Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 99 of 213
Found at i:27790201 original size:79 final size:79
Alignment explanation
Indices: 27790048--27790212 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
27790038 GGACTAAGAT
* * **
27790048 CCGAAGGCATTTGTGAGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGCGCGAGTTACTAA
1 CCGAAGGCAATTGTGAGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
27790113 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
27790127 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGAGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
27790190 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
27790206 CCGAAGG
1 CCGAAGG
27790213 TATGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.63
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.24
Consensus pattern (79 bp):
CCGAAGGCAATTGTGAGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:27793271 original size:15 final size:16
Alignment explanation
Indices: 27793241--27793273 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
27793231 AATTAAATAG
27793241 ATGTGAGATCAAGAAA
1 ATGTGAGATCAAGAAA
27793257 ATGTGAGAT-AAGAAA
1 ATGTGAGATCAAGAAA
27793272 AT
1 AT
27793274 CTCACAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.52, C:0.03, G:0.24, T:0.21
Consensus pattern (16 bp):
ATGTGAGATCAAGAAA
Found at i:27794556 original size:69 final size:69
Alignment explanation
Indices: 27794475--27794729 Score: 370
Period size: 69 Copynumber: 3.7 Consensus size: 69
27794465 CATTGCAACC
* *
27794475 TCAATTGAAACATGTATTTTATACCAAC-GAAATGACATGATAATGTCCTAAAATGGATAACATT
1 TCAATTGAAACATATATTTTATA-CAACAGAAATGACATGATAATGTCCTAAAATGGACAACATT
27794539 AAACT
65 AAACT
* * * * * *
27794544 TCTATTGAAACATACATTTTATACAATC-GAAATGACATGATGATATCTTAAAATGGACAGCATT
1 TCAATTGAAACATATATTTTATACAA-CAGAAATGACATGATAATGTCCTAAAATGGACAACATT
27794608 AAACT
65 AAACT
* * *
27794613 TCAATTGAAACATATATTTTATACCACTGAAATAACATGATAATGTCCTAAAATGGACAACATTA
1 TCAATTGAAACATATATTTTATACAACAGAAATGACATGATAATGTCCTAAAATGGACAACATTA
27794678 AACT
66 AACT
*
27794682 TCAATTGAAACATATATTTTATACAACAAAAATGACATGATAATGTCC
1 TCAATTGAAACATATATTTTATACAACAGAAATGACATGATAATGTCC
27794730 AACTGTGACA
Statistics
Matches: 164, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
68 4 0.02
69 160 0.98
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (69 bp):
TCAATTGAAACATATATTTTATACAACAGAAATGACATGATAATGTCCTAAAATGGACAACATTA
AACT
Found at i:27794917 original size:90 final size:90
Alignment explanation
Indices: 27794760--27794940 Score: 344
Period size: 90 Copynumber: 2.0 Consensus size: 90
27794750 CTTAATTAAG
* *
27794760 TCATGTATTCCAACTCAACAATATACCATGATATTGTCTAGCCTTGAATAGCAATTAACCCCGAA
1 TCATGTATTCCAACTCAACAATATACCATGATATTGTCTAGCCTTGAATAACAATTAACCCCCAA
27794825 GTACAACATGCTTCAAGTTGTGCAT
66 GTACAACATGCTTCAAGTTGTGCAT
27794850 TCATGTATTCCAACTCAACAATATACCATGATATTGTCTAGCCTTGAATAACAATTAACCCCCAA
1 TCATGTATTCCAACTCAACAATATACCATGATATTGTCTAGCCTTGAATAACAATTAACCCCCAA
27794915 GTACAACATGCTTCAAGTTGTGCAT
66 GTACAACATGCTTCAAGTTGTGCAT
27794940 T
1 T
27794941 TTAGAACAAC
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (90 bp):
TCATGTATTCCAACTCAACAATATACCATGATATTGTCTAGCCTTGAATAACAATTAACCCCCAA
GTACAACATGCTTCAAGTTGTGCAT
Found at i:27798498 original size:25 final size:24
Alignment explanation
Indices: 27798421--27798500 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 24
27798411 TGGTCTTCAA
*
27798421 AGATTTCGCCAAAAATGCTTTCTAG
1 AGATTTCGCCAAAAAGGCTTT-TAG
* ** * *
27798446 GGATTTCGATAGAAAGGCTTTTCTG
1 AGATTTCGCCAAAAAGGCTTTT-AG
*
27798471 AGATTTCGCCATAAAGGCTTTTAAG
1 AGATTTCGCCAAAAAGGCTTTT-AG
27798496 AGATT
1 AGATT
27798501 CCTTGAGTTT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
24 1 0.02
25 41 0.98
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (24 bp):
AGATTTCGCCAAAAAGGCTTTTAG
Found at i:27802826 original size:35 final size:35
Alignment explanation
Indices: 27802804--27802893 Score: 171
Period size: 35 Copynumber: 2.6 Consensus size: 35
27802794 TGGGAGAAGG
27802804 GATTGTATTTTAGGGGGGATTTCTAGAGAGGAATC
1 GATTGTATTTTAGGGGGGATTTCTAGAGAGGAATC
27802839 GATTGTATTTTAGGGGGGATTTCTAGAGAGGAATC
1 GATTGTATTTTAGGGGGGATTTCTAGAGAGGAATC
*
27802874 GATTGTATTTTGGGGGGGAT
1 GATTGTATTTTAGGGGGGAT
27802894 ATATATATTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.23, C:0.04, G:0.37, T:0.36
Consensus pattern (35 bp):
GATTGTATTTTAGGGGGGATTTCTAGAGAGGAATC
Found at i:27803686 original size:15 final size:15
Alignment explanation
Indices: 27803668--27803717 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
27803658 AATTATTTTC
27803668 CTATTATTTATTATA
1 CTATTATTTATTATA
*
27803683 CTA-T-TTT-TTACA
1 CTATTATTTATTATA
27803695 CTATTATTTATTATA
1 CTATTATTTATTATA
27803710 CTTATTAT
1 C-TATTAT
27803718 ATCATTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 7 0.24
13 4 0.14
14 4 0.14
15 8 0.28
16 6 0.21
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (15 bp):
CTATTATTTATTATA
Found at i:27815963 original size:44 final size:45
Alignment explanation
Indices: 27815838--27816323 Score: 499
Period size: 44 Copynumber: 11.0 Consensus size: 45
27815828 ATAGGTCCTA
* * *
27815838 TCTTCCTATATTGGTAG-GAAGTGGATCAAAGAT-GCAGATCTTG
1 TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
* * *
27815881 TCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
* * * * * *
27815926 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAGCAGATCCTA
1 TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
* *
27815970 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GCAGATCTTG
1 TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
* * * *
27816013 TCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
* * * * * *
27816058 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAGCAGATCCTA
1 TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
* * *
27816102 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GCAGATCTCG
1 TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
* * * *
27816145 TCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
* * * * * *
27816190 TCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGGTCCTA
1 TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
* * * *
27816234 TCTTCCTATATTGATAG-GAAGTGGATCCAAGATA-CAGATCTTG
1 TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
* * *
27816277 TCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTG
1 TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
27816322 TC
1 TC
27816324 CCTGTATTTG
Statistics
Matches: 356, Mismatches: 76, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
43 79 0.22
44 201 0.56
45 76 0.21
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (45 bp):
TCTTCCTATATTGGTGGTGAAGTAGATCGAAGATAGCAGATCTTG
Found at i:27816070 original size:132 final size:132
Alignment explanation
Indices: 27815833--27816323 Score: 883
Period size: 132 Copynumber: 3.7 Consensus size: 132
27815823 CGTAAATAGG
*
27815833 TCCTATCTTCCTATATTGGTAGGAAGTGGATCAAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
27815898 CGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
66 CGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
27815963 GA
131 GA
27815965 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
*
27816030 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
66 CGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
27816095 GA
131 GA
*
27816097 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTCGTCTTCCCATATTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
* *
27816162 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCA
66 CGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
*
27816227 GG
131 GA
* * * *
27816229 TCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATACTGGTGG
1 TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
*
27816294 TGAAGTAGATCGAAGAAAGCAGATCTTGTC
66 CGAAGTAGATCGAAGAAAGCAGATCTTGTC
27816324 CCTGTATTTG
Statistics
Matches: 347, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 347 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (132 bp):
TCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGG
CGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAGCA
GA
Found at i:27817279 original size:34 final size:34
Alignment explanation
Indices: 27817241--27817326 Score: 165
Period size: 34 Copynumber: 2.6 Consensus size: 34
27817231 ATGGGAGAAG
27817241 GATTGTATTTTAGGGGGATTTCTAGAGAGGAATC
1 GATTGTATTTTAGGGGGATTTCTAGAGAGGAATC
27817275 GATTGTATTTTAGGGGGATTTCTAGAGAGGAATC
1 GATTGTATTTTAGGGGGATTTCTAGAGAGGAATC
27817309 GATTGTATTTT-GGGGGAT
1 GATTGTATTTTAGGGGGAT
27817327 ATATATATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 7 0.13
34 45 0.87
ACGTcount: A:0.24, C:0.05, G:0.34, T:0.37
Consensus pattern (34 bp):
GATTGTATTTTAGGGGGATTTCTAGAGAGGAATC
Found at i:27818151 original size:16 final size:15
Alignment explanation
Indices: 27818103--27818153 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
27818093 AATTATTTTC
27818103 CTATTATTTATTATA
1 CTATTATTTATTATA
*
27818118 CTATT-TTT-TTACA
1 CTATTATTTATTATA
27818131 CTATTATTTATTATA
1 CTATTATTTATTATA
27818146 CTTATTAT
1 C-TATTAT
27818154 ATCATTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 9 0.29
14 6 0.19
15 10 0.32
16 6 0.19
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (15 bp):
CTATTATTTATTATA
Found at i:27818800 original size:132 final size:130
Alignment explanation
Indices: 27818455--27818804 Score: 343
Period size: 129 Copynumber: 2.7 Consensus size: 130
27818445 AGACTTGATA
* * * *
27818455 TTTGGCAATTCGCGGAATAGTGCCCTAACATGTTGGGTTGCAATTTCTCGTTTG-CTCAAAATAA
1 TTTGGCAGTTCGAGGAATAGTGCCCTATCGTGTTGGGTTGCAATTTCTCGTTTGTC-CAAAATAA
* * * * *
27818519 TCGAATATTCCTTTAGG-TTTTCACTCATGTTTATTAAAAACCTTTCAATACAAAGGATGTTCGA
65 TCGAATATTCC-TTCGGAATTTCACTCACGTTTATTAAAAACCTTTCAAAACAAAGAATGTTCGA
27818583 TG
129 TG
* * ** * * * * *
27818585 TTTGGC-GATTTGAGG-ATCGTGCCCTATCGTGTTGGGTTGCGCTTTTTCATTTGTTCTAAACAA
1 TTTGGCAG-TTCGAGGAATAGTGCCCTATCGTGTTGGGTTGCAATTTCTCGTTTGTCCAAAATAA
* * * *
27818648 TCGAAGATTCCTTCGAAATTTCATTCACGTTT-TCTAAAAACCTTTTAAAACGAAAGAAGTGTTC
65 TCGAATATTCCTTCGGAATTTCACTCACGTTTAT-TAAAAACCTTTCAAAAC-AAAGAA-TGTTC
27818712 GATG
127 GATG
* * * * *
27818716 TTTGGCAGTTCGGGGAATAGTGCCCTATCGTGCTGGGCTGCAATCTCCCGTTTGTCCAAAATAAT
1 TTTGGCAGTTCGAGGAATAGTGCCCTATCGTGTTGGGTTGCAATTTCTCGTTTGTCCAAAATAAT
*
27818781 CGAATA-TCTCTCCGGAATTTCACT
66 CGAATATTC-CTTCGGAATTTCACT
27818805 TGTACTTTTC
Statistics
Matches: 171, Mismatches: 40, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
128 4 0.02
129 74 0.43
130 16 0.09
131 22 0.13
132 55 0.32
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (130 bp):
TTTGGCAGTTCGAGGAATAGTGCCCTATCGTGTTGGGTTGCAATTTCTCGTTTGTCCAAAATAAT
CGAATATTCCTTCGGAATTTCACTCACGTTTATTAAAAACCTTTCAAAACAAAGAATGTTCGATG
Found at i:27820270 original size:3 final size:3
Alignment explanation
Indices: 27820264--27820314 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
27820254 TCAAAAAAAA
27820264 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
27820312 AAG
1 AAG
27820315 CAATTCATCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:27825554 original size:18 final size:17
Alignment explanation
Indices: 27825526--27825560 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27825516 ATTATTAAGA
*
27825526 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
27825543 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
27825561 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:27825698 original size:18 final size:17
Alignment explanation
Indices: 27825670--27825704 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
27825660 ATTATTAACC
*
27825670 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
27825687 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
27825705 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:27825955 original size:45 final size:44
Alignment explanation
Indices: 27825866--27825960 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 44
27825856 TTACACCTCT
*
27825866 ATTACATTCAACCAAACACAATTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAATTTTACTATTACACCTCTATTCC
** *
27825910 ATTACATTCAACCAAACA-GTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAAT--TTTACTATTACACCTCTATTCC
27825955 ATTACA
1 ATTACA
27825961 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.40
45 26 0.58
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAATTTTACTATTACACCTCTATTCC
Found at i:27825960 original size:16 final size:16
Alignment explanation
Indices: 27825939--27825971 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27825929 TTGATTTGCT
*
27825939 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
27825955 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
27825971 A
1 A
27825972 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:27825981 original size:21 final size:21
Alignment explanation
Indices: 27825952--27825994 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
27825942 ACACCTCTAT
*
27825952 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
27825973 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
27825994 T
1 T
27825995 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:27832161 original size:23 final size:22
Alignment explanation
Indices: 27832118--27832173 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
27832108 AAAGGGTATC
* *
27832118 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
27832139 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
27832162 TACATATCATAT
1 TACAAATCATAT
27832174 TTAAGATTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 16 0.53
23 11 0.37
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:27832180 original size:19 final size:19
Alignment explanation
Indices: 27832131--27832228 Score: 97
Period size: 19 Copynumber: 4.8 Consensus size: 19
27832121 AAATTAAATC
*
27832131 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
27832151 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
* *
27832173 TTTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
27832194 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
27832213 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
27832229 CTCGAAAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
19 32 0.48
21 17 0.25
22 7 0.10
23 11 0.16
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:27832191 original size:21 final size:21
Alignment explanation
Indices: 27832165--27832227 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
27832155 CTAAGATTAC
*
27832165 ATATCATATTTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
27832186 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
27832205 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
27832226 AT
1 AT
27832228 CCTCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
19 19 0.49
21 20 0.51
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:27860491 original size:11 final size:11
Alignment explanation
Indices: 27860475--27860503 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
27860465 TGAAATCTAT
27860475 TTGTTCTTACC
1 TTGTTCTTACC
27860486 TTGTTCTTACC
1 TTGTTCTTACC
27860497 TTGTTCT
1 TTGTTCT
27860504 ATTGATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.24, G:0.10, T:0.59
Consensus pattern (11 bp):
TTGTTCTTACC
Found at i:27867880 original size:51 final size:50
Alignment explanation
Indices: 27867705--27867939 Score: 312
Period size: 51 Copynumber: 4.7 Consensus size: 50
27867695 TCATTCGATA
*
27867705 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
*
27867755 CACGTAGTAGCCTTCACATAGTACTACA-ACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
*
27867804 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-CGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACGGTT
* * * * * *** *
27867855 CACATTGTAGCCTTCGCTTAGTACTACACATGTGACCATCATTTATGGATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGG-TT
*
27867906 CACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
27867940 TTCATCGATA
Statistics
Matches: 162, Mismatches: 18, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
49 52 0.32
50 38 0.23
51 68 0.42
52 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTT
Found at i:27867937 original size:102 final size:99
Alignment explanation
Indices: 27867705--27867939 Score: 310
Period size: 99 Copynumber: 2.3 Consensus size: 99
27867695 TCATTCGATA
* * *
27867705 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCACGTAGTAGCCTTC
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTACACATAGTAGCCTTC
* **
27867770 ACATAGTACTACAACGTGATCAAGTTTTACGGTT
66 ACATAGTACTACAACGTGACCAACATTTACGGTT
*
27867804 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTT-CGGTACACATTGTAGCCT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACC-AAG-TTTTACGGTACACATAGTAGCCT
* * * * *
27867868 TCGCTTAGTACTACACATGTGACCATCATTTATGGATT
64 TCACATAGTACTACA-ACGTGACCAACATTTACGG-TT
*
27867906 CACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
27867940 TTCATCGATA
Statistics
Matches: 119, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
99 36 0.30
100 31 0.26
101 17 0.14
102 35 0.29
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (99 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAGTTTTACGGTACACATAGTAGCCTTC
ACATAGTACTACAACGTGACCAACATTTACGGTT
Found at i:27868444 original size:31 final size:30
Alignment explanation
Indices: 27868408--27868466 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
27868398 GCTTCGACTG
*
27868408 AACTTTTGTCAAAATTACGA-TTTTGTCCCTA
1 AACTTTT-ACAAAATTAC-ATTTTTGTCCCTA
*
27868439 AACTTTTACATAATTACATTTTTGTCCC
1 AACTTTTACAAAATTACATTTTTGTCCC
27868467 CAAGCTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 17 0.68
31 7 0.28
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (30 bp):
AACTTTTACAAAATTACATTTTTGTCCCTA
Found at i:27869169 original size:11 final size:12
Alignment explanation
Indices: 27869141--27869173 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
27869131 GCCCAAACGT
27869141 CGAAATTTTCGAA
1 CGAAATTTTC-AA
27869154 CGAAATTTTC-A
1 CGAAATTTTCAA
27869165 CGAAATTTT
1 CGAAATTTT
27869174 TCTGTGCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (12 bp):
CGAAATTTTCAA
Found at i:27872891 original size:25 final size:29
Alignment explanation
Indices: 27872857--27872917 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 29
27872847 TTTTCTTAAA
27872857 ATTTGTTAATTT-TAAATA-ATGTA-ATT-
1 ATTT-TTAATTTATAAATATATGTATATTC
*
27872883 ATTTTTAATTTATATATATATGTATATTC
1 ATTTTTAATTTATAAATATATGTATATTC
27872912 ATTTTT
1 ATTTTT
27872918 TTCTTATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.23
26 9 0.30
27 5 0.17
28 3 0.10
29 6 0.20
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (29 bp):
ATTTTTAATTTATAAATATATGTATATTC
Found at i:27872916 original size:29 final size:27
Alignment explanation
Indices: 27872857--27872932 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 27
27872847 TTTTCTTAAA
*
27872857 ATTTGTTAATTT-TAAATA-ATGTAATT
1 ATTT-TTAATTTATATATATATGTAATT
27872883 ATTTTTAATTTATATATATATGTATATT
1 ATTTTTAATTTATATATATATGTA-ATT
*
27872911 CATTTTT-TTCTTATATATATAT
1 -ATTTTTAAT-TTATATATATAT
27872933 ATTTTGCAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 7 0.16
26 9 0.21
27 5 0.12
28 4 0.09
29 18 0.42
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (27 bp):
ATTTTTAATTTATATATATATGTAATT
Found at i:27873425 original size:18 final size:17
Alignment explanation
Indices: 27873404--27873447 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
27873394 CTTTGCATGT
27873404 TATTGATTTATTT-TTATA
1 TATT-ATTTATTTGTT-TA
27873422 TATTTATTTATTTGTTTA
1 TA-TTATTTATTTGTTTA
27873440 TATTATTT
1 TATTATTT
27873448 CTATGTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.25
18 14 0.58
19 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
TATTATTTATTTGTTTA
Found at i:27873477 original size:15 final size:15
Alignment explanation
Indices: 27873457--27873485 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27873447 TCTATGTCAT
27873457 TATTGTATTTGTTAC
1 TATTGTATTTGTTAC
27873472 TATTGTATTTGTTA
1 TATTGTATTTGTTA
27873486 TCACGATATT
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:0.21, C:0.03, G:0.14, T:0.62
Consensus pattern (15 bp):
TATTGTATTTGTTAC
Found at i:27880855 original size:40 final size:40
Alignment explanation
Indices: 27880781--27880964 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
27880771 GCTACTCGTT
*
27880781 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
27880820 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
27880860 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
27880899 CAATTGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
27880940 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27880965 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 43 0.35
40 67 0.54
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:27880880 original size:79 final size:80
Alignment explanation
Indices: 27880781--27880964 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 80
27880771 GCTACTCGTT
* * *
27880781 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
* *
27880844 GATTTAGTAAC-TCGCA
64 GATATAGTAACTTAGCA
* * **
27880860 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAATTGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
27880925 TATGGTCACTTAGCA
66 TATAGTAACTTAGCA
27880940 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
27880965 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
78 3 0.03
79 67 0.74
80 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:27889032 original size:40 final size:40
Alignment explanation
Indices: 27888995--27889179 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
27888985 GCTACTCGTT
*
27888995 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
27889035 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
27889075 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
27889114 CAATTGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
27889155 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27889180 CATCATTCAA
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 79 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:27889106 original size:79 final size:82
Alignment explanation
Indices: 27888995--27889179 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
27888985 GCTACTCGTT
* *
27888995 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
27889058 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* * **
27889075 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAATTGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
27889138 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
27889155 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
27889180 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:27896103 original size:25 final size:26
Alignment explanation
Indices: 27896056--27896104 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
27896046 CAGAATTTGT
27896056 TTGTTCTTGTAATACTTTATTCTTCA
1 TTGTTCTTGTAATACTTTATTCTTCA
27896082 TTGTTCTTG-AATATCTTT-TTCTT
1 TTGTTCTTGTAATA-CTTTATTCTT
27896105 TTCAAGACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.16, C:0.14, G:0.08, T:0.61
Consensus pattern (26 bp):
TTGTTCTTGTAATACTTTATTCTTCA
Found at i:27897159 original size:44 final size:43
Alignment explanation
Indices: 27897050--27897713 Score: 420
Period size: 44 Copynumber: 15.1 Consensus size: 43
27897040 AGTGGATTGA
* * *
27897050 AGATCTTGTCTTCCCATATTG-GTGGCAAAGTTA-ATCAAAGAAAGC
1 AGATCTTGTCTTCCTATATTGAGT-G--AAG-TAGATCGAAGATAGC
* * *
27897095 AGATCCTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATTGA-GTGAAGTAGATCGAAGATAGC
* * * * * *
27897139 ATATCCTGTCTTCCTATATTG-GT-AGGGAG-T-G--GATCGA
1 AGATCTTGTCTTCCTATATTGAGTGAAGTAGATCGAAGATAGC
* * *
27897176 AGATCTTGTCTTCCCATATTG-GTGGCGAAGTAGATCAAAGAAAGC
1 AGATCTTGTCTTCCTATATTGAGT---GAAGTAGATCGAAGATAGC
* * *
27897221 AGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATT-GAGTGAAGTAGATCGAAGATAGC
* *
27897265 AGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATT-G-AGTGAAGTAGATCGAAGATAGC
* * *
27897309 AGATCTTGTCTTCCCATACTGGTG-GCGAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCCTATA-T--TGAGTGAAGTAGATCGAAGATAGC
* * * *
27897354 AGATCTTGTCTTCATGTATTGGCGTGAAATAGATCGAAGATAGC
1 AGATCTTGTCTTCCTATATT-GAGTGAAGTAGATCGAAGATAGC
* * *
27897398 AGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT-GC
1 AGATCTTGTCTTCCTATATT-G-AGTGAAGTAGATCGAAGATAGC
* * * * * *
27897442 AGATCTTGTCTTCATGTATTGGCGTGAAATAGATCGAAGAAATC
1 AGATCTTGTCTTCCTATATT-GAGTGAAGTAGATCGAAGATAGC
* * * * **
27897486 AAATCTTGTCTTTCTATATTGGTAGCGAAGTGGATTAAAGATAGC
1 AGATCTTGTCTTCCTATATT-G-AGTGAAGTAGATCGAAGATAGC
* * * * *
27897531 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAAC
1 AGATCTTGTCTTCCTATATT-GAGTGAAGTAGATCGAAGATAGC
* * * * *
27897575 AAATCCTGTCTTCCTATATTGGTAGCGAAGTGGATTGAAGATAGC
1 AGATCTTGTCTTCCTATATT-G-AGTGAAGTAGATCGAAGATAGC
* * * * **
27897620 AAATCTTATCTTCCCATACTAGTG-GTGAAGTAGATCGAAGAAAAT
1 AGATCTTGTCTT-CC-TA-TATTGAGTGAAGTAGATCGAAGATAGC
* * * *
27897665 AGATCTTGTCTTCATGTATTG-GCATGAAGTAGATCAAAAATAGC
1 AGATCTTGTCTTCCTATATTGAG--TGAAGTAGATCGAAGATAGC
27897709 AGATC
1 AGATC
27897714 ATATCCAGTC
Statistics
Matches: 478, Mismatches: 112, Indels: 59
0.74 0.17 0.09
Matches are distributed among these distances:
37 24 0.05
39 1 0.00
40 1 0.00
41 8 0.02
42 9 0.02
43 18 0.04
44 231 0.48
45 170 0.36
46 5 0.01
47 8 0.02
48 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (43 bp):
AGATCTTGTCTTCCTATATTGAGTGAAGTAGATCGAAGATAGC
Found at i:27897163 original size:126 final size:127
Alignment explanation
Indices: 27897008--27897439 Score: 674
Period size: 126 Copynumber: 3.4 Consensus size: 127
27896998 TAGGTTGAAA
*
27897008 ATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAGTGGATTGAAGATCTTGTCTTCCCATATTGG
1 ATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATCTTGTCTTCCCATATTGG
* *
27897072 TGGCAAAGTTA-ATCAAAGAAAGCAGATCCTGTCTTCATGTATTGACGTGAAGTAGATCGAAG
66 TGGCGAAG-TAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAG
* *
27897134 ATAGCATATCCTGTCTTCCTATATTGGTAG-GGAGTGGATCGAAGATCTTGTCTTCCCATATTGG
1 ATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATCTTGTCTTCCCATATTGG
27897198 TGGCGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATT-AGCGTGAAGTAGATCGAAG
66 TGGCGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGA-CGTGAAGTAGATCGAAG
*
27897260 ATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCA
1 ATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATC---GA---AGATCTTGTCTTCCCA
* * * *
27897325 TACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAATAGATCG
60 TATTGGTGGCGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCG
27897390 AAG
125 AAG
27897393 ATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT
1 ATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT
27897440 GCAGATCTTG
Statistics
Matches: 284, Mismatches: 12, Indels: 19
0.90 0.04 0.06
Matches are distributed among these distances:
125 3 0.01
126 145 0.51
127 13 0.05
130 4 0.01
133 119 0.42
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (127 bp):
ATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATCTTGTCTTCCCATATTGG
TGGCGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAG
Found at i:27897339 original size:89 final size:88
Alignment explanation
Indices: 27897246--27897632 Score: 490
Period size: 89 Copynumber: 4.4 Consensus size: 88
27897236 GTATTAGCGT
* * * * * * *
27897246 GAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAG
1 GAAGTGGATCGAAGATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATGCAA
* * * *
27897311 ATCTTGTCTTCCCATACTGGTGGC
65 ATCCTGTCTTCCTATATTGGTAGC
* * * *
27897335 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAATAGATCGAAGATAGCAG
1 GAAGTGGATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT-GCAA
27897400 ATCCTGTCTTCCTATATTGGTAGC
65 ATCCTGTCTTCCTATATTGGTAGC
*
27897424 GAAGTGGATCGAAGAT-GCAGATCTTGTCTTCATGTATTGGCGTGAAATAGATCGAAGAAAT-CA
1 GAAGTGGATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG--ATGCA
* *
27897487 AATCTTGTCTTTCTATATTGGTAGC
64 AATCCTGTCTTCCTATATTGGTAGC
** **
27897512 GAAGTGGATTAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAAAACAA
1 GAAGTGGATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-ATGCAA
27897577 ATCCTGTCTTCCTATATTGGTAGC
65 ATCCTGTCTTCCTATATTGGTAGC
* * *
27897601 GAAGTGGATTGAAGATAGCAAATCTTATCTTC
1 GAAGTGGATCGAAGATAGCAGATCTTGTCTTC
27897633 CCATACTAGT
Statistics
Matches: 268, Mismatches: 25, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
88 97 0.36
89 169 0.63
90 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (88 bp):
GAAGTGGATCGAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATGCAAA
TCCTGTCTTCCTATATTGGTAGC
Found at i:27897366 original size:133 final size:134
Alignment explanation
Indices: 27897008--27897713 Score: 700
Period size: 133 Copynumber: 5.4 Consensus size: 134
27896998 TAGGTTGAAA
*
27897008 ATAGCAGATCCTGTCTTCCTATATTGGTAG-GAAGTGGAT------TGAAGATCTTGTCTTCCCA
1 ATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCA
* * * *
27897066 TATTGGTGGCAAAGTTA-ATCAAAGAAAGCAGATCCTGTCTTCATGTATT-GACGTGAAGTAGAT
66 TATTGGTGGCGAAG-TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTAGTCGTGAAGTAGAT
27897129 CGAAG
130 CGAAG
* *
27897134 ATAGCATATCCTGTCTTCCTATATTGGTAG-GGAGTGGATC---GA---AGATCTTGTCTTCCCA
1 ATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCA
*
27897192 TATTGGTGGCGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTAG-CGTGAAGTAGATC
66 TATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTAGTCGTGAAGTAGATC
27897256 GAAG
131 GAAG
27897260 ATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCA
1 ATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCA
* * *
27897325 TACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATT-GGCGTGAAATAGATC
66 TATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTAGTCGTGAAGTAGATC
27897389 GAAG
131 GAAG
* ***
27897393 ATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCATG
1 ATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCA
* * * * * * * * * *
27897458 TATTGG-CGTGAAATAGATCGAAGAAATCAAATCTTGTCTTTC-TATATTGGTAGCGAAGTGGAT
66 TATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTC-TTCATGTATTAGTCGTGAAGTAGAT
**
27897521 TAAAG
130 CGAAG
* * * * * ** * * *
27897526 ATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAACAAATCCTGTCTTCCT
1 ATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAG-ATGCAGATCTTGTCTTCCC
* * * * * * *** * *
27897590 ATATTGGTAGCGAAGTGGATTGAAGATAGCAAATCTTATCTTCCCATACTAGTGGTGAAGTAGAT
65 ATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTAGTCGTGAAGTAGAT
27897655 CGAAG
130 CGAAG
* ** * * * * * * *
27897660 AAAATAGATCTTGTCTTCATGTATTGGCA-TGAAGTAGATCAAAAATAGCAGATC
1 ATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGAT-GCAGATC
27897714 ATATCCAGTC
Statistics
Matches: 496, Mismatches: 64, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
125 2 0.00
126 143 0.29
127 10 0.02
130 2 0.00
132 47 0.09
133 208 0.42
134 84 0.17
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (134 bp):
ATAGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCA
TATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTAGTCGTGAAGTAGATC
GAAG
Found at i:27897454 original size:177 final size:177
Alignment explanation
Indices: 27897206--27897660 Score: 556
Period size: 177 Copynumber: 2.6 Consensus size: 177
27897196 GGTGGCGAAG
* * * * * * * *
27897206 TAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTAG-CGTGAAGTAGATCGAAGATAGCAGATC
1 TAGATCGAAGAAAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATAGCAGATC
* * * *
27897270 CTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATACTGGTGGC
66 TTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGAT-CAAATCTTGTCTTCCCATACTGGTAGC
*
27897335 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAA
130 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAA
*
27897383 TAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT-GCAGATC
1 TAGATCGAAGAAAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATAGCAGATC
* * * * * * *
27897447 TTGTCTTCATGTATTGG-CGTGAAATAGATCGAAGAAATCAAATCTTGTCTTTCTATATTGGTAG
66 TTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAG--ATCAAATCTTGTCTTCCCATACTGGTAG
* * * *
27897511 CGAAGTGGATTAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAG
129 CGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAA
* * * *
27897560 TAGATCGAAGAAAACAAATCCTGTCTTCCTATATTGGTAGCGAAGTGGATTGAAGATAGCAAATC
1 TAGATCGAAGAAAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATAGCAGATC
* * * * *
27897625 TTATCTTCCCATACTAGTGGTGAAGTAGATCGAAGA
66 TTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGA
27897661 AAATAGATCT
Statistics
Matches: 235, Mismatches: 38, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
176 14 0.06
177 171 0.73
178 35 0.15
179 15 0.06
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (177 bp):
TAGATCGAAGAAAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATAGCAGATC
TTGTCTTCCTATATTGGTAGTGAAGTAGATCGAAGATCAAATCTTGTCTTCCCATACTGGTAGCG
AAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAA
Found at i:27897694 original size:89 final size:89
Alignment explanation
Indices: 27897202--27897713 Score: 480
Period size: 89 Copynumber: 5.8 Consensus size: 89
27897192 TATTGGTGGC
* * * * * *
27897202 GAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTAGC-GTGAAGTAGATCGAAGATAGCA
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATATTGGCAGCGAAGTGGATCGAAGATAGCA
* * * * *
27897266 GATCCTGTCTTCCTATATTGGTAGT
66 GATCTTGTCTTCATGTAGTGG-CGT
* ** ** * ** * *
27897291 GAAGTGGATCGAAG-ATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCA
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATATTGGCAGCGAAGTGGATCGAAGATAGCA
*
27897355 GATCTTGTCTTCATGTATTGGCGT
66 GATCTTGTCTTCATGTAGTGGCGT
* * * * * *
27897379 GAAATAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGAT-GCA
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATATTGGCAGCGAAGTGGATCGAAGATAGCA
*
27897443 GATCTTGTCTTCATGTATTGGCGT
66 GATCTTGTCTTCATGTAGTGGCGT
* * * * **
27897467 GAAATAGATCGAAGAAATCAAATCTTGTCTTTC-TATATTGGTAGCGAAGTGGATTAAAGATAGC
1 GAAGTAGATCGAAGAAAACAGATCTTGTC-TTCATATATTGGCAGCGAAGTGGATCGAAGATAGC
*
27897531 AGATCTTGTCTTCATGTATTGGCGT
65 AGATCTTGTCTTCATGTAGTGGCGT
* * * * *
27897556 GAAGTAGATCGAAGAAAACAAATCCTGTCTTCCTATATTGGTAGCGAAGTGGATTGAAGATAGCA
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATATTGGCAGCGAAGTGGATCGAAGATAGCA
* * *
27897621 AATCTTATCTTCCCATACTAGT-G-GT
66 GATCTTGTCTT--CAT-GTAGTGGCGT
* * * * * *
27897646 GAAGTAGATCGAAGAAAATAGATCTTGTCTTCATGTATTGGCA-TGAAGTAGATCAAAAATAGCA
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATATTGGCAGCGAAGTGGATCGAAGATAGCA
27897710 GATC
66 GATC
27897714 ATATCCAGTC
Statistics
Matches: 364, Mismatches: 51, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
88 115 0.32
89 203 0.56
90 39 0.11
91 4 0.01
92 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (89 bp):
GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATATTGGCAGCGAAGTGGATCGAAGATAGCA
GATCTTGTCTTCATGTAGTGGCGT
Found at i:27897862 original size:44 final size:44
Alignment explanation
Indices: 27897722--27897876 Score: 136
Period size: 44 Copynumber: 3.5 Consensus size: 44
27897712 TCATATCCAG
* * *
27897722 TCTTATC-CTCCTGAAGTTGCAGT-GAGGCGGACTGAAGATGACAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCGGA-TTAAAATCACAAA
* * * * **
27897767 TCTCATCTCCTTGAAGTTGCAGTGGAGCAGATTAGAGCCA-ATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACA-AA
* * *
27897811 TCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAAA
*
27897855 TCTTATCTCTCTGAAGTTGCAG
1 TCTTATCTCCCTGAAGTTGCAG
27897877 AGAGTAGATC
Statistics
Matches: 86, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
43 1 0.01
44 58 0.67
45 24 0.28
46 3 0.03
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAAA
Found at i:27903370 original size:43 final size:43
Alignment explanation
Indices: 27903097--27903422 Score: 309
Period size: 43 Copynumber: 7.6 Consensus size: 43
27903087 TTTTAGAAAT
* * * * * *
27903097 AAACGCCGCTAAAGAACAAGACATTTAACGGCGCTATTCCAAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
27903140 AAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTCCCAT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * ** *
27903183 AAACGCCGCTAAAGACCAAGACCTTTAGTAGCGCTTCTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * * * *
27903226 AAATGGCACTAAAGACCAAGACCTTTAGCGGCACTTCTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* *
27903269 AAACGCCGCTAAAG-ACTATGACCTTTAGCGGCGATTTCCCCAC
1 AAACGCCGCTAAAGAAC-ATGACCTTTAGCGGCGCTTTTCCCAC
* **
27903312 AAACGCCTCTAAAGAACATGACCTTTAGCGGCGCTTTTATCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * ** * *
27903355 AAACGCCGCTAAAGAA-TTAACCTTTTCCGGCGCTTCTT-GCAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTT-TTCCCAC
*
27903397 AAACGCCGCTAAA-AACATAACCTTTA
1 AAACGCCGCTAAAGAACATGACCTTTA
27903423 AAAAATATAT
Statistics
Matches: 236, Mismatches: 43, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.01
42 39 0.17
43 193 0.82
44 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:27903608 original size:52 final size:52
Alignment explanation
Indices: 27903550--27903653 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
27903540 ATTTTCTATG
27903550 AAAATTTTAACTTTAAAATTAAATATAAAAATTAATGAATTTAGTTTCAGAA
1 AAAATTTTAACTTTAAAATTAAATATAAAAATTAATGAATTTAGTTTCAGAA
27903602 AAAATTTTAACTTTAAAATTAAATATAAAAATTAATGAATTTAGTTTCAGAA
1 AAAATTTTAACTTTAAAATTAAATATAAAAATTAATGAATTTAGTTTCAGAA
27903654 TTTAAAATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (52 bp):
AAAATTTTAACTTTAAAATTAAATATAAAAATTAATGAATTTAGTTTCAGAA
Found at i:27910076 original size:41 final size:41
Alignment explanation
Indices: 27909811--27910093 Score: 377
Period size: 41 Copynumber: 6.9 Consensus size: 41
27909801 TATGATAAAT
* *
27909811 CTGAGCATTAGCAGCGCTTTTCAAAAAACGCCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCC
* * *
27909852 CTGAGCATTAGCAGCGCTTTTTGAAAAATGCCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCC
* * * *
27909893 TTGAGCATTAGCGGCGCTTATTGAAAAATGCCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCC
* * *
27909934 CTAAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAATCC
1 CTGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCC
* *
27909975 CTGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCC
1 CTGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCC
*
27910016 CTGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACC
1 CTGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCC
* *** * *
27910057 CTGAACATTAGCAATGCTTTTTCAAAATCGCCGCTAA
1 CTGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAA
27910094 TGCCTCAAAA
Statistics
Matches: 218, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 218 1.00
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (41 bp):
CTGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGCC
Found at i:27910235 original size:40 final size:40
Alignment explanation
Indices: 27910184--27910269 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
27910174 TTTAGCTACG
*
27910184 TTTTTAAAAAGCACCGCTAATACTTGATCTTTAGTGGCGT
1 TTTTTAAAAAGCACCGCTAATACTTGATCTTTAGCGGCGT
* * *
27910224 TTTTTAAAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGT
1 TTTTTAAAAAGCACCGCTAATACTTGATCTTTAGCGGCGT
27910264 TTTTTA
1 TTTTTA
27910270 TCCAAGCGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (40 bp):
TTTTTAAAAAGCACCGCTAATACTTGATCTTTAGCGGCGT
Found at i:27912873 original size:30 final size:30
Alignment explanation
Indices: 27912818--27912876 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
27912808 TACATATAAC
*
27912818 CCTTTAATCATTCATATTTGCATATCATAT
1 CCTTTAATCATTCATATTAGCATATCATAT
27912848 CCTTTAATCAATCTCA-ATTAG-ATATCATA
1 CCTTTAATC-AT-TCATATTAGCATATCATA
27912877 CCCTATAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 17 0.65
31 6 0.23
32 3 0.12
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.42
Consensus pattern (30 bp):
CCTTTAATCATTCATATTAGCATATCATAT
Found at i:27925004 original size:25 final size:25
Alignment explanation
Indices: 27924971--27925030 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
27924961 TCGATAAGCC
*
27924971 CATACGAGCTG-AGAATCGGTAACCT
1 CATATGAGCTGCA-AATCGGTAACCT
*
27924996 C-TCATGAGCTGCAAATCGGTAAGCT
1 CAT-ATGAGCTGCAAATCGGTAACCT
27925021 CATATGAGCT
1 CATATGAGCT
27925031 ATGGTGAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 1 0.03
25 27 0.90
26 2 0.07
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (25 bp):
CATATGAGCTGCAAATCGGTAACCT
Found at i:27932425 original size:3 final size:3
Alignment explanation
Indices: 27932417--27932444 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27932407 CAGCAACATT
27932417 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
27932445 AAGGGAGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:27936013 original size:95 final size:95
Alignment explanation
Indices: 27935850--27936641 Score: 929
Period size: 95 Copynumber: 8.4 Consensus size: 95
27935840 TTAGTTTATT
* * * *
27935850 TATCATGAAAAATCTTCTCTAAGTTAGCTGATTTAATATCGATGCTCCAAACAGCTCGCTACTTT
1 TATCATGAACAATCTTCTCTAAGTTAGCTGATTTAATATCGCTGCTCCAAACGGCTCGCTAATTT
*
27935915 AAGATCGCAAGTTAAGTTCATTTGATTTAC
66 AAGATCGCAAGCTAAGTTCATTTGATTTAC
* * * *
27935945 TATCATGAACAATCTCCTCTAAGTTAGCTTATTTAATATCGCTGCTCCAAGCAGCTCGCTAATTT
1 TATCATGAACAATCTTCTCTAAGTTAGCTGATTTAATATCGCTGCTCCAAACGGCTCGCTAATTT
* *
27936010 AAGATCAC-AGCTTAAGTTTATTTGATTTAC
66 AAGATCGCAAGC-TAAGTTCATTTGATTTAC
* * * * *
27936040 TATTATAAACAATCATCTCTAAGTTAGCTGATTTAATATTGCTGCTCCAAACGGTTCGCTAATTT
1 TATCATGAACAATCTTCTCTAAGTTAGCTGATTTAATATCGCTGCTCCAAACGGCTCGCTAATTT
* * * *
27936105 AAGATCACAACCAAAGTTCATTTAATTTAC
66 AAGATCGCAAGCTAAGTTCATTTGATTTAC
* * * *
27936135 TATCATGAACAATCTTCTCTGAGTTAACTGATTTAATATCGTTGCTCCAAACGGCTCACTAATTT
1 TATCATGAACAATCTTCTCTAAGTTAGCTGATTTAATATCGCTGCTCCAAACGGCTCGCTAATTT
*
27936200 AAGAT--CATAGCTTGAGTTCATTTGATTTAC
66 AAGATCGCA-AGC-TAAGTTCATTTGATTTAC
* * * * * *
27936230 TATCATGAACAATCTTCTTTGAGTTAACTGATTTAATATCGCTACTCCAAACGGCTCACTCATTT
1 TATCATGAACAATCTTCTCTAAGTTAGCTGATTTAATATCGCTGCTCCAAACGGCTCGCTAATTT
27936295 AAGATCGC-AGCCTAAGTTCATTTGATTTAC
66 AAGATCGCAAG-CTAAGTTCATTTGATTTAC
* * * * * *
27936325 TATCATGAACAATCTTCTCTGAGTTAGTTTATTTAATATTGTTGCTCCAAACGGCTCGCTGATTT
1 TATCATGAACAATCTTCTCTAAGTTAGCTGATTTAATATCGCTGCTCCAAACGGCTCGCTAATTT
* *
27936390 AATATCAC-AGTCTAAGTTCATTTGATTTAC
66 AAGATCGCAAG-CTAAGTTCATTTGATTTAC
* *
27936420 TATCATG-ACTAATCTTCTCTGAGTTAGCTGATTTAATATCGCTGCTCCAAACGACT-GCTAATT
1 TATCATGAAC-AATCTTCTCTAAGTTAGCTGATTTAATATCGCTGCTCCAAACGGCTCGCTAATT
* *
27936483 TAAGATAGCAACCTAAGTTCATTTGATTTAC
65 TAAGATCGCAAGCTAAGTTCATTTGATTTAC
* * * * * * **
27936514 TATCATGAATAGTCTTCTCTAAGTTA-CTTGAATTGATATCTCTGCTTCAAACAACTCGCTAATT
1 TATCATGAACAATCTTCTCTAAGTTAGC-TGATTTAATATCGCTGCTCCAAACGGCTCGCTAATT
* * *
27936578 TAATATTGCAA-CTAAGTTCATTTGATTTAT
65 TAAGATCGCAAGCTAAGTTCATTTGATTTAC
* * *
27936608 TATCATGAAAAATCTTAC-CTGAGTTAGTTGATTT
1 TATCATGAACAATCTT-CTCTAAGTTAGCTGATTT
27936642 CCAAACCACC
Statistics
Matches: 605, Mismatches: 78, Indels: 29
0.85 0.11 0.04
Matches are distributed among these distances:
93 3 0.00
94 125 0.21
95 473 0.78
96 3 0.00
97 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (95 bp):
TATCATGAACAATCTTCTCTAAGTTAGCTGATTTAATATCGCTGCTCCAAACGGCTCGCTAATTT
AAGATCGCAAGCTAAGTTCATTTGATTTAC
Found at i:27936361 original size:285 final size:285
Alignment explanation
Indices: 27935850--27936641 Score: 1024
Period size: 285 Copynumber: 2.8 Consensus size: 285
27935840 TTAGTTTATT
* * * *
27935850 TATCATGAAAAATCTTCTCTAAGTTAGCTGATTTAATATCGATGCTCCAAACAGCTCGCTACTTT
1 TATCATGAACAATCTTCTCTGAGTTAGCTGATTTAATATCGATGCTCCAAACGGCTCGCTAATTT
* * *
27935915 AAGATCGCAAG-TTAAGTTCATTTGATTTACTATCATGAACAATCTCCTCTAAGTTAGCTTATTT
66 AAGAT-GCAAGCTTAAGTTCATTTGATTTACTATCATGAACAATCTTCTCTAAGTTAACTGATTT
* * * * *
27935979 AATATCGCTGCTCCAAGCAGCTCGCTAATTTAAGATCACAGCTTAAGTTTATTTGATTTACTATT
130 AATATCGCTGCTCCAAACAGCTCGCTAATTTAAGATCGCAGCCTAAGTTCATTTGATTTACTATC
* * * * *
27936044 ATAAACAATCATCTCTAAGTTAGCTGATTTAATATTGCTGCTCCAAACGGTTCGCTAATTTAAGA
195 ATGAACAATCTTCTCTGAGTTAGTTGATTTAATATTGCTGCTCCAAACGGCTCGCTAATTTAAGA
27936109 TCACAACCAAAGTTCATTTAATTTAC
260 TCACAACCAAAGTTCATTTAATTTAC
* * *
27936135 TATCATGAACAATCTTCTCTGAGTTAACTGATTTAATATCGTTGCTCCAAACGGCTCACTAATTT
1 TATCATGAACAATCTTCTCTGAGTTAGCTGATTTAATATCGATGCTCCAAACGGCTCGCTAATTT
* * *
27936200 AAGAT-CATAGCTTGAGTTCATTTGATTTACTATCATGAACAATCTTCTTTGAGTTAACTGATTT
66 AAGATGCA-AGCTTAAGTTCATTTGATTTACTATCATGAACAATCTTCTCTAAGTTAACTGATTT
* * * *
27936264 AATATCGCTACTCCAAACGGCTCACTCATTTAAGATCGCAGCCTAAGTTCATTTGATTTACTATC
130 AATATCGCTGCTCCAAACAGCTCGCTAATTTAAGATCGCAGCCTAAGTTCATTTGATTTACTATC
* * * *
27936329 ATGAACAATCTTCTCTGAGTTAGTTTATTTAATATTGTTGCTCCAAACGGCTCGCTGATTTAATA
195 ATGAACAATCTTCTCTGAGTTAGTTGATTTAATATTGCTGCTCCAAACGGCTCGCTAATTTAAGA
** * *
27936394 TCACAGTCTAAGTTCATTTGATTTAC
260 TCACAACCAAAGTTCATTTAATTTAC
* *
27936420 TATCATG-ACTAATCTTCTCTGAGTTAGCTGATTTAATATCGCTGCTCCAAACGACT-GCTAATT
1 TATCATGAAC-AATCTTCTCTGAGTTAGCTGATTTAATATCGATGCTCCAAACGGCTCGCTAATT
* * * *
27936483 TAAGATAGCAA-CCTAAGTTCATTTGATTTACTATCATGAATAGTCTTCTCTAAGTT-ACTTGAA
65 TAAGAT-GCAAGCTTAAGTTCATTTGATTTACTATCATGAACAATCTTCTCTAAGTTAAC-TGAT
* * * * * * * *
27936546 TTGATATCTCTGCTTCAAACAACTCGCTAATTTAATATTGCA-ACTAAGTTCATTTGATTTATTA
128 TTAATATCGCTGCTCCAAACAGCTCGCTAATTTAAGATCGCAGCCTAAGTTCATTTGATTTACTA
*
27936610 TCATGAAAAATCTTAC-CTGAGTTAGTTGATTT
193 TCATGAACAATCTT-CTCTGAGTTAGTTGATTT
27936642 CCAAACCACC
Statistics
Matches: 440, Mismatches: 60, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
283 52 0.12
284 91 0.21
285 295 0.67
286 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (285 bp):
TATCATGAACAATCTTCTCTGAGTTAGCTGATTTAATATCGATGCTCCAAACGGCTCGCTAATTT
AAGATGCAAGCTTAAGTTCATTTGATTTACTATCATGAACAATCTTCTCTAAGTTAACTGATTTA
ATATCGCTGCTCCAAACAGCTCGCTAATTTAAGATCGCAGCCTAAGTTCATTTGATTTACTATCA
TGAACAATCTTCTCTGAGTTAGTTGATTTAATATTGCTGCTCCAAACGGCTCGCTAATTTAAGAT
CACAACCAAAGTTCATTTAATTTAC
Found at i:27938526 original size:6 final size:6
Alignment explanation
Indices: 27938510--27938540 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
27938500 TATGTTTCCA
*
27938510 AAAATG GAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG AAAATG A
27938541 TCCGTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:27938740 original size:26 final size:26
Alignment explanation
Indices: 27938687--27938758 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
27938677 TATTTTCTTG
* * *
27938687 AAATTTTA-CAAGGGGAAAATCGTTA
1 AAATTTTACCAAAGGTAAAATCGTAA
*
27938712 AAATTTTACCAATGGTAAAATCGTAA
1 AAATTTTACCAAAGGTAAAATCGTAA
* *
27938738 AAATTTTGCTAAAGGTAAAAT
1 AAATTTTACCAAAGGTAAAAT
27938759 AGGGATGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 8 0.20
26 32 0.80
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (26 bp):
AAATTTTACCAAAGGTAAAATCGTAA
Found at i:27940348 original size:75 final size:75
Alignment explanation
Indices: 27940217--27940357 Score: 178
Period size: 75 Copynumber: 1.9 Consensus size: 75
27940207 GCTTACATAT
* * * * *
27940217 ATGTATATGTTCTTTTATTGAATTTAGGAAGGACATTTATATAATTTTATATAAGATTCAATTAT
1 ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAATTGTATATAAGATTCAATTAT
27940282 GCAGGTATAC
66 GCAGGTATAC
* * *
27940292 ATGTATATGTTCTTGTAATGAATTTAAGTATGAAATTTATAT-A-TGTATATGGAAGATTCGATT
1 ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAATTGTATAT--AAGATTCAATT
27940355 ATG
64 ATG
27940358 TATATATATT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
73 6 0.11
74 1 0.02
75 49 0.88
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (75 bp):
ATGTATATGTTCTTGTAATGAATTTAAGAAGGAAATTTATATAATTGTATATAAGATTCAATTAT
GCAGGTATAC
Found at i:27940487 original size:41 final size:41
Alignment explanation
Indices: 27940439--27940518 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
27940429 TGATCGAATG
* * *
27940439 TTTCAGACTTTACGTCTAGCAGGTTTGATGCCGGTGAAATA
1 TTTCAGACTTTACGTCTAGCAGGCTTAATGCCGATGAAATA
*
27940480 TTTCAGACTTTATGTCTAGCAGGCTTAATGCCGATGAAA
1 TTTCAGACTTTACGTCTAGCAGGCTTAATGCCGATGAAA
27940519 CAATTCAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTCAGACTTTACGTCTAGCAGGCTTAATGCCGATGAAATA
Found at i:27940743 original size:31 final size:31
Alignment explanation
Indices: 27940702--27940806 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 31
27940692 GGCATATGTA
*
27940702 TATATGCATTCAGCTATTCATGTTTAAAGTG
1 TATATACATTCAGCTATTCATGTTTAAAGTG
* ** * *
27940733 TATATACATTC-GGTGATAAAAT-TTGTTATGTG
1 TATATACATTCAGCT-AT-TCATGTT-TAAAGTG
*
27940765 TATA-AGCATTCAACTATTCATGTTTAAAGTG
1 TATATA-CATTCAGCTATTCATGTTTAAAGTG
27940796 TATATACATTC
1 TATATACATTC
27940807 GATGATAATA
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
30 2 0.04
31 31 0.56
32 21 0.38
33 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (31 bp):
TATATACATTCAGCTATTCATGTTTAAAGTG
Found at i:27940746 original size:69 final size:67
Alignment explanation
Indices: 27940662--27940881 Score: 250
Period size: 63 Copynumber: 3.2 Consensus size: 67
27940652 TTGAAGAACA
* *
27940662 TGTATATACAGTCGGTGATAATACTTGTTAGGCATATGTATATATGCATTCAGCTATTCATGTTT
1 TGTATATACATTCGGTGATAATATTTGTTA-GCATATGTATATA-GCATTCAGCTATTCATGTTT
27940727 AAAG
64 AAAG
* * *
27940731 TGTATATACATTCGGTGATAAAATTTGTT---ATGTGTATA-AGCATTCAACTATTCATGTTTAA
1 TGTATATACATTCGGTGATAATATTTGTTAGCATATGTATATAGCATTCAGCTATTCATGTTTAA
27940792 AG
66 AG
* * * *
27940794 TGTATATACATTCGATGATAATATTTGTTAAGCATATATGTATATACACATTCGGCTATTCAAGT
1 TGTATATACATTCGGTGATAATATTTGTT-AGC--ATATGTATATA-GCATTCAGCTATTCATG-
*
27940859 TTTAAAT
61 TTTAAAG
*
27940866 TGTATATGCATTCGGT
1 TGTATATACATTCGGT
27940882 TTTAAGTGTT
Statistics
Matches: 127, Mismatches: 15, Indels: 15
0.81 0.10 0.10
Matches are distributed among these distances:
63 50 0.39
64 1 0.01
65 8 0.06
69 34 0.27
70 1 0.01
71 13 0.10
72 20 0.16
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (67 bp):
TGTATATACATTCGGTGATAATATTTGTTAGCATATGTATATAGCATTCAGCTATTCATGTTTAA
AG
Found at i:27943432 original size:27 final size:27
Alignment explanation
Indices: 27943402--27943453 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
27943392 CCTTGTAGGG
*
27943402 TTCGGCACAAAGACTTTTCTTTCATGA
1 TTCGCCACAAAGACTTTTCTTTCATGA
**
27943429 TTCGCCACAAAGGTTTTTCTTTCAT
1 TTCGCCACAAAGACTTTTCTTTCAT
27943454 AACGTGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (27 bp):
TTCGCCACAAAGACTTTTCTTTCATGA
Found at i:27946825 original size:45 final size:45
Alignment explanation
Indices: 27946774--27946860 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
27946764 TTAAACAAAA
* *
27946774 CTAACTTCATATATTTAAATATTCCACAAGTTTGTTTGATTAGTC
1 CTAACTTCATAAACTTAAATATTCCACAAGTTTGTTTGATTAGTC
27946819 CTAACTTCATAAACTTAAATATTCCACAAGTTTGTTTGATTA
1 CTAACTTCATAAACTTAAATATTCCACAAGTTTGTTTGATTA
27946861 CTCTTATGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (45 bp):
CTAACTTCATAAACTTAAATATTCCACAAGTTTGTTTGATTAGTC
Found at i:27955840 original size:18 final size:17
Alignment explanation
Indices: 27955790--27955841 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
27955780 CCTATAAAAA
*
27955790 AAAATTAATATGAAAAGT
1 AAAATTAATATGAATA-T
**
27955808 AAAACCAATAT-AATAT
1 AAAATTAATATGAATAT
27955824 ATAAATTAATATGAATAT
1 A-AAATTAATATGAATAT
27955842 TGAGAGATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 2 0.07
17 11 0.41
18 14 0.52
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (17 bp):
AAAATTAATATGAATAT
Found at i:27960019 original size:37 final size:37
Alignment explanation
Indices: 27959969--27960044 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
27959959 TAATGTTCCC
27959969 TTCATGTTATGGATTCCTCTAGTGAATCGAACTCTCT
1 TTCATGTTATGGATTCCTCTAGTGAATCGAACTCTCT
27960006 TTCATGTTATGGATTCCTCTAGTGAATCGAACTCTCT
1 TTCATGTTATGGATTCCTCTAGTGAATCGAACTCTCT
27960043 TT
1 TT
27960045 TGCTTCCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (37 bp):
TTCATGTTATGGATTCCTCTAGTGAATCGAACTCTCT
Found at i:27965377 original size:21 final size:21
Alignment explanation
Indices: 27965351--27965393 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
27965341 AAGACCAATC
27965351 ATGAGATGATTGTAATTACAT
1 ATGAGATGATTGTAATTACAT
27965372 ATGAGATGATTGTAATTACAT
1 ATGAGATGATTGTAATTACAT
27965393 A
1 A
27965394 CTCGTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (21 bp):
ATGAGATGATTGTAATTACAT
Found at i:27968644 original size:25 final size:25
Alignment explanation
Indices: 27968607--27968660 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
27968597 TTAAGGTTAT
* *
27968607 CGATTTATGGCTCGTGAGAGCATAC
1 CGATTTATAGCTCATGAGAGCATAC
27968632 CGATTTATAGCTCATGAGAGCATAC
1 CGATTTATAGCTCATGAGAGCATAC
27968657 CGAT
1 CGAT
27968661 CTTCAGCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (25 bp):
CGATTTATAGCTCATGAGAGCATAC
Found at i:27968668 original size:25 final size:25
Alignment explanation
Indices: 27968607--27968670 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
27968597 TTAAGGTTAT
** *
27968607 CGATTTATGGCTCGTGAGAGCATAC
1 CGATTTACAGCTCATGAGAGCATAC
*
27968632 CGATTTATAGCTCATGAGAGCATAC
1 CGATTTACAGCTCATGAGAGCATAC
27968657 CGATCTT-CAGCTCA
1 CGAT-TTACAGCTCA
27968671 AATGACCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (25 bp):
CGATTTACAGCTCATGAGAGCATAC
Found at i:27970307 original size:23 final size:24
Alignment explanation
Indices: 27970264--27970318 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
27970254 ATTTATTTTA
* *
27970264 AAAATAAATATATATTAAAAT-AG
1 AAAATAAATATAAATTAAAATAAC
27970287 AAAATAAATATAAAATT-AAATAAC
1 AAAATAAATAT-AAATTAAAATAAC
27970311 AAAATAAA
1 AAAATAAA
27970319 AATTTACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (24 bp):
AAAATAAATATAAATTAAAATAAC
Found at i:27972296 original size:29 final size:28
Alignment explanation
Indices: 27972237--27972305 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
27972227 TAATAACAAT
* *
27972237 TTTAAATTAAAACAAAAAAGGAAATGAC
1 TTTAAATTAAAAAAAAAAAGGAAAAGAC
* *
27972265 TTTAATTTCAAAAAAAAAAAGGAAAAGGC
1 TTTAAATT-AAAAAAAAAAAGGAAAAGAC
27972294 TTTCAAA-TAAAA
1 TTT-AAATTAAAA
27972306 TAAGTAGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
28 11 0.32
29 21 0.62
30 2 0.06
ACGTcount: A:0.59, C:0.07, G:0.10, T:0.23
Consensus pattern (28 bp):
TTTAAATTAAAAAAAAAAAGGAAAAGAC
Found at i:27973699 original size:20 final size:20
Alignment explanation
Indices: 27973674--27973713 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
27973664 AATATTTTCT
*
27973674 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
27973694 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
27973714 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:27973716 original size:34 final size:35
Alignment explanation
Indices: 27973662--27973728 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
27973652 CAAACACCAG
* *
27973662 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
27973697 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
27973729 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:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:27974390 original size:12 final size:12
Alignment explanation
Indices: 27974375--27974399 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27974365 ATAATTTATT
27974375 AAAAAATTATAA
1 AAAAAATTATAA
27974387 AAAAAATTATAA
1 AAAAAATTATAA
27974399 A
1 A
27974400 TTTTATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAATTATAA
Found at i:27976751 original size:13 final size:13
Alignment explanation
Indices: 27976713--27976751 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
27976703 TTAAACACTT
27976713 TAAATTTTTTTTA
1 TAAATTTTTTTTA
* * *
27976726 GAAATATTCTTTA
1 TAAATTTTTTTTA
27976739 TAAATTTTTTTTA
1 TAAATTTTTTTTA
27976752 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (13 bp):
TAAATTTTTTTTA
Found at i:27979474 original size:19 final size:20
Alignment explanation
Indices: 27979433--27979475 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
27979423 GTGAATTTTA
*
27979433 ATAAAATTAAAATTTAATGT
1 ATAAAATTAAAATTTAATAT
*
27979453 ATAAAATT-AAATTTTATAT
1 ATAAAATTAAAATTTAATAT
27979472 ATAA
1 ATAA
27979476 CATTGCACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAAAATTAAAATTTAATAT
Found at i:27983570 original size:22 final size:23
Alignment explanation
Indices: 27983545--27983601 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
27983535 TTAACCTTTA
27983545 TTTTATAAATTTTGTTCA-TAAT
1 TTTTATAAATTTTGTTCATTAAT
* * *
27983567 TTTTATAACTTTTTTTTTATTAAT
1 TTTTATAA-ATTTTGTTCATTAAT
27983591 TTTTA-AAATTT
1 TTTTATAAATTT
27983602 AAAAGGGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 11 0.38
23 9 0.31
24 9 0.31
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTATAAATTTTGTTCATTAAT
Found at i:27984307 original size:19 final size:18
Alignment explanation
Indices: 27984280--27984315 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
27984270 ATTACATAAA
27984280 AAATTTAAAATATAAAAG
1 AAATTTAAAATATAAAAG
*
27984298 AAATTATAAATTATAAAA
1 AAATT-TAAAATATAAAA
27984316 ATATATGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AAATTTAAAATATAAAAG
Found at i:27984308 original size:18 final size:17
Alignment explanation
Indices: 27984275--27984316 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
27984265 ATAAAATTAC
*
27984275 ATAAAAAATTTAAAA-T
1 ATAAAAAAATTAAAATT
27984291 ATAAAAGAAATTATAAATT
1 ATAAAA-AAATTA-AAATT
27984310 ATAAAAA
1 ATAAAAA
27984317 TATATGTAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.27
17 5 0.23
18 4 0.18
19 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAAAAAAATTAAAATT
Found at i:27991599 original size:44 final size:44
Alignment explanation
Indices: 27991517--27992018 Score: 284
Period size: 44 Copynumber: 10.7 Consensus size: 44
27991507 TTTTGATCCG
* * * *
27991517 CTCCACTGTAATCTGAGGGAGATAGGATTACTAACTTCAATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTA
** *
27991561 CTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGA
1 CTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATC---T---A
* * * *
27991611 TCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTT-T-GTTTTAATCCA
1 -CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TTCTAGCTTCAATCTA
* * * *
27991659 CTCCACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTA
* *
27991703 CTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGA
1 CTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATC---T---A
* * * * *
27991753 TCTACTCTACTGTAA-CTTCAGAGAGATAAGATCTT-TTGTTTTAATCCA
1 -CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT-TTCTAGCTTCAATCTA
* *
27991801 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTTAATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTA
* * *
27991845 CTCCGCTGTAATCTCAGGAAGATAAGATTTCTGGCTTCAATCTGATGCGA
1 CTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATC---T---A
* * *
27991895 TCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTT-T-GTTTTAAT-TCA
1 -CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TTCTAGCTTCAATCT-A
* *
27991943 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTA
* *
27991987 CTCCGCTGTAATCTCAGGGACATAAGATTTCT
1 CTCCACTGTAATCTCAGGGAGATAAGATTTCT
27992019 TCTGTTTGCT
Statistics
Matches: 353, Mismatches: 58, Indels: 94
0.70 0.11 0.19
Matches are distributed among these distances:
42 2 0.01
43 3 0.01
44 221 0.63
45 7 0.02
46 3 0.01
47 9 0.03
48 3 0.01
50 3 0.01
51 6 0.02
52 3 0.01
53 5 0.01
54 80 0.23
55 4 0.01
56 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTA
Found at i:27991698 original size:98 final size:95
Alignment explanation
Indices: 27991566--27991986 Score: 272
Period size: 98 Copynumber: 4.4 Consensus size: 95
27991556 ATCTACTCTG
* *
27991566 CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAA-CTTC
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT-AT--GATCTACTCTACTGTAATC-TC
27991630 AGAGAGATAAGATCCTTTGTTTTAATCCACTCCA
62 AGAGAGATAAGATCCTTTGTTTTAATCCACTCCA
* * * *
27991664 CTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATC--TG--CT-C-C-GCTGTAATCTCAGGG
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTATGATCTACTCTACTGTAATCTCAGAG
* *
27991722 AGATAAGAT--TTCTGGCTTCAATCTGATGCGATCTACTCTA
66 AGATAAGATCCTT-T-G-TT---T-T-A----ATCCACTCCA
* * * * *
27991762 CTGTAA-CTTCAGAGAGATAAGATCT-TTTG-TT---T-TA--ATCCACTCCACTGTAATCTCAG
1 CTGTAATC-TCAGGGAGATAAGAT-TACTAGCTTCAATCTATGATCTACTCTACTGTAATCTCAG
* * * * * *
27991818 GGAGATAAGATTAC-TAGCTTTAATCTACTCCG
64 AGAGATAAGA-TCCTTTGTTTTAATCCACTCCA
* * *
27991850 CTGTAATCTCAGGAAGATAAGATTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAA-CTTC
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCT-AT--GATCTACTCTACTGTAATC-TC
*
27991914 AGAGAGATAAGATCCTTTGTTTTAATTCACTCCA
62 AGAGAGATAAGATCCTTTGTTTTAATCCACTCCA
*
27991948 CTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTA
27991987 CTCCGCTGTA
Statistics
Matches: 248, Mismatches: 36, Indels: 79
0.68 0.10 0.22
Matches are distributed among these distances:
86 2 0.01
87 2 0.01
88 50 0.20
89 7 0.03
90 1 0.00
91 2 0.01
92 3 0.01
93 4 0.02
94 4 0.02
95 2 0.01
96 1 0.00
97 9 0.04
98 158 0.64
99 2 0.01
100 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (95 bp):
CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTATGATCTACTCTACTGTAATCTCAGAG
AGATAAGATCCTTTGTTTTAATCCACTCCA
Found at i:27991711 original size:142 final size:142
Alignment explanation
Indices: 27991452--27992018 Score: 990
Period size: 142 Copynumber: 4.0 Consensus size: 142
27991442 TGCTGCTGTA
* * * * *
27991452 GCTTCAATCTAATGCGATCTACTCTACTGTGACTTCAGAGAAATAAGATCCTTTGTTTTGATCCG
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCA
* * *
27991517 CTCCACTGTAATCTGAGGGAGATAGGATTACTAACTTCAATCTACTCTGCTGTAATCTCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAG
27991582 ATAAGATTTCTG
131 ATAAGATTTCTG
27991594 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCA
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCA
* *
27991659 CTCCACTGTAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAG
27991724 ATAAGATTTCTG
131 ATAAGATTTCTG
*
27991736 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTGTTTTAATCCA
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCA
* * *
27991801 CTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTTAATCTACTCCGCTGTAATCTCAGGAAG
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAG
27991866 ATAAGATTTCTG
131 ATAAGATTTCTG
*
27991878 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATTCA
1 GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCA
*
27991943 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAC
66 CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAG
27992008 ATAAGATTTCT
131 ATAAGATTTCT
27992019 TCTGTTTGCT
Statistics
Matches: 404, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 404 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
GCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCA
CTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAG
ATAAGATTTCTG
Found at i:28002169 original size:14 final size:14
Alignment explanation
Indices: 28002150--28002181 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28002140 CTATAAATCT
28002150 GCCTTCACCAGCTC
1 GCCTTCACCAGCTC
*
28002164 GCCTTCACTAGCTC
1 GCCTTCACCAGCTC
28002178 GCCT
1 GCCT
28002182 ACACGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.47, G:0.16, T:0.25
Consensus pattern (14 bp):
GCCTTCACCAGCTC
Found at i:28011197 original size:12 final size:12
Alignment explanation
Indices: 28011180--28011246 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
28011170 CCAATTCAAA
28011180 AAAAATCAAAAT
1 AAAAATCAAAAT
*
28011192 AAAAATCAAAAG
1 AAAAATCAAAAT
** *
28011204 ACAAAAAAAAGAAG
1 A-AAAATCAA-AAT
**
28011218 AAAAAGAAAAAT
1 AAAAATCAAAAT
*
28011230 CAAAATCAAAAT
1 AAAAATCAAAAT
28011242 AAAAA
1 AAAAA
28011247 AATGAAATAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
12 27 0.61
13 13 0.30
14 4 0.09
ACGTcount: A:0.78, C:0.07, G:0.06, T:0.09
Consensus pattern (12 bp):
AAAAATCAAAAT
Found at i:28011235 original size:38 final size:36
Alignment explanation
Indices: 28011187--28011264 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
28011177 AAAAAAAATC
28011187 AAAATAAAAATCAAAAGACAAAAAAAAGAAGA-AAAAGA
1 AAAATAAAAATC-AAA-ACAAAAAAAAGAA-ATAAAAGA
* * *
28011225 AAAATCAAAATCAAAATAAAAAAATGAAATAAAAGA
1 AAAATAAAAATCAAAACAAAAAAAAGAAATAAAAGA
28011261 AAAA
1 AAAA
28011265 AAGAAAGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 1 0.03
36 21 0.58
37 3 0.08
38 11 0.31
ACGTcount: A:0.78, C:0.05, G:0.08, T:0.09
Consensus pattern (36 bp):
AAAATAAAAATCAAAACAAAAAAAAGAAATAAAAGA
Found at i:28011241 original size:44 final size:44
Alignment explanation
Indices: 28011180--28011270 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 44
28011170 CCAATTCAAA
* *
28011180 AAAAATCAAAATAAAAATCAAAAGA-CAAAAAAAAGAAGAAAAAG
1 AAAAATCAAAATAAAAATAAAAAAATCAAAAAAAAGAA-AAAAAG
* * *
28011224 AAAAATCAAAATCAAAATAAAAAAATGAAATAAAAGAAAAAAAG
1 AAAAATCAAAATAAAAATAAAAAAATCAAAAAAAAGAAAAAAAG
28011268 AAA
1 AAA
28011271 GAGAAAAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 31 0.76
45 10 0.24
ACGTcount: A:0.78, C:0.05, G:0.08, T:0.09
Consensus pattern (44 bp):
AAAAATCAAAATAAAAATAAAAAAATCAAAAAAAAGAAAAAAAG
Found at i:28011654 original size:7 final size:7
Alignment explanation
Indices: 28011637--28011687 Score: 52
Period size: 7 Copynumber: 7.0 Consensus size: 7
28011627 TTTCAAAAAA
28011637 AAAAGATG
1 AAAA-ATG
28011645 AAAAATG
1 AAAAATG
28011652 -AAAATG
1 AAAAATG
28011658 AAAAATG
1 AAAAATG
28011665 AAAAAAATG
1 --AAAAATG
28011674 AAAAA-G
1 AAAAATG
28011680 TAAAAATG
1 -AAAAATG
28011688 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
6 7 0.18
7 19 0.50
8 5 0.13
9 7 0.18
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:28011655 original size:20 final size:20
Alignment explanation
Indices: 28011631--28011669 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28011621 AATGAATTTC
*
28011631 AAAAAAAAAAGATGAAAAATG
1 AAAATAAAAA-ATGAAAAATG
*
28011652 AAAATGAAAAATGAAAAA
1 AAAATAAAAAATGAAAAA
28011670 AATGAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (20 bp):
AAAATAAAAAATGAAAAATG
Found at i:28011658 original size:13 final size:13
Alignment explanation
Indices: 28011642--28011668 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28011632 AAAAAAAAAG
28011642 ATGAAAAATGAAA
1 ATGAAAAATGAAA
28011655 ATGAAAAATGAAA
1 ATGAAAAATGAAA
28011668 A
1 A
28011669 AAATGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:28011670 original size:22 final size:23
Alignment explanation
Indices: 28011645--28011687 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
28011635 AAAAAAGATG
*
28011645 AAAAATGAAAATG-AAAAATGAA
1 AAAAATGAAAAAGTAAAAATGAA
28011667 AAAAATGAAAAAGTAAAAATG
1 AAAAATGAAAAAGTAAAAATG
28011688 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (23 bp):
AAAAATGAAAAAGTAAAAATGAA
Found at i:28011685 original size:16 final size:16
Alignment explanation
Indices: 28011635--28011678 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
28011625 AATTTCAAAA
28011635 AAAAAAGATGAAAAATG
1 AAAAAA-ATGAAAAATG
28011652 ---AAAATGAAAAATG
1 AAAAAAATGAAAAATG
28011665 AAAAAAATGAAAAA
1 AAAAAAATGAAAAA
28011679 GTAAAAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 10 0.42
14 3 0.12
16 11 0.46
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (16 bp):
AAAAAAATGAAAAATG
Found at i:28013149 original size:50 final size:50
Alignment explanation
Indices: 28013090--28013553 Score: 301
Period size: 50 Copynumber: 9.3 Consensus size: 50
28013080 GCAGTAGAGC
* * *
28013090 AGATTAAAGCTACATCGGAGAATCTCGCTTCCCCGACATTACAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
* * * * * * ** **
28013140 AGATTAAAGCCACAGCGGCGAATC-CTACTTCCCTGGCAGTGCAGTGGAGC
1 AGATTAAAGCCACATCGGTGAATCTC-GCTTCCCCGACATTGCAGTTAAAA
* *
28013190 AGATTAAAGACACATCAGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
* * * * *** ** **
28013240 AGATTAAAGCCACAACGGCGAATC-CTACTTCCCTTG-TGGTGCAGTGGAGC
1 AGATTAAAGCCACATCGGTGAATCTC-GCTTCCC-CGACATTGCAGTTAAAA
28013290 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
* * ** ** * ** *** *
28013340 AGATTAAAGCTACAGCAATGAATCTTAC-TCCCCAAGCGGTGCAGAGGAAC
1 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGA-CATTGCAGTTAAAA
*
28013390 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
* * *** ** ** ** ** *
28013440 AGATTAGAGCTACAAT-AACGAATCTTACTTCCCAAACGGTGCAGTGGAAC
1 AGATTAAAGCCAC-ATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
* * * * *
28013490 AGATTAAAGCCACAACAGTGGATCTTGCTTCCCTGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
28013540 AGATTTAAA-CCACA
1 AGA-TTAAAGCCACA
28013554 ATGGCGAATC
Statistics
Matches: 303, Mismatches: 100, Indels: 22
0.71 0.24 0.05
Matches are distributed among these distances:
49 10 0.03
50 277 0.91
51 16 0.05
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGACATTGCAGTTAAAA
Found at i:28013235 original size:100 final size:100
Alignment explanation
Indices: 28013061--28013569 Score: 642
Period size: 100 Copynumber: 5.1 Consensus size: 100
28013051 AGAATTACAG
* * * * *
28013061 ATCCTACTTCCTTGGCGGTGCAGTAGAGCAGATTAAAGCTACATCGGAGAATCTCGCTTCCCCGA
1 ATCCTACTTCCCTAGCGGTGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGA
* *
28013126 CATTACAGTTAAAAAGATTAAAGCCACAGCGGCGA
66 CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGA
* * * *
28013161 ATCCTACTTCCCTGGCAGTGCAGTGGAGCAGATTAAAGACACATCAGTGAATCTCGCTTCCCCGA
1 ATCCTACTTCCCTAGCGGTGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGA
28013226 CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGA
66 CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGA
* *
28013261 ATCCTACTTCCCTTGTGGTGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGA
1 ATCCTACTTCCCTAGCGGTGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGA
* * ***
28013326 CATTGCAGTTAAAAAGATTAAAGCTACAGCAATGA
66 CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGA
* * * * * *
28013361 ATCTTACTCCCCAAGCGGTGCAGAGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGA
1 ATCCTACTTCCCTAGCGGTGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGA
* * ***
28013426 CATTGCAGTTAAAAAGATTAGAGCTACAATAACGA
66 CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGA
* * * * * * * * *
28013461 ATCTTACTTCCCAAACGGTGCAGTGGAACAGATTAAAGCCACAACAGTGGATCTTGCTTCCCTGA
1 ATCCTACTTCCCTAGCGGTGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGA
*
28013526 CATTGCAGTTAAAAAGATTTAAA-CCACAATGGCGA
66 CATTGCAGTTAAAAAGA-TTAAAGCCACAACGGCGA
*
28013561 ATCTTACTT
1 ATCCTACTT
28013570 TCCAAAAGTT
Statistics
Matches: 366, Mismatches: 42, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
100 362 0.99
101 4 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
ATCCTACTTCCCTAGCGGTGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTCGCTTCCCCGA
CATTGCAGTTAAAAAGATTAAAGCCACAACGGCGA
Found at i:28017433 original size:14 final size:14
Alignment explanation
Indices: 28017414--28017440 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28017404 AGATAAAATC
28017414 TGATAGAAATATCA
1 TGATAGAAATATCA
28017428 TGATAGAAATATC
1 TGATAGAAATATC
28017441 TGAGTTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (14 bp):
TGATAGAAATATCA
Found at i:28021295 original size:29 final size:28
Alignment explanation
Indices: 28021241--28021295 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
28021231 TATTAATAAT
*
28021241 TTATAAAAATTAAATTTAATATATAAAA
1 TTATAAAAATTAAATTTAATAAATAAAA
28021269 TTATACAAAATTAAAATTT-ATAAATAA
1 TTATA-AAAATT-AAATTTAATAAATAA
28021296 TATTTGGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 5 0.21
29 13 0.54
30 6 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
TTATAAAAATTAAATTTAATAAATAAAA
Found at i:28024158 original size:16 final size:16
Alignment explanation
Indices: 28024137--28024167 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28024127 CTATGCATGC
*
28024137 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
28024153 AAAATACAAAAGACA
1 AAAATACAAAAGACA
28024168 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:28039037 original size:21 final size:21
Alignment explanation
Indices: 28039013--28039069 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
28039003 CCGTTCAGCT
*
28039013 CTTATGAGCTTCTGTTCAACC
1 CTTATGAGCTTCTGTTCAACA
* * * *
28039034 CTTATGGGTTTCTGTTTAGCA
1 CTTATGAGCTTCTGTTCAACA
*
28039055 CTTATGTGCTTCTGT
1 CTTATGAGCTTCTGT
28039070 GCAGCCTTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (21 bp):
CTTATGAGCTTCTGTTCAACA
Found at i:28041531 original size:25 final size:25
Alignment explanation
Indices: 28041503--28041556 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
28041493 ACATGAGCCA
*
28041503 TGAATCAGAATGCTCACACGAGTTG
1 TGAATCAAAATGCTCACACGAGTTG
28041528 TGAATCAAAATGCTCACACGAGTTG
1 TGAATCAAAATGCTCACACGAGTTG
28041553 TGAA
1 TGAA
28041557 AATGGGCCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (25 bp):
TGAATCAAAATGCTCACACGAGTTG
Found at i:28046802 original size:25 final size:25
Alignment explanation
Indices: 28046774--28046881 Score: 189
Period size: 25 Copynumber: 4.3 Consensus size: 25
28046764 TCAAAATAAC
* * *
28046774 TCAAAAAAATTTCTATTTTATTACT
1 TCAAATAAACTTCTATTTTATTACA
28046799 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAACTTCTATTTTATTACA
28046824 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAACTTCTATTTTATTACA
28046849 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAACTTCTATTTTATTACA
28046874 TCAAATAA
1 TCAAATAA
28046882 TATAAAAAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 80 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.44
Consensus pattern (25 bp):
TCAAATAAACTTCTATTTTATTACA
Found at i:28046912 original size:44 final size:44
Alignment explanation
Indices: 28046849--28046942 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
28046839 TTTTATTACA
* **
28046849 TCAAATAAACTTCTATTTTATTACATCAAATAATATAAAAAAAC
1 TCAAAAAAACTTCTATTTTATTACAAAAAATAATATAAAAAAAC
* * * *
28046893 TCAAAAAAATTTCTATTTTATTACAAAAAATAATATCAAAATAT
1 TCAAAAAAACTTCTATTTTATTACAAAAAATAATATAAAAAAAC
28046937 TCAAAA
1 TCAAAA
28046943 TATTTGTACA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (44 bp):
TCAAAAAAACTTCTATTTTATTACAAAAAATAATATAAAAAAAC
Found at i:28047382 original size:18 final size:18
Alignment explanation
Indices: 28047356--28047393 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28047346 CTCAGAAAAA
*
28047356 GATACATATAAGGGTTAG
1 GATACATATAAGGGCTAG
*
28047374 GATATATATAAGGGCTAG
1 GATACATATAAGGGCTAG
28047392 GA
1 GA
28047394 AACGCACCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.26
Consensus pattern (18 bp):
GATACATATAAGGGCTAG
Found at i:28049117 original size:11 final size:11
Alignment explanation
Indices: 28049101--28049143 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
28049091 ATTTTTATAG
28049101 TTTAAAAAAAT
1 TTTAAAAAAAT
28049112 TTTAAAAAAAT
1 TTTAAAAAAAT
*
28049123 TTT-AAAAATT
1 TTTAAAAAAAT
28049133 ATTTAAAAAAA
1 -TTTAAAAAAA
28049144 GGGAGTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 6 0.21
11 17 0.61
12 5 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TTTAAAAAAAT
Found at i:28051904 original size:11 final size:11
Alignment explanation
Indices: 28051888--28051922 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28051878 CATCTCAGAA
28051888 AGAAATTTCAT
1 AGAAATTTCAT
28051899 AGAAATTTCAT
1 AGAAATTTCAT
* *
28051910 AAAAAATTCAT
1 AGAAATTTCAT
28051921 AG
1 AG
28051923 CACAATTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (11 bp):
AGAAATTTCAT
Found at i:28058998 original size:35 final size:35
Alignment explanation
Indices: 28058912--28059023 Score: 181
Period size: 35 Copynumber: 3.2 Consensus size: 35
28058902 TACTCTCTGT
*
28058912 TTGGTGTGTTTCAGTTGGACTAGCTCTTATGAGTA
1 TTGGTGTGTTTCAGTTGGACTAGCTCTTATGAGCA
* *
28058947 TTGGT-TGTTTTAGTTGGACTAGCTCTTATCAGCA
1 TTGGTGTGTTTCAGTTGGACTAGCTCTTATGAGCA
*
28058981 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGTTGGACTAGCTCTTATGAGCA
28059016 TTGGTGTG
1 TTGGTGTG
28059024 ATTTGGATGG
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
34 31 0.44
35 39 0.56
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.43
Consensus pattern (35 bp):
TTGGTGTGTTTCAGTTGGACTAGCTCTTATGAGCA
Found at i:28059071 original size:36 final size:35
Alignment explanation
Indices: 28058912--28059073 Score: 137
Period size: 35 Copynumber: 4.6 Consensus size: 35
28058902 TACTCTCTGT
** * * * *
28058912 TTGGTGTGTTTCAGTTGGACTAGCTCTTATGAGTA
1 TTGGTGTGTTTTGGTTGGATTGGCTCATATGAGCA
* * * * *
28058947 TTGGT-TGTTTTAGTTGGACTAGCTCTTATCAGCA
1 TTGGTGTGTTTTGGTTGGATTGGCTCATATGAGCA
* * * *
28058981 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTTGGTTGGATTGGCTCATATGAGCA
* * *
28059016 TTGGTGTGATTTGGATGGATTGGCTCATGTGAGCA
1 TTGGTGTGTTTTGGTTGGATTGGCTCATATGAGCA
*
28059051 TCTGTTGTGTTTTGGTTGGATTG
1 T-TGGTGTGTTTTGGTTGGATTG
28059074 ACGATGTACT
Statistics
Matches: 109, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
34 31 0.28
35 60 0.55
36 18 0.17
ACGTcount: A:0.15, C:0.11, G:0.31, T:0.43
Consensus pattern (35 bp):
TTGGTGTGTTTTGGTTGGATTGGCTCATATGAGCA
Found at i:28067980 original size:43 final size:43
Alignment explanation
Indices: 28067825--28067981 Score: 124
Period size: 43 Copynumber: 3.7 Consensus size: 43
28067815 TGTGATTATG
* * *
28067825 TGTAAGACCACGTTTGGGATGTTGGTATCGAT-TTGTGATTTACA
1 TGTAAGACCACGTCTGGGATGTTGGCATCGGTATT-TGATTT-CA
* ** ** ** * *
28067869 TGTAAGACCATGTCTGGGACATCAGCATC-GTATACGAGTTCG
1 TGTAAGACCACGTCTGGGATGTTGGCATCGGTATTTGATTTCA
* *
28067911 TGTAAGACC-CTGTCGGGGACAG-TGGCATCGGTATTTGATTTCA
1 TGTAAGACCAC-GTCTGGGA-TGTTGGCATCGGTATTTGATTTCA
28067954 TGTAAGACCACGTCTGGGATGTTGGCAT
1 TGTAAGACCACGTCTGGGATGTTGGCAT
28067982 TGTATGAGTT
Statistics
Matches: 83, Mismatches: 24, Indels: 13
0.69 0.20 0.11
Matches are distributed among these distances:
42 23 0.28
43 36 0.43
44 24 0.29
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGATGTTGGCATCGGTATTTGATTTCA
Found at i:28075650 original size:43 final size:43
Alignment explanation
Indices: 28075494--28075651 Score: 135
Period size: 43 Copynumber: 3.7 Consensus size: 43
28075484 AAGTGATTAT
28075494 GTGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGTGATTTAC
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATT-TGATTT-C
* * * ** * ** *
28075538 GTGTAAGACCATGTCTTGGACATCAGTATCG-TATACGAGTTC
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTC
* *
28075580 GTGTAAGACC-CTGTCGGGGATAG-TGGCATCGATATTTGATTTC
1 GTGTAAGACCAC-GTCTGGGA-CGTTGGCATCGATATTTGATTTC
* *
28075623 ATGTAAGACCACGTCTAGGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGACGTTGGCAT
28075652 TGTATGAGCT
Statistics
Matches: 84, Mismatches: 24, Indels: 13
0.69 0.20 0.11
Matches are distributed among these distances:
42 23 0.27
43 34 0.40
44 27 0.32
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTC
Found at i:28077633 original size:24 final size:24
Alignment explanation
Indices: 28077587--28077633 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28077577 TGATCTAAAA
* *
28077587 TCAAACCATTTCATGCATAATTTC
1 TCAAACCACTTCAAGCATAATTTC
28077611 TCAAACCACTT-AAGCATACATTT
1 TCAAACCACTTCAAGCATA-ATTT
28077634 AATGGGTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (24 bp):
TCAAACCACTTCAAGCATAATTTC
Found at i:28078604 original size:16 final size:15
Alignment explanation
Indices: 28078580--28078609 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
28078570 CTTTAATTAC
28078580 TTTTAATTTTATATG
1 TTTTAATTTTATATG
28078595 TTTTATATTTTATAT
1 TTTTA-ATTTTATAT
28078610 TTTATTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTAATTTTATATG
Found at i:28088177 original size:15 final size:17
Alignment explanation
Indices: 28088146--28088178 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
28088136 CTTTATATTT
28088146 AATACATAAATTTTATA
1 AATACATAAATTTTATA
28088163 AATA-ATAAA-TTTATA
1 AATACATAAATTTTATA
28088178 A
1 A
28088179 GTTTATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AATACATAAATTTTATA
Found at i:28098594 original size:19 final size:20
Alignment explanation
Indices: 28098572--28098620 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
28098562 AAAAAACCTA
*
28098572 TAAAATTA-TTAAAAATTAT
1 TAAAATTATTTAAAAAGTAT
*
28098591 TAAATTTATTTAAAAAGTA-
1 TAAAATTATTTAAAAAGTAT
*
28098610 TAAAAATATTT
1 TAAAATTATTT
28098621 TTCAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAAATTATTTAAAAAGTAT
Found at i:28098997 original size:5 final size:6
Alignment explanation
Indices: 28098979--28099004 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28098969 ATAATCACAA
28098979 TTCTTT TTCTTT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TT
28099005 AAATACATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTCTTT
Found at i:28104013 original size:19 final size:17
Alignment explanation
Indices: 28103974--28104011 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
28103964 TTTCTTTTTT
*
28103974 TAAA-AAAATATATGTA
1 TAAATAAAATATATATA
28103990 TAAATAAAATATATAATA
1 TAAATAAAATATAT-ATA
28104008 TAAA
1 TAAA
28104012 ATCAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 9 0.47
18 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
TAAATAAAATATATATA
Found at i:28104173 original size:18 final size:18
Alignment explanation
Indices: 28104150--28104186 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28104140 AAAAAAGTAG
28104150 ATAAATATATAA-ACTAAT
1 ATAAATA-ATAATACTAAT
28104168 ATAAATAATAATACTAAT
1 ATAAATAATAATACTAAT
28104186 A
1 A
28104187 ATAATGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAATAATACTAAT
Found at i:28105759 original size:44 final size:44
Alignment explanation
Indices: 28105683--28106211 Score: 246
Period size: 44 Copynumber: 12.2 Consensus size: 44
28105673 ACTTGATGAG
* * * *
28105683 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTAT-TACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATCGACTTCA
*
28105727 AT-TCGCTCCACTACAACTTCAGGGAGATAAGATTATCGACTTCA
1 ATCT-GCTCCACTGCAACTTCAGGGAGATAAGATTATCGACTTCA
* **
28105771 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATT-TGCTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-CGACTTCA
* * ** * * * ***
28105815 GTCTGCCCCACTGTGACTTCAGGGGGATAAAACTTGTTTTC-TCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTATCGACTTCA
* ** * *
28105859 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CCT-GA-TGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGACTTCA
** * * ** * * *
28105900 ATCCACTCTACTGCAACTTTAAAGAAATAAGATCTAT-TACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATCGACTTCA
* * * * *
28105944 ATCCGCTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGACTTCA
* * ** *
28105988 ATCTGCTCTACTGTAACTTCAGGGAGATAAGATT-TGCTTCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAT-CGACTTCA
* * **
28106032 ATCTGC-CCTACTGCAACTTCA-GTAGGATAAGACT-T-GTTTTATCA
1 ATCTGCTCC-ACTGCAACTTCAGGGA-GATAAGATTATCG-ACT-TCA
* * * * ** * *
28106076 GTCTGCTCCATTGCAACTTTAGGAAGATAAGA-CCT-GA-TGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGACTTCA
** * * * *
28106117 ATCCACTCTACTGCAACTTCAGAGAGATAAGATCTAT-TACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TATCGACTTCA
** * * * *
28106161 ATCCACTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGACTTCA
28106205 ATCTGCT
1 ATCTGCT
28106212 TCCTTACACT
Statistics
Matches: 362, Mismatches: 100, Indels: 46
0.71 0.20 0.09
Matches are distributed among these distances:
41 50 0.14
42 2 0.01
43 21 0.06
44 278 0.77
45 10 0.03
46 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTATCGACTTCA
Found at i:28106069 original size:217 final size:217
Alignment explanation
Indices: 28105670--28106211 Score: 843
Period size: 217 Copynumber: 2.5 Consensus size: 217
28105660 TCTAGTCGGC
* * ** *
28105670 AAGACTTGATGAGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATTCGCTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
* * *
28105735 CACTACAACTTCAGGGAGATAAGATTATCGACTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
66 CACTACAACTTTAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
** * *
28105800 AGATTTGCTTCTTCAGTCTGCCCCACTGTGACTTCAGGGGGATAAAACTTGTTTTCTCAGTCTGC
131 AGATTTGCTTCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAAACTTGTTTTATCAGTCTGC
*
28105865 TCCACTGCAACTTCAGGGAGAT
196 TCCACTGCAACTTCAGGAAGAT
* * *
28105887 AAGACCTGATGCGATCCACTCTACTGCAACTTTAAAGAAATAAGATCTATTACTTTAATCCGCTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
* * *
28105952 CACTACAACTTTAGGGAGATAGGATTATCGGCTTCAATCTGCTCTACTGTAACTTCAGGGAGATA
66 CACTACAACTTTAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
* * *
28106017 AGATTTGCTTCTTC-GATCTGCCCTACTGCAACTTCAGTAGGATAAGACTTGTTTTATCAGTCTG
131 AGATTTGCTTCTTCAG-TCTGCCCCACTGCAACTTCAGGAGGATAAAACTTGTTTTATCAGTCTG
* *
28106081 CTCCATTGCAACTTTAGGAAGAT
195 CTCCACTGCAACTTCAGGAAGAT
*
28106104 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCACTC
1 AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
28106169 CACTACAACTTTAGGGAGATAGGATTATCGGCTTCAATCTGCT
66 CACTACAACTTTAGGGAGATAGGATTATCGGCTTCAATCTGCT
28106212 TCCTTACACT
Statistics
Matches: 296, Mismatches: 28, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
216 1 0.00
217 295 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (217 bp):
AAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTC
CACTACAACTTTAGGGAGATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATA
AGATTTGCTTCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAAACTTGTTTTATCAGTCTGC
TCCACTGCAACTTCAGGAAGAT
Found at i:28107729 original size:14 final size:14
Alignment explanation
Indices: 28107710--28107760 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 14
28107700 CCTTAGCCTC
28107710 TTCATTTTTACTTT
1 TTCATTTTTACTTT
*
28107724 TTCATTTTTTCATTT
1 TTCATTTTTAC-TTT
*
28107739 TTCATTTTCA-TTT
1 TTCATTTTTACTTT
28107752 TTCATTTTT
1 TTCATTTTT
28107761 TTGACTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.34
14 10 0.31
15 11 0.34
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCATTTTTACTTT
Found at i:28107732 original size:8 final size:7
Alignment explanation
Indices: 28107710--28107760 Score: 70
Period size: 7 Copynumber: 7.3 Consensus size: 7
28107700 CCTTAGCCTC
28107710 TTCATTT
1 TTCATTT
28107717 TT-ACTTT
1 TTCA-TTT
28107724 TTCATTTT
1 TTCA-TTT
28107732 TTCATTT
1 TTCATTT
28107739 TTCA-TT
1 TTCATTT
28107745 TTCATTT
1 TTCATTT
28107752 TTCATTT
1 TTCATTT
28107759 TT
1 TT
28107761 TTGACTCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
6 7 0.17
7 25 0.62
8 8 0.20
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCATTT
Found at i:28108690 original size:6 final size:6
Alignment explanation
Indices: 28108681--28108729 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
28108671 TTTCTCTCAT
* * *
28108681 TTTTTA TTTTTTA TTTTGA TTTTTGA TTTTGA TTTTTA TTTTGA TTTTT
1 TTTTTA -TTTTTA TTTTTA TTTTT-A TTTTTA TTTTTA TTTTTA TTTTT
28108730 TTTGAAAGGA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
6 24 0.69
7 11 0.31
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:28108702 original size:13 final size:13
Alignment explanation
Indices: 28108681--28108730 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
28108671 TTTCTCTCAT
*
28108681 TTTTTATTTTTTA
1 TTTTGATTTTTTA
*
28108694 TTTTGATTTTTGA
1 TTTTGATTTTTTA
28108707 TTTTGA-TTTTTA
1 TTTTGATTTTTTA
28108719 TTTTGATTTTTT
1 TTTTGATTTTTT
28108731 TTGAAAGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 11 0.33
13 22 0.67
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (13 bp):
TTTTGATTTTTTA
Found at i:28108704 original size:7 final size:7
Alignment explanation
Indices: 28108679--28108729 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
28108669 CTTTTCTCTC
*
28108679 ATTTTTT
1 ATTTTTG
*
28108686 ATTTTTT
1 ATTTTTG
28108693 A-TTTTG
1 ATTTTTG
28108699 ATTTTTG
1 ATTTTTG
28108706 A-TTTTG
1 ATTTTTG
28108712 ATTTTT-
1 ATTTTTG
28108718 A-TTTTG
1 ATTTTTG
28108724 ATTTTT
1 ATTTTT
28108730 TTTGAAAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 4 0.10
6 13 0.33
7 22 0.56
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (7 bp):
ATTTTTG
Found at i:28113750 original size:18 final size:18
Alignment explanation
Indices: 28113727--28113763 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28113717 AAAAATGTAG
28113727 ATAAATATATAA-ACTAAT
1 ATAAATA-ATAATACTAAT
28113745 ATAAATAATAATACTAAT
1 ATAAATAATAATACTAAT
28113763 A
1 A
28113764 ATAATGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAATAATACTAAT
Found at i:28115397 original size:27 final size:27
Alignment explanation
Indices: 28115325--28115448 Score: 144
Period size: 27 Copynumber: 4.7 Consensus size: 27
28115315 AACCCTGATC
* *
28115325 TACAGCTTGTGCGAGCAACCTAAATAT
1 TACAGCTTGTGTGAGCAATCTAAATAT
* *
28115352 CACAAC-T-TGTGAGCAATCTAAATAT
1 TACAGCTTGTGTGAGCAATCTAAATAT
* *
28115377 TACAGCTTGTGTGAGAAATCTAAACAT
1 TACAGCTTGTGTGAGCAATCTAAATAT
* *
28115404 TATAGCTTGTGTGAGCAATCTACATAT
1 TACAGCTTGTGTGAGCAATCTAAATAT
* *
28115431 TACAACTTGTGTAAGCAA
1 TACAGCTTGTGTGAGCAA
28115449 ACCTAAATGA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
25 20 0.25
26 2 0.03
27 58 0.73
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (27 bp):
TACAGCTTGTGTGAGCAATCTAAATAT
Found at i:28116411 original size:25 final size:25
Alignment explanation
Indices: 28116383--28116431 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
28116373 TAACAAATCA
* **
28116383 AGCAGAATAGAATTAAACAGAGCAG
1 AGCAGAACAGAACAAAACAGAGCAG
28116408 AGCAGAACAGAACAAAACAGAGCA
1 AGCAGAACAGAACAAAACAGAGCA
28116432 TATTAGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.55, C:0.16, G:0.22, T:0.06
Consensus pattern (25 bp):
AGCAGAACAGAACAAAACAGAGCAG
Found at i:28116439 original size:25 final size:25
Alignment explanation
Indices: 28116397--28116446 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28116387 GAATAGAATT
*
28116397 AAACAGAGCAGAGCAGAACAGAACA
1 AAACAGAGCAGAGCAGAACAAAACA
* **
28116422 AAACAGAGCATATTAGAACAAAACA
1 AAACAGAGCAGAGCAGAACAAAACA
28116447 GAGTAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.58, C:0.18, G:0.18, T:0.06
Consensus pattern (25 bp):
AAACAGAGCAGAGCAGAACAAAACA
Done.