Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 6 of 131
Found at i:1935168 original size:3 final size:3
Alignment explanation
Indices: 1935153--1935191 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1935143 TACTATGACT
*
1935153 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1935192 CTGTACATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1935466 original size:16 final size:16
Alignment explanation
Indices: 1935433--1935466 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1935423 TATTGTACAC
**
1935433 ATATATATGTATTTGA
1 ATATATATGTATGCGA
1935449 ATATATATGTATGCGA
1 ATATATATGTATGCGA
1935465 AT
1 AT
1935467 TTTCATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (16 bp):
ATATATATGTATGCGA
Found at i:1938601 original size:9 final size:8
Alignment explanation
Indices: 1938584--1938608 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1938574 CCTGCCCGAT
1938584 AATAAAAA
1 AATAAAAA
1938592 AATAAAAA
1 AATAAAAA
1938600 AATAAAAA
1 AATAAAAA
1938608 A
1 A
1938609 TAGTCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAAAA
Found at i:1941635 original size:48 final size:47
Alignment explanation
Indices: 1941577--1941729 Score: 198
Period size: 48 Copynumber: 3.2 Consensus size: 47
1941567 AACAACATTC
1941577 GGACAGCATTAATTTGTACAAAAATGGACAGCATTTAAGCACCAATTT
1 GGACAGCATTAATTTGT-CAAAAATGGACAGCATTTAAGCACCAATTT
* ** * * *
1941625 GGACAACATTAATATACTCAAAAATGGACAGCAATTAATCATCAATTT
1 GGACAGCATTAAT-TTGTCAAAAATGGACAGCATTTAAGCACCAATTT
* * *
1941673 GGACAGCATTAATATGCTCAAAAATGGATAGCATTTAAGCACTAATTT
1 GGACAGCATTAATTTG-TCAAAAATGGACAGCATTTAAGCACCAATTT
1941721 GGACAGCAT
1 GGACAGCAT
1941730 CTTATCATCA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
48 86 0.98
49 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (47 bp):
GGACAGCATTAATTTGTCAAAAATGGACAGCATTTAAGCACCAATTT
Found at i:1941663 original size:26 final size:25
Alignment explanation
Indices: 1941624--1941707 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
1941614 AGCACCAATT
*
1941624 TGGACAACATTAATATACTCAAAAA
1 TGGACAGCATTAATATACTCAAAAA
* **
1941649 TGGACAGCAATTAAT-CA-TC-AATT
1 TGGACAGC-ATTAATATACTCAAAAA
*
1941672 TGGACAGCATTAATATGCTCAAAAA
1 TGGACAGCATTAATATACTCAAAAA
*
1941697 TGGATAGCATT
1 TGGACAGCATT
1941708 TAAGCACTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
22 6 0.13
23 10 0.22
24 4 0.09
25 20 0.43
26 6 0.13
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.27
Consensus pattern (25 bp):
TGGACAGCATTAATATACTCAAAAA
Found at i:1941728 original size:23 final size:23
Alignment explanation
Indices: 1941601--1941729 Score: 73
Period size: 23 Copynumber: 5.4 Consensus size: 23
1941591 TGTACAAAAA
*
1941601 TGGACAGCATTTAAGCACCAATT
1 TGGACAGCATTTAAGCACAAATT
* * **
1941624 TGGACAACATTAATATA-CTCAAAAA
1 TGGACAGCATT--TA-AGCACAAATT
* *
1941649 TGGACAGCAATTAATCATC-AATT
1 TGGACAGCATTTAAGCA-CAAATT
* * **
1941672 TGGACAGCATTAATATGCTCAAAAA
1 TGGACAGCATT--TAAGCACAAATT
* *
1941697 TGGATAGCATTTAAGCACTAATT
1 TGGACAGCATTTAAGCACAAATT
1941720 TGGACAGCAT
1 TGGACAGCAT
1941730 CTTATCATCA
Statistics
Matches: 75, Mismatches: 23, Indels: 16
0.66 0.20 0.14
Matches are distributed among these distances:
22 1 0.01
23 41 0.55
24 2 0.03
25 30 0.40
26 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (23 bp):
TGGACAGCATTTAAGCACAAATT
Found at i:1944360 original size:12 final size:12
Alignment explanation
Indices: 1944345--1944370 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1944335 AATCTTGATG
1944345 AAAATCTGCTTC
1 AAAATCTGCTTC
1944357 AAAATCTGCTTC
1 AAAATCTGCTTC
1944369 AA
1 AA
1944371 TGGTGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (12 bp):
AAAATCTGCTTC
Found at i:1950271 original size:22 final size:23
Alignment explanation
Indices: 1950234--1950276 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1950224 ACTATTTGGT
*
1950234 AGTTTGACTTTTTTTATATTTAA
1 AGTTTGACCTTTTTTATATTTAA
1950257 AGTTT-ACCTTTTTTATATTT
1 AGTTTGACCTTTTTTATATTT
1950277 GGAATTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (23 bp):
AGTTTGACCTTTTTTATATTTAA
Found at i:1950284 original size:22 final size:23
Alignment explanation
Indices: 1950243--1950292 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
1950233 TAGTTTGACT
1950243 TTTTTTATATTTAAAGTTTA-CC
1 TTTTTTATATTTAAAGTTTATCC
*
1950265 TTTTTTATATTTGGAA-TTTATCC
1 TTTTTTATATTT-AAAGTTTATCC
1950288 TTTTT
1 TTTTT
1950293 ATTTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.64
Consensus pattern (23 bp):
TTTTTTATATTTAAAGTTTATCC
Found at i:1961290 original size:9 final size:10
Alignment explanation
Indices: 1961263--1961291 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1961253 AATCATATCA
1961263 TTTAGAAAAT
1 TTTAGAAAAT
1961273 TTTAGAAAAT
1 TTTAGAAAAT
1961283 TTTA-AAAAT
1 TTTAGAAAAT
1961292 AATTTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
TTTAGAAAAT
Found at i:1962197 original size:22 final size:22
Alignment explanation
Indices: 1962169--1962212 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1962159 CAAAAAGAAA
1962169 AAAAAAAGCATTTTTTTTCAAT
1 AAAAAAAGCATTTTTTTTCAAT
1962191 AAAAAAAGCATTTTTTTTCAAT
1 AAAAAAAGCATTTTTTTTCAAT
1962213 CTTGAGATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (22 bp):
AAAAAAAGCATTTTTTTTCAAT
Found at i:1962651 original size:125 final size:126
Alignment explanation
Indices: 1962420--1962671 Score: 497
Period size: 125 Copynumber: 2.0 Consensus size: 126
1962410 ATATTATATG
1962420 TGTTTATATTTAACTATATTTATAATATGTTTGAGGATCAAATTGATAGATTGTATAAGTATTGA
1 TGTTTATATTTAACTATATTTATAATATGTTTGAGGATCAAATTGATAGATTGTATAAGTATTGA
1962485 TAACTAAATATGTTATTATACCGGTTAGAAAAAAATCTCATCATCACTTTAGTTAATAGAA
66 TAACTAAATATGTTATTATACCGGTTAGAAAAAAATCTCATCATCACTTTAGTTAATAGAA
1962546 TGTTTATA-TTAACTATATTTATAATATGTTTGAGGATCAAATTGATAGATTGTATAAGTATTGA
1 TGTTTATATTTAACTATATTTATAATATGTTTGAGGATCAAATTGATAGATTGTATAAGTATTGA
1962610 TAACTAAATATGTTATTATACCGGTTAGAAAAAAATCTCATCATCACTTTAGTTAATAGAA
66 TAACTAAATATGTTATTATACCGGTTAGAAAAAAATCTCATCATCACTTTAGTTAATAGAA
1962671 T
1 T
1962672 AACCAAAATA
Statistics
Matches: 126, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
125 118 0.94
126 8 0.06
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.40
Consensus pattern (126 bp):
TGTTTATATTTAACTATATTTATAATATGTTTGAGGATCAAATTGATAGATTGTATAAGTATTGA
TAACTAAATATGTTATTATACCGGTTAGAAAAAAATCTCATCATCACTTTAGTTAATAGAA
Found at i:1968728 original size:107 final size:106
Alignment explanation
Indices: 1968503--1968773 Score: 314
Period size: 107 Copynumber: 2.5 Consensus size: 106
1968493 TTTTCGAGTA
* * ** *
1968503 TTGGTCTATCAATGGCCGGCACCAAAATACGAAAAAAG-TAAGAAATTTTTTTTTGTGGTGGCCT
1 TTGGTCTGTCAATGGCCGGCACCAATATACGAAAAAAGTTAA-AAA-AATTTTTGGTGGTGGCCT
* * * **
1968567 GCCAATGGCCGGCACCACCTTTATGGAATTTTTTTTTTATATT
64 ACCAATGGCCAGCAACACCTTTATCAAATTTTTTTTTTATATT
* * * **
1968610 TT-TTCATGTCAATGGCAGGCACTAATATACGAAAAAAGTTAAAAAAAAATTTGGTGGTGGCCTA
1 TTGGTC-TGTCAATGGCCGGCACCAATATACGAAAAAAGTTAAAAAAATTTTTGGTGGTGGCCTA
*
1968674 CCAATGGCCAGCAACACCTTT-TCCAAATTTTTTTTTTTTACTT
65 CCAATGGCCAGCAACACCTTTAT-CAAATTTTTTTTTTATA-TT
*
1968717 TTGGTCTGTCAATGGCCGGCACCAGTATACGAAAAAAGTTTAAAAAAATTTTTGGTG
1 TTGGTCTGTCAATGGCCGGCACCAATATACGAAAAAAG-TTAAAAAAATTTTTGGTG
1968774 ACAACCTCCA
Statistics
Matches: 136, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
105 1 0.01
106 48 0.35
107 66 0.49
108 21 0.15
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (106 bp):
TTGGTCTGTCAATGGCCGGCACCAATATACGAAAAAAGTTAAAAAAATTTTTGGTGGTGGCCTAC
CAATGGCCAGCAACACCTTTATCAAATTTTTTTTTTATATT
Found at i:1970332 original size:107 final size:106
Alignment explanation
Indices: 1970171--1970615 Score: 476
Period size: 107 Copynumber: 4.2 Consensus size: 106
1970161 AAATTGTTGT
* * *
1970171 AAAGGTGGTGCCGGCCATTGGTAAGCCACCACCAAAATTTCTTTTTTTATTTTTTTCGTATACTG
1 AAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTT-TTTTTTTACTTTTTTCGTATACTG
*
1970236 GTGACGACCATTGACAGACCAAAAGTAAAAAAAACATTTGGAA
65 GTGACGACCATTGACAAACCAAAAGTAAAAAAAA-ATTTGGAA
* * *
1970279 AAAGGTAGTGCCGGTCATTGGCAGGCCACCACCCAAATTTTTTTTTTACTTTTTTCGTATACTGG
1 AAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTTTTTTTTTACTTTTTTCGTATACTGG
* *
1970344 TGCCGACCATTGACAAACCAAAAGTAAAAAAAAAAATTGGAA
66 TGACGACCATTGACAAACCAAAAGT-AAAAAAAAATTTGGAA
* *
1970386 AAAGGTGGTGCCGACCATTGGTAGGCC-CCAACCAAAATTTTTTTTTTAACTTTTTTCGTATACT
1 AAAGGTGGTGCCGGCCATTGGCAGGCCACC-ACCAAAATTTTTTTTTT-ACTTTTTTCGTATACT
* * *** *
1970450 GGTGTCTG-CCATTGACACAA-AAAAAGTAAAAAAAAATTCCCAT
64 GGTGAC-GACCATTGACA-AACCAAAAGTAAAAAAAAATTTGGAA
***** ** *
1970493 AAAGGTGGTGCCGGCCATTGGCAGGCCACCA-CAAAAAAAAATTTAAACTTTTTTCGTATACTAG
1 AAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTTTTTTTTTACTTTTTTCGTATACTGG
* *
1970557 TGATTG-CCATTGACACGAA--AAAAGTAAAAAAAAATTCT-CATA
66 TGA-CGACCATTGACA--AACCAAAAGTAAAAAAAAATT-TGGA-A
1970599 AAA-GTGGTGCCGGCCAT
1 AAAGGTGGTGCCGGCCAT
1970616 GGACAGACCA
Statistics
Matches: 291, Mismatches: 36, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
105 62 0.21
106 15 0.05
107 130 0.45
108 81 0.28
109 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (106 bp):
AAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATTTTTTTTTTACTTTTTTCGTATACTGG
TGACGACCATTGACAAACCAAAAGTAAAAAAAAATTTGGAA
Found at i:1970590 original size:215 final size:214
Alignment explanation
Indices: 1970171--1970590 Score: 512
Period size: 215 Copynumber: 2.0 Consensus size: 214
1970161 AAATTGTTGT
* *
1970171 AAAGGTGGTGCCGGCCATTGGTAAGCCACCACCAAAATTTCTTTTTTTATTTTTTTCGTATACTG
1 AAAGGTGGTGCCGACCATTGGTAAGCCACCACCAAAATTTCTTTTTTTACTTTTTTCGTATACTG
* ** *** *
1970236 GTGACGACCATTGACAGACCAAAAGTAAAAAAAACATTTGGAAAAAGGTAGTGCCGGTCATTGGC
66 GTGACGACCATTGACACAAAAAAAGTAAAAAAAACATTCCCAAAAAGGTAGTGCCGGCCATTGGC
* ***** ** *
1970301 AGGCCACCACCCAAATTTTTTTTTTACTTTTTTCGTATACTGGTGCCGACCATTGACAAACCAAA
131 AGGCCACCACCAAAAAAAAATTTAAACTTTTTTCGTATACTAGTGCCGACCATTGACAAA-CAAA
1970366 AGTAAAAAAAAAAATTGGAA
195 AGTAAAAAAAAAAATTGGAA
*
1970386 AAAGGTGGTGCCGACCATTGGTAGGCC-CCAACCAAAATTT-TTTTTTTAACTTTTTTCGTATAC
1 AAAGGTGGTGCCGACCATTGGTAAGCCACC-ACCAAAATTTCTTTTTTT-ACTTTTTTCGTATAC
* * *
1970449 TGGTGTCTG-CCATTGACACAAAAAAAGTAAAAAAAA-ATTCCCATAAAGGTGGTGCCGGCCATT
64 TGGTGAC-GACCATTGACACAAAAAAAGTAAAAAAAACATTCCCAAAAAGGTAGTGCCGGCCATT
**
1970512 GGCAGGCCACCA-CAAAAAAAAATTTAAACTTTTTTCGTATACTAGTGATTG-CCATTGACACGA
128 GGCAGGCCACCACCAAAAAAAAATTTAAACTTTTTTCGTATACTAGTG-CCGACCATTGACA--A
1970575 A-AAAAGTAAAAAAAAA
190 ACAAAAGTAAAAAAAAA
1970591 TTCTCATAAA
Statistics
Matches: 175, Mismatches: 24, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
213 50 0.29
214 43 0.25
215 81 0.46
216 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (214 bp):
AAAGGTGGTGCCGACCATTGGTAAGCCACCACCAAAATTTCTTTTTTTACTTTTTTCGTATACTG
GTGACGACCATTGACACAAAAAAAGTAAAAAAAACATTCCCAAAAAGGTAGTGCCGGCCATTGGC
AGGCCACCACCAAAAAAAAATTTAAACTTTTTTCGTATACTAGTGCCGACCATTGACAAACAAAA
GTAAAAAAAAAAATTGGAA
Found at i:1970615 original size:49 final size:48
Alignment explanation
Indices: 1970562--1970665 Score: 138
Period size: 49 Copynumber: 2.1 Consensus size: 48
1970552 ACTAGTGATT
* *
1970562 GCCATTGACACGA-AAAAAGTAAAAAAAAATTCTCATAAAAGTGGTGCCG
1 GCCATTGACA-GACAAAAAGTAAAAAAAAATT-GCAAAAAAGTGGTGCCG
* * *
1970611 GCCATGGACAGACCAAAAGTAAAAAAAAATTGGAAAAAAGTGGTGCCG
1 GCCATTGACAGACAAAAAGTAAAAAAAAATTGCAAAAAAGTGGTGCCG
1970659 GCCATTG
1 GCCATTG
1970666 GCAGGCCACC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
48 22 0.46
49 26 0.54
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.16
Consensus pattern (48 bp):
GCCATTGACAGACAAAAAGTAAAAAAAAATTGCAAAAAAGTGGTGCCG
Found at i:1970635 original size:105 final size:105
Alignment explanation
Indices: 1970433--1970641 Score: 305
Period size: 105 Copynumber: 2.0 Consensus size: 105
1970423 TTTTTTTTTT
* *
1970433 AACTTTTTTCGTATACTGGTGTCTGCCATTGACACAAAAAAAGTAAAAAAAAATTCCCATAAAGG
1 AACTTTTTTCGTATACTAGTGTCTGCCATTGACACAAAAAAAGTAAAAAAAAATTCCCATAAAAG
* **
1970498 TGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAATTTA
66 TGGTGCCGGCCATTGGCAGACCAAAACAAAAAAAAATTTA
* *
1970538 AACTTTTTTCGTATACTAGTGAT-TGCCATTGACACGAAAAAAGTAAAAAAAAATTCTCATAAAA
1 AACTTTTTTCGTATACTAGTG-TCTGCCATTGACACAAAAAAAGTAAAAAAAAATTCCCATAAAA
*
1970602 GTGGTGCCGGCCA-TGGACAGACCAAAAGTAAAAAAAAATT
65 GTGGTGCCGGCCATTGG-CAGACCAAAA-CAAAAAAAAATT
1970642 GGAAAAAAGT
Statistics
Matches: 93, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
104 3 0.03
105 78 0.84
106 12 0.13
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.24
Consensus pattern (105 bp):
AACTTTTTTCGTATACTAGTGTCTGCCATTGACACAAAAAAAGTAAAAAAAAATTCCCATAAAAG
TGGTGCCGGCCATTGGCAGACCAAAACAAAAAAAAATTTA
Found at i:1970731 original size:151 final size:153
Alignment explanation
Indices: 1970471--1970777 Score: 431
Period size: 151 Copynumber: 2.0 Consensus size: 153
1970461 TTGACACAAA
* *
1970471 AAAAGTAAAAAAAAATTCCCATAAAGGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAATT
1 AAAAGTAAAAAAAAATTCCCAAAAAAGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAA-T
* * *
1970536 TAAACTTTTTTCGTATACTAGTGATTGCCATTGACACGAAAAAAGTAAAAAAAAATTCTCATAAA
65 TAAACTTTTTTCGTATACTAGTGACTGCCATTGACACGAAAAAAGTAAAAAAAAATTCCCACAAA
*
1970601 AGTGGTGCCGGCCATGGACAGACC
130 AGTGGTGCCAGCCATGGACAGACC
**
1970625 AAAAGTAAAAAAAAATT-GGAAAAAAGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAAAAAA-
1 AAAAGTAAAAAAAAATTCCCAAAAAAGTGGTGCCGGCCATTGGCAGGCCACCA-CAAAAAAAAAT
* * * * *
1970688 T-AACTTTTTTCGTATACTGGTGCCTGCTATTGATACGAAAAAAGTAAAAAAAATTTCCCACAAA
65 TAAACTTTTTTCGTATACTAGTGACTGCCATTGACACGAAAAAAGTAAAAAAAAATTCCCACAAA
* * *
1970752 GGTGGTGCCAGCTATTGACAGACC
130 AGTGGTGCCAGCCATGGACAGACC
1970776 AA
1 AA
1970778 TACCTGAATT
Statistics
Matches: 136, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
151 77 0.57
152 1 0.01
153 31 0.23
154 27 0.20
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (153 bp):
AAAAGTAAAAAAAAATTCCCAAAAAAGTGGTGCCGGCCATTGGCAGGCCACCACAAAAAAAAATT
AAACTTTTTTCGTATACTAGTGACTGCCATTGACACGAAAAAAGTAAAAAAAAATTCCCACAAAA
GTGGTGCCAGCCATGGACAGACC
Found at i:1981941 original size:2 final size:2
Alignment explanation
Indices: 1981934--1981959 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1981924 GAAAGAGAAC
1981934 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
1981960 ATGAGGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1988246 original size:20 final size:20
Alignment explanation
Indices: 1988204--1988246 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1988194 TTAAAATTAG
*
1988204 AAAATATCAAAATTTAGTTT
1 AAAATATCAAAATTTAGTAT
*
1988224 AAAATATTAAAATATTA-TAT
1 AAAATATCAAAAT-TTAGTAT
1988244 AAA
1 AAA
1988247 TCATTACAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATATCAAAATTTAGTAT
Found at i:1989211 original size:20 final size:19
Alignment explanation
Indices: 1989164--1989262 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 19
1989154 TGGTGTAGGG
*
1989164 TTAGAAATTTTGGTAAAGTC
1 TTAGAAATATTGGTAAA-TC
** *
1989184 CCATAAATATTGGTAAATC
1 TTAGAAATATTGGTAAATC
*
1989203 TATAGAAATTTTGGTAAATC
1 T-TAGAAATATTGGTAAATC
* * ** *
1989223 GTCAGATATATTAATAAGTCC
1 -TTAGAAATATTGGTAAAT-C
1989244 TTAGAAATATTGGTAAATC
1 TTAGAAATATTGGTAAATC
1989263 GTCGAATGTT
Statistics
Matches: 57, Mismatches: 19, Indels: 7
0.69 0.23 0.08
Matches are distributed among these distances:
19 3 0.05
20 52 0.91
21 2 0.04
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (19 bp):
TTAGAAATATTGGTAAATC
Found at i:1989234 original size:40 final size:40
Alignment explanation
Indices: 1989164--1989299 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
1989154 TGGTGTAGGG
* * *
1989164 TTAGAAATTTTGGTAAAGTC-CCATAAATATTGGTAAAT-C
1 TTAGAAATTTTGGTAAA-TCGTCAGATATATTGGTAAATCC
** *
1989203 TATAGAAATTTTGGTAAATCGTCAGATATATTAATAAGTCC
1 T-TAGAAATTTTGGTAAATCGTCAGATATATTGGTAAATCC
* * *
1989244 TTAGAAATATTGGTAAATCGTC-GAATGTTTTGGTAAATCC
1 TTAGAAATTTTGGTAAATCGTCAG-ATATATTGGTAAATCC
* *
1989284 TTTGAAAATTTGGTAA
1 TTAGAAATTTTGGTAA
1989300 TTGTTAAGAC
Statistics
Matches: 78, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (40 bp):
TTAGAAATTTTGGTAAATCGTCAGATATATTGGTAAATCC
Found at i:1989356 original size:20 final size:21
Alignment explanation
Indices: 1989331--1989455 Score: 93
Period size: 20 Copynumber: 6.2 Consensus size: 21
1989321 TTTAGAAAAT
1989331 TTAGAAATATTGGTAAAAT-A
1 TTAGAAATATTGGTAAAATCA
* *
1989351 TTAGAAATTTTGGTAAAGTCCA
1 TTAGAAATATTGGTAAAAT-CA
* * *
1989373 --ATAAATATTGATAAAATGA
1 TTAGAAATATTGGTAAAATCA
* *
1989392 -TAGAAATTTTGGT-AAATCC
1 TTAGAAATATTGGTAAAATCA
* *
1989411 TTAGAAATGTTGGT-AAATCG
1 TTAGAAATATTGGTAAAATCA
* *
1989431 TTAGATATATTGGTAAATTC-
1 TTAGAAATATTGGTAAAATCA
1989451 TTAGA
1 TTAGA
1989456 TATTTTGATA
Statistics
Matches: 83, Mismatches: 17, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
19 5 0.06
20 73 0.88
21 4 0.05
22 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.37
Consensus pattern (21 bp):
TTAGAAATATTGGTAAAATCA
Found at i:1989598 original size:20 final size:20
Alignment explanation
Indices: 1989553--1989640 Score: 65
Period size: 20 Copynumber: 4.4 Consensus size: 20
1989543 AAAATGATAT
* *
1989553 AAATTTTGGTAACTCATTA-
1 AAATTTTGATAAATCATTAG
*
1989572 AATATTTTGATAAATCCTTAG
1 AA-ATTTTGATAAATCATTAG
*
1989593 AAATTTT-AGTAAATCGTT-G
1 AAATTTTGA-TAAATCATTAG
* * *
1989612 AATATATTGATAAAACAATAG
1 AA-ATTTTGATAAATCATTAG
1989633 AAATTTTG
1 AAATTTTG
1989641 GTAATTGTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
19 6 0.11
20 42 0.78
21 6 0.11
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (20 bp):
AAATTTTGATAAATCATTAG
Found at i:1989616 original size:40 final size:40
Alignment explanation
Indices: 1989535--1989644 Score: 112
Period size: 40 Copynumber: 2.8 Consensus size: 40
1989525 AGTTTCATAA
* ** * *
1989535 ATATTGGTAAAATGATATAAATTTTGGTAACTCATTAAAT
1 ATATTGATAAAACAATAGAAATTTTGGTAAATCATTAAAT
* * ** * * *
1989575 ATTTTGATAAATCCTTAGAAATTTTAGTAAATCGTTGAAT
1 ATATTGATAAAACAATAGAAATTTTGGTAAATCATTAAAT
1989615 ATATTGATAAAACAATAGAAATTTTGGTAA
1 ATATTGATAAAACAATAGAAATTTTGGTAA
1989645 TTGTTAAGAC
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.39
Consensus pattern (40 bp):
ATATTGATAAAACAATAGAAATTTTGGTAAATCATTAAAT
Found at i:1989622 original size:158 final size:158
Alignment explanation
Indices: 1989319--1989624 Score: 388
Period size: 158 Copynumber: 1.9 Consensus size: 158
1989309 CTTCGTATAG
* *
1989319 GGTTTAGAAAATTTAGAAATATTGGTAAAATATTAGAAATTTTGGTAAAGTCCAATAAATATTGA
1 GGTTTAGAAAATTTAGAAATATTGGTAAAATATTAAAAATTATGGTAAAGTCCAATAAATATTGA
* * * * *
1989384 TAAAATGATAGAAATTTTGGTAAATCCTTAGAAATGTTGGTAAATCGTTAGATATATTGGTAAAT
66 TAAAATGATAGAAATTTTGGTAAATCATTAGAAATGTTGATAAATCCTTAGAAATATTAGTAAAT
*
1989449 TCTTAGATATTTTGATAAGGCCATTGAA
131 TCTTAGATATATTGATAAGGCCATTGAA
* * *
1989477 GGTTTAGAAAATTT-GAAAATATTGGTAAAATCTTAAAAATTATGGTGAAGTTTC-ATAAATATT
1 GGTTTAGAAAATTTAG-AAATATTGGTAAAATATTAAAAATTATGGTAAAG-TCCAATAAATATT
* * * * *
1989540 GGTAAAATGATATAAATTTTGGTAACTCATTA-AATATTTTGATAAATCCTTAGAAATTTTAGTA
64 GATAAAATGATAGAAATTTTGGTAAATCATTAGAA-ATGTTGATAAATCCTTAGAAATATTAGTA
1989604 AA-TCGTT-GAATATATTGATAA
128 AATTC-TTAG-ATATATTGATAA
1989625 AACAATAGAA
Statistics
Matches: 127, Mismatches: 16, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
157 6 0.05
158 119 0.94
159 2 0.02
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (158 bp):
GGTTTAGAAAATTTAGAAATATTGGTAAAATATTAAAAATTATGGTAAAGTCCAATAAATATTGA
TAAAATGATAGAAATTTTGGTAAATCATTAGAAATGTTGATAAATCCTTAGAAATATTAGTAAAT
TCTTAGATATATTGATAAGGCCATTGAA
Found at i:1989722 original size:20 final size:19
Alignment explanation
Indices: 1989671--1989725 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
1989661 TGATGTTTAG
*
1989671 AAAATTTGGAAATATTGAT
1 AAAATTTGTAAATATTGAT
* * *
1989690 AAAATTTTATAAATTTTGGT
1 AAAA-TTTGTAAATATTGAT
1989710 AAAATCTTGTAAATAT
1 AAAAT-TTGTAAATAT
1989726 CGGCAAAACC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (19 bp):
AAAATTTGTAAATATTGAT
Found at i:1991455 original size:25 final size:25
Alignment explanation
Indices: 1991413--1991460 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1991403 GACATTTTCA
*
1991413 TAATTTCCTAATCAAGTTAGTACAT
1 TAATTTCCTAACCAAGTTAGTACAT
* *
1991438 TAATTTCCTAACCGAGTTGGTAC
1 TAATTTCCTAACCAAGTTAGTAC
1991461 CCGGTTAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (25 bp):
TAATTTCCTAACCAAGTTAGTACAT
Found at i:1994356 original size:10 final size:10
Alignment explanation
Indices: 1994341--1994386 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
1994331 TAAATTTGAG
1994341 TATAATTATT
1 TATAATTATT
1994351 TATAATTA-T
1 TATAATTATT
* *
1994360 TATTACT-TT
1 TATAATTATT
*
1994369 GATAATTATT
1 TATAATTATT
1994379 TATAATTA
1 TATAATTA
1994387 AAGTATTTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
9 11 0.39
10 17 0.61
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (10 bp):
TATAATTATT
Found at i:1995928 original size:16 final size:17
Alignment explanation
Indices: 1995909--1995950 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1995899 AATCCTTTCA
*
1995909 AAATTTATAT-AATTAT
1 AAATTTATATAAATGAT
*
1995925 AAATTAATATAAATGAT
1 AAATTTATATAAATGAT
*
1995942 AAAATTATA
1 AAATTTATA
1995951 CTTTAGTCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATTTATATAAATGAT
Found at i:2000551 original size:4 final size:4
Alignment explanation
Indices: 2000544--2000590 Score: 85
Period size: 4 Copynumber: 11.8 Consensus size: 4
2000534 TTGATTGATT
*
2000544 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GACG GAT
1 GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GATG GAT
2000591 TAAGAAGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.26, C:0.02, G:0.49, T:0.23
Consensus pattern (4 bp):
GATG
Found at i:2006746 original size:21 final size:21
Alignment explanation
Indices: 2006722--2006765 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2006712 CTTCAACGAA
2006722 AACCCAGAATAAAGATTTTTT
1 AACCCAGAATAAAGATTTTTT
2006743 AACCCAGAATAAAGATTTTTT
1 AACCCAGAATAAAGATTTTTT
2006764 AA
1 AA
2006766 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (21 bp):
AACCCAGAATAAAGATTTTTT
Found at i:2008093 original size:33 final size:33
Alignment explanation
Indices: 2008051--2008118 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
2008041 TAATATATTA
2008051 TTATGGATGGTTTGTGCATGATTTTAACAATTG
1 TTATGGATGGTTTGTGCATGATTTTAACAATTG
2008084 TTATGGATGGTTTGTGCATGATTTTAACAATTG
1 TTATGGATGGTTTGTGCATGATTTTAACAATTG
2008117 TT
1 TT
2008119 TTCTTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.47
Consensus pattern (33 bp):
TTATGGATGGTTTGTGCATGATTTTAACAATTG
Found at i:2016580 original size:23 final size:24
Alignment explanation
Indices: 2016554--2016692 Score: 79
Period size: 23 Copynumber: 5.6 Consensus size: 24
2016544 TAGTGTATGA
2016554 AAATTTAAAATAATAT-TAATAAT
1 AAATTTAAAATAATATATAATAAT
* * *
2016577 AAATTTAGAGTAAT-TATGATAAT
1 AAATTTAAAATAATATATAATAAT
* *
2016600 AAACTAAAAATAATA-ATACATGAA-
1 AAATTTAAAATAATATATA-AT-AAT
** * *
2016624 AAACCTAAAATAATACATATATAAAAA
1 AAATTTAAAATAAT--ATATA-ATAAT
*
2016651 AAACTTTTAAAATAATAATACAATAAT
1 AAA--TTTAAAATAAT-ATATAATAAT
*
2016678 AAATTTATAATAATA
1 AAATTTAAAATAATA
2016693 AGTTTAATTA
Statistics
Matches: 87, Mismatches: 19, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
22 1 0.01
23 30 0.34
24 15 0.17
25 12 0.14
26 3 0.03
27 13 0.15
28 4 0.05
29 9 0.10
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (24 bp):
AAATTTAAAATAATATATAATAAT
Found at i:2020422 original size:68 final size:69
Alignment explanation
Indices: 2020291--2020428 Score: 176
Period size: 68 Copynumber: 2.0 Consensus size: 69
2020281 TTCCACCTTT
* *
2020291 TCTTTTAAATGGCATCAAAACATTTCCAAGATACCAATCAAGTCCAAAAAATATCAACCAATAAG
1 TCTTTCAAATGGCATCAAAACATGTCCAAGATACCAATCAAGTCCAAAAAATATCAACCAATAAG
2020356 CCAA
66 CCAA
* * *
2020360 TCTTTCAAATGGCATCAAAAC-TAGT-CAATATACTAGTCAAGTCCAACAGAAA-A-CAACCAAT
1 TCTTTCAAATGGCATCAAAACAT-GTCCAAGATACCAATCAAGTCCAA-A-AAATATCAACCAAT
2020421 AAGCCAA
63 AAGCCAA
2020428 T
1 T
2020429 AGTCTATTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
68 35 0.57
69 23 0.38
70 3 0.05
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.22
Consensus pattern (69 bp):
TCTTTCAAATGGCATCAAAACATGTCCAAGATACCAATCAAGTCCAAAAAATATCAACCAATAAG
CCAA
Found at i:2021219 original size:427 final size:427
Alignment explanation
Indices: 2020424--2021278 Score: 1710
Period size: 427 Copynumber: 2.0 Consensus size: 427
2020414 AACCAATAAG
2020424 CCAATAGTCTATTATACAGACTCATGAACAAGTTCAAGCTGACTCGGATAAAAAGGTGAAACCAA
1 CCAATAGTCTATTATACAGACTCATGAACAAGTTCAAGCTGACTCGGATAAAAAGGTGAAACCAA
2020489 GCTTGAAGCAGACTAATTAGTTCCAAAAAGCATTTGAGGCTTGAATAGGCACAACCAATTTCATG
66 GCTTGAAGCAGACTAATTAGTTCCAAAAAGCATTTGAGGCTTGAATAGGCACAACCAATTTCATG
2020554 AATCTGTGATTATATTATGTACCTCATTTGCCTCTGCTTCTATGCAGCAATGCATATATGAACAT
131 AATCTGTGATTATATTATGTACCTCATTTGCCTCTGCTTCTATGCAGCAATGCATATATGAACAT
2020619 CAGAAGATTACTAACAAAGAAAGATCTTTACTATGTAAAACCACTTAGCTACTCTACCACATGGC
196 CAGAAGATTACTAACAAAGAAAGATCTTTACTATGTAAAACCACTTAGCTACTCTACCACATGGC
2020684 TAACATAATAAGATCCATGAATCACATAAGACAACCAACATTTGCCTCTTTCATGGCAACATGCA
261 TAACATAATAAGATCCATGAATCACATAAGACAACCAACATTTGCCTCTTTCATGGCAACATGCA
2020749 AACCAAAGGTTTAATACTATTATTAATTTCAAAGAAGAGAACAAGTAGCATTTCCATCTGCTGAA
326 AACCAAAGGTTTAATACTATTATTAATTTCAAAGAAGAGAACAAGTAGCATTTCCATCTGCTGAA
2020814 AAGATTACCTCGTCCGGAGAAAAGAAAGCCACTGAAT
391 AAGATTACCTCGTCCGGAGAAAAGAAAGCCACTGAAT
2020851 CCAATAGTCTATTATACAGACTCATGAACAAGTTCAAGCTGACTCGGATAAAAAGGTGAAACCAA
1 CCAATAGTCTATTATACAGACTCATGAACAAGTTCAAGCTGACTCGGATAAAAAGGTGAAACCAA
2020916 GCTTGAAGCAGACTAATTAGTTCCAAAAAGCATTTGAGGCTTGAATAGGCACAACCAATTTCATG
66 GCTTGAAGCAGACTAATTAGTTCCAAAAAGCATTTGAGGCTTGAATAGGCACAACCAATTTCATG
2020981 AATCTGTGATTATATTATGTACCTCATTTGCCTCTGCTTCTATGCAGCAATGCATATATGAACAT
131 AATCTGTGATTATATTATGTACCTCATTTGCCTCTGCTTCTATGCAGCAATGCATATATGAACAT
2021046 CAGAAGATTACTAACAAAGAAAGATCTTTACTATGTAAAACCACTTAGCTACTCTACCACATGGC
196 CAGAAGATTACTAACAAAGAAAGATCTTTACTATGTAAAACCACTTAGCTACTCTACCACATGGC
2021111 TAACATAATAAGATCCATGAATCACATAAGACAACCAACATTTGCCTCTTTCATGGCAACATGCA
261 TAACATAATAAGATCCATGAATCACATAAGACAACCAACATTTGCCTCTTTCATGGCAACATGCA
2021176 AACCAAAGGTTTAATACTATTATTAATTTCAAAGAAGAGAACAAGTAGCATTTCCATCTGCTGAA
326 AACCAAAGGTTTAATACTATTATTAATTTCAAAGAAGAGAACAAGTAGCATTTCCATCTGCTGAA
2021241 AAGATTACCTCGTCCGGAGAAAAGAAAGCCACTGAAT
391 AAGATTACCTCGTCCGGAGAAAAGAAAGCCACTGAAT
2021278 C
1 C
2021279 TGGATCTGTT
Statistics
Matches: 428, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
427 428 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.26
Consensus pattern (427 bp):
CCAATAGTCTATTATACAGACTCATGAACAAGTTCAAGCTGACTCGGATAAAAAGGTGAAACCAA
GCTTGAAGCAGACTAATTAGTTCCAAAAAGCATTTGAGGCTTGAATAGGCACAACCAATTTCATG
AATCTGTGATTATATTATGTACCTCATTTGCCTCTGCTTCTATGCAGCAATGCATATATGAACAT
CAGAAGATTACTAACAAAGAAAGATCTTTACTATGTAAAACCACTTAGCTACTCTACCACATGGC
TAACATAATAAGATCCATGAATCACATAAGACAACCAACATTTGCCTCTTTCATGGCAACATGCA
AACCAAAGGTTTAATACTATTATTAATTTCAAAGAAGAGAACAAGTAGCATTTCCATCTGCTGAA
AAGATTACCTCGTCCGGAGAAAAGAAAGCCACTGAAT
Found at i:2024314 original size:21 final size:22
Alignment explanation
Indices: 2024278--2024320 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2024268 TTTGACCCCC
2024278 TAAAATTATAAAAATTCAATTT
1 TAAAATTATAAAAATTCAATTT
*
2024300 TAAAATTAT-AAAATTCGATTT
1 TAAAATTATAAAAATTCAATTT
2024321 AATCCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAAATTATAAAAATTCAATTT
Found at i:2025499 original size:57 final size:55
Alignment explanation
Indices: 2025387--2025500 Score: 131
Period size: 57 Copynumber: 2.0 Consensus size: 55
2025377 CCTGCAGAGA
** *
2025387 AGTTGAACACCTTTTAGTTTGCTTATGTATTTTTTTTCCACCATTTGGTTTATTCTT
1 AGTTGAACACCTTTTAGTTTGCTTATGTA--TTTTTTCCACCATTACGTTCATTCTT
* *
2025444 AGTTGAACTCCTTTTAGTAGTCTGCTTATGTA-TTTTTCCTCCATTACGTTCATTCTT
1 AGTTGAACACCTTTTAGT--T-TGCTTATGTATTTTTTCCACCATTACGTTCATTCTT
2025501 GGTCAAACAC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
57 38 0.78
59 1 0.02
60 10 0.20
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (55 bp):
AGTTGAACACCTTTTAGTTTGCTTATGTATTTTTTCCACCATTACGTTCATTCTT
Found at i:2028377 original size:28 final size:29
Alignment explanation
Indices: 2028346--2028401 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2028336 TTTAAATAAA
* * *
2028346 AAAATATAT-GACTTAATTTTTAATTTTT
1 AAAATATATGGACTAAAATTTAAATTTTT
2028374 AAAATATATGGACTAAAATTTAAATTTT
1 AAAATATATGGACTAAAATTTAAATTTT
2028402 ATCAAAGTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (29 bp):
AAAATATATGGACTAAAATTTAAATTTTT
Found at i:2028402 original size:28 final size:28
Alignment explanation
Indices: 2028346--2028402 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
2028336 TTTAAATAAA
** *
2028346 AAAATATATGACTTAATTTTTAATTTTT
1 AAAATATATGACTTAAAATTTAAATTTT
2028374 AAAATATATGGAC-TAAAATTTAAATTTT
1 AAAATATAT-GACTTAAAATTTAAATTTT
2028402 A
1 A
2028403 TCAAAGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (28 bp):
AAAATATATGACTTAAAATTTAAATTTT
Found at i:2029865 original size:21 final size:22
Alignment explanation
Indices: 2029841--2029895 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
2029831 AATAGCGGTG
* *
2029841 GCGGTGAGATTAG-TTACTGTA
1 GCGGTGAGATTAGCATAATGTA
2029862 GCGGTGAGATT-GCATAATGTA
1 GCGGTGAGATTAGCATAATGTA
2029883 GCGGTGAGATTAG
1 GCGGTGAGATTAG
2029896 AAACAATGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.29
Consensus pattern (22 bp):
GCGGTGAGATTAGCATAATGTA
Found at i:2047979 original size:18 final size:18
Alignment explanation
Indices: 2047958--2047993 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2047948 TAATATTTTA
2047958 AAATAATTAGAATTATTC
1 AAATAATTAGAATTATTC
*
2047976 AAATAATTATAATTATTC
1 AAATAATTAGAATTATTC
2047994 GATCGATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (18 bp):
AAATAATTAGAATTATTC
Found at i:2053810 original size:14 final size:15
Alignment explanation
Indices: 2053778--2053810 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2053768 TTTTTTTAAG
*
2053778 AAAATATATAAAATT
1 AAAATATATAAAATA
2053793 AAAAT-TATAAAATA
1 AAAATATATAAAATA
2053807 AAAA
1 AAAA
2053811 ATTAGCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATATATAAAATA
Found at i:2055811 original size:17 final size:17
Alignment explanation
Indices: 2055791--2055824 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2055781 GGGAGTTTTC
2055791 GGTAAAAACATACCACA
1 GGTAAAAACATACCACA
2055808 GGTAAAAACATACCACA
1 GGTAAAAACATACCACA
2055825 TTGTTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.12
Consensus pattern (17 bp):
GGTAAAAACATACCACA
Found at i:2057778 original size:31 final size:31
Alignment explanation
Indices: 2057734--2057925 Score: 169
Period size: 31 Copynumber: 6.3 Consensus size: 31
2057724 TGTTTATAGT
*
2057734 TATACATTGTCGAAATTGATTTGCATATGAA
1 TATACATTGTCGAAATTGATTTGTATATGAA
*
2057765 TATA-AGTTGTCG-AATTGATTTGTATATGAT
1 TATACA-TTGTCGAAATTGATTTGTATATGAA
* * * **
2057795 TGTACATTGTTGAAATTAATTTGTATATGGT
1 TATACATTGTCGAAATTGATTTGTATATGAA
* * *
2057826 TATACATTGTTGAAATTGAATTGTATATGGA
1 TATACATTGTCGAAATTGATTTGTATATGAA
* * **
2057857 TATA-AGTTG-CCAAATTGATTCGTATATGGT
1 TATACA-TTGTCGAAATTGATTTGTATATGAA
* * *
2057887 TATACATTGAT-GAATTTAATTTGTATATGAT
1 TATACATTG-TCGAAATTGATTTGTATATGAA
2057918 TATACATT
1 TATACATT
2057926 ACCGAACTTG
Statistics
Matches: 134, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
30 49 0.37
31 85 0.63
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (31 bp):
TATACATTGTCGAAATTGATTTGTATATGAA
Found at i:2057801 original size:61 final size:62
Alignment explanation
Indices: 2057736--2057854 Score: 152
Period size: 61 Copynumber: 1.9 Consensus size: 62
2057726 TTTATAGTTA
* *
2057736 TACATTGTCGAAATTGATTTGCATATGAATATA-AGTTGTCG-AATTGATTTGTATATGATTG
1 TACATTGTCGAAATTAATTTGCATATGAATATACA-TTGTCGAAATTGAATTGTATATGATTG
* * ** *
2057797 TACATTGTTGAAATTAATTTGTATATGGTTATACATTGTTGAAATTGAATTGTATATG
1 TACATTGTCGAAATTAATTTGCATATGAATATACATTGTCGAAATTGAATTGTATATG
2057855 GATATAAGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
61 33 0.67
62 16 0.33
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (62 bp):
TACATTGTCGAAATTAATTTGCATATGAATATACATTGTCGAAATTGAATTGTATATGATTG
Found at i:2057833 original size:92 final size:92
Alignment explanation
Indices: 2057732--2057925 Score: 280
Period size: 92 Copynumber: 2.1 Consensus size: 92
2057722 ACTGTTTATA
* * * * *
2057732 GTTATACATTGTCGAAATTGATTTGCATATGAATATAAGTTGTCGAATTGATTTGTATATGATTG
1 GTTATACATTGTCGAAATTGAATTGCATATGAATATAAGTTGCCAAATTGATTCGTATATGATTA
*
2057797 TACATTGTTGAAATTAATTTGTATATG
66 TACATTGATGAAATTAATTTGTATATG
* * * *
2057824 GTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGGTTA
1 GTTATACATTGTCGAAATTGAATTGCATATGAATATAAGTTGCCAAATTGATTCGTATATGATTA
*
2057889 TACATTGATGAATTTAATTTGTATATG
66 TACATTGATGAAATTAATTTGTATATG
*
2057916 ATTATACATT
1 GTTATACATT
2057926 ACCGAACTTG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (92 bp):
GTTATACATTGTCGAAATTGAATTGCATATGAATATAAGTTGCCAAATTGATTCGTATATGATTA
TACATTGATGAAATTAATTTGTATATG
Found at i:2057945 original size:92 final size:92
Alignment explanation
Indices: 2057733--2057983 Score: 245
Period size: 92 Copynumber: 2.7 Consensus size: 92
2057723 CTGTTTATAG
** * ** * * * * *
2057733 TTATACATTGTCGAAATTGATTTGCATATGAATATAAGTTGTCGAATTGATTTGTATATGATTGT
1 TTATACATTACCGAAATTGAATTATATATGGATATAAGTTGCCAAATTGATTCGTATATGATTAT
* *
2057798 ACATTGTTGAAATTAATTTGTATATGG
66 ACATTGATGAAATTAATTTGTATATGA
*** * *
2057825 TTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGGTTAT
1 TTATACATTACCGAAATTGAATTATATATGGATATAAGTTGCCAAATTGATTCGTATATGATTAT
*
2057890 ACATTGATGAATTTAATTTGTATATGA
66 ACATTGATGAAATTAATTTGTATATGA
* * * * * *
2057917 TTATACATTACCGAACTTG-ATTCATATATGGTTGTACA-TTGCCAAATTTGGTTCGTACATGAA
1 TTATACATTACCGAAATTGAATT-ATATATGGATATA-AGTTGCCAAA-TTGATTCGTATATGAT
2057980 TATA
63 TATA
2057984 TATATTGTTG
Statistics
Matches: 133, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
91 3 0.02
92 113 0.85
93 17 0.13
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (92 bp):
TTATACATTACCGAAATTGAATTATATATGGATATAAGTTGCCAAATTGATTCGTATATGATTAT
ACATTGATGAAATTAATTTGTATATGA
Found at i:2058184 original size:31 final size:31
Alignment explanation
Indices: 2058104--2058280 Score: 152
Period size: 31 Copynumber: 5.8 Consensus size: 31
2058094 GACATGATAT
* *
2058104 ATTAA-TTGTATATGGATATA-AGTTGTCG-A
1 ATTAATTTGTATATGGTTATACA-TTGTTGAA
* * * *
2058133 ATTGATTTTTATATGATTATATATTGTTGAA
1 ATTAATTTGTATATGGTTATACATTGTTGAA
*
2058164 ATTAATTTGTACATGGTTATACATTGTTGAA
1 ATTAATTTGTATATGGTTATACATTGTTGAA
*
2058195 ATTGAA-TTGTATATGGATATA-A--GTTGCCAA
1 ATT-AATTTGTATATGGTTATACATTGTTG--AA
* * *
2058225 ATTGATTCGTATATGGTTATACATTGATGAA
1 ATTAATTTGTATATGGTTATACATTGTTGAA
* *
2058256 TTTAATTTGTATATGATTATACATT
1 ATTAATTTGTATATGGTTATACATT
2058281 ACCGAACTTG
Statistics
Matches: 118, Mismatches: 20, Indels: 18
0.76 0.13 0.12
Matches are distributed among these distances:
28 4 0.03
29 5 0.04
30 36 0.31
31 68 0.58
32 2 0.02
33 3 0.03
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (31 bp):
ATTAATTTGTATATGGTTATACATTGTTGAA
Found at i:2058243 original size:61 final size:62
Alignment explanation
Indices: 2058131--2058312 Score: 176
Period size: 61 Copynumber: 3.0 Consensus size: 62
2058121 ATAAGTTGTC
* * *** * * * *
2058131 GAATTG-ATTTTTATATGATTATATATTGTTGAAATTAATTTGTACATGGTTATACATTGTT
1 GAATTGAATTTGTATATGATTATACATTACCGAAATTGATTCGTATATGGTTATACATTGAT
*
2058192 GAAATTGAA-TTGTATATGGA-TATA-AGTTGCC-AAATTGATTCGTATATGGTTATACATTGAT
1 G-AATTGAATTTGTATAT-GATTATACA-TTACCGAAATTGATTCGTATATGGTTATACATTGAT
* * * *
2058253 GAATTTAATTTGTATATGATTATACATTACCGAACTTGATTCATATATGGTTGTACATTG
1 GAATTGAATTTGTATATGATTATACATTACCGAAATTGATTCGTATATGGTTATACATTG
2058313 CCAAATTTGG
Statistics
Matches: 101, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
60 8 0.08
61 45 0.45
62 45 0.45
63 3 0.03
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (62 bp):
GAATTGAATTTGTATATGATTATACATTACCGAAATTGATTCGTATATGGTTATACATTGAT
Found at i:2058264 original size:92 final size:92
Alignment explanation
Indices: 2058107--2058280 Score: 258
Period size: 92 Copynumber: 1.9 Consensus size: 92
2058097 ATGATATATT
* * ** * *
2058107 AATTGTATATGGATATAAGTTGTCGAATTGATTTTTATATGATTATATATTGTTGAAATTAATTT
1 AATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGATTATACATTGATGAAATTAATTT
*
2058172 GTACATGGTTATACATTGTTGAAATTG
66 GTACATGATTATACATTGTTGAAATTG
* *
2058199 AATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGGTTATACATTGATGAATTTAATTT
1 AATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGATTATACATTGATGAAATTAATTT
*
2058264 GTATATGATTATACATT
66 GTACATGATTATACATT
2058281 ACCGAACTTG
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
92 72 1.00
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (92 bp):
AATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGATTATACATTGATGAAATTAATTT
GTACATGATTATACATTGTTGAAATTG
Found at i:2058300 original size:92 final size:92
Alignment explanation
Indices: 2058107--2058338 Score: 234
Period size: 92 Copynumber: 2.5 Consensus size: 92
2058097 ATGATATATT
* * * ** * *
2058107 AATTGTATATGGATATAAGTTGTCGAATTGATTTTTATATGATTATATATTGTTGAAATTAATTT
1 AATTATATATGGATATAAGTTGCCAAATTGATTCGTATATGATTATACATTGATGAAATTAATTT
* ***
2058172 GTACATGGTTATACATTGTTGAAATTG
66 GTACATGATTATACATTACCGAAATTG
* * *
2058199 AATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGGTTATACATTGATGAATTTAATTT
1 AATTATATATGGATATAAGTTGCCAAATTGATTCGTATATGATTATACATTGATGAAATTAATTT
* *
2058264 GTATATGATTATACATTACCGAACTTG
66 GTACATGATTATACATTACCGAAATTG
* * * * *
2058291 -ATTCATATATGGTTGTACA-TTGCCAAATTTGGTTCGTACATGAATATA
1 AATT-ATATATGGATATA-AGTTGCCAAA-TTGATTCGTATATGATTATA
2058339 TATATTGTTG
Statistics
Matches: 116, Mismatches: 21, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
91 3 0.03
92 96 0.83
93 17 0.15
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (92 bp):
AATTATATATGGATATAAGTTGCCAAATTGATTCGTATATGATTATACATTGATGAAATTAATTT
GTACATGATTATACATTACCGAAATTG
Found at i:2058415 original size:355 final size:355
Alignment explanation
Indices: 2057758--2058458 Score: 1357
Period size: 355 Copynumber: 2.0 Consensus size: 355
2057748 ATTGATTTGC
* *
2057758 ATATGAATATAAGTTGTCGAATTGATTTGTATATGATTGTACATTGTTGAAATTAATTTGTATAT
1 ATATGAATATAAGTTGTCGAATTGATTTGTATATGATTATACATTGTTGAAATTAATTTGTACAT
2057823 GGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGGTT
66 GGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGGTT
2057888 ATACATTGATGAATTTAATTTGTATATGATTATACATTACCGAACTTGATTCATATATGGTTGTA
131 ATACATTGATGAATTTAATTTGTATATGATTATACATTACCGAACTTGATTCATATATGGTTGTA
2057953 CATTGCCAAATTTGGTTCGTACATGAATATATATATTGTTGAATTGATTTGAGCATTGGATTACT
196 CATTGCCAAATTTGGTTCGTACATGAATATATATATTGTTGAATTGATTTGAGCATTGGATTACT
2058018 GGTTTCGTGCATGAAATGATTTAATTAAGAAGTCTATAGCTTTGAATGAACCTTAGAAAATGTAT
261 GGTTTCGTGCATGAAATGATTTAATTAAGAAGTCTATAGCTTTGAATGAACCTTAGAAAATGTAT
2058083 TTGATATTGATGACATGATATATTAATTGT
326 TTGATATTGATGACATGATATATTAATTGT
* * *
2058113 ATATGGATATAAGTTGTCGAATTGATTTTTATATGATTATATATTGTTGAAATTAATTTGTACAT
1 ATATGAATATAAGTTGTCGAATTGATTTGTATATGATTATACATTGTTGAAATTAATTTGTACAT
2058178 GGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGGTT
66 GGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGGTT
2058243 ATACATTGATGAATTTAATTTGTATATGATTATACATTACCGAACTTGATTCATATATGGTTGTA
131 ATACATTGATGAATTTAATTTGTATATGATTATACATTACCGAACTTGATTCATATATGGTTGTA
2058308 CATTGCCAAATTTGGTTCGTACATGAATATATATATTGTTGAATTGATTTGAGCATTGGATTACT
196 CATTGCCAAATTTGGTTCGTACATGAATATATATATTGTTGAATTGATTTGAGCATTGGATTACT
2058373 GGTTTCGTGCATGAAATGATTTAATTAAGAAGTCTATAGCTTTGAATGAACCTTAGAAAATGTAT
261 GGTTTCGTGCATGAAATGATTTAATTAAGAAGTCTATAGCTTTGAATGAACCTTAGAAAATGTAT
2058438 TTGATATTGATGACATGATAT
326 TTGATATTGATGACATGATAT
2058459 TAGGACTTCT
Statistics
Matches: 341, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
355 341 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (355 bp):
ATATGAATATAAGTTGTCGAATTGATTTGTATATGATTATACATTGTTGAAATTAATTTGTACAT
GGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCAAATTGATTCGTATATGGTT
ATACATTGATGAATTTAATTTGTATATGATTATACATTACCGAACTTGATTCATATATGGTTGTA
CATTGCCAAATTTGGTTCGTACATGAATATATATATTGTTGAATTGATTTGAGCATTGGATTACT
GGTTTCGTGCATGAAATGATTTAATTAAGAAGTCTATAGCTTTGAATGAACCTTAGAAAATGTAT
TTGATATTGATGACATGATATATTAATTGT
Found at i:2059089 original size:99 final size:99
Alignment explanation
Indices: 2058966--2059823 Score: 1664
Period size: 99 Copynumber: 8.7 Consensus size: 99
2058956 AGAAAAAGAA
* * *
2058966 TCATATCCAGTAG-GTTAGGACACAATGTCTCGAATTCCCGATACGAGAATAAATGCCAAAAATT
1 TCATATCCAAT-GCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATT
2059030 TATTAGAAAAATCCTCATCTTGAGAAAATGACATG
65 TATTAGAAAAATCCTCATCTTGAGAAAATGACATG
2059065 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
1 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
2059130 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
66 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
2059164 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
1 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
2059229 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
66 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
2059263 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
1 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
2059328 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
66 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
2059362 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
1 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
2059427 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
66 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
2059461 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
1 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
2059526 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
66 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
2059560 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
1 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
2059625 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
66 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
2059659 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
1 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
2059724 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
66 ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
*
2059758 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCGAAAATTT
1 TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
2059823 A
66 A
2059824 CTTATTTAAA
Statistics
Matches: 754, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
98 1 0.00
99 753 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (99 bp):
TCATATCCAATGCGTTAGGACACAACGTATCGAATTCCCGATACGAGAATAAATGCCAAAAATTT
ATTAGAAAAATCCTCATCTTGAGAAAATGACATG
Found at i:2063640 original size:59 final size:59
Alignment explanation
Indices: 2063525--2063640 Score: 135
Period size: 59 Copynumber: 2.0 Consensus size: 59
2063515 AAGTTTAGAA
* * ** * * *
2063525 ACTAACTTGGACAAAAAAAAGTTCAAGTCATAATGTGGAAACGATTGTCAAGTTCAAGG
1 ACTAACCTAGACAAAAAAAAGTTCAAACCATAATGTGAAAACGATTGCCAAATTCAAGG
* *
2063584 ACTAACCTAGACAAAAAAAAGTTCAAACCTTAATTTGAAAAC-ACTTGCCAAATTCAA
1 ACTAACCTAGACAAAAAAAAGTTCAAACCATAATGTGAAAACGA-TTGCCAAATTCAA
2063641 ATCCCAAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.02
59 46 0.98
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (59 bp):
ACTAACCTAGACAAAAAAAAGTTCAAACCATAATGTGAAAACGATTGCCAAATTCAAGG
Found at i:2068374 original size:12 final size:12
Alignment explanation
Indices: 2068357--2068381 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2068347 GGTGTTCATT
2068357 CGGTTAACCGAC
1 CGGTTAACCGAC
2068369 CGGTTAACCGAC
1 CGGTTAACCGAC
2068381 C
1 C
2068382 CGAAATTACT
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:2068556 original size:9 final size:9
Alignment explanation
Indices: 2068542--2068582 Score: 82
Period size: 9 Copynumber: 4.6 Consensus size: 9
2068532 TTTGGTTAAA
2068542 AATTACCCG
1 AATTACCCG
2068551 AATTACCCG
1 AATTACCCG
2068560 AATTACCCG
1 AATTACCCG
2068569 AATTACCCG
1 AATTACCCG
2068578 AATTA
1 AATTA
2068583 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.37, C:0.29, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:2069947 original size:13 final size:13
Alignment explanation
Indices: 2069929--2070003 Score: 105
Period size: 13 Copynumber: 5.8 Consensus size: 13
2069919 TTCTTCATTT
2069929 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
2069942 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
2069955 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
***
2069968 CTGCGGAAAAGTG
1 CTTTTGAAAAGTG
* *
2069981 CTTCTGAGAAGTG
1 CTTTTGAAAAGTG
2069994 CTTTTGAAAA
1 CTTTTGAAAA
2070004 ATTTGAGTGT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 54 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:2073169 original size:20 final size:20
Alignment explanation
Indices: 2073144--2073188 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
2073134 ATTATCAGCC
2073144 AAAAGCACTTCAAGCTAAAG
1 AAAAGCACTTCAAGCTAAAG
2073164 AAAAGCACTTCAAGCTAAAG
1 AAAAGCACTTCAAGCTAAAG
2073184 AAAAG
1 AAAAG
2073189 GAGAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.53, C:0.18, G:0.16, T:0.13
Consensus pattern (20 bp):
AAAAGCACTTCAAGCTAAAG
Found at i:2073596 original size:9 final size:9
Alignment explanation
Indices: 2073584--2073686 Score: 52
Period size: 9 Copynumber: 11.2 Consensus size: 9
2073574 AAAAAAAACA
2073584 TAAAAATAT
1 TAAAAATAT
2073593 TAAAAATAT
1 TAAAAATAT
2073602 ATATAAAAGCTA-
1 -TA-AAAA--TAT
* *
2073614 AAAAAAAAT
1 TAAAAATAT
* *
2073623 TAAAATTTT
1 TAAAAATAT
* * *
2073632 TAGAATTTT
1 TAAAAATAT
2073641 TAAAAAT-T
1 TAAAAATAT
2073649 ATAAAAATA-
1 -TAAAAATAT
2073658 TAAAAATTAT
1 TAAAAA-TAT
*
2073668 TAAAAATAA
1 TAAAAATAT
2073677 TAAAAA-AT
1 TAAAAATAT
2073685 TA
1 TA
2073687 TTTAAGAATT
Statistics
Matches: 74, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
8 11 0.15
9 44 0.59
10 12 0.16
11 5 0.07
13 2 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (9 bp):
TAAAAATAT
Found at i:2073663 original size:17 final size:18
Alignment explanation
Indices: 2073641--2073687 Score: 69
Period size: 17 Copynumber: 2.6 Consensus size: 18
2073631 TTAGAATTTT
2073641 TAAAAATTATAAAAAT-A
1 TAAAAATTATAAAAATAA
2073658 TAAAAATTATTAAAAATAA
1 TAAAAATTA-TAAAAATAA
2073677 TAAAAAATTAT
1 T-AAAAATTAT
2073688 TTAAGAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.33
18 7 0.26
19 3 0.11
20 8 0.30
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAAATTATAAAAATAA
Found at i:2073682 original size:10 final size:9
Alignment explanation
Indices: 2073641--2073786 Score: 73
Period size: 10 Copynumber: 15.6 Consensus size: 9
2073631 TTAGAATTTT
2073641 TAAAAATTA
1 TAAAAATTA
2073650 TAAAAA-TA
1 TAAAAATTA
2073658 TAAAAATTA
1 TAAAAATTA
*
2073667 TTAAAAATAA
1 -TAAAAATTA
2073677 TAAAAAATTA
1 T-AAAAATTA
*
2073687 TTTAAGAATTA
1 --TAAAAATTA
* **
2073698 T-GAAAGCA
1 TAAAAATTA
*
2073706 TAACAAACTA
1 TAA-AAATTA
*
2073716 TAAAAATATT
1 TAAAAAT-TA
*
2073726 TAAAAACTA
1 TAAAAATTA
**
2073735 TAAAAGCTA
1 TAAAAATTA
2073744 TTAAAAATTA
1 -TAAAAATTA
*
2073754 CAAAATATTA
1 TAAAA-ATTA
**
2073764 TAATGCATTA
1 TAA-AAATTA
2073774 TAAAAA-TA
1 TAAAAATTA
2073782 TAAAA
1 TAAAA
2073787 TATTTAGTAA
Statistics
Matches: 103, Mismatches: 23, Indels: 23
0.69 0.15 0.15
Matches are distributed among these distances:
8 19 0.18
9 27 0.26
10 49 0.48
11 7 0.07
12 1 0.01
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:2073759 original size:37 final size:36
Alignment explanation
Indices: 2073641--2073762 Score: 99
Period size: 37 Copynumber: 3.3 Consensus size: 36
2073631 TTAGAATTTT
* **
2073641 TAAAAAT-TATAAAAATATAAAAATTATTAAAAATAA
1 TAAAAATATTTAAAAATATAAAAGCTATTAAAAAT-A
* *
2073677 TAAAAAATTATTTAAGAATTATGAAAGC-A-TAACAAACTA
1 T-AAAAA-TATTTAA-AAATATAAAAGCTATTAA-AAA-TA
2073716 TAAAAATATTTAAAAACTATAAAAGCTATTAAAAAT-
1 TAAAAATATTTAAAAA-TATAAAAGCTATTAAAAATA
2073752 TACAAAATATT
1 TA-AAAATATT
2073763 ATAATGCATT
Statistics
Matches: 69, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
36 5 0.07
37 29 0.42
38 13 0.19
39 13 0.19
40 9 0.13
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.30
Consensus pattern (36 bp):
TAAAAATATTTAAAAATATAAAAGCTATTAAAAATA
Found at i:2081209 original size:38 final size:39
Alignment explanation
Indices: 2081137--2081214 Score: 115
Period size: 38 Copynumber: 2.0 Consensus size: 39
2081127 ATAGAATTAT
2081137 ACATTTACAAAAAGTGGAAAACGTTTTTGAAATTAAAATA
1 ACATTTACAAAAAGT-GAAAACGTTTTTGAAATTAAAATA
*
2081177 ACATTTAC-AAAAGT-AAAACGTTTTTTGAAATTAGAATA
1 ACATTTACAAAAAGTGAAAACG-TTTTTGAAATTAAAATA
2081215 TATATATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
37 6 0.17
38 16 0.44
39 6 0.17
40 8 0.22
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.32
Consensus pattern (39 bp):
ACATTTACAAAAAGTGAAAACGTTTTTGAAATTAAAATA
Found at i:2083243 original size:44 final size:44
Alignment explanation
Indices: 2083089--2083252 Score: 143
Period size: 44 Copynumber: 3.7 Consensus size: 44
2083079 ACCAATATAG
* *
2083089 GAAGACAGGACCTACTATCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTACTATCTTTGATCTACTTCACGCCAGTACAT
* ** * * * * * ***
2083133 GAAGACACGATCTGTTTTCTTCGACCTAC-TCTACCACCGGTATGG
1 GAAGACAAGATCTACTATCTTTGATCTACTTC-A-CGCCAGTACAT
* * *
2083178 GGAGACAAGATCT-GTTTCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTACTATCTTTGATCTACTTCACGCCAGTACAT
*
2083221 GAAGACAAGATCTACTATCTTTGATCCACTTC
1 GAAGACAAGATCTACTATCTTTGATCTACTTC
2083253 GCTACCAATA
Statistics
Matches: 90, Mismatches: 26, Indels: 8
0.73 0.21 0.06
Matches are distributed among these distances:
43 20 0.22
44 51 0.57
45 19 0.21
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTACTATCTTTGATCTACTTCACGCCAGTACAT
Found at i:2083272 original size:88 final size:90
Alignment explanation
Indices: 2083078--2083272 Score: 220
Period size: 88 Copynumber: 2.2 Consensus size: 90
2083068 NNNNNNNNNT
* *
2083078 TACCAATATAGGAAGACAGGACCTACTATCTTTGATCTACTTCACGCCAGTACATGAAGACACGA
1 TACCAATATAGGAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGA
** *
2083143 TCTGTTTTCTTCGACCTACTCTACC
66 TCTACTATCTTCGACCTACTCTACC
** * * * * *
2083168 -ACCGGTATGGGGAGACAAGATCT-GTTTCTTTGATCTACTTCACGCCAGTACATGAAGACAAGA
1 TACCAATATAGGAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGA
*
2083231 TCTACTATCTTTGATCC-ACT-T-CGC
66 TCTACTATCTTCGA-CCTACTCTAC-C
2083255 TACCAATATAGGAAGACA
1 TACCAATATAGGAAGACA
2083273 GGANNNNNNN
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
86 1 0.01
87 2 0.02
88 63 0.74
89 19 0.22
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (90 bp):
TACCAATATAGGAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGA
TCTACTATCTTCGACCTACTCTACC
Found at i:2084196 original size:6 final size:6
Alignment explanation
Indices: 2084177--2084227 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
2084167 CCTTTTCCTC
* * *
2084177 TTCTTCT TTATTT TTCTTT TTCTTT TT-TCTT TTCTTT TTATTT TCCTTT
1 TTCTT-T TTCTTT TTCTTT TTCTTT TTCT-TT TTCTTT TTCTTT TTCTTT
2084226 TT
1 TT
2084228 TCCATCATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
5 1 0.03
6 30 0.83
7 5 0.14
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (6 bp):
TTCTTT
Found at i:2085072 original size:24 final size:25
Alignment explanation
Indices: 2085022--2085078 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
2085012 AGAAGATCTG
*
2085022 AAAGAATGAAAATATAATTATTTAA
1 AAAGAATGAAAATATAATTATTCAA
*
2085047 AAAGAAT-AAAATAT-ATTGGTTCAA
1 AAAGAATGAAAATATAATT-ATTCAA
*
2085071 AATGAATG
1 AAAGAATG
2085079 CAAAGATGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.11
24 17 0.63
25 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (25 bp):
AAAGAATGAAAATATAATTATTCAA
Found at i:2092385 original size:20 final size:20
Alignment explanation
Indices: 2092360--2092399 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2092350 TAAAGGTCTT
*
2092360 TAATACATATGATGTGATGC
1 TAATACATATGATGCGATGC
2092380 TAATACATATGATGCGATGC
1 TAATACATATGATGCGATGC
2092400 ATGAGGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TAATACATATGATGCGATGC
Found at i:2093047 original size:20 final size:20
Alignment explanation
Indices: 2093022--2093059 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2093012 GGCTTTGCGC
*
2093022 TTTTCTTTTCTCAGGCCTAT
1 TTTTCTTTCCTCAGGCCTAT
2093042 TTTTCTTTCCTCAGGCCT
1 TTTTCTTTCCTCAGGCCT
2093060 TCGGTTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.29, G:0.11, T:0.53
Consensus pattern (20 bp):
TTTTCTTTCCTCAGGCCTAT
Found at i:2096126 original size:45 final size:45
Alignment explanation
Indices: 2096062--2096150 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
2096052 GGTATGTTAC
*
2096062 GGTTAATGTACAATGTGAAACAAAACTTTAATGTAAAACATATAA
1 GGTTAAGGTACAATGTGAAACAAAACTTTAATGTAAAACATATAA
2096107 GGTTAAGGTACAATGTGAAACAAAACTTTAATGTAAAACATATA
1 GGTTAAGGTACAATGTGAAACAAAACTTTAATGTAAAACATATA
2096151 TGAATATGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (45 bp):
GGTTAAGGTACAATGTGAAACAAAACTTTAATGTAAAACATATAA
Found at i:2100016 original size:6 final size:6
Alignment explanation
Indices: 2100005--2100029 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2099995 TCTATCTATC
2100005 TATCTA TATCTA TATCTA TATCTA T
1 TATCTA TATCTA TATCTA TATCTA T
2100030 CTATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (6 bp):
TATCTA
Found at i:2100016 original size:10 final size:10
Alignment explanation
Indices: 2100001--2100035 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
2099991 TAAATCTATC
2100001 TATCTATCTA
1 TATCTATCTA
2100011 TATCTATATCTA
1 TATC--TATCTA
2100023 TATCTATCTA
1 TATCTATCTA
2100033 TAT
1 TAT
2100036 ATATGACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (10 bp):
TATCTATCTA
Found at i:2100022 original size:16 final size:16
Alignment explanation
Indices: 2100001--2100035 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2099991 TAAATCTATC
*
2100001 TATCTATCTATATCTA
1 TATCTATATATATCTA
*
2100017 TATCTATATCTATCTA
1 TATCTATATATATCTA
2100033 TAT
1 TAT
2100036 ATATGACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (16 bp):
TATCTATATATATCTA
Found at i:2100548 original size:29 final size:29
Alignment explanation
Indices: 2100506--2100583 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 29
2100496 AAGTTGTGGG
* * *
2100506 TTTAGTC-TCTATACTTTTATTTGATTAAT
1 TTTAGTCAT-TATACTTTTAATTGATCAAA
*
2100535 TTTAGTCATTATACATTTCGAATTGATCAAA
1 TTTAGTCATTATAC-TTT-TAATTGATCAAA
*
2100566 TTTAGTCATTGTACTTTT
1 TTTAGTCATTATACTTTT
2100584 TAAAATTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
29 12 0.30
30 7 0.17
31 21 0.52
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.53
Consensus pattern (29 bp):
TTTAGTCATTATACTTTTAATTGATCAAA
Found at i:2102554 original size:33 final size:33
Alignment explanation
Indices: 2102482--2102559 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
2102472 TAATTTTGAT
* *
2102482 TATATAAATAAAATTTTAATTGTAATTTAAATA
1 TATATATATAAAATTTTAATTGTAATTCAAATA
* * * *
2102515 TGTATATATAAAATTTTAATTTTGATTCAATTA
1 TATATATATAAAATTTTAATTGTAATTCAAATA
*
2102548 TATATATTTAAA
1 TATATATATAAA
2102560 TAAATAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (33 bp):
TATATATATAAAATTTTAATTGTAATTCAAATA
Found at i:2105586 original size:2 final size:2
Alignment explanation
Indices: 2105581--2105614 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2105571 TGTCTCTCTA
2105581 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2105615 AGAGAGAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2105619 original size:2 final size:2
Alignment explanation
Indices: 2105614--2105657 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2105604 GTGTGTGTGT
2105614 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2105656 GA
1 GA
2105658 CTTTGCTAGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2106818 original size:2 final size:2
Alignment explanation
Indices: 2106811--2106837 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2106801 TGTTGATGTT
2106811 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2106838 CAGGTGGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2111227 original size:15 final size:15
Alignment explanation
Indices: 2111209--2111247 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2111199 TTAGTCTTAA
2111209 TTAATTAATAAAAAC
1 TTAATTAATAAAAAC
* *
2111224 TTAATTAATCAAACC
1 TTAATTAATAAAAAC
2111239 TTAACTTAA
1 TTAA-TTAA
2111248 ATTTAGCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATTAATAAAAAC
Found at i:2115744 original size:3 final size:3
Alignment explanation
Indices: 2115738--2115803 Score: 62
Period size: 3 Copynumber: 21.0 Consensus size: 3
2115728 ATTTTTTTAC
* * *
2115738 ATT ATT ATT A-T ATT TTT ATT ATT ACTT GTTT ATT ATT CTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT -ATT ATT ATT ATT ATT ATT
2115784 ATTT ATT ATT ATTT ATT ATT
1 A-TT ATT ATT A-TT ATT ATT
2115804 TTCATGTACA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 2 0.04
3 40 0.77
4 10 0.19
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2115761 original size:20 final size:19
Alignment explanation
Indices: 2115738--2115803 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
2115728 ATTTTTTTAC
*
2115738 ATTATTATTATATTTTTATT
1 ATTATTATT-TATTATTATT
* *
2115758 ATTACTTGTTTATTATTCTT
1 ATTA-TTATTTATTATTATT
2115778 ATTATTATTTATTATTATTT
1 ATTATTATTTATTATTA-TT
2115798 ATTATT
1 ATTATT
2115804 TTCATGTACA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
19 11 0.28
20 24 0.62
21 4 0.10
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTATTATTTATTATTATT
Found at i:2115779 original size:23 final size:21
Alignment explanation
Indices: 2115742--2115803 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 21
2115732 TTTTACATTA
2115742 TTATTA-TATTTTTATTATTACT
1 TTATTATTA-TTTTATTATTA-T
2115764 TGT-TTATTATTCTTATTATTAT
1 T-TATTATTATT-TTATTATTAT
2115786 TTATTATTA-TTTATTATT
1 TTATTATTATTTTATTATT
2115804 TTCATGTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
20 8 0.22
21 2 0.06
22 14 0.39
23 12 0.33
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (21 bp):
TTATTATTATTTTATTATTAT
Found at i:2115801 original size:17 final size:18
Alignment explanation
Indices: 2115738--2115804 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 18
2115728 ATTTTTTTAC
2115738 ATTATTATTATATT-TTT
1 ATTATTATTATATTATTT
*
2115755 ATTATTACTTGT-TTA-TT
1 ATTATTA-TTATATTATTT
*
2115772 ATTCTTA-T-TATTATTT
1 ATTATTATTATATTATTT
2115788 ATTATTATT-TATTATTT
1 ATTATTATTATATTATTT
2115805 TCATGTACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
14 1 0.02
15 4 0.10
16 8 0.19
17 26 0.62
18 3 0.07
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (18 bp):
ATTATTATTATATTATTT
Found at i:2128156 original size:51 final size:52
Alignment explanation
Indices: 2128059--2128164 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
2128049 TCAACGAACA
2128059 ATTCTGGGTTTCTTTTTTTCTTTCTAGATTTTTTTGTACAATTTTTTTGTTT
1 ATTCTGGGTTTCTTTTTTTCTTTCTAGATTTTTTTGTACAATTTTTTTGTTT
2128111 ATTCTGGGTTTCTTTTTTTCTTTCTAGATTTTTTTGTACAA-TTTTTTGTTT
1 ATTCTGGGTTTCTTTTTTTCTTTCTAGATTTTTTTGTACAATTTTTTTGTTT
2128162 ATT
1 ATT
2128165 AGAAATTGTT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 13 0.24
52 41 0.76
ACGTcount: A:0.12, C:0.09, G:0.11, T:0.67
Consensus pattern (52 bp):
ATTCTGGGTTTCTTTTTTTCTTTCTAGATTTTTTTGTACAATTTTTTTGTTT
Found at i:2128476 original size:14 final size:14
Alignment explanation
Indices: 2128457--2128484 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2128447 TTTCAAGTTA
2128457 TAAAAATCTTCAAG
1 TAAAAATCTTCAAG
2128471 TAAAAATCTTCAAG
1 TAAAAATCTTCAAG
2128485 AATTATACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
TAAAAATCTTCAAG
Found at i:2129552 original size:13 final size:14
Alignment explanation
Indices: 2129528--2129556 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2129518 CTTAAATTGA
2129528 TAATTGAATTTTTT
1 TAATTGAATTTTTT
2129542 TAATT-AATTTTTT
1 TAATTGAATTTTTT
2129555 TA
1 TA
2129557 TAATTCTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
TAATTGAATTTTTT
Found at i:2130780 original size:17 final size:17
Alignment explanation
Indices: 2130760--2130797 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2130750 GTTATCAAAA
*
2130760 TAATAACAAT-AATAATT
1 TAATAA-AATGAATAAAT
2130777 TAATAAAATGAATAAAT
1 TAATAAAATGAATAAAT
2130794 TAAT
1 TAAT
2130798 CTTTTTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
TAATAAAATGAATAAAT
Found at i:2137414 original size:20 final size:20
Alignment explanation
Indices: 2137385--2137429 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2137375 TGTTGCTATA
*
2137385 TTTTAGTTTTAGACTTTTAC
1 TTTTACTTTTAGACTTTTAC
* *
2137405 TTTTACTTTTAGATTTTTAT
1 TTTTACTTTTAGACTTTTAC
2137425 TTTTA
1 TTTTA
2137430 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTTACTTTTAGACTTTTAC
Found at i:2138527 original size:14 final size:14
Alignment explanation
Indices: 2138498--2138536 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2138488 AATTTACAGC
*
2138498 ATATACGAATAAAT
1 ATATACAAATAAAT
* *
2138512 ATTTACAAATATAT
1 ATATACAAATAAAT
2138526 ATATACAAATA
1 ATATACAAATA
2138537 CAATGTACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATACAAATAAAT
Found at i:2140747 original size:88 final size:88
Alignment explanation
Indices: 2140592--2140757 Score: 205
Period size: 88 Copynumber: 1.9 Consensus size: 88
2140582 TGGGGTCTTC
* * *
2140592 GATCTGCTCCACTACTGCTTAGGGAGATAAGAATACTGGCTTTAATGTACTCCACTGTAACCACA
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGAATACTGGCTTCAATCTACTCCACTGTAACCACA
*
2140657 GGGAGGTAAAATTCACCATATTT
66 GGGAAGTAAAATTCACCATATTT
* * *
2140680 GATCTGCTCCACTACTGCTTAGGGAGACAAG-AT-CTGAAATCTTCAATCTATTCCACTGCT-GC
1 GATCTGCTCCACTACTGCTTAGGGAGACAAGAATACTG---GCTTCAATCTACTCCACTG-TAAC
2140742 C-CAGGGAAGTAAAATT
62 CACAGGGAAGTAAAATT
2140758 TTTGGCTTCA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
86 3 0.04
87 2 0.03
88 44 0.66
89 17 0.25
90 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (88 bp):
GATCTGCTCCACTACTGCTTAGGGAGACAAGAATACTGGCTTCAATCTACTCCACTGTAACCACA
GGGAAGTAAAATTCACCATATTT
Found at i:2140748 original size:132 final size:132
Alignment explanation
Indices: 2140627--2141597 Score: 1418
Period size: 132 Copynumber: 7.5 Consensus size: 132
2140617 GATAAGAATA
* * * *
2140627 CTGGCTTTAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATATTTGATCTGCTCCAC
1 CTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCAC
*
2140692 TACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAAAAT
66 TACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT
2140757 TT
131 TT
* * * *
2140759 TTGGCTTCAATGTACTCCACTGTAACCACGGGGAGGTAAAATCCGCCATCTTTGACCTGTTCCAC
1 CTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCAC
* * *
2140824 TACTGCTTAGGGAGGCAAGATCTGAAATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAAAAT
66 TACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT
2140889 TT
131 TT
* * * *
2140891 TTGGCTTCAATGTACTCCACTGTAACCACGGGGAGGTAAAATCCGCCATCTTTGACCTGTTCCAC
1 CTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCAC
* *
2140956 TACTGCTTAGGGAGGCAAGATCTGAAATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT
66 TACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT
*
2141021 TA
131 TT
* * * * *
2141023 CTGGCTTCAATGTACTCCACTATAACCATAGAGAGGTAAAATTCACCATCTTTGATCTGCTCCAC
1 CTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCAC
* * ** *
2141088 TACTGCTT-GAGGAGACAAGATCTAAAATCTTTAATCTATTCCACTGCTGCTTAGAGAAGTAGAA
66 TACTGCTTAG-GGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
*
2141152 TTA
130 TTT
* * *
2141155 CTGGTTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCGTCATCTTTGATCTGCTCCAC
1 CTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCAC
* *
2141220 TACTGCTTAGCGAGAC-A-A---G--ATC-TCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAA
66 TACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT
2141277 TT
131 TT
* *
2141279 CTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTAATCTGCTCCAC
1 CTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCAC
* *
2141344 TACTGCTTAGCGAGAC-A-A---G--ATC-TCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAA
66 TACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT
2141401 TT
131 TT
*
2141403 CTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCAC
1 CTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCAC
* * *
2141468 TACTGGTTAGGGAGACAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAA
66 TACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT
2141533 TT
131 TT
*
2141535 CTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCC
1 CTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCC
2141598 GCTGTCTATG
Statistics
Matches: 778, Mismatches: 51, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
124 228 0.29
125 4 0.01
126 1 0.00
130 1 0.00
131 5 0.01
132 538 0.69
133 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
CTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCAC
TACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAAT
TT
Found at i:2140880 original size:44 final size:44
Alignment explanation
Indices: 2140700--2141012 Score: 121
Period size: 44 Copynumber: 7.1 Consensus size: 44
2140690 ACTACTGCTT
* * *
2140700 AGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGGCAAAATCTGAAATCTTTAATCTATTCCACTGCTGCCC
* * ***** * * * *
2140744 AGGGAAGTAAAAT-TTTTGGCTTCAATGTACTCCACTG-TAACCAC
1 AGGGAGGCAAAATCTGAAATCTTTAATCTATTCCACTGCT-GCC-C
* * * ** * * * * **
2140788 GGGGAGGTAAAATCCGCCATCTTTGACCTGTTCCACTACTGCTT
1 AGGGAGGCAAAATCTGAAATCTTTAATCTATTCCACTGCTGCCC
*
2140832 AGGGAGGCAAGATCTGAAATCTTTAATCTATTCCACTGCTGCCC
1 AGGGAGGCAAAATCTGAAATCTTTAATCTATTCCACTGCTGCCC
* * ***** * * * *
2140876 AGGGAAGTAAAAT-TTTTGGCTTCAATGTACTCCACTG-TAACCAC
1 AGGGAGGCAAAATCTGAAATCTTTAATCTATTCCACTGCT-GCC-C
* * * ** * * * * **
2140920 GGGGAGGTAAAATCCGCCATCTTTGACCTGTTCCACTACTGCTT
1 AGGGAGGCAAAATCTGAAATCTTTAATCTATTCCACTGCTGCCC
*
2140964 AGGGAGGCAAGATCTGAAATCTTTAATCTATTCCACTGCTGCCC
1 AGGGAGGCAAAATCTGAAATCTTTAATCTATTCCACTGCTGCCC
2141008 AGGGA
1 AGGGA
2141013 AGTAGAATTA
Statistics
Matches: 177, Mismatches: 84, Indels: 16
0.64 0.30 0.06
Matches are distributed among these distances:
42 2 0.01
43 37 0.21
44 112 0.63
45 24 0.14
46 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (44 bp):
AGGGAGGCAAAATCTGAAATCTTTAATCTATTCCACTGCTGCCC
Found at i:2141648 original size:45 final size:45
Alignment explanation
Indices: 2141591--2141708 Score: 114
Period size: 43 Copynumber: 2.7 Consensus size: 45
2141581 CATCTTTGAT
*
2141591 CTGCTCCGCTGTCTATGCAGGAAGGCAAGAGCTGCTATCTTCAAC
1 CTGCTCCACTGTCTATGCAGGAAGGCAAGAGCTGCTATCTTCAAC
** * * * * * * *
2141636 CTGCTCCACTGTCTCCG-AGGGAGGCGAG-GTTGGTGTCTTCGAT
1 CTGCTCCACTGTCTATGCAGGAAGGCAAGAGCTGCTATCTTCAAC
* *
2141679 CTGCTTCACTGTCGATGCAGGAAGGCAAGA
1 CTGCTCCACTGTCTATGCAGGAAGGCAAGA
2141709 TCTATTATCA
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
43 23 0.42
44 18 0.33
45 14 0.25
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.25
Consensus pattern (45 bp):
CTGCTCCACTGTCTATGCAGGAAGGCAAGAGCTGCTATCTTCAAC
Found at i:2142962 original size:14 final size:13
Alignment explanation
Indices: 2142953--2142983 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
2142943 CATTTTCATC
2142953 TTTTCATTTTTCA
1 TTTTCATTTTTCA
2142966 TTTTCATCTTTTCA
1 TTTTCAT-TTTTCA
2142980 TTTT
1 TTTT
2142984 TCACATCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:2142965 original size:7 final size:7
Alignment explanation
Indices: 2142945--2142986 Score: 59
Period size: 8 Copynumber: 5.9 Consensus size: 7
2142935 AGCCTCTCCA
2142945 TTTTCAT
1 TTTTCAT
2142952 CTTTTCAT
1 -TTTTCAT
2142960 TTTTCA-
1 TTTTCAT
2142966 TTTTCAT
1 TTTTCAT
2142973 CTTTTCAT
1 -TTTTCAT
2142981 TTTTCA
1 TTTTCA
2142987 CATCACTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.19
7 12 0.38
8 14 0.44
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTTCAT
Found at i:2142969 original size:21 final size:21
Alignment explanation
Indices: 2142943--2142986 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2142933 TTAGCCTCTC
2142943 CATTTTCATCTTTTCATTTTT
1 CATTTTCATCTTTTCATTTTT
2142964 CATTTTCATCTTTTCATTTTT
1 CATTTTCATCTTTTCATTTTT
2142985 CA
1 CA
2142987 CATCACTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (21 bp):
CATTTTCATCTTTTCATTTTT
Found at i:2142996 original size:21 final size:21
Alignment explanation
Indices: 2142948--2142998 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
2142938 CTCTCCATTT
**
2142948 TCATCTTTTCATTTTTCATTT
1 TCATCTTTTCATTTTTCATCA
2142969 TCATCTTTTCATTTTTCA-CA
1 TCATCTTTTCATTTTTCATCA
2142989 TCACTCTTTT
1 TCA-TCTTTT
2142999 TTTTTTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 3 0.11
21 24 0.89
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (21 bp):
TCATCTTTTCATTTTTCATCA
Found at i:2148128 original size:14 final size:14
Alignment explanation
Indices: 2148099--2148137 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2148089 AATTTACAGC
*
2148099 ATATACGAATAAAT
1 ATATACAAATAAAT
* *
2148113 ATTTACAAATATAT
1 ATATACAAATAAAT
2148127 ATATACAAATA
1 ATATACAAATA
2148138 CAATGTACCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATACAAATAAAT
Found at i:2168644 original size:32 final size:36
Alignment explanation
Indices: 2168616--2168689 Score: 112
Period size: 38 Copynumber: 2.0 Consensus size: 36
2168606 CAAGAGATCA
2168616 CAACAGATTTCTATCCTTAATTATAGAGATTCCAATAC
1 CAACAGATTTCTATCCTTAATTATAGAGATTCC-A-AC
* *
2168654 CATCAGATTTCTATCCTTAATTATAGGGATTCCAAC
1 CAACAGATTTCTATCCTTAATTATAGAGATTCCAAC
2168690 AATATACTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 2 0.06
37 1 0.03
38 31 0.91
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (36 bp):
CAACAGATTTCTATCCTTAATTATAGAGATTCCAAC
Found at i:2169537 original size:5 final size:5
Alignment explanation
Indices: 2169527--2169552 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2169517 ATATTATTTA
2169527 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
2169553 TTTATACTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2169638 original size:25 final size:23
Alignment explanation
Indices: 2169600--2169650 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
2169590 NNNNNNNNNC
2169600 TATTTTTAATTTAATAATTTAATA
1 TATTTTTAATTTAA-AATTTAATA
* *
2169624 TATTTTTTATATTAAAATTTTATA
1 TATTTTTAAT-TTAAAATTTAATA
2169648 TAT
1 TAT
2169651 GATCATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTTTTAATTTAAAATTTAATA
Found at i:2181415 original size:3 final size:3
Alignment explanation
Indices: 2181407--2181435 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2181397 TTCAGTAGTT
2181407 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2181436 TTTTCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2187754 original size:8 final size:7
Alignment explanation
Indices: 2187732--2187776 Score: 65
Period size: 7 Copynumber: 6.4 Consensus size: 7
2187722 AAAAAAAGAG
2187732 ATGAATAA
1 ATGAA-AA
2187740 ATGAAAA
1 ATGAAAA
2187747 ATGAAAA
1 ATGAAAA
2187754 ATGAAAA
1 ATGAAAA
2187761 ATG-AAA
1 ATGAAAA
*
2187767 GTGAAAA
1 ATGAAAA
2187774 ATG
1 ATG
2187777 GAGAGGCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 5 0.15
7 24 0.71
8 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (7 bp):
ATGAAAA
Found at i:2187771 original size:13 final size:14
Alignment explanation
Indices: 2187732--2187776 Score: 65
Period size: 13 Copynumber: 3.2 Consensus size: 14
2187722 AAAAAAAGAG
2187732 ATGAATAAATGAAAA
1 ATGAA-AAATGAAAA
2187747 ATGAAAAATGAAAA
1 ATGAAAAATGAAAA
*
2187761 ATG-AAAGTGAAAA
1 ATGAAAAATGAAAA
2187774 ATG
1 ATG
2187777 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.41
14 12 0.41
15 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (14 bp):
ATGAAAAATGAAAA
Found at i:2191866 original size:46 final size:45
Alignment explanation
Indices: 2191771--2192321 Score: 338
Period size: 46 Copynumber: 12.6 Consensus size: 45
2191761 NNNNNNNNAG
* * * * *
2191771 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---G-CATCA
1 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACTTCA
* * *
2191812 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCA
1 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAC-TTCA
* *
2191858 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACAT-A
1 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACTTCA
* * * * * **
2191902 -ATCCTATCTCCCTGAAGTTACAGTGGAGCGGAT-TAA-AATAAA
1 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACTTCA
* * * * *
2191944 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---G-CATCA
1 -GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACTTCA
* * *
2191986 GGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCA
1 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAC-TTCA
* * *
2192032 GATCTTATCCCCCTGAGGTTACAGCGGAGCAGATCGAAGACAT-A
1 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACTTCA
* * * * * **
2192076 -ATCCTATCTCCCTGAAGTTACAGTGGAGCGGAT-TAA-AATAAA
1 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACTTCA
* * * * *
2192118 GGATCTTACCTCTCTGAAGTTACAGTAGAGCAGATC--ACAC--CA
1 -GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACTTCA
* * * * * * *
2192160 GGTCTTATCTCCCTGATGATACAGTAGAGTAGACCGAAGAATTTCA
1 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAG-ACTTCA
* * *
2192206 GATCTTATCCCCCTGAGGTTACAGCGGAGCAGATCGAAGAC-AC-
1 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACTTCA
* * * * * * * **
2192249 TATCCTATCTCCCTGAAGTTACAGCGGAGCGGAT-TAAAACCACA
1 GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACTTCA
* * *
2192293 GAGCTTATCTCCCTGAAGTTGCAGTGGAG
1 GATCTTATCTCCCTGAGGTTACAGTGGAG
2192322 TAAATTAAAA
Statistics
Matches: 396, Mismatches: 87, Indels: 51
0.74 0.16 0.10
Matches are distributed among these distances:
41 90 0.23
42 12 0.03
43 90 0.23
44 87 0.22
45 5 0.01
46 112 0.28
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (45 bp):
GATCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGACTTCA
Found at i:2191949 original size:87 final size:86
Alignment explanation
Indices: 2191857--2192308 Score: 385
Period size: 87 Copynumber: 5.2 Consensus size: 86
2191847 GAAGACTTTC
2191857 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
2191922 CAGTGGAGCGGATTAAAATAA
66 CAGTGGAGCGGATTAAAATAA
* * ** * * * ** * *
2191943 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCA-TCA-GGTCTTATCTCCCTGAGGTT
1 A-GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTT
** ** * **
2192006 ACAGTGGAGTAGACCGAAGACTTTC
65 ACAGTGGAGCGGA-TTAA-A-ATAA
*
2192031 AGATCTTATCCCCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
2192096 CAGTGGAGCGGATTAAAATAA
66 CAGTGGAGCGGATTAAAATAA
* * * ** * ** * * *
2192117 AGGATCTTACCTCTCTGAAGTTACAGTAGAGCAGATC-ACA-CCA-GGTCTTATCTCCCTGATGA
1 A-GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGA-AGACATAATCCTATCTCCCTGAAGT
* ** ** **
2192179 TACAGTAGAGTAGACCGAAGAATTTC
64 TACAGTGGAGCGGA-TTAA-AA-TAA
*
2192205 AGATCTTATCCCCCTGAGGTTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCCTGAAGTT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACA-TAATCCTATCTCCCTGAAGTT
* * *
2192269 ACAGCGGAGCGGATTAAAACCAC
65 ACAGTGGAGCGGATTAAAA-TAA
*
2192292 AGAGCTTATCTCCCTGA
1 AGATCTTATCTCCCTGA
2192309 AGTTGCAGTG
Statistics
Matches: 273, Mismatches: 78, Indels: 29
0.72 0.21 0.08
Matches are distributed among these distances:
85 52 0.19
86 12 0.04
87 145 0.53
88 13 0.05
89 51 0.19
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (86 bp):
AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAATAA
Found at i:2191962 original size:44 final size:44
Alignment explanation
Indices: 2191858--2192331 Score: 193
Period size: 43 Copynumber: 10.9 Consensus size: 44
2191848 AAGACTTTCA
* * * * * *
2191858 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACATA-
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGAT-TAAAATAAAG
* *
2191902 -ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* * * *** *
2191945 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGA-TCGCAT-CAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* * ** * **
2191987 G-TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGACTTTCA-
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-A-ATAAAG
* * * * * * *
2192032 GATCTTATCCCCCTGAGGTTACAGCGGAGCAGATCGAAGACATA-
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGAT-TAAAATAAAG
* *
2192076 -ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* * * * * **
2192119 GATCTTACCTCTCTGAAGTTACAGTAGAGCAGA-TCACA-CCAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* * * * ** **
2192161 G-TCTTATCTCCCTGATGATACAGTAGAGTAGACCGAAGAATTTCA-
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AA-TAAAG
* * * ** * * *
2192206 GATCTTATCCCCCTGAGGTTACAGCGGAGCAGA-TCGAAGACAC
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* * * * * *
2192249 TATCCTATCTCCCTGAAGTTACAGCGGAGCGGATTAAAACCACA-
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAA-TAAAG
* * * *
2192293 GAGCTTATCTCCCTGAAGTTGCAGTGGAGTAAATTAAAA
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAA
2192332 CCATGAATCT
Statistics
Matches: 322, Mismatches: 88, Indels: 40
0.72 0.20 0.09
Matches are distributed among these distances:
41 54 0.17
42 18 0.06
43 94 0.29
44 90 0.28
45 6 0.02
46 60 0.19
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (44 bp):
GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
Found at i:2192059 original size:174 final size:174
Alignment explanation
Indices: 2191769--2192323 Score: 934
Period size: 174 Copynumber: 3.2 Consensus size: 174
2191759 NNNNNNNNNN
2191769 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTAC
1 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTAC
*
2191834 AGTGGAGTAGACCGAAGACTTTCAGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAC
66 AGTGGAGTAGACCGAAGACTTTCAGATCTTATCCCCCTGAGGTTACAGCGGAGCAGATCGAAGAC
2191899 ATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
131 ATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
2191943 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTAC
1 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTAC
2192008 AGTGGAGTAGACCGAAGACTTTCAGATCTTATCCCCCTGAGGTTACAGCGGAGCAGATCGAAGAC
66 AGTGGAGTAGACCGAAGACTTTCAGATCTTATCCCCCTGAGGTTACAGCGGAGCAGATCGAAGAC
2192073 ATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
131 ATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
* * * * * *
2192117 AGGATCTTACCTCTCTGAAGTTACAGTAGAGCAGATCACACCAGGTCTTATCTCCCTGATGATAC
1 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTAC
* *
2192182 AGTAGAGTAGACCGAAGAATTTCAGATCTTATCCCCCTGAGGTTACAGCGGAGCAGATCGAAGAC
66 AGTGGAGTAGACCGAAGACTTTCAGATCTTATCCCCCTGAGGTTACAGCGGAGCAGATCGAAGAC
* * *
2192247 ACT-ATCCTATCTCCCTGAAGTTACAGCGGAGCGGATTAAAACCAC
131 A-TAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAA-TAA
* * * *
2192292 A-GAGCTTATCTCCCTGAAGTTGCAGTGGAGTA
1 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
2192324 AATTAAAACC
Statistics
Matches: 361, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
174 358 0.99
175 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (174 bp):
AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTAC
AGTGGAGTAGACCGAAGACTTTCAGATCTTATCCCCCTGAGGTTACAGCGGAGCAGATCGAAGAC
ATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
Found at i:2193723 original size:3 final size:3
Alignment explanation
Indices: 2193715--2193759 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2193705 TTCAGTAGTT
2193715 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2193760 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2199632 original size:21 final size:20
Alignment explanation
Indices: 2199606--2199645 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2199596 GACTTTTATA
*
2199606 GTTATTATTATTGTTGTTTTT
1 GTTATTATTATGGTT-TTTTT
*
2199627 GTTATTTTTATGGTTTTTT
1 GTTATTATTATGGTTTTTT
2199646 ATTATTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.72
Consensus pattern (20 bp):
GTTATTATTATGGTTTTTTT
Found at i:2201343 original size:15 final size:14
Alignment explanation
Indices: 2201289--2201344 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
2201279 TAACAATATA
2201289 GTAATAATAATAA-
1 GTAATAATAATAAG
2201302 GTACATAAATAATAAGG
1 GTA-AT-AATAATAA-G
2201319 GTAA-AATAATAATG
1 GTAATAATAATAA-G
2201333 GTAATAATAATA
1 GTAATAATAATA
2201345 TTAATTTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
13 3 0.08
14 15 0.41
15 15 0.41
16 1 0.03
17 3 0.08
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (14 bp):
GTAATAATAATAAG
Found at i:2202136 original size:4 final size:4
Alignment explanation
Indices: 2202129--2202154 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2202119 AAAAAAGGGA
2202129 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
2202155 GAAATCAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2219174 original size:3 final size:3
Alignment explanation
Indices: 2219166--2219197 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2219156 AGGCAACCCA
*
2219166 TCT TCT TCT TCT TCT TCT TCT TCA TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
2219198 ACTTGGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:2220539 original size:25 final size:23
Alignment explanation
Indices: 2220511--2220562 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
2220501 AATGTGTACG
* *
2220511 ATTAAATTAAAAAATTATGTATATA
1 ATTAAA-TAAAAAATAATATAT-TA
2220536 ATTAAATAAAAAATAATATATTA
1 ATTAAATAAAAAATAATATATTA
2220559 ATTA
1 ATTA
2220563 TGTCAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.24
24 13 0.52
25 6 0.24
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
ATTAAATAAAAAATAATATATTA
Found at i:2221217 original size:18 final size:18
Alignment explanation
Indices: 2221164--2221221 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
2221154 TTTTATTGGA
*
2221164 TTTTAAAATTTTTATGTAT
1 TTTTAAAATTTTTAAG-AT
* *
2221183 TTTTTAATTTTATTAAGAT
1 TTTTAAAATTT-TTAAGAT
*
2221202 TTTTAAAATTTGTAAGAT
1 TTTTAAAATTTTTAAGAT
2221220 TT
1 TT
2221222 ACTTGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 8 0.25
19 20 0.62
20 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
TTTTAAAATTTTTAAGAT
Found at i:2221266 original size:18 final size:17
Alignment explanation
Indices: 2221229--2221269 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
2221219 TTTACTTGAA
2221229 AATTTTATTATTTTTGG
1 AATTTTATTATTTTTGG
2221246 AATTTATATATATTTTT-G
1 AATTT-TAT-TATTTTTGG
2221264 AATTTT
1 AATTTT
2221270 TTTAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.27
18 9 0.41
19 7 0.32
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (17 bp):
AATTTTATTATTTTTGG
Found at i:2223946 original size:20 final size:22
Alignment explanation
Indices: 2223908--2223955 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
2223898 CTCTCTCAAT
2223908 AAAAATTACAAAAAGAATTTTC
1 AAAAATTACAAAAAGAATTTTC
* *
2223930 AAAAATT-C-AAAATAATTTTT
1 AAAAATTACAAAAAGAATTTTC
2223950 AAAAAT
1 AAAAAT
2223956 CACATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.67
21 1 0.04
22 7 0.29
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAATTACAAAAAGAATTTTC
Found at i:2236206 original size:56 final size:56
Alignment explanation
Indices: 2236108--2236242 Score: 180
Period size: 56 Copynumber: 2.4 Consensus size: 56
2236098 GGTATTTATG
* * **
2236108 ATCTTTTAGCAATTTGATTCCTAATGGGATATTATAGGATATTACTATGGAATATT
1 ATCTTTTAGCAATTTGATTCCTAATGAGATATTACAAAATATTACTATGGAATATT
* * * *
2236164 ATCTCTTAGCAATTTGATTCCTAATGAGATGTTACAAAATATTATTATGGTATATT
1 ATCTTTTAGCAATTTGATTCCTAATGAGATATTACAAAATATTACTATGGAATATT
* *
2236220 ATCTTTTGGTAATTTGATTCCTA
1 ATCTTTTAGCAATTTGATTCCTA
2236243 TATAATTATT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.44
Consensus pattern (56 bp):
ATCTTTTAGCAATTTGATTCCTAATGAGATATTACAAAATATTACTATGGAATATT
Found at i:2253133 original size:23 final size:23
Alignment explanation
Indices: 2253091--2253134 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2253081 GTAAAACCGA
*
2253091 ATAATTGTCACATGTTTATTACC
1 ATAATTGTCACATGTATATTACC
2253114 ATAATTG-CACATGTAATATTA
1 ATAATTGTCACATGT-ATATTA
2253135 TTAACCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (23 bp):
ATAATTGTCACATGTATATTACC
Done.