Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 105 of 189
Found at i:29310528 original size:165 final size:165
Alignment explanation
Indices: 29310248--29310575 Score: 516
Period size: 165 Copynumber: 2.0 Consensus size: 165
29310238 ATATAATTTG
* *
29310248 GAATAACACCTTAATTATCGGGAGATAAGTATGTATTGATAACTTGTTGAGACCAAATGTTAAGC
1 GAATAACACCTTAATTATCGGCAAATAAGTATGTATTGATAACTTGTTGAGACCAAATGTTAAGC
*
29310313 AATTGTGGTTTATATTCAGAGACATATGTTCCTTCATGTTGATCTTTATAAATATTATTCTTATA
66 AATTGTGGTTTATATTCAGAGACATATGTTCCTTCATGTTGATCTTTATAAATATTAGTCTTATA
29310378 CTT-TTTTACCAGTTGTTCTTAATCTAGAGTTGAAA
131 -TTCTTTTACCAGTTGTTCTTAATCTAGAGTTGAAA
* *
29310413 GAATAATACCTTAATTATC-GCACAATAAGTATGTATTGATAACTTGTTGAGACCAAATGTTGAG
1 GAATAACACCTTAATTATCGGCA-AATAAGTATGTATTGATAACTTGTTGAGACCAAATGTTAAG
** * * *
29310477 CAATTGTGGTTTATATTTTGAGACATATGTTCCTTCATGTTTATTTTTATAAATATTCGTCTTAT
65 CAATTGTGGTTTATATTCAGAGACATATGTTCCTTCATGTTGATCTTTATAAATATTAGTCTTAT
* *
29310542 ATTCTTTTACTAGTTGTTCTTACTCTAGAGTTGA
130 ATTCTTTTACCAGTTGTTCTTAATCTAGAGTTGA
29310576 GGGAAGAAGA
Statistics
Matches: 149, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
164 4 0.03
165 145 0.97
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (165 bp):
GAATAACACCTTAATTATCGGCAAATAAGTATGTATTGATAACTTGTTGAGACCAAATGTTAAGC
AATTGTGGTTTATATTCAGAGACATATGTTCCTTCATGTTGATCTTTATAAATATTAGTCTTATA
TTCTTTTACCAGTTGTTCTTAATCTAGAGTTGAAA
Found at i:29310981 original size:164 final size:163
Alignment explanation
Indices: 29310752--29311626 Score: 1164
Period size: 164 Copynumber: 5.3 Consensus size: 163
29310742 TTCCTTTACA
* *
29310752 TTGATCATTATAAATATTCTTGTTATATTTTTTTACCAGTTGTTCTTGCCCTAGGGTTGAGGGAA
1 TTGATCATTATAAATATTCTTCTTAT-TTTTTTTACCAGTTGTTCTTGCCCTAGAGTTGAGGGAA
* * * * * *
29310817 TAATACCATACTTACCGTGCGGTATGTATATATTTAAAACTTGTTGAGACCAAATGTTGAGCAAT
65 TAATACCTTAATTACAGCGCGGTAAGTAT-TATTTATAACTTGTTGAGACCAAATGTTGAGCAAT
* * * * *
29310882 TGAGGTTTATATTCGAAGACATGCATTCCTTCATG
129 TGTGGTTTATATTCTAAGACATACGTTCTTTCATG
* * * *
29310917 TTGGTCATTATAAATATTCTTCTTATTTTTTTTACCAGTTATTATTGCTCTAGAGTTGAGGGAAT
1 TTGATCATTATAAATATTCTTCTTATTTTTTTTACCAGTTGTTCTTGCCCTAGAGTTGAGGGAAT
* * * * *
29310982 AATGCCTTAATTACAGCGCGGT-A-T-GTATTGATAACTTGTTAAGACCAAATTTTGAGCAATTG
66 AATACCTTAATTACAGCGCGGTAAGTATTATTTATAACTTGTTGAGACCAAATGTTGAGCAATTG
* * * *
29311044 TAGTTTATATTCTAATACATACATTCTTTCAAG
131 TGGTTTATATTCTAAGACATACGTTCTTTCATG
* *
29311077 TTGATCATTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTCTTGCCCAAGAGTTGAGGGAAT
1 TTGATCATTATAAATATTCTTCTTATTTTTTTTACCAGTTGTTCTTGCCCTAGAGTTGAGGGAAT
* * * *
29311142 AATACCTTAAGTACAGCACGGTAAGTATCT-TTTGATAACTTCTTGAGACCAAATGTTGAACAAT
66 AATACCTTAATTACAGCGCGGTAAGTAT-TATTT-ATAACTTGTTGAGACCAAATGTTGAGCAAT
*
29311206 AGTGGTTTATATTCTAAGACATACGTTCTTTCATG
129 TGTGGTTTATATTCTAAGACATACGTTCTTTCATG
* *
29311241 TTGATCATTATAAATATTCTTCTTATATTTTTTACCAGTTGTTCTTGCCCAAGAGTTGAGGGAAT
1 TTGATCATTATAAATATTCTTCTTATTTTTTTTACCAGTTGTTCTTGCCCTAGAGTTGAGGGAAT
* * * * **
29311306 AATACCTTAATTACAGCACGGTAAGTATCTATTTATAACTTCTTGAGACAAAATGTTGAACAACA
66 AATACCTTAATTACAGCGCGGTAAGTAT-TATTTATAACTTGTTGAGACCAAATGTTGAGCAATT
*
29311371 GTGGTTTATATTCTAAGACATATGTTCTTTCATG
130 GTGGTTTATATTCTAAGACATACGTTCTTTCATG
** *
29311405 TTGATCATTATAAATATTCTTCTTATGCTTTTTACCAGTTGTTCTTACCCCTAGAGTTGAGGGAA
1 TTGATCATTATAAATATTCTTCTTATTTTTTTTACCAGTTGTTCTT-GCCCTAGAGTTGAGGGAA
* * *
29311470 TAATACCTTAATTACTGCGCGGTAAGTATGATTGATAACTTGTTGAGACCAAATGTTGAGCAATT
65 TAATACCTTAATTACAGCGCGGTAAGTATTATTTATAACTTGTTGAGACCAAATGTTGAGCAATT
* * * *
29311535 GTGGTTTATATTCCAAGACATATGTTCCTTCACG
130 GTGGTTTATATTCTAAGACATACGTTCTTTCATG
* * *
29311569 TTAATCTTTATAAATATTCTTCTTATGTTTTTTTACCAGTTGTTCTTGCTCTAGAGTT
1 TTGATCATTATAAATATTCTTCTTAT-TTTTTTTACCAGTTGTTCTTGCCCTAGAGTT
29311627 TATGGAAGAA
Statistics
Matches: 631, Mismatches: 71, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
160 137 0.22
161 1 0.00
162 2 0.00
163 2 0.00
164 401 0.64
165 88 0.14
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (163 bp):
TTGATCATTATAAATATTCTTCTTATTTTTTTTACCAGTTGTTCTTGCCCTAGAGTTGAGGGAAT
AATACCTTAATTACAGCGCGGTAAGTATTATTTATAACTTGTTGAGACCAAATGTTGAGCAATTG
TGGTTTATATTCTAAGACATACGTTCTTTCATG
Found at i:29311524 original size:328 final size:324
Alignment explanation
Indices: 29310752--29311626 Score: 1194
Period size: 324 Copynumber: 2.7 Consensus size: 324
29310742 TTCCTTTACA
* * *
29310752 TTGATCATTATAAATATTCTTGTTATATTTTTTTACCAGTTGTTCTTGCCCTAGGGTTGAGGGAA
1 TTGATCATTATAAATATTCTTCTTAT-GTTTTTTACCAGTTGTTCTTGCCCTAGAGTTGAGGGAA
* * * * * * *
29310817 TAATACCATACTTACCGTGCGGTATGTATATATTTAAAACTTGTTGAGACCAAATGTTGAGCAAT
65 TAATACCTTAATTACAGCGCGGTAAGTATATATTGATAACTTGTTGAGACCAAATGTTGAGCAAT
* * * * *
29310882 TGAGGTTTATATTCGAAGACATGCATTCCTTCATGTTGGTCATTATAAATATTCTTCTTATTTTT
130 TGTGGTTTATATTCCAAGACATACGTTCCTTCATGTTGATCATTATAAATATTCTTCTTATTTTT
* * * * *
29310947 TTTACCAGTTATTATTGCTCTAGAGTTGAGGGAATAATGCCTTAATTACAGCGCGGTATGTATTG
195 TTTACCAGTTGTTCTTGCTCTAGAGTTGAGGGAATAATACCTTAATTACAGCACGGTATCTATTG
* * * * ** *
29311012 ATAACTTGTTAAGACCAAATTTTGAGCAATTGTAGTTTATATTCTAATACATACATTCTTTCAAG
260 ATAACTTCTTAAGACAAAATGTTGAACAACAGTAGTTTATATTCTAAGACATACATTCTTTCAAG
*
29311077 TTGATCATTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTCTTGCCCAAGAGTTGAGGGAAT
1 TTGATCATTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTCTTGCCCTAGAGTTGAGGGAAT
* * * * * * *
29311142 AATACCTTAAGTACAGCACGGTAAGTATCTTTTGATAACTTCTTGAGACCAAATGTTGAACAATA
66 AATACCTTAATTACAGCGCGGTAAGTATATATTGATAACTTGTTGAGACCAAATGTTGAGCAATT
* * *
29311207 GTGGTTTATATTCTAAGACATACGTTCTTTCATGTTGATCATTATAAATATTCTTCTTATATTTT
131 GTGGTTTATATTCCAAGACATACGTTCCTTCATGTTGATCATTATAAATATTCTTCTTATTTTTT
* *
29311272 TTACCAGTTGTTCTTGCCCAAGAGTTGAGGGAATAATACCTTAATTACAGCACGGTAAGTATCTA
196 TTACCAGTTGTTCTTGCTCTAGAGTTGAGGGAATAATACCTTAATTACAGCAC-G---GTATCTA
* * * **
29311337 TTTATAACTTCTTGAGACAAAATGTTGAACAACAGTGGTTTATATTCTAAGACATATGTTCTTTC
257 TTGATAACTTCTTAAGACAAAATGTTGAACAACAGTAGTTTATATTCTAAGACATACATTCTTTC
*
29311402 ATG
322 AAG
* *
29311405 TTGATCATTATAAATATTCTTCTTATGCTTTTTACCAGTTGTTCTTACCCCTAGAGTTGAGGGAA
1 TTGATCATTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTCTT-GCCCTAGAGTTGAGGGAA
* *
29311470 TAATACCTTAATTACTGCGCGGTAAGTAT-GATTGATAACTTGTTGAGACCAAATGTTGAGCAAT
65 TAATACCTTAATTACAGCGCGGTAAGTATATATTGATAACTTGTTGAGACCAAATGTTGAGCAAT
* * * *
29311534 TGTGGTTTATATTCCAAGACATATGTTCCTTCACGTTAATCTTTATAAATATTCTTCTTATGTTT
130 TGTGGTTTATATTCCAAGACATACGTTCCTTCATGTTGATCATTATAAATATTCTTCTTAT-TTT
29311599 TTTTACCAGTTGTTCTTGCTCTAGAGTT
194 TTTTACCAGTTGTTCTTGCTCTAGAGTT
29311627 TATGGAAGAA
Statistics
Matches: 479, Mismatches: 65, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
324 192 0.40
325 26 0.05
328 191 0.40
329 70 0.15
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (324 bp):
TTGATCATTATAAATATTCTTCTTATGTTTTTTACCAGTTGTTCTTGCCCTAGAGTTGAGGGAAT
AATACCTTAATTACAGCGCGGTAAGTATATATTGATAACTTGTTGAGACCAAATGTTGAGCAATT
GTGGTTTATATTCCAAGACATACGTTCCTTCATGTTGATCATTATAAATATTCTTCTTATTTTTT
TTACCAGTTGTTCTTGCTCTAGAGTTGAGGGAATAATACCTTAATTACAGCACGGTATCTATTGA
TAACTTCTTAAGACAAAATGTTGAACAACAGTAGTTTATATTCTAAGACATACATTCTTTCAAG
Found at i:29312723 original size:165 final size:163
Alignment explanation
Indices: 29312053--29312929 Score: 614
Period size: 165 Copynumber: 5.3 Consensus size: 163
29312043 ATTACCCGAG
* * * * * * * *
29312053 GTTGAGACCAAATGTGGGGAAATTGTGGTTAATATTACGAGGCATACGTTCCTTCACGTTGATCA
1 GTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGACATACGTTCTTTCATGTTGATCA
* * * * ** * * * * * *
29312118 TTATAAATCTTCTTCTAATGTTTTTTTTTTCCAATTATTCTCACTCAAGTGTTGTGAGAAGGATA
66 TTATAAATCTTCTTCTTATG--TTTTTTTACCAGTTGTT-TTTCTCCAGAGTTGAGGGAAGAAGA
** * * *
29312183 GCGTAAGTATTGCACGA-TAAGTATGTATTGATGACTT
128 AAGTAATTAAT-C-CGAGTAAGTATGTATTGATAACTT
* * * * * * *
29312220 ATTGAGACCAAATGTTGAGCAATTTTGGTTTATATTTCGAGGCATATGTTCCTTCATATTGATTA
1 GTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGACATACGTTCTTTCATGTTGATCA
* * * * * * * *
29312285 TTATAAATCTTCTGCTAATG-TTTTTTGCTAGATCTTCTTGCTCCAGAGTTGAGGCAAGAAGAAA
66 TTATAAATCTTCTTCTTATGTTTTTTTACCAGTTGTT-TTTCTCCAGAGTTGAGGGAAGAAGAAA
* * * *
29312349 GTAATTAATCTGGGGTAAATATGCATTGATAACTT
130 GTAATTAATC-CGAGTAAGTATGTATTGATAACTT
* * * ** ***
29312384 GTTGAGACCAAATATTAAGCAAATT-TGGTTTATATTCTGCTA-ATGTTTTTTGCTAGATCTTCA
1 GTTGAGACCAAATGTTGAGC-AATTGTGGTTTATATT-T-CGAGACATACGTT-C----T-TTCA
* * *
29312447 TATTGATCATTGTAAATCTTCTTCTTTTTATG-TTTTTTACCAGTTGTTCTTTCTCCAGAGTGGA
57 TGTTGATCATTATAAATCTTCTTC---TTATGTTTTTTTACCAGTTGTT-TTTCTCCAGAGTTGA
* * ** * * *
29312511 GGGAATAA-TACCTAAATT-ATAGCGCAGTCAGTATGTATAGATAACTT
118 GGGAAGAAGAAAGT-AATTAAT-CCG-AGTAAGTATGTATTGATAACTT
*
29312558 GTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGACATACGTTCTTTCATGTTGATCT
1 GTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGACATACGTTCTTTCATGTTGATCA
* *
29312623 TTATAAATATTCTTCTTATGTTTTTTTACCAGTTGTTTTTGCTCAAGAGTTGAGGGAAGAAGAAA
66 TTATAAATCTTCTTCTTATGTTTTTTTACCAGTTGTTTTT-CTCCAGAGTTGAGGGAAGAAGAAA
* **
29312688 GTAATTAATCCGAGGTAAGTCTACATTGATAACTT
130 GTAATTAATCCGA-GTAAGTATGTATTGATAACTT
* * * * *
29312723 GTTGAGACCAAATATTGAG-AGAATGTGATTTATATTTTGAGACATACGTT-TCTTCATGTTGGT
1 GTTGAGACCAAATGTTGAGCA-ATTGTGGTTTATATTTCGAGACATACGTTCT-TTCATGTTGAT
* * * *
29312786 CGTTATAAATCTTCTTCTTA--TTTTTTTACCAGTTGTTCTTTCTCCAGAGTTGGGGGAATAATA
64 CATTATAAATCTTCTTCTTATGTTTTTTTACCAGTTGTT-TTTCTCCAGAGTTGAGGGAAGAAGA
* * * **
29312849 CATTAATT-A--CGATGT-ACTATGTATTGACCACTT
128 AAGTAATTAATCCGA-GTAAGTATGTATTGATAACTT
* * *
29312882 GTTGAGACCAAATGTTGAGTAATTGTGGTTTATAATTCTAAGACATAC
1 GTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTC-GAGACATAC
29312930 ATTTTTTCTT
Statistics
Matches: 564, Mismatches: 118, Indels: 63
0.76 0.16 0.08
Matches are distributed among these distances:
159 43 0.08
160 14 0.02
162 1 0.00
163 43 0.08
164 94 0.17
165 136 0.24
166 7 0.01
167 97 0.17
168 1 0.00
171 25 0.04
172 3 0.01
173 14 0.02
174 86 0.15
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (163 bp):
GTTGAGACCAAATGTTGAGCAATTGTGGTTTATATTTCGAGACATACGTTCTTTCATGTTGATCA
TTATAAATCTTCTTCTTATGTTTTTTTACCAGTTGTTTTTCTCCAGAGTTGAGGGAAGAAGAAAG
TAATTAATCCGAGTAAGTATGTATTGATAACTT
Found at i:29316564 original size:23 final size:23
Alignment explanation
Indices: 29316538--29316590 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
29316528 CTATTAATAT
29316538 TGTAAGACCCCAAAAATTACTAC
1 TGTAAGACCCCAAAAATTACTAC
* * **
29316561 TGTAATATCCTGAAAATTACTAC
1 TGTAAGACCCCAAAAATTACTAC
*
29316584 AGTAAGA
1 TGTAAGA
29316591 AAGTAGATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (23 bp):
TGTAAGACCCCAAAAATTACTAC
Found at i:29319043 original size:22 final size:21
Alignment explanation
Indices: 29319017--29319058 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
29319007 CCCTGAATCC
29319017 TAAACTCCAAATCTATAAACCT
1 TAAACTCCAAATCT-TAAACCT
**
29319039 TAAACTTTAAATCTTAAACC
1 TAAACTCCAAATCTTAAACC
29319059 CTAATACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (21 bp):
TAAACTCCAAATCTTAAACCT
Found at i:29319069 original size:21 final size:21
Alignment explanation
Indices: 29319015--29319084 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
29319005 AACCCTGAAT
**
29319015 CCTAAACTCCAAATCTATAAAC
1 CCTAAACTTTAAATCT-TAAAC
*
29319037 CTTAAACTTTAAATCTTAAAC
1 CCTAAACTTTAAATCTTAAAC
* *
29319058 CCTAATAC-TTAAGTCTCAAAC
1 CCTAA-ACTTTAAATCTTAAAC
29319079 CC-AAAC
1 CCTAAAC
29319085 ACTGAACTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 22 0.54
22 15 0.37
ACGTcount: A:0.43, C:0.29, G:0.01, T:0.27
Consensus pattern (21 bp):
CCTAAACTTTAAATCTTAAAC
Found at i:29319326 original size:28 final size:28
Alignment explanation
Indices: 29319295--29319350 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
29319285 AAATATTTGT
29319295 TTATAATTTAAAAAATTAATTATTTTAA
1 TTATAATTTAAAAAATTAATTATTTTAA
29319323 TTATAATTTAAAAAATTAATTATTTTAA
1 TTATAATTTAAAAAATTAATTATTTTAA
29319351 GTAATTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TTATAATTTAAAAAATTAATTATTTTAA
Found at i:29319369 original size:28 final size:27
Alignment explanation
Indices: 29319296--29319359 Score: 103
Period size: 28 Copynumber: 2.4 Consensus size: 27
29319286 AATATTTGTT
29319296 TATAATTTAAAAAATTAATTATTTTAA
1 TATAATTTAAAAAATTAATTATTTTAA
29319323 TTATAATTTAAAAAATTAATTATTTTAA
1 -TATAATTTAAAAAATTAATTATTTTAA
*
29319351 -GTAATTTAA
1 TATAATTTAA
29319360 TTAAAGTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 8 0.23
28 27 0.77
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TATAATTTAAAAAATTAATTATTTTAA
Found at i:29319632 original size:6 final size:6
Alignment explanation
Indices: 29319621--29319646 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29319611 TTTTTAACTA
29319621 ATAATT ATAATT ATAATT ATAATT AT
1 ATAATT ATAATT ATAATT ATAATT AT
29319647 CACACCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:29324626 original size:19 final size:19
Alignment explanation
Indices: 29324588--29324627 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29324578 AACTTAAATA
*
29324588 TATATATATTTAATTTTTT
1 TATATATATTTAATTATTT
29324607 TATATATATTT-ATTAATTT
1 TATATATATTTAATT-ATTT
29324626 TA
1 TA
29324628 AATTTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATATATATTTAATTATTT
Found at i:29331946 original size:28 final size:28
Alignment explanation
Indices: 29331914--29332011 Score: 142
Period size: 28 Copynumber: 3.5 Consensus size: 28
29331904 TGACTTTCGA
29331914 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
29331942 CACTAAGTGTGCGAGTTTAATGGAAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * **
29331970 CACTAAGTGTGCGAGTTTGATTATTTAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
29331998 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
29332012 ACTTATTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:29332771 original size:25 final size:24
Alignment explanation
Indices: 29332743--29333025 Score: 161
Period size: 23 Copynumber: 12.0 Consensus size: 24
29332733 TTATGCTTAA
*
29332743 ATGCTGCACAATTTCTTGTATATAT
1 ATGCTGC-CAATTTGTTGTATATAT
29332768 ATGCTGCTCAATTTGTTGTATAT-T
1 ATGCTGC-CAATTTGTTGTATATAT
*
29332792 -TGCCGCCAATTTGTTGTATATA-
1 ATGCTGCCAATTTGTTGTATATAT
* * *
29332814 A-GCTGTCCAATTT-TTGGTGTAAAA
1 ATGCTG-CCAATTTGTT-GTATATAT
29332838 ATGCTGCTCAATTTGTTGTATAT-T
1 ATGCTGC-CAATTTGTTGTATATAT
29332862 -TGCTGCCAATTTGTT-T-TATAT
1 ATGCTGCCAATTTGTTGTATATAT
* * * *
29332883 AAGCTGTCCAATTT-TTGGTGTAAAA
1 ATGCTG-CCAATTTGTT-GTATATAT
*
29332908 ATGCTGCTCAATTTGTTGTGTA-AT
1 ATGCTGC-CAATTTGTTGTATATAT
*
29332932 -TGCTGTCCAATTTGTTGTGTATA-
1 ATGCTG-CCAATTTGTTGTATATAT
* * * *
29332955 A-GTTGTCCAATTTTGGTGCA-A-AA
1 ATGCTG-CCAA-TTTGTTGTATATAT
*
29332978 ATGCTGCTCAATATGTTG--TATAT
1 ATGCTGC-CAATTTGTTGTATATAT
* *
29333001 ATGCTGCGTAAATTGTTGTATATAT
1 ATGCTGC-CAATTTGTTGTATATAT
29333026 GTTGTCCAAA
Statistics
Matches: 205, Mismatches: 26, Indels: 54
0.72 0.09 0.19
Matches are distributed among these distances:
20 3 0.01
21 2 0.01
22 37 0.18
23 80 0.39
24 20 0.10
25 59 0.29
26 4 0.02
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (24 bp):
ATGCTGCCAATTTGTTGTATATAT
Found at i:29332849 original size:70 final size:70
Alignment explanation
Indices: 29332768--29333054 Score: 405
Period size: 70 Copynumber: 4.1 Consensus size: 70
29332758 TTGTATATAT
*
29332768 ATGCTGCTCAATTTGTTGTATATTTGCCGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTG
1 ATGCTGCTCAATTTGTTGTATATTTGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTG
29332833 TAAAA
66 TAAAA
*
29332838 ATGCTGCTCAATTTGTTGTATATTTGCTGCCAATTTGTTTTATATAAGCTGTCCAATTTTTGGTG
1 ATGCTGCTCAATTTGTTGTATATTTGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTG
29332903 TAAAA
66 TAAAA
* * * *
29332908 ATGCTGCTCAATTTGTTGTGTAATTGCTGTCCAATTTGTTGTGTATAAGTTGTCCAA-TTTTGGT
1 ATGCTGCTCAATTTGTTGTATATTTGCTG-CCAATTTGTTGTATATAAGCTGTCCAATTTTTGGT
*
29332972 GCAAAA
65 GTAAAA
* * * * * * *
29332978 ATGCTGCTCAATATGTTGTATATATGCTGCGTAAATTGTTGTATATATGTTGTCCAAATTTTGGT
1 ATGCTGCTCAATTTGTTGTATATTTGCTGC-CAATTTGTTGTATATAAGCTGTCCAATTTTTGGT
*
29333043 GTGAAA
65 GTAAAA
*
29333049 TTGCTG
1 ATGCTG
29333055 TTTAGTTTGG
Statistics
Matches: 195, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
69 1 0.01
70 154 0.79
71 40 0.21
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.44
Consensus pattern (70 bp):
ATGCTGCTCAATTTGTTGTATATTTGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTG
TAAAA
Found at i:29332857 original size:48 final size:47
Alignment explanation
Indices: 29332741--29333007 Score: 157
Period size: 47 Copynumber: 5.7 Consensus size: 47
29332731 TTTTATGCTT
* *
29332741 AAATGCTG-CACAATTTCTTGTATATATATGCTGCTCAATTTG-T-TGTAT
1 AAATGCTGTC-CAATTTGTTGTATATA-A-GCTGC-CAATTTGTTGTGTAA
** *
29332789 ATTTGCCG-CCAATTTGTTGTATATAAGCTGTCCAATTT-TTGGTGTAA
1 AAATGCTGTCCAATTTGTTGTATATAAGCTG-CCAATTTGTT-GTGTAA
**
29332836 AAATGCTG-CTCAATTTGTTGTATATTTGCTGCCAATTTGTT-T-TATA
1 AAATGCTGTC-CAATTTGTTGTATATAAGCTGCCAATTTGTTGTGTA-A
* * *
29332882 TAA-GCTGTCCAATTT-TTGGTGTAAAAATGCTGCTCAATTTGTTGTGT--
1 AAATGCTGTCCAATTTGTT-GTAT-ATAA-GCTGC-CAATTTGTTGTGTAA
* * * * *
29332929 AATTGCTGTCCAATTTGTTGTGTATAAGTTGTCCAATTT-TGGTGCAA
1 AAATGCTGTCCAATTTGTTGTATATAAGCTG-CCAATTTGTTGTGTAA
* *
29332976 AAATGCTG-CTCAATATGTTGTATATATGCTGC
1 AAATGCTGTC-CAATTTGTTGTATATAAGCTGC
29333008 GTAAATTGTT
Statistics
Matches: 173, Mismatches: 26, Indels: 42
0.72 0.11 0.17
Matches are distributed among these distances:
44 2 0.01
45 30 0.17
46 19 0.11
47 66 0.38
48 52 0.30
49 3 0.02
50 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (47 bp):
AAATGCTGTCCAATTTGTTGTATATAAGCTGCCAATTTGTTGTGTAA
Found at i:29333077 original size:141 final size:141
Alignment explanation
Indices: 29332797--29333081 Score: 365
Period size: 141 Copynumber: 2.0 Consensus size: 141
29332787 ATATTTGCCG
* * *
29332797 CCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGTATATT
1 CCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGCAAAAATGCTGCTCAATATGTTGTATATA
* * * * *
29332862 TGCTGCCAATTTGTTTTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTGT
66 TGCTGCCAAATTGTTGTATATAAGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTAT
** *
29332927 GTAATTGCTGT
131 AAAAATGCTGT
* *
29332938 CCAATTTGTTGTGTATAAGTTGTCCAA-TTTTGGTGCAAAAATGCTGCTCAATATGTTGTATATA
1 CCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGCAAAAATGCTGCTCAATATGTTGTATATA
* * * * * * * *
29333002 TGCTGCGTAAATTGTTGTATATATGTTGTCCAAATTTTGGTGTGAAATTGCTGTTTAGTTTGGTA
66 TGCTGC-CAAATTGTTGTATATAAGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTA
29333067 TAAAAATGCTGT
130 TAAAAATGCTGT
29333079 CCA
1 CCA
29333082 TATTGACATA
Statistics
Matches: 122, Mismatches: 21, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
140 40 0.33
141 82 0.67
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (141 bp):
CCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGCAAAAATGCTGCTCAATATGTTGTATATA
TGCTGCCAAATTGTTGTATATAAGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGTAT
AAAAATGCTGT
Found at i:29339472 original size:28 final size:28
Alignment explanation
Indices: 29339440--29339537 Score: 142
Period size: 28 Copynumber: 3.5 Consensus size: 28
29339430 TGACTTTCGA
29339440 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
29339468 CACTAAGTGTGCGAGTTTAATGGAAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * **
29339496 CACTAAGTGTGCGAGTTTGATTATTTAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
29339524 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
29339538 ACTTATTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:29340374 original size:70 final size:70
Alignment explanation
Indices: 29340293--29340569 Score: 412
Period size: 70 Copynumber: 3.9 Consensus size: 70
29340283 TTGTATATAT
*
29340293 ATGCTGCTCAATTTGTTGTATATTTGCTGTCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTG
1 ATGCTGCTCAATTTGTTGTATATTTGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTG
29340358 TAAAA
66 TAAAA
*
29340363 ATGCTGCTCAATTTGTTGTATATTTGCTGCCAATTTGTTTTATATAAGCTGTCCAATTTTTGGTG
1 ATGCTGCTCAATTTGTTGTATATTTGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTG
29340428 TAAAA
66 TAAAA
* * *
29340433 ATGCTGCTCAATTTGTTGTGTAATTGCTGTCCAATTTGTTGTGTATAAGCTGTCCAA-TTTTGGT
1 ATGCTGCTCAATTTGTTGTATATTTGCTG-CCAATTTGTTGTATATAAGCTGTCCAATTTTTGGT
*
29340497 GCAAAA
65 GTAAAA
* * * * * * *
29340503 ATGCTGCTCAATATGTTTTATATATGCTACCTAAATTGTTGTATATATGCTGTCCAAATTTTGGT
1 ATGCTGCTCAATTTGTTGTATATTTGCTGCC-AATTTGTTGTATATAAGCTGTCCAATTTTTGGT
29340568 GT
65 GT
29340570 GAAATTACTG
Statistics
Matches: 187, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
69 2 0.01
70 152 0.81
71 33 0.18
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.44
Consensus pattern (70 bp):
ATGCTGCTCAATTTGTTGTATATTTGCTGCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTG
TAAAA
Found at i:29340562 original size:23 final size:23
Alignment explanation
Indices: 29340288--29340559 Score: 191
Period size: 23 Copynumber: 11.7 Consensus size: 23
29340278 ATTTCTTGTA
29340288 TATATATGCTG-CTCAATTTGTTG
1 TATATATGCTGTC-CAATTTGTTG
*
29340311 TATATTTGCTGT-CAATTTGTTG
1 TATATATGCTGTCCAATTTGTTG
* *
29340333 TATATAAGCTGTCCAATTTTTGGTG
1 TATATATGCTGTCCAA--TTTGTTG
* *
29340358 TAAAAATGCTG-CTCAATTTGTTG
1 TATATATGCTGTC-CAATTTGTTG
* *
29340381 TATATTTGCTG-CCAATTTGTTT
1 TATATATGCTGTCCAATTTGTTG
* *
29340403 TATATAAGCTGTCCAATTTTTGGTG
1 TATATATGCTGTCCAA--TTTGTTG
* *
29340428 TAAAAATGCTG-CTCAATTTGTTG
1 TATATATGCTGTC-CAATTTGTTG
*
29340451 TGTA-ATTGCTGTCCAATTTGTTG
1 TATATA-TGCTGTCCAATTTGTTG
* * *
29340474 TGTATAAGCTGTCCAATTTTGGTG
1 TATATATGCTGTCCAA-TTTGTTG
* * * * *
29340498 CAAAAATGCTG-CTCAATATGTTT
1 TATATATGCTGTC-CAATTTGTTG
* *
29340521 TATATATGCT-ACCTAAATTGTTG
1 TATATATGCTGTCC-AATTTGTTG
29340544 TATATATGCTGTCCAA
1 TATATATGCTGTCCAA
29340560 ATTTTGGTGT
Statistics
Matches: 193, Mismatches: 39, Indels: 34
0.73 0.15 0.13
Matches are distributed among these distances:
22 40 0.21
23 99 0.51
24 21 0.11
25 33 0.17
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.44
Consensus pattern (23 bp):
TATATATGCTGTCCAATTTGTTG
Found at i:29340605 original size:141 final size:141
Alignment explanation
Indices: 29340317--29340606 Score: 359
Period size: 141 Copynumber: 2.1 Consensus size: 141
29340307 GTTGTATATT
* *
29340317 TGCTGT-CAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTGTTG
1 TGCTGTCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGCAAAAATGCTGCTCAATATGTTG
* * * * * *
29340381 TATATTTGCTGCCAATTTGTTTTATATAAGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATT
66 TATATATGCTACCAAATTGTTGTATATAAGCTGTCCAAATTTTGGTGTAAAAATACTGCTCAATT
* * ** *
29340446 TGTTGTGTAAT
131 TGGTATAAAAA
* *
29340457 TGCTGTCCAATTTGTTGTGTATAAGCTGTCCAA-TTTTGGTGCAAAAATGCTGCTCAATATGTTT
1 TGCTGTCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGCAAAAATGCTGCTCAATATGTTG
* * * * * *
29340521 TATATATGCTACCTAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAATTACTGTTTAGT
66 TATATATGCTACC-AAATTGTTGTATATAAGCTGTCCAAATTTTGGTGTAAAAATACTGCTCAAT
29340586 TTGGTATAAAAA
130 TTGGTATAAAAA
*
29340598 TGTTGTCCA
1 TGCTGTCCA
29340607 TATTGACATA
Statistics
Matches: 126, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
140 45 0.36
141 81 0.64
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (141 bp):
TGCTGTCCAATTTGTTGTATATAAGCTGTCCAATTTTTGGTGCAAAAATGCTGCTCAATATGTTG
TATATATGCTACCAAATTGTTGTATATAAGCTGTCCAAATTTTGGTGTAAAAATACTGCTCAATT
TGGTATAAAAA
Found at i:29341247 original size:42 final size:43
Alignment explanation
Indices: 29341195--29341358 Score: 192
Period size: 43 Copynumber: 3.9 Consensus size: 43
29341185 TAGGGTTATC
*
29341195 GAGATTTCGTGTAAGACCATATCTGGGATA-TGGCATCGATAT
1 GAGAATTCGTGTAAGACCATATCTGGGATATTGGCATCGATAT
* *
29341237 GAGAATTCGTGTAAGACCATCTCTGGGACATTGGCATCGATAT
1 GAGAATTCGTGTAAGACCATATCTGGGATATTGGCATCGATAT
* * * * * *
29341280 GTGATTTCGTGTAAGACCATGGT-TGGGCTATTGGCATCAATAC
1 GAGAATTCGTGTAAGACCAT-ATCTGGGATATTGGCATCGATAT
*
29341323 GAG-ATTACATGTAAGACCATATCTGGGATA-TGGCAT
1 GAGAATT-CGTGTAAGACCATATCTGGGATATTGGCAT
29341359 GGTTATGGTA
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
42 36 0.35
43 66 0.64
44 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (43 bp):
GAGAATTCGTGTAAGACCATATCTGGGATATTGGCATCGATAT
Found at i:29342059 original size:34 final size:34
Alignment explanation
Indices: 29342016--29342083 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
29342006 GAAACGGTGT
29342016 AAGCAAAAGAATCTTGTATTATGAGATATTTGAA
1 AAGCAAAAGAATCTTGTATTATGAGATATTTGAA
29342050 AAGCAAAAGAATCTTGTATTATGAGATATTTGAA
1 AAGCAAAAGAATCTTGTATTATGAGATATTTGAA
29342084 TTTTTGTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (34 bp):
AAGCAAAAGAATCTTGTATTATGAGATATTTGAA
Found at i:29347832 original size:6 final size:6
Alignment explanation
Indices: 29347821--29347848 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29347811 GGAAGCTTAT
29347821 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
29347849 TAAGAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.54
Consensus pattern (6 bp):
ATTTGG
Found at i:29347914 original size:15 final size:15
Alignment explanation
Indices: 29347865--29347907 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
29347855 TTTATATTTG
29347865 AAATTTTTTATTTCT
1 AAATTTTTTATTTCT
** *
29347880 AAATTCATAATTTCT
1 AAATTTTTTATTTCT
29347895 AAATTTTTTATTT
1 AAATTTTTTATTT
29347908 GAAAATTAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
AAATTTTTTATTTCT
Found at i:29349441 original size:20 final size:19
Alignment explanation
Indices: 29349374--29349445 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 19
29349364 AATTTTTTTA
* *
29349374 AACTTGAACCCTGAATCCTG
1 AACTTGAACCCTAAATTC-G
*
29349394 AACTTCGAACCTTAAATCTCG
1 AACTT-GAACCCTAAAT-TCG
29349415 AATCTTGAACCCTAAATTCG
1 AA-CTTGAACCCTAAATTCG
29349435 AACCTTGAACC
1 AA-CTTGAACC
29349446 TTGAACCTCG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 18 0.41
21 22 0.50
22 4 0.09
ACGTcount: A:0.33, C:0.29, G:0.11, T:0.26
Consensus pattern (19 bp):
AACTTGAACCCTAAATTCG
Found at i:29349463 original size:34 final size:34
Alignment explanation
Indices: 29349371--29349465 Score: 95
Period size: 34 Copynumber: 2.8 Consensus size: 34
29349361 GATAATTTTT
*
29349371 TTAAA-CTTGAACC-CTGAATCCTGAACTTCGAACC
1 TTAAACCTTGAACCTC-GAATCCT-AAATTCGAACC
* * * * *
29349405 TTAAATCTCGAATCTTGAACCCTAAATTCGAACC
1 TTAAACCTTGAACCTCGAATCCTAAATTCGAACC
*
29349439 TTGAACCTTGAACCTCGAATCCTAAAT
1 TTAAACCTTGAACCTCGAATCCTAAAT
29349466 CAAAAGGTCA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
34 36 0.75
35 12 0.25
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (34 bp):
TTAAACCTTGAACCTCGAATCCTAAATTCGAACC
Found at i:29349502 original size:21 final size:21
Alignment explanation
Indices: 29349478--29349548 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
29349468 AAAGGTCAAG
29349478 TTTAGGGTTCAAGATTTAGGA
1 TTTAGGGTTCAAGATTTAGGA
* *
29349499 TTTAAGGTTC-AGAGTTTGGGA
1 TTTAGGGTTCAAGA-TTTAGGA
* *
29349520 TTTAGGATTCAAGATTCAGG-
1 TTTAGGGTTCAAGATTTAGGA
29349540 TTT-GGGTTC
1 TTTAGGGTTC
29349549 GAAGTTCGAG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.12
20 6 0.15
21 27 0.66
22 3 0.07
ACGTcount: A:0.24, C:0.07, G:0.30, T:0.39
Consensus pattern (21 bp):
TTTAGGGTTCAAGATTTAGGA
Found at i:29349537 original size:28 final size:27
Alignment explanation
Indices: 29349490--29349545 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
29349480 TAGGGTTCAA
* *
29349490 GATTTAGGATTTAAGGTTCAGAGTTTGG
1 GATTTAGGATTCAAGATTCAG-GTTTGG
29349518 GATTTAGGATTCAAGATTCAGGTTTGG
1 GATTTAGGATTCAAGATTCAGGTTTGG
29349545 G
1 G
29349546 TTCGAAGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.25, C:0.05, G:0.32, T:0.38
Consensus pattern (27 bp):
GATTTAGGATTCAAGATTCAGGTTTGG
Found at i:29349657 original size:21 final size:21
Alignment explanation
Indices: 29349633--29349672 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29349623 ATTATATATC
29349633 AATGACATAAAAAAATTATTA
1 AATGACATAAAAAAATTATTA
* * *
29349654 AATGTCATTAAATAATTAT
1 AATGACATAAAAAAATTAT
29349673 AAAGTGATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (21 bp):
AATGACATAAAAAAATTATTA
Found at i:29356290 original size:29 final size:30
Alignment explanation
Indices: 29356248--29356313 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
29356238 AATTATTCTC
*
29356248 TATATTTCTTTTTCTTGCGTGGAGAACT-T
1 TATATATCTTTTTCTTGCGTGGAGAACTCT
*
29356277 TATATATCTTTTTCTTGCTTGGAGAACTCT
1 TATATATCTTTTTCTTGCGTGGAGAACTCT
29356307 TAATATA
1 T-ATATA
29356314 AATATCATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 26 0.79
30 2 0.06
31 5 0.15
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (30 bp):
TATATATCTTTTTCTTGCGTGGAGAACTCT
Found at i:29356827 original size:25 final size:26
Alignment explanation
Indices: 29356782--29356840 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
29356772 GTTTGTATTT
* *
29356782 TTTTTTTAATTTAAAGGGATTAG-TA
1 TTTTTTTAATATAAAGAGATTAGTTA
29356807 TTTTTTTAA-ATAGAAGAGATTAGTTA
1 TTTTTTTAATATA-AAGAGATTAGTTA
*
29356833 TTCTTTTA
1 TTTTTTTA
29356841 TGTAGTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 2 0.07
25 18 0.62
26 9 0.31
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.53
Consensus pattern (26 bp):
TTTTTTTAATATAAAGAGATTAGTTA
Found at i:29357049 original size:83 final size:82
Alignment explanation
Indices: 29356952--29357108 Score: 262
Period size: 83 Copynumber: 1.9 Consensus size: 82
29356942 TTTTAAAAAC
*
29356952 TTTTTAATGTTATTTTGTCAGTAATTTATGATTAGATTATATATTGTTTGTGTTTAGTTTAGTGT
1 TTTTTAATGTTATTTTGTCAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAGTTTAGTGT
29357017 TTATTGTGATCTTAATTT
66 TTA-TGTGATCTTAATTT
* *
29357035 TTTTTAAAT-TTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTTAGTG
1 TTTTT-AATGTTATTTTGTCAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAGTTTAGTG
29357099 TTTATGTGAT
65 TTTATGTGAT
29357109 TTTTTATGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
82 6 0.09
83 61 0.87
84 3 0.04
ACGTcount: A:0.24, C:0.01, G:0.17, T:0.59
Consensus pattern (82 bp):
TTTTTAATGTTATTTTGTCAGTAATTTATGATTAGATTATAAATTGTTTGTGTTTAGTTTAGTGT
TTATGTGATCTTAATTT
Found at i:29359669 original size:49 final size:49
Alignment explanation
Indices: 29359577--29359848 Score: 336
Period size: 49 Copynumber: 5.6 Consensus size: 49
29359567 CAAAAATACC
* * * *
29359577 AACTTCGTAATTTAAATT-AAATTAATTGGAGCATTAAAAATTGGAACA
1 AACTTCGTAATTTAAATTGAGATTCATTGCAACATTAAAAATTGGAACA
* *
29359625 AACTTTGTAATTTAGATTGAGATTCATTGCAACATTAAAAATTGGAACA
1 AACTTCGTAATTTAAATTGAGATTCATTGCAACATTAAAAATTGGAACA
** *
29359674 AACTTCGTAATTTAAATTGAGATTCACCGCAACACTAAAAATTGGAACA
1 AACTTCGTAATTTAAATTGAGATTCATTGCAACATTAAAAATTGGAACA
* * * *
29359723 AACTTCGTAATTTCAATTGAGATTCATTACAACATTAAAATTTGGAATA
1 AACTTCGTAATTTAAATTGAGATTCATTGCAACATTAAAAATTGGAACA
** *
29359772 AACTTTATAATTTAAATT-AGATTAATTGCAACATTAAAACGA-T-GAACA
1 AACTTCGTAATTTAAATTGAGATTCATTGCAACATTAAAA--ATTGGAACA
* *
29359820 AACTTTGTAACTTAAATTGAGATTCATTG
1 AACTTCGTAATTTAAATTGAGATTCATTG
29359849 GAGTACATTA
Statistics
Matches: 192, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
48 55 0.29
49 137 0.71
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.34
Consensus pattern (49 bp):
AACTTCGTAATTTAAATTGAGATTCATTGCAACATTAAAAATTGGAACA
Found at i:29359800 original size:146 final size:145
Alignment explanation
Indices: 29359577--29359845 Score: 371
Period size: 146 Copynumber: 1.8 Consensus size: 145
29359567 CAAAAATACC
** * * *
29359577 AACTTCGTAATTTAAATTAAATTAATTGGAGCATTAAAAATTGGAACAAACTTTGTAATTTAGAT
1 AACTTCGTAATTTAAATTAAATTAATTACAACATTAAAAATTGGAACAAACTTTATAATTTAAAT
* *
29359642 TGAGATTCATTGCAACATTAAAA-ATTGGAACAAACTTCGTAATTTAAATTGAGATTCACCGCAA
66 TGAGATTAATTGCAACATTAAAACA-T-GAACAAACTTCGTAACTTAAATTGAGATTCACCGCAA
29359706 CACTAAAAATTGGAACA
129 CACTAAAAATTGGAACA
* * * * *
29359723 AACTTCGTAATTTCAATTGAGATTCATTACAACATTAAAATTTGGAATAAACTTTATAATTTAAA
1 AACTTCGTAATTTAAATT-AAATTAATTACAACATTAAAAATTGGAACAAACTTTATAATTTAAA
*
29359788 TT-AGATTAATTGCAACATTAAAACGATGAACAAACTTTGTAACTTAAATTGAGATTCA
65 TTGAGATTAATTGCAACATTAAAAC-ATGAACAAACTTCGTAACTTAAATTGAGATTCA
29359846 TTGGAGTACA
Statistics
Matches: 107, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
146 66 0.62
147 40 0.37
148 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (145 bp):
AACTTCGTAATTTAAATTAAATTAATTACAACATTAAAAATTGGAACAAACTTTATAATTTAAAT
TGAGATTAATTGCAACATTAAAACATGAACAAACTTCGTAACTTAAATTGAGATTCACCGCAACA
CTAAAAATTGGAACA
Found at i:29362731 original size:17 final size:17
Alignment explanation
Indices: 29362709--29362744 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29362699 TCCTTTAATC
29362709 TTCTCTACTAATTTTTT
1 TTCTCTACTAATTTTTT
* *
29362726 TTCTCTTCTACTTTTTT
1 TTCTCTACTAATTTTTT
29362743 TT
1 TT
29362745 ACTACTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCTCTACTAATTTTTT
Found at i:29362882 original size:27 final size:27
Alignment explanation
Indices: 29362809--29362882 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
29362799 CCTCTCAAAT
* **
29362809 AGGGGCCACTAGTGCCGTGTACCTAAG
1 AGGGGTCACTAGTGCCGCCTACCTAAG
** *
29362836 AGGGGTCACTAGTGTTGCCTACTTAAG
1 AGGGGTCACTAGTGCCGCCTACCTAAG
*
29362863 AGGGGTCACTAGTACCGCCT
1 AGGGGTCACTAGTGCCGCCT
29362883 CTTTGAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.23
Consensus pattern (27 bp):
AGGGGTCACTAGTGCCGCCTACCTAAG
Found at i:29366282 original size:30 final size:30
Alignment explanation
Indices: 29366246--29366305 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
29366236 TATTTATAAC
29366246 TCCACACAATGCCAATGAGAGGATATCATT
1 TCCACACAATGCCAATGAGAGGATATCATT
29366276 TCCACACAATGCCAATGAGAGGATATCATT
1 TCCACACAATGCCAATGAGAGGATATCATT
29366306 AACTCTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (30 bp):
TCCACACAATGCCAATGAGAGGATATCATT
Found at i:29372618 original size:9 final size:9
Alignment explanation
Indices: 29372600--29372636 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
29372590 TTATAGTTAA
*
29372600 TATTCAAAT
1 TATTCGAAT
29372609 TATTCGAAT
1 TATTCGAAT
*
29372618 TATTCGATT
1 TATTCGAAT
29372627 TATTCGAAT
1 TATTCGAAT
29372636 T
1 T
29372637 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:29372706 original size:9 final size:9
Alignment explanation
Indices: 29372689--29372719 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29372679 TTGAGTTGAT
29372689 TCGAATAAC
1 TCGAATAAC
*
29372698 TCGATTAAC
1 TCGAATAAC
29372707 TCGAATAAC
1 TCGAATAAC
29372716 TCGA
1 TCGA
29372720 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:29380753 original size:13 final size:13
Alignment explanation
Indices: 29380721--29380763 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
29380711 TTTTTATTCT
*
29380721 TTGGACTTTAGAC
1 TTGGACATTAGAC
* *
29380734 TTTGACATTGGAC
1 TTGGACATTAGAC
29380747 TTGGACATTA-AC
1 TTGGACATTAGAC
29380759 TTGGA
1 TTGGA
29380764 TTTTGAACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (13 bp):
TTGGACATTAGAC
Found at i:29381194 original size:29 final size:29
Alignment explanation
Indices: 29381152--29381209 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
29381142 GTTTGATCCT
* *
29381152 TTTATCTTAATTCTAAAATTAAATTAAAA
1 TTTAGCTTAATTCTAAAATTAAACTAAAA
*
29381181 TTTAGCTTGATTCTAAAATTAAACTAAAA
1 TTTAGCTTAATTCTAAAATTAAACTAAAA
29381210 AGTAGATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (29 bp):
TTTAGCTTAATTCTAAAATTAAACTAAAA
Found at i:29391525 original size:30 final size:31
Alignment explanation
Indices: 29391489--29391551 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
29391479 TTCTTCCTTC
29391489 ACATTATTTATCTTATACTTT-TATATATAT
1 ACATTATTTATCTTATACTTTATATATATAT
* *
29391519 ACATTATTTATTTTATCCTTTATATATATAT
1 ACATTATTTATCTTATACTTTATATATATAT
29391550 AC
1 AC
29391552 TTTTTTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (31 bp):
ACATTATTTATCTTATACTTTATATATATAT
Found at i:29396921 original size:21 final size:21
Alignment explanation
Indices: 29396895--29396935 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29396885 AGATCTACCC
29396895 AATAAAAGAAGAAAAGAGAAG
1 AATAAAAGAAGAAAAGAGAAG
* *
29396916 AATAAAAGAGGAAAGGAGAA
1 AATAAAAGAAGAAAAGAGAA
29396936 TTAGCGTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (21 bp):
AATAAAAGAAGAAAAGAGAAG
Found at i:29399834 original size:33 final size:33
Alignment explanation
Indices: 29399790--29399902 Score: 113
Period size: 33 Copynumber: 3.4 Consensus size: 33
29399780 TGTTGACTAC
* *
29399790 TAGGGAAGGTGATGTTGAAGGGGTAGAATTTGA
1 TAGGGAGGGTGATGTTGAAGGGGTAGAATCTGA
*
29399823 TAGGGAGGGTGATGATGAAGGGGTAGAATCTGA
1 TAGGGAGGGTGATGTTGAAGGGGTAGAATCTGA
* * * * *
29399856 T-GGTAAAGGTGATCTGGAAAGGGTAGAATCT-A
1 TAGG-GAGGGTGATGTTGAAGGGGTAGAATCTGA
*
29399888 TTGGGGAGGGTGATG
1 -TAGGGAGGGTGATG
29399903 GTGGAGAGGT
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
32 3 0.05
33 60 0.92
34 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.43, T:0.25
Consensus pattern (33 bp):
TAGGGAGGGTGATGTTGAAGGGGTAGAATCTGA
Found at i:29400115 original size:51 final size:51
Alignment explanation
Indices: 29400039--29400141 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 51
29400029 AAGTTGTTGT
* * * *
29400039 TGATGAATATGTTGTTTATTTTGCAACATTAGATGGAGTAGATAATGATGC
1 TGATGAATATGGTGGTGATTTTGCAACATCAGATGGAGTAGATAATGATGC
* *
29400090 TGATGAATATGGTGGTGATTTTGCAACATCAGATGGAGTGGATAATGTTGC
1 TGATGAATATGGTGGTGATTTTGCAACATCAGATGGAGTAGATAATGATGC
29400141 T
1 T
29400142 TCTACAAGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (51 bp):
TGATGAATATGGTGGTGATTTTGCAACATCAGATGGAGTAGATAATGATGC
Found at i:29405455 original size:37 final size:40
Alignment explanation
Indices: 29405414--29405511 Score: 97
Period size: 37 Copynumber: 2.6 Consensus size: 40
29405404 TAATATTATA
29405414 TTAATAGTTTAATATTAAATTTAAT-TT-AA-T-ACGTATC
1 TTAATAGTTTAATATTAAATTTAATCTTAAAGTGA-GTATC
* *
29405451 TTAATAGTATT-TTATT-AATTTAATCTTAAAGTGATTATC
1 TTAATAGT-TTAATATTAAATTTAATCTTAAAGTGAGTATC
29405490 TTAATA--TTAA-ATTAAATTTAAT
1 TTAATAGTTTAATATTAAATTTAAT
29405512 ATTTATCTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
36 13 0.25
37 22 0.43
38 4 0.08
39 11 0.22
40 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (40 bp):
TTAATAGTTTAATATTAAATTTAATCTTAAAGTGAGTATC
Found at i:29405493 original size:25 final size:26
Alignment explanation
Indices: 29405448--29405499 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
29405438 TTTAATACGT
*
29405448 ATCTTAATAGTATTTTATTAAT-TTA
1 ATCTTAATAGTATTATATTAATATTA
*
29405473 ATCTTAA-AGTGATTATCTTAATATTA
1 ATCTTAATAGT-ATTATATTAATATTA
29405499 A
1 A
29405500 ATTAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.13
25 16 0.70
26 4 0.17
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (26 bp):
ATCTTAATAGTATTATATTAATATTA
Found at i:29406860 original size:28 final size:28
Alignment explanation
Indices: 29406828--29406884 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
29406818 ATTTGGAAAG
29406828 TATGTGAAATTATGCTTAATTACATTAT
1 TATGTGAAATTATGCTTAATTACATTAT
29406856 TATGTGAAATTATGCTTAATTACATTAT
1 TATGTGAAATTATGCTTAATTACATTAT
29406884 T
1 T
29406885 TTCATGCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.47
Consensus pattern (28 bp):
TATGTGAAATTATGCTTAATTACATTAT
Found at i:29422113 original size:14 final size:15
Alignment explanation
Indices: 29422094--29422124 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29422084 CTGATTTTAA
29422094 AGATAC-ACTTTATT
1 AGATACTACTTTATT
29422108 AGATACTACTTTATT
1 AGATACTACTTTATT
29422123 AG
1 AG
29422125 TATCAAGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (15 bp):
AGATACTACTTTATT
Found at i:29425135 original size:26 final size:26
Alignment explanation
Indices: 29425093--29425167 Score: 91
Period size: 25 Copynumber: 2.9 Consensus size: 26
29425083 ACATATTTCC
29425093 TCAAAATTTTAAC-AGGGGTAAAATCA
1 TCAAAATTTT-ACTAGGGGTAAAATCA
* *
29425119 TCAAAATATTACTA-GGGTAAAATCG
1 TCAAAATTTTACTAGGGGTAAAATCA
* *
29425144 TTAAAATTTTACTGGGGGTAAAAT
1 TCAAAATTTTACTAGGGGTAAAAT
29425168 AGGGATGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 23 0.55
26 19 0.45
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (26 bp):
TCAAAATTTTACTAGGGGTAAAATCA
Found at i:29438153 original size:17 final size:19
Alignment explanation
Indices: 29438115--29438154 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
29438105 TCTTTGTTCC
*
29438115 CAATACATTTCATCTTTAT
1 CAATACATTTCATCTGTAT
29438134 CAATACATTTC-TC-GTAT
1 CAATACATTTCATCTGTAT
29438151 CAAT
1 CAAT
29438155 TATCTATGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 2 0.10
19 11 0.55
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.42
Consensus pattern (19 bp):
CAATACATTTCATCTGTAT
Found at i:29447473 original size:23 final size:22
Alignment explanation
Indices: 29447413--29447473 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
29447403 ATAATTTTGA
29447413 TATTTTATAATATATAAACAATTT
1 TATTTTAT-ATA-ATAAACAATTT
* * *
29447437 TATTTCAATGTAATAATCAATTT
1 TATTT-TATATAATAAACAATTT
29447460 TACTTTTATATAAT
1 TA-TTTTATATAAT
29447474 GATAATAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
23 18 0.60
24 10 0.33
25 2 0.07
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTTTATATAATAAACAATTT
Found at i:29449196 original size:20 final size:20
Alignment explanation
Indices: 29449142--29449196 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
29449132 GATACTAACT
* **
29449142 TAAAAATATCGATAATTTTA
1 TAAAAATATCGATACTCGTA
* *
29449162 TAAAAATATCAATACTCGTG
1 TAAAAATATCGATACTCGTA
29449182 TAAAAATATCGATAC
1 TAAAAATATCGATAC
29449197 CACTAAGGCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (20 bp):
TAAAAATATCGATACTCGTA
Found at i:29457925 original size:47 final size:47
Alignment explanation
Indices: 29457874--29458239 Score: 635
Period size: 47 Copynumber: 7.7 Consensus size: 47
29457864 TTAGGATTCT
* * *
29457874 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
29457921 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
29457968 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
29458015 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
29458064 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
29458111 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
29458158 ATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
29458205 ATGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
29458240 TCCCGAAGGG
Statistics
Matches: 307, Mismatches: 9, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
46 1 0.00
47 260 0.85
49 46 0.15
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:29457949 original size:25 final size:25
Alignment explanation
Indices: 29457921--29457999 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
29457911 CTAATGGCCG
29457921 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
29457946 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
29457968 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
29457993 ATGTGAT
1 ATGTGAT
29458000 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:29458054 original size:143 final size:141
Alignment explanation
Indices: 29457874--29458239 Score: 635
Period size: 143 Copynumber: 2.6 Consensus size: 141
29457864 TTAGGATTCT
* * *
29457874 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
29457938 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
65 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
29458003 GCCTAATGGCCG
130 GCCTAATGGCCG
*
29458015 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
29458080 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
64 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
29458145 GGCCTAATGGCCG
129 GGCCTAATGGCCG
* *
29458158 ATGTGATGAATGTGAAAGTGTATATATGTGATAGGGCCTAATGGCCGATGTGATGGATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
29458223 TGTATAAATGTGATAAG
66 TGTATATATGTGATAAG
29458240 TCCCGAAGGG
Statistics
Matches: 214, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
140 1 0.00
141 75 0.35
143 138 0.64
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.30
Consensus pattern (141 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCTAATGGCCG
Found at i:29458157 original size:190 final size:188
Alignment explanation
Indices: 29457874--29458239 Score: 653
Period size: 190 Copynumber: 1.9 Consensus size: 188
29457864 TTAGGATTCT
*
29457874 ATGTGATGGATGTGAACATGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
29457939 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
66 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
29458004 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCA
131 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATA-A-ATGTGATAAGGCCTAATGGCCA
* *
29458064 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
*
29458128 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAGG
65 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
*
29458193 GCCTAATGGCCGATGTGATGGATGTGAAAGTGTATAAATGTGATAAG
130 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGATAAG
29458240 TCCCGAAGGG
Statistics
Matches: 170, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
188 10 0.06
189 2 0.01
190 158 0.93
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.30
Consensus pattern (188 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGATAAGGCCTAATGGCCA
Found at i:29458416 original size:37 final size:37
Alignment explanation
Indices: 29458358--29458436 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
29458348 CCGAGCTCTA
* * * *
29458358 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
*
29458395 AAGACCCGATAACTTCATGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
29458432 AAGAC
1 AAGAC
29458437 TTTGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACATGTGGAGATTATGTCCGGGT
Found at i:29460256 original size:40 final size:40
Alignment explanation
Indices: 29459652--29460244 Score: 940
Period size: 40 Copynumber: 14.8 Consensus size: 40
29459642 GAGAATTGAG
* *
29459652 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* *
29459692 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
*
29459732 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
29459772 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
29459812 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
*
29459852 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* *
29459892 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
*
29459932 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTG-CT
29459973 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
29460013 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* *
29460053 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
*
29460093 AGTGATATATCCGGGCTAAG-TCCTG-AGAAGCATTCGTGAT
1 AGTGATATATCCGGGCTAAGTTCC-GAAG-AGCATTCGTGCT
* *
29460133 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* ***
29460173 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
* * *
29460213 GGTGTTATATCCGGGCT-AGGTCTCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTTC-CGAAGAGCA
29460245 ATCATGCTGG
Statistics
Matches: 517, Mismatches: 30, Indels: 12
0.92 0.05 0.02
Matches are distributed among these distances:
39 7 0.01
40 468 0.91
41 42 0.08
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
Found at i:29463997 original size:47 final size:47
Alignment explanation
Indices: 29463946--29464311 Score: 599
Period size: 47 Copynumber: 7.7 Consensus size: 47
29463936 TTAGGATTCT
* * *
29463946 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
29463993 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
29464040 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
29464087 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
29464134 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
29464183 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
29464230 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
29464277 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
29464312 TCCCGAAGGG
Statistics
Matches: 303, Mismatches: 13, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 255 0.84
49 47 0.16
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:29464184 original size:190 final size:190
Alignment explanation
Indices: 29463967--29464311 Score: 609
Period size: 190 Copynumber: 1.8 Consensus size: 190
29463957 GTGAACATGC
29463967 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
* * * *
29464032 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAA
66 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAA
*
29464097 TGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
131 TGTGAAAGTGTATAAATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
*
29464157 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
* * *
29464222 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGA
66 AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAA
29464287 TGTGAAAGTGTATAAATGTGATAAG
131 TGTGAAAGTGTATAAATGTGATAAG
29464312 TCCCGAAGGG
Statistics
Matches: 146, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
190 146 1.00
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (190 bp):
ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
AATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCAACGTGATGAA
TGTGAAAGTGTATAAATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:29464486 original size:37 final size:37
Alignment explanation
Indices: 29464430--29464508 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
29464420 CCGAGCTCTA
* * *
29464430 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
29464467 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
29464504 AAGAC
1 AAGAC
29464509 TTTGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:29466738 original size:17 final size:16
Alignment explanation
Indices: 29466711--29466743 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
29466701 CTATGTTAGA
29466711 AAAAATTTTAAAAATT
1 AAAAATTTTAAAAATT
29466727 AAAAATTATTAAAAATT
1 AAAAATT-TTAAAAATT
29466744 TAATTCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAAATTTTAAAAATT
Found at i:29471061 original size:21 final size:21
Alignment explanation
Indices: 29471035--29471076 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
29471025 AAAAATAAAA
*
29471035 AAAATATAGAAAATAGTTTAT
1 AAAATAAAGAAAATAGTTTAT
29471056 AAAATAAAGAAAATAGTTTAT
1 AAAATAAAGAAAATAGTTTAT
29471077 CTAATTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAATAAAGAAAATAGTTTAT
Found at i:29473282 original size:20 final size:20
Alignment explanation
Indices: 29473247--29473301 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
29473237 AACACGCTCA
*
29473247 TGTGAAGGAGGCACACACCCG
1 TGTGAA-GAAGCACACACCCG
* *
29473268 TGTGAAGAAGCACACGCTCG
1 TGTGAAGAAGCACACACCCG
29473288 TGTGAAGAAGCACA
1 TGTGAAGAAGCACA
29473302 AGCCTATGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 25 0.81
21 6 0.19
ACGTcount: A:0.33, C:0.24, G:0.31, T:0.13
Consensus pattern (20 bp):
TGTGAAGAAGCACACACCCG
Found at i:29478840 original size:26 final size:26
Alignment explanation
Indices: 29478810--29478862 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
29478800 TTCCAAAATT
*
29478810 TAGTCCAA-ATTAGTACTTTACAAAAA
1 TAGTCCAAGATTA-AACTTTACAAAAA
*
29478836 TAGTCCAAGATTAAAGTTTACAAAAA
1 TAGTCCAAGATTAAACTTTACAAAAA
29478862 T
1 T
29478863 CTGGAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.30
Consensus pattern (26 bp):
TAGTCCAAGATTAAACTTTACAAAAA
Found at i:29484494 original size:20 final size:20
Alignment explanation
Indices: 29484451--29484495 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29484441 CATATGACCG
* * **
29484451 TGTGAAGATGCACTCATCTG
1 TGTGAAGAAGCACTCACCCA
29484471 TGTGAAGAAGCACTCACCCA
1 TGTGAAGAAGCACTCACCCA
29484491 TGTGA
1 TGTGA
29484496 GAGGAGGCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.24
Consensus pattern (20 bp):
TGTGAAGAAGCACTCACCCA
Found at i:29485229 original size:5 final size:6
Alignment explanation
Indices: 29485200--29485226 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29485190 ATTTAGACTT
29485200 AAAACA AAAACA AAAACA AAAACA AAA
1 AAAACA AAAACA AAAACA AAAACA AAA
29485227 CAACTCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:29487623 original size:9 final size:9
Alignment explanation
Indices: 29487611--29487635 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29487601 TAAAACTATT
29487611 AAAAATTAA
1 AAAAATTAA
29487620 AAAAATTAA
1 AAAAATTAA
29487629 AAAAATT
1 AAAAATT
29487636 GGATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAAATTAA
Found at i:29487627 original size:16 final size:18
Alignment explanation
Indices: 29487594--29487631 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
29487584 TAATTATTTC
*
29487594 AAAATTATAAAACTATTA
1 AAAATTATAAAACAATTA
29487612 AAAATTA-AAAA-AATTA
1 AAAATTATAAAACAATTA
29487628 AAAA
1 AAAA
29487632 AATTGGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 4 0.21
18 7 0.37
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTATAAAACAATTA
Found at i:29487786 original size:14 final size:15
Alignment explanation
Indices: 29487765--29487802 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
29487755 GATTGAATGA
29487765 ATAAATTTTGTATAC
1 ATAAATTTTGTATAC
*
29487780 A-AAA-TTTGTATAT
1 ATAAATTTTGTATAC
29487793 ATAAATTTTG
1 ATAAATTTTG
29487803 AATATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 9 0.45
14 6 0.30
15 5 0.25
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (15 bp):
ATAAATTTTGTATAC
Found at i:29487802 original size:15 final size:15
Alignment explanation
Indices: 29487765--29487808 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
29487755 GATTGAATGA
*
29487765 ATAAATTTTGTATAC
1 ATAAATTTTGTATAT
29487780 A-AAA-TTTGTATAT
1 ATAAATTTTGTATAT
*
29487793 ATAAATTTTGAATAT
1 ATAAATTTTGTATAT
29487808 A
1 A
29487809 AAAAGTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 9 0.36
14 6 0.24
15 10 0.40
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (15 bp):
ATAAATTTTGTATAT
Found at i:29490406 original size:30 final size:30
Alignment explanation
Indices: 29490358--29490415 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
29490348 ATTTTAGGAG
* * *
29490358 CCACGCGGGCTGGGCACACACCCATGTGAC
1 CCACACGGGCTAGACACACACCCATGTGAC
*
29490388 CCACACGGGCTAGACACACGCCCATGTG
1 CCACACGGGCTAGACACACACCCATGTG
29490416 CCAGCTCGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.40, G:0.28, T:0.10
Consensus pattern (30 bp):
CCACACGGGCTAGACACACACCCATGTGAC
Found at i:29495078 original size:26 final size:26
Alignment explanation
Indices: 29495038--29495112 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 26
29495028 TCTTTCCTTT
29495038 TTCTTTTTATTTATTTATTTATTATTA
1 TTCTTTTTA-TTATTTATTTATTATTA
*
29495065 TTCTTTTTATTATTTATTCT-TTTTTA
1 TTCTTTTTATTATTTATT-TATTATTA
* *
29495091 TTATTCTTATTATTTATTTATT
1 TTCTTTTTATTATTTATTTATT
29495113 TTTCATTTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 1 0.02
26 32 0.74
27 10 0.23
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (26 bp):
TTCTTTTTATTATTTATTTATTATTA
Found at i:29495120 original size:11 final size:11
Alignment explanation
Indices: 29495043--29495112 Score: 55
Period size: 9 Copynumber: 6.9 Consensus size: 11
29495033 CCTTTTTCTT
29495043 TTTATTTATTTA
1 TTTATTTA-TTA
29495055 TTTA-TTATTA
1 TTTATTTATTA
*
29495065 -TTCTTT-TTA
1 TTTATTTATTA
*
29495074 -TTATTTATTC
1 TTTATTTATTA
29495084 TTT-TTTATTA
1 TTTATTTATTA
*
29495094 -TT-CTTATTA
1 TTTATTTATTA
29495103 TTTATTTATT
1 TTTATTTATT
29495113 TTTCATTTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
9 18 0.38
10 15 0.32
11 10 0.21
12 4 0.09
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:29496896 original size:21 final size:21
Alignment explanation
Indices: 29496872--29496912 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29496862 TTCTTTTCTT
29496872 TTTAGTTTTAGTTTTATTTTC
1 TTTAGTTTTAGTTTTATTTTC
* *
29496893 TTTATTTTTATTTTTATTTT
1 TTTAGTTTTAGTTTTATTTT
29496913 TAGTTGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (21 bp):
TTTAGTTTTAGTTTTATTTTC
Found at i:29496900 original size:27 final size:27
Alignment explanation
Indices: 29496857--29496929 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
29496847 GATCATTGAA
*
29496857 TTTA-TTTCTTTTCTTTTTAGTTTTAGT
1 TTTATTTTC-TTTATTTTTAGTTTTAGT
* *
29496884 TTTATTTTCTTTATTTTTATTTTTATT
1 TTTATTTTCTTTATTTTTAGTTTTAGT
*
29496911 TTTAGTTGT-TTTATTTTTA
1 TTTA-TTTTCTTTATTTTTA
29496930 TGTCTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
27 33 0.82
28 7 0.17
ACGTcount: A:0.14, C:0.04, G:0.05, T:0.77
Consensus pattern (27 bp):
TTTATTTTCTTTATTTTTAGTTTTAGT
Found at i:29496901 original size:15 final size:14
Alignment explanation
Indices: 29496877--29496930 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
29496867 TTCTTTTTAG
*
29496877 TTTTAGTTTTATTT
1 TTTTATTTTTATTT
29496891 TCTTTATTTTTA--T
1 T-TTTATTTTTATTT
*
29496904 TTTTATTTTTAGTTG
1 TTTTATTTTTA-TTT
29496919 TTTTATTTTTAT
1 TTTTATTTTTAT
29496931 GTCTTTAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 10 0.29
13 2 0.06
14 2 0.06
15 20 0.59
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.78
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:29496928 original size:6 final size:6
Alignment explanation
Indices: 29496865--29496930 Score: 51
Period size: 6 Copynumber: 10.0 Consensus size: 6
29496855 AATTTATTTC
* * *
29496865 TTTTCT TTTTAG TTTTAGT TTTATTT TCTTTAT TTTTAT TTTTAT TTTTAGTT
1 TTTTAT TTTTAT TTTTA-T TTT-TAT T-TTTAT TTTTAT TTTTAT TTTTA--T
29496918 GTTTTAT TTTTAT
1 -TTTTAT TTTTAT
29496931 GTCTTTAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
6 31 0.63
7 9 0.18
8 4 0.08
9 5 0.10
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:29509049 original size:26 final size:26
Alignment explanation
Indices: 29508993--29509068 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
29508983 TACCAATATT
* * * * *
29508993 GCAGCAGAGCTGCCAGTGATAATGAC
1 GCAGCAAAGCTGCCAGTAACAGTAAC
*
29509019 ACAGCAAAGCTGCCAGTAACAGTAAC
1 GCAGCAAAGCTGCCAGTAACAGTAAC
* *
29509045 GCAGCAAGGCTGCCCGTAACAGTA
1 GCAGCAAAGCTGCCAGTAACAGTA
29509069 TATGTGGCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.34, C:0.26, G:0.26, T:0.13
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAACAGTAAC
Found at i:29509264 original size:27 final size:27
Alignment explanation
Indices: 29509241--29509392 Score: 173
Period size: 27 Copynumber: 5.7 Consensus size: 27
29509231 AGAGGTATAA
*
29509241 CAGTAATTTTACCCTTCGGGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
*
29509268 C-GATAATTTTACCCTTCGAGAGTATTT
1 CAG-TAATTTTACCCTTCGAGGGTATTT
* * *
29509295 TAGTAATTTTACCCTTTGAGGGTGTTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
**
29509322 TGGTAATTTT-CCCTTCGAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
* * * *
29509348 TAGTACTTTTACCTTTCTAGGGTATTT
1 CAGTAATTTTACCCTTCGAGGGTATTT
*
29509375 TAGTAATTTTACCCTTCG
1 CAGTAATTTTACCCTTCG
29509393 GCAATCTTAC
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
26 23 0.22
27 82 0.77
28 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45
Consensus pattern (27 bp):
CAGTAATTTTACCCTTCGAGGGTATTT
Found at i:29509358 original size:53 final size:54
Alignment explanation
Indices: 29509242--29509392 Score: 198
Period size: 53 Copynumber: 2.8 Consensus size: 54
29509232 GAGGTATAAC
* * * *
29509242 AGTAATTTTACCCTTCGGGGGTATTTCGATAATTTTACCCTTCGAGAGTATTTT
1 AGTAATTTTACCCTTTGAGGGTATTTTGGTAATTTTACCCTTCGAGAGTATTTT
* *
29509296 AGTAATTTTACCCTTTGAGGGTGTTTTGGTAATTTT-CCCTTCGAGGGTATTTT
1 AGTAATTTTACCCTTTGAGGGTATTTTGGTAATTTTACCCTTCGAGAGTATTTT
* * *
29509349 AGTACTTTTA-CCTTTCTAGGGTATTTTAGTAATTTTACCCTTCG
1 AGTAATTTTACCCTTT-GAGGGTATTTTGGTAATTTTACCCTTCG
29509393 GCAATCTTAC
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
52 5 0.06
53 42 0.49
54 38 0.45
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.46
Consensus pattern (54 bp):
AGTAATTTTACCCTTTGAGGGTATTTTGGTAATTTTACCCTTCGAGAGTATTTT
Found at i:29509451 original size:27 final size:27
Alignment explanation
Indices: 29509421--29509485 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
29509411 GATATTTTAG
*
29509421 TAATTTTACCCTTCGGGGGTAATTCAA
1 TAATTTTACCCTTCGGGGGTAAGTCAA
*
29509448 TAATTTTACCCTTCGGGGGTAAGTCGA
1 TAATTTTACCCTTCGGGGGTAAGTCAA
*
29509475 TCATTTTACCC
1 TAATTTTACCC
29509486 ACGATTCGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (27 bp):
TAATTTTACCCTTCGGGGGTAAGTCAA
Found at i:29516173 original size:20 final size:20
Alignment explanation
Indices: 29516135--29516173 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29516125 AACTTAGACT
*
29516135 TGTTGATAAAATTCATTTCA
1 TGTTGATAAAACTCATTTCA
*
29516155 TGTTGATAAAACTCGTTTC
1 TGTTGATAAAACTCATTTC
29516174 GTTAATTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (20 bp):
TGTTGATAAAACTCATTTCA
Found at i:29516695 original size:30 final size:31
Alignment explanation
Indices: 29516659--29516717 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
29516649 ATAGTACGGT
*
29516659 GTGGGCCTAAGCCCAGTACAATAA-CAGTGA
1 GTGGGCCTAAGCCCAATACAATAATCAGTGA
* *
29516689 GTGGGCCTTAGCCCAATACAGTAATCAGT
1 GTGGGCCTAAGCCCAATACAATAATCAGT
29516718 ACGATGCAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.20
Consensus pattern (31 bp):
GTGGGCCTAAGCCCAATACAATAATCAGTGA
Found at i:29517107 original size:27 final size:27
Alignment explanation
Indices: 29517072--29517247 Score: 171
Period size: 27 Copynumber: 6.5 Consensus size: 27
29517062 AGAGGTATAA
* * *
29517072 CAGTCATTTTACCTTTTGGGGGTATGTT
1 CAGTAATTTTACCCTTTGAGGGTAT-TT
* *
29517100 -AGTAATTTTACCCTTTAAGGGCATTT
1 CAGTAATTTTACCCTTTGAGGGTATTT
*
29517126 TAGTAATTTTACCCTTTGAGGGTATTT
1 CAGTAATTTTACCCTTTGAGGGTATTT
*
29517153 CAGTAATTTTACCCTTTGAAGGTATTT
1 CAGTAATTTTACCCTTTGAGGGTATTT
* * *
29517180 CGGTAATTTTACTCTTTAAGGGTAATTT
1 CAGTAATTTTACCCTTTGAGGGT-ATTT
* *
29517208 -GGTAATTTTACCCTTCT-AGGGTAATT
1 CAGTAATTTTACCCTT-TGAGGGTATTT
*
29517234 C-GATCATTTTACCC
1 CAG-TAATTTTACCC
29517248 ATGATTCACA
Statistics
Matches: 127, Mismatches: 16, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
26 6 0.05
27 116 0.91
28 5 0.04
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (27 bp):
CAGTAATTTTACCCTTTGAGGGTATTT
Found at i:29518194 original size:18 final size:19
Alignment explanation
Indices: 29518157--29518194 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
29518147 AATTGGCAAC
*
29518157 AAGAGAAGAAGAAACCAAA
1 AAGAGAAGAAGAAAACAAA
*
29518176 AAGA-AAGAAGAAAAGAAA
1 AAGAGAAGAAGAAAACAAA
29518194 A
1 A
29518195 GATGAGAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (19 bp):
AAGAGAAGAAGAAAACAAA
Found at i:29529770 original size:50 final size:50
Alignment explanation
Indices: 29529711--29529834 Score: 126
Period size: 50 Copynumber: 2.5 Consensus size: 50
29529701 CGCCATTGCG
* *
29529711 GCTTCAATCTGTTCCACTGCACCGTCTGGGAAGCAAAATTC-GCTGCAGTA
1 GCTTTAATCTGTTCCACTGCACCGTCAGGGAAGCAAAATTCAGC-GCAGTA
** ** * ** *
29529761 GCTTTAATCT-TCTTAACTGCAATGTCAGGGAAGCAAGATTCAGCGTTGTG
1 GCTTTAATCTGT-TCCACTGCACCGTCAGGGAAGCAAAATTCAGCGCAGTA
29529811 GCTTTAATCTGTTCCACTGCACCG
1 GCTTTAATCTGTTCCACTGCACCG
29529835 CTAGGGGAGT
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
49 1 0.02
50 53 0.93
51 3 0.05
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (50 bp):
GCTTTAATCTGTTCCACTGCACCGTCAGGGAAGCAAAATTCAGCGCAGTA
Found at i:29530076 original size:46 final size:46
Alignment explanation
Indices: 29530003--29530120 Score: 191
Period size: 46 Copynumber: 2.6 Consensus size: 46
29529993 TCTGCTCCGT
** *
29530003 TGTAATCTCAGGGAGATAAGATTTGAAATTCCTCGGTCTATTCCAC
1 TGTAATCTCAGGGAGATAAGACCTGAAATGCCTCGGTCTATTCCAC
* *
29530049 TGTAATCTCAGGGAGATAAGACCTGAAATGCTTTGGTCTATTCCAC
1 TGTAATCTCAGGGAGATAAGACCTGAAATGCCTCGGTCTATTCCAC
29530095 TGTAATCTCAGGGAGATAAGACCTGA
1 TGTAATCTCAGGGAGATAAGACCTGA
29530121 TGCGATCTAC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 67 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (46 bp):
TGTAATCTCAGGGAGATAAGACCTGAAATGCCTCGGTCTATTCCAC
Found at i:29530226 original size:44 final size:43
Alignment explanation
Indices: 29529947--29530244 Score: 181
Period size: 46 Copynumber: 6.8 Consensus size: 43
29529937 CCTTTATATT
* * *
29529947 AATCCACTCCACTGTAATCTCAGGGAGGTAGGATTACTAGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACT-GCTTC
* ** * * *
29529991 AATCTGCTCCGTTGTAATCTCAGGGAGATAAGATTTGAAATTCCTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGA-TT--ACTGCTTC
** * * * *
29530037 GGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGAAATGCTTT
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGA--T-TACTGCTTC
** * * * *
29530083 GGTCTATTCCACTGTAATCTCAGGGAGATAAGA--CCTGATGC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTGCTTC
* * * * ** *
29530124 GATCTACTCTACTGTAA-CTTCAGAGAGATAAGA-TCCTTTATTT
1 AATCTACTCCACTGTAATC-TCAGGGAGATAAGATTAC-TGCTTC
*** *
29530167 AATCCGGTCCACTGTAATCTCAGGGAGATAGGATTACTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACT-GCTTC
*
29530211 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT
29530245 CTGAAATTCT
Statistics
Matches: 197, Mismatches: 46, Indels: 22
0.74 0.17 0.08
Matches are distributed among these distances:
40 1 0.01
41 30 0.15
42 2 0.01
43 28 0.14
44 63 0.32
45 2 0.01
46 68 0.35
47 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (43 bp):
AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTGCTTC
Found at i:29538122 original size:69 final size:70
Alignment explanation
Indices: 29537990--29538122 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 70
29537980 TAGTTTATTA
* * * * *
29537990 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
29538055 CTTAG
66 CTTAG
29538060 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
29538123 GTTATGTGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 35 0.60
70 23 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:29539649 original size:47 final size:47
Alignment explanation
Indices: 29539595--29539905 Score: 496
Period size: 47 Copynumber: 6.6 Consensus size: 47
29539585 TATTTGAATA
29539595 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
29539642 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
29539691 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
29539738 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
29539785 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * *
29539832 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
29539879 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
29539906 TCCCGAAGGG
Statistics
Matches: 250, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
47 205 0.82
49 45 0.18
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:29551193 original size:14 final size:14
Alignment explanation
Indices: 29551174--29551203 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29551164 TATAAAAATG
*
29551174 TAAGTATGTATGTA
1 TAAGTATGTATATA
29551188 TAAGTATGTATATA
1 TAAGTATGTATATA
29551202 TA
1 TA
29551204 TAACATAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (14 bp):
TAAGTATGTATATA
Found at i:29552720 original size:44 final size:43
Alignment explanation
Indices: 29552566--29553209 Score: 315
Period size: 44 Copynumber: 14.9 Consensus size: 43
29552556 TGTGGTTTTA
* * * *
29552566 GTCTACTCCACTGCAACTTCAGGGAGATAAGACTGG--ATGC-
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTTCT
* * * *
29552606 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTTGTGGTTTT-A
1 G-TCTGCTCCACTGCAACTTCAGGGAGATAAGA--TTG-GTTTTTCT
* * * *
29552652 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTT
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTT-TTCT
* * **
29552696 GTCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGTGATCT
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGG-T-TTTTCT
* * * *
29552741 GT-T-CT--ACTGCAACTTCAGAGAGATAAGATCTTGTGGTTTCA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGGT-TTTTCT
* * *
29552782 ATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTT-TTCT
* * * * * *
29552826 ATCTGCTCCACTACAACTTCAGTGAGATAAGACTGG---ATGT
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTTCT
* * * * * *
29552866 GATCTGCTCTACTCCAACTTTAGAGAGATAAGATCTTGTGGTTTT-A
1 G-TCTGCTCCACTGCAACTTCAGGGAGATAAGA--TTG-GTTTTTCT
* ** * *
29552912 ATCCACTCTACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTT-TTCT
* * * * *
29552956 GTCTGCTCCACTGCAACTTCAGAGAGATATGACTGG--ATGC-
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTTCT
* * * *
29552996 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTTGTGGTTTT-A
1 G-TCTGCTCCACTGCAACTTCAGGGAGATAAGA--TTG-GTTTTTCT
* ** * *
29553042 ATCCACTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCT
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTT-TTCT
* * * *
29553086 GTCTACTCCACTACAACTTCAGGGAGATAAGACTT-G---ATGT
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTTTTTCT
* * * **
29553126 GATCTGCTCTACTGCAACTTAAGAGAGATAAGATCTGTGATTTTAAT
1 G-TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-G-TTTTTCT
* * *
29553173 -CCT-CTCCAATGCAACTTCAGGGAGATAGGATTGGTTT
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTT
29553210 CTTTCGTCTA
Statistics
Matches: 456, Mismatches: 104, Indels: 87
0.70 0.16 0.13
Matches are distributed among these distances:
40 8 0.02
41 142 0.31
42 12 0.03
43 29 0.06
44 152 0.33
45 108 0.24
46 3 0.01
47 2 0.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (43 bp):
GTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTTTCT
Found at i:29552747 original size:130 final size:130
Alignment explanation
Indices: 29552566--29553212 Score: 1062
Period size: 130 Copynumber: 5.0 Consensus size: 130
29552556 TGTGGTTTTA
* *
29552566 GTCTACTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
* *
29552631 AGATAAGATCTTGTGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTTT
66 AGATAAGATCTTGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
* *
29552696 GTCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGTGATCTGTTCTACTGCAACTTCAGAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
* *
29552761 AGATAAGATCTTGTGGTTTCAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
66 AGATAAGATCTTGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
* * * * *
29552826 ATCTGCTCCACTACAACTTCAGTGAGATAAGACTGGATGTGATCTGCTCTACTCCAACTTTAGAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
*
29552891 AGATAAGATCTTGTGGTTTTAATCCACTCTACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
66 AGATAAGATCTTGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
* * *
29552956 GTCTGCTCCACTGCAACTTCAGAGAGATATGACTGGATGCGATCTGCTCTACTGCAACTTCAGAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
*
29553021 AGATAAGATCTTGTGGTTTTAATCCACTCCACTGCAACTTTAGGGAGATAGGATTGGTTTCTTCT
66 AGATAAGATCTTGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
* * * *
29553086 GTCTACTCCACTACAACTTCAGGGAGATAAGACTTGATGTGATCTGCTCTACTGCAACTTAAGAG
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
* * *
29553151 AGATAAGATC-TGTGATTTTAATCCTCTCCAATGCAACTTCAGGGAGATAGGATTGGTTTCTT
66 AGATAAGATCTTGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTT
29553213 TCGTCTATTT
Statistics
Matches: 481, Mismatches: 36, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
129 48 0.10
130 433 0.90
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (130 bp):
GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTACTGCAACTTCAGAG
AGATAAGATCTTGTGGTTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTCT
Found at i:29553472 original size:100 final size:99
Alignment explanation
Indices: 29553220--29553774 Score: 655
Period size: 100 Copynumber: 5.6 Consensus size: 99
29553210 CTTTCGTCTA
* * * * * * *
29553220 TTTAACTGCAATGTCAGGGAAACAAGATTCGCCTTCGTAGCTTCAATTTGTTCCATTACACCGCC
1 TTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCC
* * *
29553285 AGAGAAGTAAGATTCACTGTCGTGGCTTCAATC-T
66 AG-GAAGTAAGATTCGCCGTTGTGGCTTCAATCTT
* ** * * *
29553319 TTTAACTGCAATGTCAGGGAAATAAGATTCACTGTTGTAGCTTCAATCTGTTCCACTACACCGCC
1 TTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCC
29553384 AGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCTT
66 AG-GAAGTAAGATTCGCCGTTGTGGCTTCAATCTT
* * * *
29553419 TTTAATTGCAATGTCGGGGAAGCAAGATTCATCGTCGTAGCTTCAATCTGTTCCACTACACCACC
1 TTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCC
* *
29553484 TGGAAAGTAAGATTCGCCATTGTGGCTTCAATCTT
66 AGG-AAGTAAGATTCGCCGTTGTGGCTTCAATCTT
* * * * *
29553519 TTTAATTACAATGTCAGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTACTCCACTGCATCGCC
1 TTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCC
* *
29553584 AGGAAAGTAAGATTCACCGTTGCGGCTTCAATCTT
66 AGG-AAGTAAGATTCGCCGTTGTGGCTTCAATCTT
* * ** * * ** *
29553619 TTAAATTGCAATATCAGGGAAGCAAGATTCGTCGTCATAGCTTTAATCTGCTCCACTGTACTGCC
1 TTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCC
* *
29553684 AGGGAAGTAAGATTCGTCGTCGTGGCTTCAAT-TT
66 A-GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTT
* * * *
29553718 TTAAATTGCAATATCAGGTAAGCAAGATTCACCGTCGTAGCTTTAATCTGCTCCACT
1 TTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACT
29553775 GCACTGCTAG
Statistics
Matches: 402, Mismatches: 51, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
99 144 0.36
100 256 0.64
101 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (99 bp):
TTTAATTGCAATGTCAGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACACCGCC
AGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTT
Found at i:29553646 original size:50 final size:50
Alignment explanation
Indices: 29553223--29553766 Score: 313
Period size: 50 Copynumber: 10.9 Consensus size: 50
29553213 TCGTCTATTT
** * * *
29553223 AACTGCAATGTCAGGGAAACAAGATTCGCCTTCGTAGCTTCAAT-TTGTTC
1 AACTGCAATGTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTT-TTC
* * * ** * * *
29553273 CATTACACCGCCAGAGAAGTAAGATTCACTGTCGTGGCTTCAATCTTTT-
1 AACTGCAATGTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTC
* * * * *
29553322 AACTGCAATGTCAGGGAAATAAGATTCACTGTTGTAGCTTCAATCTGTTC
1 AACTGCAATGTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTC
* * ** * * * * *
29553372 CACTACACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTT
1 AACTGCAATGTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTC
* * * * * *
29553422 AATTGCAATGTCGGGGAAGCAAGATTCATCGTCGTAGCTTCAATCTGTTC
1 AACTGCAATGTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTC
* * **** * * * * * *
29553472 CACTACACCACCTGGAAAGTAAGATTCGCCATTGTGGCTTCAATCTTTTT
1 AACTGCAATGTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTC
* * * * * **
29553522 AATTACAATGTCAGGGAAGCAAGATTCGCCGTCGTAGCTTCAATCTACTC
1 AACTGCAATGTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTC
* * * * * *
29553572 CACTGC-ATCGCCAGGAAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTA
1 AACTGCAAT-GTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTC
* * * ** * * * **
29553622 AATTGCAATATCAGGGAAGCAAGATTCGTCGTCATAGCTTTAATCTGCTC
1 AACTGCAATGTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTC
* * * * ** *
29553672 CACTGTACTGCCAGGGAAGTAAGATTCGTCGTCGTGGCTTCAAT-TTTTA
1 AACTGCAATGTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTC
* * * * * *
29553721 AATTGCAATATCAGGTAAGCAAGATTCACCGTCGTAGCTTTAATCT
1 AACTGCAATGTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCT
29553767 GCTCCACTGC
Statistics
Matches: 352, Mismatches: 137, Indels: 10
0.71 0.27 0.02
Matches are distributed among these distances:
49 74 0.21
50 274 0.78
51 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (50 bp):
AACTGCAATGTCAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTC
Found at i:29560009 original size:16 final size:16
Alignment explanation
Indices: 29559990--29560020 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29559980 AGTATAAATA
*
29559990 ATATATATCTAAGTAG
1 ATATATATATAAGTAG
29560006 ATATATATATAAGTA
1 ATATATATATAAGTA
29560021 AACTTGGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (16 bp):
ATATATATATAAGTAG
Found at i:29560144 original size:21 final size:19
Alignment explanation
Indices: 29560120--29560158 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 19
29560110 ATAAATGGGT
29560120 AAATAATAAGGCAAATAATAA
1 AAATAATAA-GC-AATAATAA
29560141 AAATAA-AAGCAATAATAA
1 AAATAATAAGCAATAATAA
29560159 TAATGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 2 0.11
20 2 0.11
21 6 0.33
ACGTcount: A:0.69, C:0.05, G:0.08, T:0.18
Consensus pattern (19 bp):
AAATAATAAGCAATAATAA
Found at i:29566484 original size:38 final size:39
Alignment explanation
Indices: 29566399--29566492 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 39
29566389 TAATTACCAT
* * *
29566399 AATTATAATAATTATAATAATGTTTGACCAAAACATTAA
1 AATTACAATAATTATAATAATATTCGACCAAAACATTAA
* **
29566438 AATTACAATAATTATAATAATATTCGATCGTAA-ATTAA
1 AATTACAATAATTATAATAATATTCGACCAAAACATTAA
29566476 AATTACAATAATTATAA
1 AATTACAATAATTATAA
29566493 CAAGGATTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.36
Consensus pattern (39 bp):
AATTACAATAATTATAATAATATTCGACCAAAACATTAA
Found at i:29569679 original size:5 final size:6
Alignment explanation
Indices: 29569656--29569686 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
29569646 TAGATTTTGG
29569656 GAAAGAA GAAAAA GAAAAA GAAAAA GAAAAA
1 GAAA-AA GAAAAA GAAAAA GAAAAA GAAAAA
29569687 TGTGGGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:29570960 original size:20 final size:18
Alignment explanation
Indices: 29570918--29570966 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
29570908 TATTCTTATA
*
29570918 TTTTTTATAATTTATTAAT
1 TTTTTT-TAATTTATTAAG
29570937 TTTTTTTAATTGTATATAAG
1 TTTTTTTAATT-TAT-TAAG
*
29570957 TTTTTATAAT
1 TTTTTTTAAT
29570967 ATTTATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 5 0.19
19 9 0.35
20 12 0.46
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTTTTTAATTTATTAAG
Found at i:29570989 original size:9 final size:9
Alignment explanation
Indices: 29570870--29570989 Score: 73
Period size: 9 Copynumber: 12.8 Consensus size: 9
29570860 AGTTTGTATA
*
29570870 AATTTTTAA
1 AATTTTTAT
29570879 ATATTTTTA-
1 A-ATTTTTAT
29570888 ATATGTTTTAT
1 A-AT-TTTTAT
*
29570899 ATTTTTTAT
1 AATTTTTAT
* *
29570908 TATTCTTAT
1 AATTTTTAT
*
29570917 ATTTTTTAT
1 AATTTTTAT
29570926 AATTTATTA-
1 AATTT-TTAT
* *
29570935 ATTTTTTTT
1 AATTTTTAT
*
29570944 AATTGTATAT
1 AATT-TTTAT
29570954 AAGTTTTTAT
1 AA-TTTTTAT
*
29570964 AATATTTAT
1 AATTTTTAT
29570973 AATATTTTAT
1 AAT-TTTTAT
*
29570983 GATTTTT
1 AATTTTT
29570990 CTTATAAGTT
Statistics
Matches: 86, Mismatches: 17, Indels: 16
0.72 0.14 0.13
Matches are distributed among these distances:
8 2 0.02
9 47 0.55
10 34 0.40
11 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (9 bp):
AATTTTTAT
Found at i:29570996 original size:22 final size:22
Alignment explanation
Indices: 29570969--29571029 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
29570959 TTTATAATAT
*
29570969 TTATAATATTTTATGA-TTTTTC
1 TTATAA-ATTTTATAAGTTTTTC
*
29570991 TTATAAGTTTTATAAGTTTTTC
1 TTATAAATTTTATAAGTTTTTC
**
29571013 TTATAAAAATTATAAGT
1 TTATAAATTTTATAAGT
29571030 GTATATAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 7 0.21
22 26 0.79
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (22 bp):
TTATAAATTTTATAAGTTTTTC
Found at i:29574314 original size:30 final size:29
Alignment explanation
Indices: 29574273--29574345 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
29574263 CTTCAAAAAA
*
29574273 TATACATATATACCCACATACTTTT-TTTT
1 TATAAATATATACCCACATA-TTTTATTTT
**
29574302 TATAATATATATACGTACATATTTTAATTTT
1 TATAA-ATATATACCCACATATTTT-ATTTT
*
29574333 TGTAAATATATAC
1 TATAAATATATAC
29574346 ATACTTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 8 0.22
30 21 0.57
31 8 0.22
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.48
Consensus pattern (29 bp):
TATAAATATATACCCACATATTTTATTTT
Found at i:29574873 original size:71 final size:70
Alignment explanation
Indices: 29574766--29574902 Score: 222
Period size: 71 Copynumber: 1.9 Consensus size: 70
29574756 CTTTTCAAAT
*
29574766 TCAAGTTTTAAACAATCTCGAGAATTAAAAAGAGATCGTGTCCTAACCTACTGGGCATGATCTCT
1 TCAAGTTTTAAACAATCTCGAGAATCAAAAAGAGATCGTGTCCTAACCTACTGGGCATGATC-CT
29574831 TTCTTC
65 TTCTTC
* *
29574837 TCAAGTTTTAAACAATCTCGGGAATCAAGAAA-AGATCGTGTCCTAACTTACTGGGCATGATCCT
1 TCAAGTTTTAAACAATCTCGAGAATCAA-AAAGAGATCGTGTCCTAACCTACTGGGCATGATCCT
29574901 TT
65 TT
29574903 TTTTAAATCC
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
70 4 0.06
71 55 0.89
72 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (70 bp):
TCAAGTTTTAAACAATCTCGAGAATCAAAAAGAGATCGTGTCCTAACCTACTGGGCATGATCCTT
TCTTC
Found at i:29575247 original size:22 final size:22
Alignment explanation
Indices: 29575220--29575264 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
29575210 TCGTGGACCA
*
29575220 AAATCGTTGTTTTAATAA-AATC
1 AAATCGTT-TATTAATAACAATC
29575242 AAATCGTTTATTAATAACAATC
1 AAATCGTTTATTAATAACAATC
29575264 A
1 A
29575265 CTTTTTGACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (22 bp):
AAATCGTTTATTAATAACAATC
Found at i:29581768 original size:23 final size:22
Alignment explanation
Indices: 29581742--29581799 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
29581732 AGTGCGCACC
29581742 CGTAGGAGAGCCCTTGAGTGGGA
1 CGTAGGAGAGCCCTTGA-TGGGA
** *
29581765 CGTATAAGAGCCCTTTATGGGA
1 CGTAGGAGAGCCCTTGATGGGA
* *
29581787 CATTGGAGAGCCC
1 CGTAGGAGAGCCC
29581800 CTCGGGGAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (22 bp):
CGTAGGAGAGCCCTTGATGGGA
Found at i:29581907 original size:26 final size:26
Alignment explanation
Indices: 29581871--29582159 Score: 152
Period size: 26 Copynumber: 11.2 Consensus size: 26
29581861 ATAAATGTGA
*
29581871 AAGTCCATCAGGACAATCTAATTGGG
1 AAGTCCGTCAGGACAATCTAATTGGG
*
29581897 AAGTCCGTCAGGACAATTTAATGTGGG
1 AAGTCCGTCAGGACAATCTAAT-TGGG
* * * * *
29581924 -AGCCCATTAGGACAAACTAATTAGG
1 AAGTCCGTCAGGACAATCTAATTGGG
*
29581949 AAGTCTG-CTAGGACAATCTAA-TGTGG
1 AAGTCCGTC-AGGACAATCTAATTG-GG
* ** *
29581975 AA-TCTTGTCAATACAATCCAATTGGG
1 AAGTC-CGTCAGGACAATCTAATTGGG
* ** *
29582001 AAGT--GTACTAAGATTATATAATAT-GG
1 AAGTCCGT-C-AGGACAATCTAAT-TGGG
** **
29582027 -AGTCTATCAGGACAATCTAA-AAGG
1 AAGTCCGTCAGGACAATCTAATTGGG
29582051 AAGTCCG-CTAGGACAATCTAA-TGAGG
1 AAGTCCGTC-AGGACAATCTAATTG-GG
* *
29582077 AAGTCCGTCAGGACAATCTATTTAGG
1 AAGTCCGTCAGGACAATCTAATTGGG
* * *
29582103 AAGTCTGCCAGGACGATCTAA-TGTGG
1 AAGTCCGTCAGGACAATCTAATTG-GG
** *
29582129 AAGTCTATTAGGACAATCTAATTGGG
1 AAGTCCGTCAGGACAATCTAATTGGG
29582155 AAGTC
1 AAGTC
29582160 TACAAGGGTG
Statistics
Matches: 199, Mismatches: 43, Indels: 42
0.70 0.15 0.15
Matches are distributed among these distances:
24 5 0.03
25 35 0.18
26 145 0.73
27 14 0.07
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.26
Consensus pattern (26 bp):
AAGTCCGTCAGGACAATCTAATTGGG
Found at i:29582160 original size:52 final size:52
Alignment explanation
Indices: 29581864--29582160 Score: 260
Period size: 52 Copynumber: 5.8 Consensus size: 52
29581854 CATTATCATA
* * * *
29581864 AATGTGAAAGTCCATCAGGACAATCTAATTGGGAAGTCCG-TCAGGACAATTT
1 AATGTGGAAGTCCATCAGGACAATCTAATTAGGAAGTCTGCT-AGGACAATCT
* * * *
29581916 AATGTGGGAGCCCATTAGGACAAACTAATTAGGAAGTCTGCTAGGACAATCT
1 AATGTGGAAGTCCATCAGGACAATCTAATTAGGAAGTCTGCTAGGACAATCT
** ** * * * * * ** *
29581968 AATGTGGAA-TCTTGTCAATACAATCCAATTGGGAAGTGTACTAAGATTATAT
1 AATGTGGAAGTC-CATCAGGACAATCTAATTAGGAAGTCTGCTAGGACAATCT
* * * *
29582020 AATATGG-AGTCTATCAGGACAATCTAA-AAGGAAGTCCGCTAGGACAATCT
1 AATGTGGAAGTCCATCAGGACAATCTAATTAGGAAGTCTGCTAGGACAATCT
* * * * *
29582070 AATGAGGAAGTCCGTCAGGACAATCTATTTAGGAAGTCTGCCAGGACGATCT
1 AATGTGGAAGTCCATCAGGACAATCTAATTAGGAAGTCTGCTAGGACAATCT
* * *
29582122 AATGTGGAAGTCTATTAGGACAATCTAATTGGGAAGTCT
1 AATGTGGAAGTCCATCAGGACAATCTAATTAGGAAGTCT
29582161 ACAAGGGTGA
Statistics
Matches: 187, Mismatches: 53, Indels: 10
0.75 0.21 0.04
Matches are distributed among these distances:
50 19 0.10
51 31 0.17
52 136 0.73
53 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.26
Consensus pattern (52 bp):
AATGTGGAAGTCCATCAGGACAATCTAATTAGGAAGTCTGCTAGGACAATCT
Found at i:29582177 original size:154 final size:155
Alignment explanation
Indices: 29581872--29582181 Score: 369
Period size: 154 Copynumber: 2.0 Consensus size: 155
29581862 TAAATGTGAA
** * * * *
29581872 AGTCCATCAGGACAATCTAATTGGGAAGTCCGTCAGGACAATTTAATGTGGGAGCCCATTAGGAC
1 AGTCCATCAGGACAATCTAATAAGGAAGTCCGTCAGGACAATCTAATGAGGAAGCCCATCAGGAC
* *
29581937 AAACTAATTAGGAAGTCTGCTAGGACAATCTAATGTGGAATCTTGTCAATACAATCCAATTGGGA
66 AAACTAATTAGGAAGTCTGCCAGGACAATCTAATGTGGAATCTTGTCAAGACAATCCAATTGGGA
* *
29582002 AGTGTACTAAGATTATATAATATGG
131 AGTCTACTAAGATGATATAATATGG
* * *
29582027 AGTCTATCAGGACAATCTAA-AAGGAAGTCCG-CTAGGACAATCTAATGAGGAAGTCCGTCAGGA
1 AGTCCATCAGGACAATCTAATAAGGAAGTCCGTC-AGGACAATCTAATGAGGAAGCCCATCAGGA
* * * * *
29582090 CAATCTATTTAGGAAGTCTGCCAGGACGATCTAATGTGGAAGTCTAT-T-AGGACAATCTAATTG
65 CAAACTAATTAGGAAGTCTGCCAGGACAATCTAATGTGGAA-TCT-TGTCAAGACAATCCAATTG
* *
29582153 GGAAGTCTAC-AAGGGTGATCTAATATGG
128 GGAAGTCTACTAA-GATGATATAATATGG
29582181 A
1 A
29582182 ATTTAGTCAG
Statistics
Matches: 131, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
153 3 0.02
154 104 0.79
155 23 0.18
156 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.26
Consensus pattern (155 bp):
AGTCCATCAGGACAATCTAATAAGGAAGTCCGTCAGGACAATCTAATGAGGAAGCCCATCAGGAC
AAACTAATTAGGAAGTCTGCCAGGACAATCTAATGTGGAATCTTGTCAAGACAATCCAATTGGGA
AGTCTACTAAGATGATATAATATGG
Found at i:29582182 original size:26 final size:25
Alignment explanation
Indices: 29582086--29582182 Score: 77
Period size: 26 Copynumber: 3.7 Consensus size: 25
29582076 GAAGTCCGTC
* * * *
29582086 AGGACAATCTATTTAGGAAGTCTGCC
1 AGGACGATCTAATT-GGAAGTCTACA
**
29582112 AGGACGATCTAATGTGGAAGTCTATT
1 AGGACGATCTAAT-TGGAAGTCTACA
*
29582138 AGGACAATCTAATTGGGAAGTCTACA
1 AGGACGATCTAATT-GGAAGTCTACA
**
29582164 AGGGTGATCTAATATGGAA
1 AGGACGATCTAAT-TGGAA
29582183 TTTAGTCAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
25 1 0.02
26 54 0.95
27 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (25 bp):
AGGACGATCTAATTGGAAGTCTACA
Found at i:29585346 original size:31 final size:30
Alignment explanation
Indices: 29585288--29585347 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
29585278 GAAAAACTGG
*
29585288 AATGAAAGAAGGGAGAAGCAAGCGAGAGAT
1 AATGAAAGAAGGGAGAAGCAAACGAGAGAT
* *
29585318 AATGTAAAGAATGGAGAAGCAAATGAGAGA
1 AATG-AAAGAAGGGAGAAGCAAACGAGAGA
29585348 ATAAGTATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.52, C:0.05, G:0.33, T:0.10
Consensus pattern (30 bp):
AATGAAAGAAGGGAGAAGCAAACGAGAGAT
Found at i:29588169 original size:19 final size:19
Alignment explanation
Indices: 29588145--29588184 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29588135 TCCCATATTG
29588145 TTTTTT-TCTTTCTTCTCTC
1 TTTTTTCTCTTTCTTC-CTC
*
29588164 TTTTTTCTTTTTCTTCCTC
1 TTTTTTCTCTTTCTTCCTC
29588183 TT
1 TT
29588185 CCTTTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTTTCTCTTTCTTCCTC
Found at i:29588190 original size:20 final size:20
Alignment explanation
Indices: 29588153--29588190 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29588143 TGTTTTTTTC
*
29588153 TTTCTTCTCTCTTTTTTCTT
1 TTTCTTCTCTCTTCTTTCTT
29588173 TTTCTTC-CTCTTCCTTTC
1 TTTCTTCTCTCTT-CTTTC
29588191 ATTTGGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTCTTCTCTCTTCTTTCTT
Found at i:29588689 original size:30 final size:30
Alignment explanation
Indices: 29588589--29588685 Score: 149
Period size: 30 Copynumber: 3.2 Consensus size: 30
29588579 TAAGCTAGGT
* *
29588589 TGGGCGTATGAACCACACGGACATGCCACA
1 TGGGCGTATGGACCACACGGACATGCCATA
29588619 TGGGCGTATGGACCACACGGACATGCCATA
1 TGGGCGTATGGACCACACGGACATGCCATA
* *
29588649 TGGGCGTGTGGACCACACAGACATGCCATA
1 TGGGCGTATGGACCACACGGACATGCCATA
*
29588679 TAGGCGT
1 TGGGCGT
29588686 GTGGGTTTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (30 bp):
TGGGCGTATGGACCACACGGACATGCCATA
Found at i:29598285 original size:13 final size:13
Alignment explanation
Indices: 29598267--29598291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29598257 GACAACCAAC
29598267 CTGCTATTACAAT
1 CTGCTATTACAAT
29598280 CTGCTATTACAA
1 CTGCTATTACAA
29598292 GGCAAGACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (13 bp):
CTGCTATTACAAT
Found at i:29600556 original size:3 final size:3
Alignment explanation
Indices: 29600548--29600581 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
29600538 AGATAAGTAG
*
29600548 ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29600582 AATTGCCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29601527 original size:17 final size:16
Alignment explanation
Indices: 29601502--29601538 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
29601492 AATCTACTGC
*
29601502 CTTTTCTTTGTTTCTTT
1 CTTTCCTTTGTTTC-TT
29601519 CTTTCCTTTGTTTCTT
1 CTTTCCTTTGTTTCTT
29601535 CTTT
1 CTTT
29601539 GCAGGTGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.00, C:0.22, G:0.05, T:0.73
Consensus pattern (16 bp):
CTTTCCTTTGTTTCTT
Found at i:29602471 original size:46 final size:46
Alignment explanation
Indices: 29602378--29603133 Score: 1041
Period size: 46 Copynumber: 16.5 Consensus size: 46
29602368 TCGCCGTTAG
* ** * * *
29602378 TACAGGAAGGCAAGATCTGC-AACTTCAATCTACTCTGTTGCCAAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
* *
29602423 TACATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCTAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
* **
29602469 TACAGGAAGACAAGATCTGCTTTTTTCGATCTACTCCGCTATCAAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
* ** *
29602515 TACAGGAAGATAAGATCTGCTTTCTTCGATCTACTATGCTGCCTAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
* * * *
29602561 TACAAGAAGACAAGATCTACTTTCTTCGATCTACTCCGCCGCCTAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
* * * * *
29602607 TACAGGAAAACAAGAACTACTATCTTCGATCTACTCCGCTGCCTAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
* *
29602653 TACAGGAAGACAAGATCTG-TTATCTTCGGTCTACTCTGCTGCCAAA
1 TACAGGAAGACAAGATCTGCTT-TCTTCGATCTACTCCGCTGCCAAA
* * *
29602699 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGTTACCAAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
*
29602745 TACAGGAAGACAAGATCTGCTATT-TTCGATCTACTCCGCTGCCTAA
1 TACAGGAAGACAAGATCTGCT-TTCTTCGATCTACTCCGCTGCCAAA
*
29602791 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCTAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
* * *
29602837 TACAGGAAGACAAGATATGCTTTTTTCGATCTACTCTGCTGCCAAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
* * * *
29602883 TACAGGAAGACAAGATCTACTATCTTCGATCTACTCCACTACCAAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
* *
29602929 TACAGGAAGACAAGATCTACTTTCTTCGATCTACTCCGCTGCCTAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
* * * *
29602975 TACAGGAAGACAAGATCTGCTTTCTTCAATCTACTTCGCTGTCTAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
* * *
29603021 TACAGGAAGACAAGATTTTCTATCTTCGATCTACTCCGCTGCCAAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
*
29603067 TACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCTGCCAAA
1 TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
29603113 TACAGGAAGACAAGATCTGCT
1 TACAGGAAGACAAGATCTGCT
29603134 GCTTCTAGTC
Statistics
Matches: 631, Mismatches: 75, Indels: 9
0.88 0.10 0.01
Matches are distributed among these distances:
45 21 0.03
46 608 0.96
47 2 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (46 bp):
TACAGGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCTGCCAAA
Done.