Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 46 of 216
Found at i:13211230 original size:21 final size:22
Alignment explanation
Indices: 13211178--13211234 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
13211168 ACATATACAC
13211178 GTATATATTTTTTATAACATAT
1 GTATATATTTTTTATAACATAT
* *
13211200 ATATGCATATTTTTTA-AATATAT
1 GTAT--ATATTTTTTATAACATAT
13211223 GTATATATTTTT
1 GTATATATTTTT
13211235 AGACTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 8 0.27
22 3 0.10
23 9 0.30
24 10 0.33
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (22 bp):
GTATATATTTTTTATAACATAT
Found at i:13211255 original size:30 final size:30
Alignment explanation
Indices: 13211209--13211265 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
13211199 TATATGCATA
* *
13211209 TTTTTTAAATATATGTATATATTTTTAGAC
1 TTTTATAAATACATGTATATATTTTTAGAC
13211239 TTTTATAAATACATGTATATATTTTTA
1 TTTTATAAATACATGTATATATTTTTA
13211266 TACATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (30 bp):
TTTTATAAATACATGTATATATTTTTAGAC
Found at i:13211270 original size:18 final size:18
Alignment explanation
Indices: 13211247--13211285 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
13211237 ACTTTTATAA
*
13211247 ATACATGTATATATTTTT
1 ATACATATATATATTTTT
13211265 ATACATATATATATTTTT
1 ATACATATATATATTTTT
13211283 ATA
1 ATA
13211286 TTTTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
ATACATATATATATTTTT
Found at i:13221667 original size:492 final size:492
Alignment explanation
Indices: 13220743--13221724 Score: 1919
Period size: 492 Copynumber: 2.0 Consensus size: 492
13220733 GCTTAATCTA
13220743 ACAAAGTGCACCTTTGGAGCCAGATCAGGGAAGTTGCTAGGCTTTATAGTCAGTGGAAAAGGAAT
1 ACAAAGTGCACCTTTGGAGCCAGATCAGGGAAGTTGCTAGGCTTTATAGTCAGTGGAAAAGGAAT
13220808 TGAGGTTGACCCAGATAAAGTCAAGGTGATACGAGATTTGCCTCCACCACACACTCAGAAAGAGG
66 TGAGGTTGACCCAGATAAAGTCAAGGTGATACGAGATTTGCCTCCACCACACACTCAGAAAGAGG
13220873 TACGAGGTTTTCTAGGAAGATTGAATTACATTGCTCGGTTCATTTCACAGTTAACTGAGAAATGT
131 TACGAGGTTTTCTAGGAAGATTGAATTACATTGCTCGGTTCATTTCACAGTTAACTGAGAAATGT
* *
13220938 GATCCCATATTCTGTCTTCTGAGGAAGCATAATCTGGGTGTATGGGATGAATAATATCAAAAAGC
196 GATCCCATATTCCGTCTTCTGAGGAAGCATAATCCGGGTGTATGGGATGAATAATATCAAAAAGC
*
13221003 TTTTGAAAAAATAAAATAGTTCTTGTCCATCACTCCAGTGCTATCACCACCTAGTCCGGATAGGC
261 TTTTGAAAAAATAAAATAGTTCTTGTCCATCACTCCAGTGCTATCACCACCTAGTCCAGATAGGC
*
13221068 CATTAATACTGTATTTAATAGTATTTGACAATTCCATGGGGTGCGTGTTAGGCTAACATGATGAG
326 CACTAATACTGTATTTAATAGTATTTGACAATTCCATGGGGTGCGTGTTAGGCTAACATGATGAG
13221133 ACAGGAAGAAAAGAAAGGGCAATATATTATCTTAGCAAGAAATTCACTGATTGTGAAGCGAGGTA
391 ACAGGAAGAAAAGAAAGGGCAATATATTATCTTAGCAAGAAATTCACTGATTGTGAAGCGAGGTA
13221198 CTCGTCTATCGAGAAGTTATGTTGTGCCCTGGTTTGG
456 CTCGTCTATCGAGAAGTTATGTTGTGCCCTGGTTTGG
13221235 ACAAAGTGCACCTTTGGAGCCAGATCAGGGAAGTTGCTAGGCTTTATAGTCAGTGGAAAAGGAAT
1 ACAAAGTGCACCTTTGGAGCCAGATCAGGGAAGTTGCTAGGCTTTATAGTCAGTGGAAAAGGAAT
13221300 TGAGGTTGACCCAGATAAAGTCAAGGTGATACGAGATTTGCCTCCACCACACACTCAGAAAGAGG
66 TGAGGTTGACCCAGATAAAGTCAAGGTGATACGAGATTTGCCTCCACCACACACTCAGAAAGAGG
13221365 TACGAGGTTTTCTAGGAAGATTGAATTACATTGCTCGGTTCATTTCACAGTTAACTGAGAAATGT
131 TACGAGGTTTTCTAGGAAGATTGAATTACATTGCTCGGTTCATTTCACAGTTAACTGAGAAATGT
*
13221430 GATCCCATATTCCGTCTTCTGAGGAAGCATAATCCGGGTGTATGGGATGAATAATATCAAAAGGC
196 GATCCCATATTCCGTCTTCTGAGGAAGCATAATCCGGGTGTATGGGATGAATAATATCAAAAAGC
13221495 TTTTGAAAAAATAAAATAGTTCTTGTCCATCACTCCAGTGCTATCACCACCTAGTCCAGATAGGC
261 TTTTGAAAAAATAAAATAGTTCTTGTCCATCACTCCAGTGCTATCACCACCTAGTCCAGATAGGC
13221560 CACTAATACTGTATTTAATAGTATTTGACAATTCCATGGGGTGCGTGTTAGGCTAACATGATGAG
326 CACTAATACTGTATTTAATAGTATTTGACAATTCCATGGGGTGCGTGTTAGGCTAACATGATGAG
13221625 ACAGGAAGAAAAGAAAGGGCAATATATTATCTTAGCAAGAAATTCACTGATTGTGAAGCGAGGTA
391 ACAGGAAGAAAAGAAAGGGCAATATATTATCTTAGCAAGAAATTCACTGATTGTGAAGCGAGGTA
13221690 CTCGTCTATCGAGAAGTTATGTTGTGCCCTGGTTT
456 CTCGTCTATCGAGAAGTTATGTTGTGCCCTGGTTT
13221725 AGAAAACTCG
Statistics
Matches: 485, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
492 485 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (492 bp):
ACAAAGTGCACCTTTGGAGCCAGATCAGGGAAGTTGCTAGGCTTTATAGTCAGTGGAAAAGGAAT
TGAGGTTGACCCAGATAAAGTCAAGGTGATACGAGATTTGCCTCCACCACACACTCAGAAAGAGG
TACGAGGTTTTCTAGGAAGATTGAATTACATTGCTCGGTTCATTTCACAGTTAACTGAGAAATGT
GATCCCATATTCCGTCTTCTGAGGAAGCATAATCCGGGTGTATGGGATGAATAATATCAAAAAGC
TTTTGAAAAAATAAAATAGTTCTTGTCCATCACTCCAGTGCTATCACCACCTAGTCCAGATAGGC
CACTAATACTGTATTTAATAGTATTTGACAATTCCATGGGGTGCGTGTTAGGCTAACATGATGAG
ACAGGAAGAAAAGAAAGGGCAATATATTATCTTAGCAAGAAATTCACTGATTGTGAAGCGAGGTA
CTCGTCTATCGAGAAGTTATGTTGTGCCCTGGTTTGG
Found at i:13225019 original size:45 final size:45
Alignment explanation
Indices: 13224882--13225243 Score: 320
Period size: 45 Copynumber: 8.0 Consensus size: 45
13224872 AACAGATCGG
* * *
13224882 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTAGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * * * * *
13224927 TGAAGATATGCAAGTCTTATCTCCATGAAGTTGCAGCGAAGCAGAT
1 TGAAGATA-GCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
*
13224973 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * * ** * * *
13225018 TGAAGATATGCAAGTCTTATCTCCCTGAAGTTACAGCAGAGCAAAC
1 TGAAGATA-GCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
* * *
13225064 TGAAGATAGCAAATCTTATCTCGCT-AATGTTGCAGTGGAGTGGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAA-GTTGCAGTGGAGTAGAT
* * *
13225109 TGAAGATAGCAAGTCTTATCCCCCTGAAGTTGCAGTGG-GATAGAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAG-TAGAT
* ** ** *
13225154 TGAAGATGGTGAA-CCTTATCTCCCTGGGGTTGCAGTGGAGCAGAT
1 TGAAGATAGCAAATCC-TATCTCCCTGAAGTTGCAGTGGAGTAGAT
** * * *
13225199 TGAAGCCA--ATAATCCTATCTCTCTAAAGTTGCAGTGGAGTGGAT
1 TGAAGATAGCA-AATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
13225243 T
1 T
13225244 AAAACATCCA
Statistics
Matches: 252, Mismatches: 56, Indels: 19
0.77 0.17 0.06
Matches are distributed among these distances:
44 30 0.12
45 146 0.58
46 76 0.30
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (45 bp):
TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGAT
Found at i:13225037 original size:91 final size:91
Alignment explanation
Indices: 13224882--13225143 Score: 404
Period size: 91 Copynumber: 2.9 Consensus size: 91
13224872 AACAGATCGG
* *
13224882 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTAGAGTGGATTGAAGATATGCAAGTCTTAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
* * *
13224947 CTCCATGAAGTTGCAGC-GAAGCAGAT
66 CTCCCTGAAGTTGCAGCAG-AGCAAAC
13224973 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
*
13225038 CTCCCTGAAGTTACAGCAGAGCAAAC
66 CTCCCTGAAGTTGCAGCAGAGCAAAC
* *
13225064 TGAAGATAGCAAATCTTATCTCGCT-AATGTTGCAGTGGAGTGGATTGAAGATA-GCAAGTCTTA
1 TGAAGATAGCAAATCCTATCTCCCTGAA-GTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTA
*
13225127 TCCCCCTGAAGTTGCAG
65 TCTCCCTGAAGTTGCAG
13225144 TGGGATAGAT
Statistics
Matches: 159, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
90 27 0.17
91 131 0.82
92 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (91 bp):
TGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAGATATGCAAGTCTTAT
CTCCCTGAAGTTGCAGCAGAGCAAAC
Found at i:13225134 original size:136 final size:136
Alignment explanation
Indices: 13224882--13225160 Score: 332
Period size: 136 Copynumber: 2.1 Consensus size: 136
13224872 AACAGATCGG
* * * *** * *
13224882 TGAAGATAGCAAATCCTATCTCCTTGAAGTTGCAGTAGAGTGGATTGAAGATATGCAAGTCTTAT
1 TGAAGATAGCAAATCCTATCTCCCTGAAGTTACAGCAGAGCAAACTGAAGATATGCAAATCTTAT
*
13224947 CTCCATGAAGTTGCAGCGAAGCAGATTGAAGATAGCAAATCCTATCTCCCTGAAGTTGCAGT-GG
66 CTCCATGAAGTTGCAGCGAAGCAGATTGAAGATAGCAAATCCTATCCCCCTGAAGTTGCAGTGGG
*
13225011 AGTGGAT
131 A-TAGAT
* *
13225018 TGAAGATATGCAAGTCTTATCTCCCTGAAGTTACAGCAGAGCAAACTGAAGATA-GCAAATCTTA
1 TGAAGATA-GCAAATCCTATCTCCCTGAAGTTACAGCAGAGCAAACTGAAGATATGCAAATCTTA
* * ** * *
13225082 TCTCGC-T-AATGTTGCAGTGGAGTGGATTGAAGATAGCAAGTCTTATCCCCCTGAAGTTGCAGT
65 TCTC-CATGAA-GTTGCAGCGAAGCAGATTGAAGATAGCAAATCCTATCCCCCTGAAGTTGCAGT
13225145 GGGATAGAT
128 GGGATAGAT
13225154 TGAAGAT
1 TGAAGAT
13225161 GGTGAACCTT
Statistics
Matches: 121, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
135 2 0.02
136 79 0.65
137 40 0.33
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (136 bp):
TGAAGATAGCAAATCCTATCTCCCTGAAGTTACAGCAGAGCAAACTGAAGATATGCAAATCTTAT
CTCCATGAAGTTGCAGCGAAGCAGATTGAAGATAGCAAATCCTATCCCCCTGAAGTTGCAGTGGG
ATAGAT
Found at i:13227130 original size:44 final size:44
Alignment explanation
Indices: 13226995--13227626 Score: 729
Period size: 44 Copynumber: 14.3 Consensus size: 44
13226985 GAAAAGCAGC
*
13226995 GGATCTTGTCTTCATGTATTGACATGAAGTAGATC-GAAGATAGC
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAGT
*** * *** *
13227039 GGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAGAT-GAT
1 GGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAGAGATAG-T
* *
13227084 GGATCTTGTCTTCATGCATTGACATGAAGTAGATCAGAGATAAT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
*
13227128 GGATCTTGTCTTCATGTATTGACATGAAGTAGATC-GAAGATAGC
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAGT
* **** * *** * *
13227172 GGATCTTATCTTCCCACACTGGTGGTGAAGTAAATC-GAAGATAAT
1 GGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAG-AGATAGT
*
13227217 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAAT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
* * *
13227261 GGATCTTATCTTCATGTATTGACATGAAGTAGATCAAAGATAGC
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
*
13227305 GGATCTTGTCTTCATGCATTGACATGAAGTAGATCAGAGATAGT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
*
13227349 GGATCTTGTCTTCATGTATTGACATGAAGTAGATC-GAAGATAGC
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAGT
* *
13227393 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAAT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
13227437 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
* *
13227481 GGATCTTGTCTTCATGTATTGACATGAAGTAGATC-GAAGATGGC
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGATAGT
* *** * *** *
13227525 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-GAAGATAAT
1 GGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAG-AGATAGT
13227570 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
* *
13227614 AGATCGTGTCTTC
1 GGATCTTGTCTTC
13227627 CCATACTAGT
Statistics
Matches: 493, Mismatches: 83, Indels: 24
0.82 0.14 0.04
Matches are distributed among these distances:
43 3 0.01
44 392 0.80
45 98 0.20
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (44 bp):
GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATAGT
Found at i:13227238 original size:133 final size:132
Alignment explanation
Indices: 13226995--13227626 Score: 730
Period size: 133 Copynumber: 4.8 Consensus size: 132
13226985 GAAAAGCAGC
* * *
13226995 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCGGATCTTGTCTTCCCATACTG
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCGGATCTTGTCTTCACACA-TG
*** * * *
13227060 GTGGTGAAGTAGATCAAAGATGATGGATCTTGTCTTCATGCATTGACATGAAGTAGATCAGAGAT
65 GACATGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGAT
13227125 AAT
130 AAT
* * *
13227128 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAGCGGATCTTATCTTCCCACACTG
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCGGATCTTGTCTTCACACA-TG
*** *
13227193 GTGGTGAAGTAAATC-GAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGA
65 GACATGAAGTAGATCAG-AGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGA
13227257 TAAT
129 TAAT
* ** *
13227261 GGATCTTATCTTCATGTATTGACATGAAGTAGATCAAAGATAGCGGATCTTGTCTTCATGCATTG
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCGGATCTTGTCTTCACACATGG
*
13227326 ACATGAAGTAGATCAGAGATAGTGGATCTTGTCTTCATGTATTGACATGAAGTAGATC-GAAGAT
66 ACATGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGAT
**
13227390 AGC
130 AAT
** *** *
13227393 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAATGGATCTTGTCTTCATGTATTG
1 GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCGGATCTTGTCTTCACACATGG
*
13227458 ACATGAAGTAGATCAGAGATAGTGGATCTTGTCTTCATGTATTGACATGAAGTAGATC-GAAGAT
66 ACATGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAG-AGAT
***
13227522 GGC
130 AAT
* *** * *** * ** *** *
13227525 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATT
1 GGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCAAAGATAGCGGATCTTGTCTTCACACATG
* * *
13227590 GACATGAAGTAGATCAGAGATAGTAGATCGTGTCTTC
65 GACATGAAGTAGATCAGAGATAATGGATCTTGTCTTC
13227627 CCATACTAGT
Statistics
Matches: 459, Mismatches: 36, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
131 1 0.00
132 199 0.43
133 259 0.56
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (132 bp):
GGATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATAGCGGATCTTGTCTTCACACATGG
ACATGAAGTAGATCAGAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCAGAGATA
AT
Found at i:13230139 original size:40 final size:40
Alignment explanation
Indices: 13230095--13230238 Score: 128
Period size: 40 Copynumber: 3.5 Consensus size: 40
13230085 TTTCGACACT
*
13230095 TATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCC
1 TATCTTCCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCC
* ** ** * * *
13230135 TATC-TCCTTGAAGTTGCAGTGGAGTGGATTAAAACATCCAAATCT
1 TATCTTCC-TGAAGTTGCAG-AGAGCAGA-T--CGCAT-CTAGTCC
*
13230180 TATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCC
1 TATCTTCCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCC
*
13230220 TATCTCCCTGAAGTTGCAG
1 TATCTTCCTGAAGTTGCAG
13230239 TGGAGTGGAT
Statistics
Matches: 77, Mismatches: 20, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
39 2 0.03
40 36 0.47
41 8 0.10
42 1 0.01
43 1 0.01
44 8 0.10
45 19 0.25
46 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (40 bp):
TATCTTCCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCC
Found at i:13230236 original size:85 final size:85
Alignment explanation
Indices: 13230093--13230275 Score: 348
Period size: 85 Copynumber: 2.2 Consensus size: 85
13230083 GGTTTCGACA
*
13230093 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCTTGAAGTTGCAGTGGA
1 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCCTGAAGTTGCAGTGGA
13230158 GTGGATTAAAACATCCAAAT
66 GTGGATTAAAACATCCAAAT
13230178 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCCTGAAGTTGCAGTGGA
1 CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCCTGAAGTTGCAGTGGA
*
13230243 GTGGATTAAAACATCCAGAT
66 GTGGATTAAAACATCCAAAT
13230263 CTTATCTTTCTGA
1 CTTATCTTTCTGA
13230276 TGTCTTATCT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 96 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (85 bp):
CTTATCTTTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCCTATCTCCCTGAAGTTGCAGTGGA
GTGGATTAAAACATCCAAAT
Found at i:13230315 original size:61 final size:61
Alignment explanation
Indices: 13230220--13230336 Score: 234
Period size: 61 Copynumber: 1.9 Consensus size: 61
13230210 CATCTAGTCC
13230220 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATCCAGATCTTATCTTTCTGATGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATCCAGATCTTATCTTTCTGATGTCT
13230281 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATCCAGATCTTATCTTTCTGA
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATCCAGATCTTATCTTTCTGA
13230337 AGTTGCAGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (61 bp):
TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACATCCAGATCTTATCTTTCTGATGTCT
Found at i:13231832 original size:3 final size:3
Alignment explanation
Indices: 13231813--13231863 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
13231803 GTTATATTGC
* * * *
13231813 ATT ATT AGT ATT -GT ATT ATTT ATT ATT ATT TTT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
13231858 ATT ATT
1 ATT ATT
13231864 TCTATACATA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 1 0.03
3 34 0.89
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:13231935 original size:23 final size:24
Alignment explanation
Indices: 13231881--13231939 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
13231871 ATATACGCAC
13231881 GTATATATTTTTTATAACATATAT
1 GTATATATTTTTTATAACATATAT
* ** *
13231905 ATGCATATTTTTTTTAA-ATATAT
1 GTATATATTTTTTATAACATATAT
13231928 GTATATATTTTT
1 GTATATATTTTT
13231940 AGACTTTTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (24 bp):
GTATATATTTTTTATAACATATAT
Found at i:13231960 original size:30 final size:30
Alignment explanation
Indices: 13231914--13231970 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
13231904 TATGCATATT
* *
13231914 TTTTTTAAATATATGTATATATTTTTAGAC
1 TTTTATAAATACATGTATATATTTTTAGAC
13231944 TTTTATAAATACATGTATATATTTTTA
1 TTTTATAAATACATGTATATATTTTTA
13231971 TACATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (30 bp):
TTTTATAAATACATGTATATATTTTTAGAC
Found at i:13231975 original size:18 final size:18
Alignment explanation
Indices: 13231952--13231990 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
13231942 ACTTTTATAA
*
13231952 ATACATGTATATATTTTT
1 ATACATATATATATTTTT
13231970 ATACATATATATATTTTT
1 ATACATATATATATTTTT
13231988 ATA
1 ATA
13231991 TTTTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (18 bp):
ATACATATATATATTTTT
Found at i:13234619 original size:41 final size:42
Alignment explanation
Indices: 13234518--13234676 Score: 121
Period size: 41 Copynumber: 3.7 Consensus size: 42
13234508 ATATCGAACA
* * * *
13234518 ATGCCAACGTCCCAGAC-GTGGTCTTACATGCTAGCTCATAT-CG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACG-TA-ATCAAATACG
*
13234561 ATGCCACTGTCCCAGACAGGGTCTTACACG-AATCAAATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATACG
* * *
13234602 ATGCCAATGTCCTAGACATGGTCTTATACGTAATCACATATATCG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCA-A-ATA-CG
* *
13234647 ATGAC-ATCATCCCAGAC-GTGGTCTTACACG
1 ATGCCAAT-GTCCCAGACAG-GGTCTTACACG
13234677 AGAACACATA
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
40 5 0.05
41 29 0.31
42 5 0.05
43 26 0.28
44 6 0.06
45 23 0.24
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATACG
Found at i:13235602 original size:28 final size:31
Alignment explanation
Indices: 13235570--13235628 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
13235560 TGTTTTGTTT
13235570 TTATTATAATAA-CATTAT-AAT-ATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
* *
13235598 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
13235629 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 3 0.12
31 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATAATAACCATTATAAATAATATAAA
Found at i:13236756 original size:30 final size:30
Alignment explanation
Indices: 13236695--13236756 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
13236685 TTACGGTCGG
* * * *
13236695 TAAAATTTTAATTTAATACTTTATAATTTA
1 TAAAATTTTAAATTAATAATGTATAAATTA
13236725 TAAAATTTTAAATTAATAATGGTA-AAATTA
1 TAAAATTTTAAATTAATAAT-GTATAAATTA
13236755 TA
1 TA
13236757 TTTTGACCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (30 bp):
TAAAATTTTAAATTAATAATGTATAAATTA
Found at i:13238056 original size:51 final size:50
Alignment explanation
Indices: 13237922--13238118 Score: 202
Period size: 51 Copynumber: 3.9 Consensus size: 50
13237912 AGAGAAAATG
** *
13237922 ATGGTCATGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TG
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GATAGTA
* * *
13237971 ATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGT-
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GATAGTA
* * * * *
13238022 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCG-ATAGTA
* * *
13238074 ATGGTCATATGTGTAGTACTATGTGCAGGCTACTATGTATACCGA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGA
13238119 ACATCATTGA
Statistics
Matches: 121, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
49 2 0.02
50 40 0.33
51 77 0.64
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGATAGTA
Found at i:13246336 original size:19 final size:19
Alignment explanation
Indices: 13246285--13246369 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 19
13246275 ATTACAAAAA
* * *
13246285 AAAAATCAAAGTAATTTTC
1 AAAATTCAAAATAATTTTT
*
13246304 AAAATTTGAAAATAATTTTT
1 AAAA-TTCAAAATAATTTTT
*
13246324 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
13246342 AGAAATTCTAAAATTTATATTTTT
1 A-AAATTC-AAAA--TA-ATTTTT
13246366 AAAA
1 AAAA
13246370 AAAATTATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
18 6 0.12
19 17 0.33
20 19 0.37
22 1 0.02
23 3 0.06
24 6 0.12
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:13246357 original size:18 final size:19
Alignment explanation
Indices: 13246312--13246360 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
13246302 TCAAAATTTG
*
13246312 AAAATAATTTTTA-AAATTC
1 AAAAT-ATTTATAGAAATTC
13246331 AAAATATTTATAGAAATTC
1 AAAATATTTATAGAAATTC
*
13246350 TAAA-ATTTATA
1 AAAATATTTATA
13246361 TTTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATATTTATAGAAATTC
Found at i:13246747 original size:21 final size:21
Alignment explanation
Indices: 13246723--13246762 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13246713 ACCTTTTCTA
13246723 AAGTTAAAAGCCAAAACTATC
1 AAGTTAAAAGCCAAAACTATC
*
13246744 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGCCAAAACTA
13246763 CGTTGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.12, T:0.17
Consensus pattern (21 bp):
AAGTTAAAAGCCAAAACTATC
Found at i:13249894 original size:18 final size:19
Alignment explanation
Indices: 13249856--13249898 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
13249846 TCTAAATGAA
13249856 TTCATTTCTCATTTTTATT
1 TTCATTTCTCATTTTTATT
13249875 TTCATTTCT-ATTTTCT-TT
1 TTCATTTCTCATTTT-TATT
13249893 TTCATT
1 TTCATT
13249899 CTGAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (19 bp):
TTCATTTCTCATTTTTATT
Found at i:13253870 original size:13 final size:13
Alignment explanation
Indices: 13253852--13253876 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13253842 TCTAAAATGG
13253852 TTCTTCTTTCTTC
1 TTCTTCTTTCTTC
13253865 TTCTTCTTTCTT
1 TTCTTCTTTCTT
13253877 AAGTGGTATT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTCTTTCTTC
Found at i:13261220 original size:31 final size:32
Alignment explanation
Indices: 13261141--13261221 Score: 78
Period size: 33 Copynumber: 2.5 Consensus size: 32
13261131 AGATTAATTT
* * *
13261141 ATATTTTATGTATCATTATATTAAATTATTTAA
1 ATATATTATGTAT-AATATATTAAATTATTAAA
13261174 ATATAATTTAT-TATAATAT-TTAAAATT-TTAAA
1 ATAT-A-TTATGTATAATATATT-AAATTATTAAA
13261206 ATATATTATGTATAAT
1 ATATATTATGTATAAT
13261222 TAATTTTACA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
30 4 0.10
31 7 0.17
32 10 0.24
33 13 0.32
34 3 0.07
35 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (32 bp):
ATATATTATGTATAATATATTAAATTATTAAA
Found at i:13261247 original size:26 final size:26
Alignment explanation
Indices: 13261197--13261249 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
13261187 TAATATTTAA
*
13261197 AATTTTAAAATATATTATGTATAATT
1 AATTTTAAAATATATTATATATAATT
13261223 AATTTTACAAATA-ATT-TATACTAATT
1 AATTTTA-AAATATATTATATA-TAATT
13261249 A
1 A
13261250 CTCAAGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.12
26 16 0.67
27 5 0.21
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (26 bp):
AATTTTAAAATATATTATATATAATT
Found at i:13268105 original size:27 final size:27
Alignment explanation
Indices: 13268075--13268133 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
13268065 TAGAGATACA
13268075 TATTTACAAATAAACAGCGCGTGCCTC
1 TATTTACAAATAAACAGCGCGTGCCTC
13268102 TATTTACAAATAAACAGCGCGTGCCTC
1 TATTTACAAATAAACAGCGCGTGCCTC
13268129 TATTT
1 TATTT
13268134 CTTACAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (27 bp):
TATTTACAAATAAACAGCGCGTGCCTC
Found at i:13269386 original size:20 final size:20
Alignment explanation
Indices: 13269361--13269398 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13269351 AATCAAGGAA
13269361 GCAATCAAGAAGGTTGATAT
1 GCAATCAAGAAGGTTGATAT
*
13269381 GCAATCAAGGAGGTTGAT
1 GCAATCAAGAAGGTTGAT
13269399 TGGATTGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GCAATCAAGAAGGTTGATAT
Found at i:13277575 original size:20 final size:20
Alignment explanation
Indices: 13277552--13277590 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13277542 CAATTTAAAA
13277552 TATAAAAAATTATTAATATG
1 TATAAAAAATTATTAATATG
* **
13277572 TATATAATTTTATTAATAT
1 TATAAAAAATTATTAATAT
13277591 ATGTAAAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAAATTATTAATATG
Found at i:13277712 original size:20 final size:20
Alignment explanation
Indices: 13277687--13277726 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13277677 AATATTTTCA
13277687 GTAAATCATTTTCCAGAAAT
1 GTAAATCATTTTCCAGAAAT
13277707 GTAAATCATTTTCCAGAAAT
1 GTAAATCATTTTCCAGAAAT
13277727 CATTTTCCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (20 bp):
GTAAATCATTTTCCAGAAAT
Found at i:13277727 original size:34 final size:33
Alignment explanation
Indices: 13277676--13277739 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
13277666 AAACACCAGA
13277676 AAATATTTTCAGTAAATCATTTTCCAGAAATGT
1 AAATATTTTCAGTAAATCATTTTCCAGAAATGT
*
13277709 AAATCATTTTCCAG-AAATCATTTTCCGGAAA
1 AAAT-ATTTT-CAGTAAATCATTTTCCAGAAA
13277740 ACATTTTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.14
34 21 0.75
35 3 0.11
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (33 bp):
AAATATTTTCAGTAAATCATTTTCCAGAAATGT
Found at i:13277728 original size:14 final size:14
Alignment explanation
Indices: 13277709--13277746 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
13277699 CCAGAAATGT
13277709 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
13277723 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
13277737 AAAACATTTT
1 AAATCATTTT
13277747 ACTGGCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:13280511 original size:32 final size:31
Alignment explanation
Indices: 13280473--13280544 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 31
13280463 TATAAAAATT
13280473 AAATCAAAACATTTAAAGTATAAAATTACATA-
1 AAATCAAAA-ATTT-AAGTATAAAATTACATAC
* *
13280505 AAATC-AAAATTTATGTATAATATTACATATC
1 AAATCAAAAATTTAAGTATAAAATTACATA-C
13280536 AAATCAAAA
1 AAATCAAAA
13280545 TTCATTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 15 0.43
30 4 0.11
31 8 0.23
32 8 0.23
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.31
Consensus pattern (31 bp):
AAATCAAAAATTTAAGTATAAAATTACATAC
Found at i:13282046 original size:17 final size:17
Alignment explanation
Indices: 13282020--13282053 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13282010 TATGGTCTAT
*
13282020 ATATAGTATACTAAAAA
1 ATATAGTATAATAAAAA
*
13282037 ATATATTATAATAAAAA
1 ATATAGTATAATAAAAA
13282054 TTTAAGTCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
ATATAGTATAATAAAAA
Found at i:13282860 original size:9 final size:9
Alignment explanation
Indices: 13282846--13282870 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
13282836 TGGAATTAAA
13282846 AAATATATT
1 AAATATATT
13282855 AAATATATT
1 AAATATATT
13282864 AAATATA
1 AAATATA
13282871 AAAATATAAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAATATATT
Found at i:13284224 original size:18 final size:18
Alignment explanation
Indices: 13284201--13284243 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
13284191 TAGCTTTGCT
*
13284201 TCGACTGCTGTGGAACCG
1 TCGACTGCCGTGGAACCG
13284219 TCGACTGCCGTGGAACCG
1 TCGACTGCCGTGGAACCG
*
13284237 TTGACTG
1 TCGACTG
13284244 GAAAAGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.28, G:0.33, T:0.23
Consensus pattern (18 bp):
TCGACTGCCGTGGAACCG
Found at i:13307131 original size:189 final size:189
Alignment explanation
Indices: 13306811--13307378 Score: 1100
Period size: 189 Copynumber: 3.0 Consensus size: 189
13306801 TATCGTGACC
* * *
13306811 AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCGTCCAGTGACCTTTGT
1 AAACTCTCCCTAATAACATACTATTACGAAAGCTAATCAATCAGTGCTCATCTAGTGACCTTTGT
*
13306876 GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
66 GTTACTCTTATATGATACTTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
13306941 TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
131 TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
13307000 AAACTCTCCCTAATAACATACTATTACGAAAGCTAATCAATCAGTGCTCATCTAGTGACCTTTGT
1 AAACTCTCCCTAATAACATACTATTACGAAAGCTAATCAATCAGTGCTCATCTAGTGACCTTTGT
13307065 GTTACTCTTATATGATACTTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
66 GTTACTCTTATATGATACTTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
13307130 TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
131 TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
13307189 AAACTCTCCCTAATAACATACTATTACGAAAGCTAATCAATCAGTGCTCATCTAGTGACCTTTGT
1 AAACTCTCCCTAATAACATACTATTACGAAAGCTAATCAATCAGTGCTCATCTAGTGACCTTTGT
13307254 GTTACTCTTATATGATACTTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
66 GTTACTCTTATATGATACTTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
13307319 TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
131 TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
13307378 A
1 A
13307379 TTAAGTCATG
Statistics
Matches: 375, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 375 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (189 bp):
AAACTCTCCCTAATAACATACTATTACGAAAGCTAATCAATCAGTGCTCATCTAGTGACCTTTGT
GTTACTCTTATATGATACTTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
Found at i:13309747 original size:43 final size:43
Alignment explanation
Indices: 13309621--13309726 Score: 151
Period size: 43 Copynumber: 2.5 Consensus size: 43
13309611 TGTATCAATA
* *
13309621 GATAAATCAAAATAAATATACTGGCACACATAGTGCATCATCG
1 GATAAATCGAAACAAATATACTGGCACACATAGTGCATCATCG
* * *
13309664 GATTAACCGAAGC-AATCATACTGGCACACATAGTGCATCATCG
1 GATAAATCGAAACAAAT-ATACTGGCACACATAGTGCATCATCG
13309707 GATAAATCGAAACAAATATA
1 GATAAATCGAAACAAATATA
13309727 TTGACATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 3 0.06
43 47 0.89
44 3 0.06
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (43 bp):
GATAAATCGAAACAAATATACTGGCACACATAGTGCATCATCG
Found at i:13311635 original size:19 final size:20
Alignment explanation
Indices: 13311611--13311649 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
13311601 AATTCATTGT
*
13311611 ATAATTTAA-AAATAAAATA
1 ATAATTGAAGAAATAAAATA
*
13311630 ATAATTGAAGTAATAAAATA
1 ATAATTGAAGAAATAAAATA
13311650 TATTTATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
ATAATTGAAGAAATAAAATA
Found at i:13314912 original size:14 final size:14
Alignment explanation
Indices: 13314893--13314919 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13314883 AGATGTCGAT
13314893 AATGGCAATTGGAC
1 AATGGCAATTGGAC
13314907 AATGGCAATTGGA
1 AATGGCAATTGGA
13314920 TAATCACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (14 bp):
AATGGCAATTGGAC
Found at i:13316107 original size:156 final size:156
Alignment explanation
Indices: 13315813--13316127 Score: 479
Period size: 156 Copynumber: 2.0 Consensus size: 156
13315803 TACCTTGTAA
* * * *
13315813 GTATATGAAAATCCACTGAATTGTTTTTCAATGTTCTTTATTGGGATTCACCATGTATCCACTAA
1 GTATATGAAAATCCACTAAATTATTTTTCAATATTCTTTATCGGGATTCACCATGTATCCACTAA
* * *
13315878 CCACACTAACTGCATATGACAAATCTAGACGTAAGCAAACCATAGTGTACATGAGAGATCCCACT
66 CCACACTAACTGCATATGACAAATCTAGACATAAGCAAACCATAGTATACACGAGAGATCCCACT
*
13315943 GCTCTAGAATATGGAACACGTGACAT
131 GCTCTAGAATATGGAACACGTAACAT
* * * *
13315969 GTATCTGAAAATTCACTAAATTATTTTTCAATATTCTTTATCGGGATTCGCCATGTATCTACTAA
1 GTATATGAAAATCCACTAAATTATTTTTCAATATTCTTTATCGGGATTCACCATGTATCCACTAA
* *
13316034 CCACACTAACTGCATATGACAAATCTGGACATAAGCAAACCATAGTATACACGAGAGATCCCATT
66 CCACACTAACTGCATATGACAAATCTAGACATAAGCAAACCATAGTATACACGAGAGATCCCACT
*
13316099 G-TATTAGAATATGGAACACGTAACAT
131 GCT-CTAGAATATGGAACACGTAACAT
13316125 GTA
1 GTA
13316128 GTCAATCTCA
Statistics
Matches: 143, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
155 1 0.01
156 142 0.99
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (156 bp):
GTATATGAAAATCCACTAAATTATTTTTCAATATTCTTTATCGGGATTCACCATGTATCCACTAA
CCACACTAACTGCATATGACAAATCTAGACATAAGCAAACCATAGTATACACGAGAGATCCCACT
GCTCTAGAATATGGAACACGTAACAT
Found at i:13321782 original size:6 final size:6
Alignment explanation
Indices: 13321771--13321837 Score: 59
Period size: 6 Copynumber: 11.2 Consensus size: 6
13321761 CAACACATAG
* * *
13321771 AATAAA AATAAA AATAATA AA-AATA AA-AAT AATAAA AATTAT AAT-AA
1 AATAAA AATAAA AATAA-A AATAA-A AATAAA AATAAA AATAAA AATAAA
13321818 AATAAA AATAAA ATATAAA A
1 AATAAA AATAAA A-ATAAA A
13321838 CTGAAAACCT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
5 6 0.12
6 37 0.71
7 9 0.17
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
AATAAA
Found at i:13321791 original size:9 final size:9
Alignment explanation
Indices: 13321777--13321828 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
13321767 ATAGAATAAA
13321777 AATAAAAAT
1 AATAAAAAT
13321786 AAT--AAA-
1 AATAAAAAT
13321792 AATAAAAAT
1 AATAAAAAT
13321801 AATAAAAAT
1 AATAAAAAT
* *
13321810 TATAATAA-
1 AATAAAAAT
13321818 AATAAAAAT
1 AATAAAAAT
13321827 AA
1 AA
13321829 AATATAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
6 3 0.09
7 3 0.09
8 9 0.26
9 20 0.57
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
AATAAAAAT
Found at i:13321791 original size:15 final size:15
Alignment explanation
Indices: 13321771--13321835 Score: 87
Period size: 15 Copynumber: 4.1 Consensus size: 15
13321761 CAACACATAG
13321771 AATAAAAATAAAAAT
1 AATAAAAATAAAAAT
13321786 AATAAAAATAAAAAT
1 AATAAAAATAAAAAT
13321801 AATAAAAATTATAATAA-
1 AATAAAAA-TA-AA-AAT
13321818 AATAAAAATAAAATAT
1 AATAAAAATAAAA-AT
13321834 AA
1 AA
13321836 AACTGAAAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.02
15 26 0.58
16 6 0.13
17 10 0.22
18 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAAAAATAAAAAT
Found at i:13321834 original size:21 final size:22
Alignment explanation
Indices: 13321771--13321835 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 22
13321761 CAACACATAG
13321771 AATAAAAATAAAAATAATAA-A-
1 AATAAAAATAAAAATAA-AATAT
* *
13321792 AATAAAAATAATAA-AAATTAT
1 AATAAAAATAAAAATAAAATAT
13321813 AAT-AAAATAAAAATAAAATAT
1 AATAAAAATAAAAATAAAATAT
13321834 AA
1 AA
13321836 AACTGAAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 1 0.03
20 12 0.32
21 24 0.65
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (22 bp):
AATAAAAATAAAAATAAAATAT
Found at i:13331083 original size:50 final size:50
Alignment explanation
Indices: 13331015--13331205 Score: 159
Period size: 50 Copynumber: 3.7 Consensus size: 50
13331005 TACTACCTAT
* * * ** * *
13331015 GCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAGGTGCCCAT
1 GCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAAC
* ** * *
13331065 GCCCTGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAAC
1 GCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAAC
* * * *
13331115 GCCATGTCCTAGACATAGTCTTACATCGGACCTCTCATAATCTCAATGATGCCAAT
1 GCCATGTCCTAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GGTGCCAAC
*
13331171 GCCATGTTCC-AGACATGGTCTTACATGGGATCTCT
1 GCCATG-TCCTAGACATGGTCTTACATGGGACCTCT
13331206 TTACCCAAAT
Statistics
Matches: 110, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
50 71 0.65
53 1 0.01
56 35 0.32
57 3 0.03
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (50 bp):
GCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAAC
Found at i:13335510 original size:16 final size:16
Alignment explanation
Indices: 13335486--13335516 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13335476 TCACCAAAGT
*
13335486 GAAGGGATGATGGTTG
1 GAAGAGATGATGGTTG
13335502 GAAGAGATGATGGTT
1 GAAGAGATGATGGTT
13335517 TTAGGGATGA
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:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (16 bp):
GAAGAGATGATGGTTG
Found at i:13339677 original size:24 final size:24
Alignment explanation
Indices: 13339627--13339688 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
13339617 ACCCCTCATT
*
13339627 TTCATCTTCATCTCGACCCTCACC
1 TTCATCTTCATCTCGACCCCCACC
** **
13339651 TTCATCTTCATCTCTTCCCCCGTC
1 TTCATCTTCATCTCGACCCCCACC
*
13339675 TTCGTCTTCATCTC
1 TTCATCTTCATCTC
13339689 CTTTTTTCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.11, C:0.44, G:0.05, T:0.40
Consensus pattern (24 bp):
TTCATCTTCATCTCGACCCCCACC
Found at i:13340427 original size:20 final size:18
Alignment explanation
Indices: 13340380--13340430 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
13340370 CAAGATAAGC
13340380 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
13340397 ATTAAGA-TAATCATTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
13340417 ATTAAATTAATATT
1 ATTAAATTAATATT
13340431 ATTTTTGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
17 8 0.28
18 3 0.10
19 3 0.10
20 15 0.52
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:13347977 original size:585 final size:581
Alignment explanation
Indices: 13346871--13348041 Score: 2225
Period size: 585 Copynumber: 2.0 Consensus size: 581
13346861 TCAATTCAAT
13346871 AATCTCTTAATCAATATATTTCATAATATACAAAATCAATCCATTTCAAATCCACTATTAATTCA
1 AATCTCTTAATCAATATATTTCATAATATACAAAATCAATCCATTTCAAATCCACTATTAATTCA
* *
13346936 ATTTAATCTCAAACTACCAAAGTACTCACCTCAAATGCTTACCATATGCAAATAATTTAAATATG
66 ATTCAATCTCAAACTAACAAAGTACTCACCTCAAATGCTTACCATATGCAAATAATTTAAATATG
13347001 CAACATTCTACTAGTTAATTCGAATTATAGAAACACAAACCGTGAATTTCGAGCTATTCAACGTC
131 CAACATTCTACTAGTTAATTCGAATTATAGAAACACAAACCGTGAATTTCGAGCTATTCAACGTC
13347066 GATTTTATCATTTCCCTTTTTACTCGAGGATTCCGGTACGACATTAGCTAAGGAATAAATTAAAA
196 GATTTTATCATTTCCCTTTTTACTCGAGGATTCCGGTACGACATTAGCTAAGGAATAAATTAAAA
*
13347131 TACGTTAATATTACACAATTAAATTTCACATTGAATTTCAATTTTTACACTATATTTTGCTTATT
261 TACGTTAATATTACACAACTAAATTTCACATTGAATTTCAATTTTTACACTATATTTTGCTTATT
* *
13347196 TTTCAATTTAGTCCCTAAACTGAGATTAGTTTTTAACCTTCATATTTAAATTTATACTTTTATAC
326 TTTCAATTTAGTCCCTAAACTGAGACTAGTTTTTAACCTTCACATTTAAATTTATACTTTTATAC
13347261 TAATTTCACTCTAACTAAATTTAGCTTCCTCTTTTCCAATTCGACCTCTTAATTTCTAATTTTTC
391 TAATTTCACTCTAACTAAATTTAGCTTCCTCTTTTCCAATTCGACCTCTTAATTTCTAATTTTTC
*
13347326 ACAATTTAGTCCTTATTACTCAAAATTAACAATTTATTCCATAATTTAGTCATTTTCCATTTTCA
456 ACAATTTAGTCATTATTACTCAAAATTAACAATTTATTCCATAATTTAGTCATTTTCCATTTTCA
13347391 ACTTAAAAATCTATCTATTTAATCCCTAATACTTAAACTATTCAACAATGTCAACACTTAA
521 ACTTAAAAATCTATCTATTTAATCCCTAATACTTAAACTATTCAACAATGTCAACACTTAA
13347452 AATCTCTTAATCAATATATTTCATAATATACAAAATCAATCCATTTCAAATCCACTATTAATTCA
1 AATCTCTTAATCAATATATTTCATAATATACAAAATCAATCCATTTCAAATCCACTATTAATTCA
13347517 ATTCAATCTCAAACTAACAAAGTACTCACCTCAAATGCTTACCATATGCAAATAATTTAAATATG
66 ATTCAATCTCAAACTAACAAAGTACTCACCTCAAATGCTTACCATATGCAAATAATTTAAATATG
13347582 CAACATTCTACTAGTTAATTCGAATTATAGAAACACAAACCGTGAATTTCGAGCTATTCAACGTC
131 CAACATTCTACTAGTTAATTCGAATTATAGAAACACAAACCGTGAATTTCGAGCTATTCAACGTC
*
13347647 GATTTTATCCTTTCCCTTTTTACTCGAGGATTCCGGTACGACATTAGCTAAGGAATACAACAATT
196 GATTTTATCATTTCCCTTTTTACTCGAGGATTCCGGTACGACATTAGCTAAGGAAT---A-AATT
13347712 AAAATACGTTAATATTACACAACTAAATTTCACATTGAATTTCAATTTTTACACTATATTTTGCT
257 AAAATACGTTAATATTACACAACTAAATTTCACATTGAATTTCAATTTTTACACTATATTTTGCT
*
13347777 TATTTTTCAATTTAGTCCCTAAACTGAGACTAGTTTTTAACCTTCACATTTAAATTTATATTTTT
322 TATTTTTCAATTTAGTCCCTAAACTGAGACTAGTTTTTAACCTTCACATTTAAATTTATACTTTT
13347842 ATACTAATTTCACTCTAACTAAATTTAGCTTCCTCTTTTCCAATTCGACCTCTTAATTTCTAATT
387 ATACTAATTTCACTCTAACTAAATTTAGCTTCCTCTTTTCCAATTCGACCTCTTAATTTCTAATT
13347907 TTTCACAATTTAGTCATTATTACTCAAAATTAACAATTTATTCCATAATTTAGTCATTTTCCATT
452 TTTCACAATTTAGTCATTATTACTCAAAATTAACAATTTATTCCATAATTTAGTCATTTTCCATT
*
13347972 TTCAACTTAAAAATCTATCTATTTAATCCTTAATACTTAAACTATTCAACAATGTCAACACTTAA
517 TTCAACTTAAAAATCTATCTATTTAATCCCTAATACTTAAACTATTCAACAATGTCAACACTTAA
13348037 AATCT
1 AATCT
13348042 TGAACAATAC
Statistics
Matches: 577, Mismatches: 9, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
581 248 0.43
584 1 0.00
585 328 0.57
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (581 bp):
AATCTCTTAATCAATATATTTCATAATATACAAAATCAATCCATTTCAAATCCACTATTAATTCA
ATTCAATCTCAAACTAACAAAGTACTCACCTCAAATGCTTACCATATGCAAATAATTTAAATATG
CAACATTCTACTAGTTAATTCGAATTATAGAAACACAAACCGTGAATTTCGAGCTATTCAACGTC
GATTTTATCATTTCCCTTTTTACTCGAGGATTCCGGTACGACATTAGCTAAGGAATAAATTAAAA
TACGTTAATATTACACAACTAAATTTCACATTGAATTTCAATTTTTACACTATATTTTGCTTATT
TTTCAATTTAGTCCCTAAACTGAGACTAGTTTTTAACCTTCACATTTAAATTTATACTTTTATAC
TAATTTCACTCTAACTAAATTTAGCTTCCTCTTTTCCAATTCGACCTCTTAATTTCTAATTTTTC
ACAATTTAGTCATTATTACTCAAAATTAACAATTTATTCCATAATTTAGTCATTTTCCATTTTCA
ACTTAAAAATCTATCTATTTAATCCCTAATACTTAAACTATTCAACAATGTCAACACTTAA
Found at i:13350126 original size:16 final size:16
Alignment explanation
Indices: 13350105--13350135 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13350095 AACATATATA
13350105 AAAAAATAATTACATG
1 AAAAAATAATTACATG
13350121 AAAAAATAATTACAT
1 AAAAAATAATTACAT
13350136 CCTAAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAAATAATTACATG
Found at i:13352037 original size:260 final size:260
Alignment explanation
Indices: 13351558--13352185 Score: 638
Period size: 260 Copynumber: 2.4 Consensus size: 260
13351548 AGTCCACCGC
* *
13351558 AACTTCAGAGAGATAAGATTTGCCAACTTTAATGTGCCTCACTGCAACTTCAGGAGGATAATACT
1 AACTTCAGAGAGATAAGATTTGCCAACTTTAATATGCCTCACTGCAACTTCAGGAGGATAAGACT
* * *
13351623 TGCTGATTTAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACCTAGTTTGCTCCAC
66 TGCTCATTTAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTAACTAGTCTGCTCCAC
* * * * * * * *
13351688 TGCAACTTCAGGAGGATGAGGCTTGCTTACCTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGA
131 TACAACTTCAGGAGGATAAGACTAGCATACCGAGTCTGCTCCACTGCAACTTCAGAGAGATAAGA
* * *
13351753 CTAGATGCGATCCGCTCTCTGCAACTTCAGAGAGATAATATCTGAGATTTTAATCCACTTACTGT
196 CTAGATGCAACCCGCTCACTGCAACTTCAGAGAGATAATATCTGAGATTTTAATCCACTTACTGT
* * * *
13351818 AACTTCAGCGAGATAGGA-TTGTCGACTTTAATATG-CTCCACTGCAACTTCAGG-GAGATAAGA
1 AACTTCAGAGAGATAAGATTTGCCAACTTTAATATGCCT-CACTGCAACTTCAGGAG-GATAAGA
* * *
13351880 TTTGC-CATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCT
64 CTTGCTCAT-TT-AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTAACTAGTCTGCT
* *
13351944 CCACTACAACTTCA-GAGAGATAAGACTAG-AT-GCGA-TCTGCT-CTCTGCAACTTCAGAGAGA
127 CCACTACAACTTCAGGAG-GATAAGACTAGCATACCGAGTCTGCTCCACTGCAACTTCAGAGAGA
* ** * * *
13352004 TAAGATCTAAGGTTTTAACCCGCTCCACTGCAACTTCAGTGAGATAGGAT-TACCG-G-CTTTAA
191 TAAGA-CT-A-GATGCAACCCGCT-CACTGCAACTTCAGAGAGATA--ATAT-CTGAGATTTTAA
** * * *
13352066 TCTGCTCCATTGC
249 TCCACT-TACTGT
* * * * * *
13352079 AACTTCAGAGAGATAAGATTTGCCATCTTCAGTCTACCTCGCTGCAACTTCAGGAGGATAAGACT
1 AACTTCAGAGAGATAAGATTTGCCAACTTTAATATGCCTCACTGCAACTTCAGGAGGATAAGACT
*
13352144 TGCTCAGTTAGTCTG-CTCCACTGCAACTTCA-G-GGATAAGACT
66 TGCTCATTTAGTCTGCCT-CACTGCAACTTCAGGAGGATAAGACT
13352186 AGATGCGATC
Statistics
Matches: 301, Mismatches: 49, Indels: 37
0.78 0.13 0.10
Matches are distributed among these distances:
256 21 0.07
257 8 0.03
258 8 0.03
259 63 0.21
260 116 0.39
261 39 0.13
262 41 0.14
263 5 0.02
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (260 bp):
AACTTCAGAGAGATAAGATTTGCCAACTTTAATATGCCTCACTGCAACTTCAGGAGGATAAGACT
TGCTCATTTAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTAACTAGTCTGCTCCAC
TACAACTTCAGGAGGATAAGACTAGCATACCGAGTCTGCTCCACTGCAACTTCAGAGAGATAAGA
CTAGATGCAACCCGCTCACTGCAACTTCAGAGAGATAATATCTGAGATTTTAATCCACTTACTGT
Found at i:13352136 original size:217 final size:217
Alignment explanation
Indices: 13351687--13352833 Score: 1856
Period size: 217 Copynumber: 5.3 Consensus size: 217
13351677 GTTTGCTCCA
* * ** *
13351687 CTGCAACTTCAGGAGGATGAGGCTTGCTTACCTAGTCTGCTCCACTGTAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
* * * * * * *
13351752 ACTAGATGCGATCCGCTCTCTGCAACTTCAGAGAGATAATATCTGAGATTTTAATCCACT-TACT
66 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACT
* ** * *
13351816 GTAACTTCAGCGAGATAGGATTGTCGACTTTAATATGCTCCACTGCAACTTCAGGGAGATAAGAT
131 GCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
13351881 TTGCCATCTTCAGTCTGCCTCG
196 TTGCCATCTTCAGTCTGCCTCG
* *
13351903 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTACAACTTCAGAGAGATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
13351968 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACT
66 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACT
* * *
13352033 GCAACTTCAGTGAGATAGGATTACCGGCTTTAATCTGCTCCATTGCAACTTCAGAGAGATAAGAT
131 GCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
13352098 TTGCCATCTTCAGTCTACCTCG
196 TTGCCATCTTCAGTCTGCCTCG
* *
13352120 CTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTCCACTGCAACTTCA-GG-GATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
13352183 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACT
66 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACT
* *
13352248 GCAACTTTAGCGAGATAGGATTACTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
131 GCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
13352313 TTGCCATCTTCAGTCTGCCTCG
196 TTGCCATCTTCAGTCTGCCTCG
* * *
13352335 CTACAACTTCAGGAGGATAAGACTTGCTTAATTAGTTTGCTCCACTACAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
13352400 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACT
66 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACT
* * * *
13352465 GCAACTTCAGTGAGATAGGATTACCGGCTTTAATCTGCTCCATTGTAACTTCAGAGAGATAAGAT
131 GCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
13352530 TTGCCATCTTCAGTCTACCTCG
196 TTGCCATCTTCAGTCTGCCTCG
* *
13352552 CTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTCCACTGCAACTTCA-GG-GATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
* *
13352615 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCAC-CCACT
66 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACT
* ** *
13352679 ACAACTTCAGCGAGATAGGATTGTCGGCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGAT
131 GCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
13352744 TTGCCATCTTCAGTCTGCCTCG
196 TTGCCATCTTCAGTCTGCCTCG
*
13352766 CTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
13352831 ACT
66 ACT
13352834 CGATCTGTTA
Statistics
Matches: 863, Mismatches: 63, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
214 136 0.16
215 267 0.31
216 126 0.15
217 334 0.39
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (217 bp):
CTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACT
GCAACTTCAGCGAGATAGGATTACCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
TTGCCATCTTCAGTCTGCCTCG
Found at i:13352360 original size:432 final size:432
Alignment explanation
Indices: 13351687--13352833 Score: 2012
Period size: 432 Copynumber: 2.7 Consensus size: 432
13351677 GTTTGCTCCA
* * * ** *
13351687 CTGCAACTTCAGGAGGATGAGGCTTGCTTACCTAGTCTGCTCCACTGTAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTCCACTGCAACTTCA-GG-GATAAG
* * * * *
13351752 ACTAGATGCGATCCGCTCTCTGCAACTTCAGAGAGATAATATCTGAGATTTTAATCCACT-TACT
64 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCACTCCACT
* * *
13351816 GTAACTTCAGCGAGATAGGATTGTCGACTTTAATATGCTCCACTGCAACTTCAGGGAGATAAGAT
129 GCAACTTCAGCGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
13351881 TTGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCC
194 TTGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCC
*
13351946 ACTACAACTTCAGAGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATC
259 ACTACAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATC
13352011 TAAGGTTTTAACCCGCTCCACTGCAACTTCAGTGAGATAGGATTACCGGCTTTAATCTGCTCCAT
324 TAAGGTTTTAACCCGCTCCACTGCAACTTCAGTGAGATAGGATTACCGGCTTTAATCTGCTCCAT
13352076 TGCAACTTCAGAGAGATAAGATTTGCCATCTTCAGTCTACCTCG
389 TGCAACTTCAGAGAGATAAGATTTGCCATCTTCAGTCTACCTCG
13352120 CTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTCCACTGCAACTTCAGGGATAAGAC
1 CTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTCCACTGCAACTTCAGGGATAAGAC
* *
13352185 TAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAACCCGCTCCACTGC
66 TAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCACTCCACTGC
* *
13352250 AACTTTAGCGAGATAGGATT-ACTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
131 AACTTCAGCGAGATAGGATTGTC-GGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
* *
13352314 TGCCATCTTCAGTCTGCCTCGCTACAACTTCAGGAGGATAAGACTTGCTTAATTAGTTTGCTCCA
195 TGCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCA
13352379 CTACAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
260 CTACAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCT
13352444 AAGGTTTTAACCCGCTCCACTGCAACTTCAGTGAGATAGGATTACCGGCTTTAATCTGCTCCATT
325 AAGGTTTTAACCCGCTCCACTGCAACTTCAGTGAGATAGGATTACCGGCTTTAATCTGCTCCATT
*
13352509 GTAACTTCAGAGAGATAAGATTTGCCATCTTCAGTCTACCTCG
390 GCAACTTCAGAGAGATAAGATTTGCCATCTTCAGTCTACCTCG
13352552 CTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTCCACTGCAACTTCAGGGATAAGAC
1 CTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTCCACTGCAACTTCAGGGATAAGAC
*
13352617 TAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCAC-CCACTAC
66 TAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCACTCCACTGC
*
13352681 AACTTCAGCGAGATAGGATTGTCGGCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGATTT
131 AACTTCAGCGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT
*
13352746 GCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTGCTCCAC
196 GCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCAC
*
13352811 TGCAACTTCAGGGAGATAAGACT
261 TACAACTTCAGGGAGATAAGACT
13352834 CGATCTGTTA
Statistics
Matches: 679, Mismatches: 32, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
431 211 0.31
432 419 0.62
433 49 0.07
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (432 bp):
CTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTCCACTGCAACTTCAGGGATAAGAC
TAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAATCCACTCCACTGC
AACTTCAGCGAGATAGGATTGTCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT
GCCATCTTCAGTCTGCCTCGCTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTCCAC
TACAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTA
AGGTTTTAACCCGCTCCACTGCAACTTCAGTGAGATAGGATTACCGGCTTTAATCTGCTCCATTG
CAACTTCAGAGAGATAAGATTTGCCATCTTCAGTCTACCTCG
Found at i:13352600 original size:44 final size:44
Alignment explanation
Indices: 13351597--13352833 Score: 351
Period size: 44 Copynumber: 28.6 Consensus size: 44
13351587 TAATGTGCCT
* * *
13351597 CACTGCAACTTCAGGAGGATAATACTTGCTGATTTAGTCTGC-C
1 CACTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTC
* ** *
13351640 TCACTGCAACTTCAGGAGGATAAGACTTGCTTACCTAGTTTGCTC
1 -CACTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTC
* * * **
13351685 CACTGCAACTTCAGGAGGATGAGGCTTGCTTACCTAGTCTGCTC
1 CACTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTC
* * * *
13351729 CACTGTAACTTCAGG-GAGATAAGACTAGATGC-G--A-TCCGCT-
1 CACTGCAACTTCAGGAG-GATAAGACTTGCT-CAGTTAGTCTGCTC
* * * * **
13351769 CTCTGCAACTTCA-GAGAGATAATA--T-CTGAGATTTTAATCCACT-
1 CACTGCAACTTCAGGAG-GATAAGACTTGCTCAG---TTAGTCTGCTC
* * * * * *
13351812 TACTGTAACTTCAGCGA-GATAGGA-TTG-TCGACTTTAATATGCTC
1 CACTGCAACTTCAG-GAGGATAAGACTTGCTC-A-GTTAGTCTGCTC
* *
13351856 CACTGCAACTTCAGG-GAGATAAGATTTGC-CATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGAG-GATAAGACTTGCTCA-GTT-AGTCTGCTC
* * *
13351900 TCGCTGCAACTTCAGGAGGATAAGACTTGCTTAATTAGTCTGCTC
1 -CACTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTC
* * *
13351945 CACTACAACTTCA-GAGAGATAAGACTAGATGC-G--A-TCTGCT-
1 CACTGCAACTTCAGGAG-GATAAGACTTGCT-CAGTTAGTCTGCTC
* * ** *
13351985 CTCTGCAACTTCA-GAGAGATAAGA--T-CTAAGGTTTTAACCCGCTC
1 CACTGCAACTTCAGGAG-GATAAGACTTGCTCA-G--TTAGTCTGCTC
* * * *
13352029 CACTGCAACTTCAGTGA-GATAGGA-TTAC-CGGCTTTAATCTGCTC
1 CACTGCAACTTCAG-GAGGATAAGACTTGCTCAG--TTAGTCTGCTC
* * * *
13352073 CATTGCAACTTCA-GAGAGATAAGATTTGC-CATCTTCAGTCTAC-C
1 CACTGCAACTTCAGGAG-GATAAGACTTGCTCA-GTT-AGTCTGCTC
*
13352117 TCGCTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTC
1 -CACTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTC
* *
13352162 CACTGCAACTTCA-G-GGATAAGACTAGATGC-G--A-TCTGCT-
1 CACTGCAACTTCAGGAGGATAAGACTTGCT-CAGTTAGTCTGCTC
* * ** *
13352200 CTCTGCAACTTCA-GAGAGATAAGA--T-CTAAGGTTTTAACCCGCTC
1 CACTGCAACTTCAGGAG-GATAAGACTTGCTCA-G--TTAGTCTGCTC
* * * * *
13352244 CACTGCAACTTTAGCGA-GATAGGA-TTACTGGC-TTTAATCTGCTC
1 CACTGCAACTTCAG-GAGGATAAGACTTGCT--CAGTTAGTCTGCTC
* *
13352288 CACTGCAACTTCAGG-GAGATAAGATTTGC-CATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGAG-GATAAGACTTGCTCA-GTT-AGTCTGCTC
* * * * *
13352332 TCGCTACAACTTCAGGAGGATAAGACTTGCTTAATTAGTTTGCTC
1 -CACTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTC
* * *
13352377 CACTACAACTTCAGG-GAGATAAGACTAGATGC-G--A-TCTGCT-
1 CACTGCAACTTCAGGAG-GATAAGACTTGCT-CAGTTAGTCTGCTC
* * ** *
13352417 CTCTGCAACTTCA-GAGAGATAAGA--T-CTAAGGTTTTAACCCGCTC
1 CACTGCAACTTCAGGAG-GATAAGACTTGCTCA-G--TTAGTCTGCTC
* * * *
13352461 CACTGCAACTTCAGTGA-GATAGGA-TTAC-CGGCTTTAATCTGCTC
1 CACTGCAACTTCAG-GAGGATAAGACTTGCTCAG--TTAGTCTGCTC
* * * * *
13352505 CATTGTAACTTCA-GAGAGATAAGATTTGC-CATCTTCAGTCTAC-C
1 CACTGCAACTTCAGGAG-GATAAGACTTGCTCA-GTT-AGTCTGCTC
*
13352549 TCGCTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTC
1 -CACTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTC
* *
13352594 CACTGCAACTTCA-G-GGATAAGACTAGATGC-G--A-TCTGCT-
1 CACTGCAACTTCAGGAGGATAAGACTTGCT-CAGTTAGTCTGCTC
* * * **
13352632 CTCTGCAACTTCA-GAGAGATAAGA--T-CTAAGGTTTTAATCCAC-C
1 CACTGCAACTTCAGGAG-GATAAGACTTGCTCA-G--TTAGTCTGCTC
* * * *
13352675 CACTACAACTTCAGCGA-GATAGGA-TTG-TCGGCTTTAATCTGCTC
1 CACTGCAACTTCAG-GAGGATAAGACTTGCTCAG--TTAGTCTGCTC
* * *
13352719 TACTGCAACTTCAGG-GAGATAAGATTTGC-CATCTTCAGTCTGC-C
1 CACTGCAACTTCAGGAG-GATAAGACTTGCTCA-GTT-AGTCTGCTC
* * *
13352763 TCGCTGCAACTTCAGGAGGATAAGACTTGCTTATTTAGTCTGCTC
1 -CACTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTC
13352808 CACTGCAACTTCAGG-GAGATAAGACT
1 CACTGCAACTTCAGGAG-GATAAGACT
13352834 CGATCTGTTA
Statistics
Matches: 899, Mismatches: 166, Indels: 256
0.68 0.13 0.19
Matches are distributed among these distances:
37 6 0.01
38 30 0.03
39 16 0.02
40 77 0.09
41 16 0.02
42 39 0.04
43 81 0.09
44 422 0.47
45 186 0.21
46 26 0.03
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
CACTGCAACTTCAGGAGGATAAGACTTGCTCAGTTAGTCTGCTC
Found at i:13360906 original size:24 final size:24
Alignment explanation
Indices: 13360877--13360922 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
13360867 ATCATCTTTT
*
13360877 GCTGCTCATT-CATTTGCTTTTGAA
1 GCTGCTC-TTGCATTTCCTTTTGAA
13360901 GCTGCTCTTGCATTTCCTTTTG
1 GCTGCTCTTGCATTTCCTTTTG
13360923 GGATTGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (24 bp):
GCTGCTCTTGCATTTCCTTTTGAA
Found at i:13365183 original size:19 final size:16
Alignment explanation
Indices: 13365142--13365175 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
13365132 ATAAACATAT
13365142 ATAAAAAAATAATTAC
1 ATAAAAAAATAATTAC
13365158 ATAAAAAAATAATTAC
1 ATAAAAAAATAATTAC
13365174 AT
1 AT
13365176 CCTAAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAAAATAATTAC
Found at i:13368330 original size:20 final size:20
Alignment explanation
Indices: 13368288--13368328 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
13368278 AGCATTCCAT
*
13368288 AACTCAGGATAACATAAAAA
1 AACTCAGGATAAAATAAAAA
13368308 AACTCA-GATAAAATAAAAA
1 AACTCAGGATAAAATAAAAA
13368327 AA
1 AA
13368329 ACATACTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.66, C:0.12, G:0.07, T:0.15
Consensus pattern (20 bp):
AACTCAGGATAAAATAAAAA
Found at i:13376214 original size:5 final size:5
Alignment explanation
Indices: 13376204--13376230 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
13376194 AGTAAAGATA
13376204 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
13376231 CGAATCACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:13381994 original size:39 final size:40
Alignment explanation
Indices: 13381925--13382020 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
13381915 TTTGAATAAA
* *
13381925 AAAATGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTGG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTAG
* *
13381965 AAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTTTTTTAG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTAG
*
13382004 AAAAGCGCCGCAAAAAA
1 AAAA-CGCCGCTAAAAA
13382021 CCTAATCCCA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 23 0.46
40 27 0.54
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTAG
Found at i:13382171 original size:41 final size:41
Alignment explanation
Indices: 13382058--13382312 Score: 330
Period size: 41 Copynumber: 6.2 Consensus size: 41
13382048 CTTTTCGAGG
* * *
13382058 CTTTAGCGGTGTTTTTGGAAAAGCGACACTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* * *
13382099 CTTTAGCGGCGTTTTTTGGAGAAGCGGCGCTAATGCTCAAAC
1 CTTTAGCGGCG-TTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* * * *
13382141 CTTTAGCTGTGTTTTTGTAAAAGTGCCGCTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* * * *
13382182 CTTTAGTGGCGTTTATGGAAAAGAGTCGCTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
* * *
13382223 CTTTAGCGGCGTTTTTGAAAAAGCGCTGCTAATGCTCTGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
*
13382264 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
*
13382305 TTTTAGCG
1 CTTTAGCG
13382313 CCGCTAATGC
Statistics
Matches: 184, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
41 149 0.81
42 35 0.19
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGAC
Found at i:13382317 original size:24 final size:24
Alignment explanation
Indices: 13382285--13382336 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
13382275 TTTTTGAAAA
*
13382285 AGCGCCGCTAATGCTCAGACTTTT
1 AGCGCCGCTAATGCTCAGACCTTT
13382309 AGCGCCGCTAATGCTCAGACCTTT
1 AGCGCCGCTAATGCTCAGACCTTT
13382333 AGCG
1 AGCG
13382337 GCGTTTATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (24 bp):
AGCGCCGCTAATGCTCAGACCTTT
Found at i:13382351 original size:65 final size:65
Alignment explanation
Indices: 13382244--13382377 Score: 223
Period size: 65 Copynumber: 2.1 Consensus size: 65
13382234 TTTTTGAAAA
* * * *
13382244 AGCGCTGCTAATGCTCTGACCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGACTTTT
1 AGCGCCGCTAATGCTCAGACCTTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCAGACCTTT
*
13382309 AGCGCCGCTAATGCTCAGACCTTTAGCGGCGTTTATGGAAAAGCGCCGCTAATGCTCAGACCTTT
1 AGCGCCGCTAATGCTCAGACCTTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCAGACCTTT
13382374 AGCG
1 AGCG
13382378 GCGTTTTTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (65 bp):
AGCGCCGCTAATGCTCAGACCTTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCAGACCTTT
Found at i:13382398 original size:41 final size:41
Alignment explanation
Indices: 13382309--13382398 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
13382299 TCAGACTTTT
*
13382309 AGCGCCGCTAATGCTCAGACCTTTAGCGGCGTTTATGGAAA
1 AGCGCCGCTAATGCTCAGACCTTTAGCGGCGTTTATGAAAA
*
13382350 AGCGCCGCTAATGCTCAGACCTTTAGCGGCGTTTTTTGAAAA
1 AGCGCCGCTAATGCTCAGACCTTTAGCGGCG-TTTATGAAAA
13382392 AG-GCCGC
1 AGCGCCGC
13382399 AAAAACATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 36 0.78
42 10 0.22
ACGTcount: A:0.23, C:0.26, G:0.27, T:0.24
Consensus pattern (41 bp):
AGCGCCGCTAATGCTCAGACCTTTAGCGGCGTTTATGAAAA
Found at i:13382398 original size:106 final size:106
Alignment explanation
Indices: 13382208--13382398 Score: 330
Period size: 106 Copynumber: 1.8 Consensus size: 106
13382198 GGAAAAGAGT
* * *
13382208 CGCTAATGCTCAGACCTTTAGCGGCGTTTTTGAAAAAGCGCTGCTAATGCTCTGACCTTTAGCGG
1 CGCTAATGCTCAGACCTTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCAGACCTTTAGCGG
13382273 CGTTTTTGAAAAAGCGCCGCTAATGCTCAGACTTTTAGCGC
66 CGTTTTTGAAAAAGCGCCGCTAATGCTCAGACTTTTAGCGC
*
13382314 CGCTAATGCTCAGACCTTTAGCGGCGTTTATGGAAAAGCGCCGCTAATGCTCAGACCTTTAGCGG
1 CGCTAATGCTCAGACCTTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCAGACCTTTAGCGG
13382379 CGTTTTTTGAAAAAG-GCCGC
66 CG-TTTTTGAAAAAGCGCCGC
13382399 AAAAACATTT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
106 68 0.85
107 12 0.15
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (106 bp):
CGCTAATGCTCAGACCTTTAGCGGCGTTTATGAAAAAGCGCCGCTAATGCTCAGACCTTTAGCGG
CGTTTTTGAAAAAGCGCCGCTAATGCTCAGACTTTTAGCGC
Found at i:13382484 original size:15 final size:16
Alignment explanation
Indices: 13382453--13382485 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13382443 TATTAATTAA
*
13382453 AATTTAATATATTTTT
1 AATTGAATATATTTTT
13382469 AATTGAATAT-TTTTT
1 AATTGAATATATTTTT
13382484 AA
1 AA
13382486 AAATGGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
AATTGAATATATTTTT
Found at i:13382828 original size:14 final size:15
Alignment explanation
Indices: 13382800--13382832 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
13382790 AAGGTTTATA
13382800 GATTATGGAATTAGG
1 GATTATGGAATTAGG
13382815 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
13382829 GATT
1 GATT
13382833 CTAGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:13383009 original size:7 final size:7
Alignment explanation
Indices: 13382999--13383024 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13382989 GGGGTTAAGG
13382999 GTTAGTA
1 GTTAGTA
13383006 GTTAGTA
1 GTTAGTA
13383013 GTTAGTA
1 GTTAGTA
13383020 GTTAG
1 GTTAG
13383025 GGGTTGGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (7 bp):
GTTAGTA
Found at i:13385652 original size:18 final size:18
Alignment explanation
Indices: 13385629--13385687 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
13385619 AACAGAACTT
13385629 ATGTAATTCTAATATAGA
1 ATGTAATTCTAATATAGA
* * ***
13385647 ATGTAA-AC-AATTTTCTT
1 ATGTAATTCTAA-TATAGA
13385664 ATGTAATTCTAATATAGA
1 ATGTAATTCTAATATAGA
13385682 ATGTAA
1 ATGTAA
13385688 CTTGTTTTAA
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
16 2 0.07
17 9 0.32
18 15 0.54
19 2 0.07
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (18 bp):
ATGTAATTCTAATATAGA
Found at i:13385949 original size:43 final size:43
Alignment explanation
Indices: 13385888--13386142 Score: 348
Period size: 43 Copynumber: 5.9 Consensus size: 43
13385878 AATTCATGTT
* * *
13385888 TTTAGTGGCGTTTGTGGGAAAAGCGCCGCTATAGGTATTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* ** * **
13385931 TTTAGCGGCGTTTGTGGGAAATGAACTGCTAAATTTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
13385974 TTTAGCAGCGTTTGTGGGATATGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
13386017 TTCAGCGGCGTTTGTGGGAAATGCGCCGCTAAAGTTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
**
13386060 TTTAGCGGCGTTTGTGGGATTAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
13386103 TTTAGCGGCGCTTGTGGGAAAAGCGCCGCTAAAGGTCTTG
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG
13386143 TTATTTAAAA
Statistics
Matches: 184, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 184 1.00
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:13386666 original size:12 final size:12
Alignment explanation
Indices: 13386649--13386673 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13386639 TTAGGACTTG
13386649 AATGATGTTGAT
1 AATGATGTTGAT
13386661 AATGATGTTGAT
1 AATGATGTTGAT
13386673 A
1 A
13386674 TTGTGAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AATGATGTTGAT
Found at i:13390849 original size:15 final size:15
Alignment explanation
Indices: 13390831--13390864 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13390821 AATAATTAGT
13390831 TAATAATAGTAATAA
1 TAATAATAGTAATAA
* *
13390846 TAATAATGGTATTAA
1 TAATAATAGTAATAA
13390861 TAAT
1 TAAT
13390865 TGGGGCACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (15 bp):
TAATAATAGTAATAA
Found at i:13391354 original size:19 final size:20
Alignment explanation
Indices: 13391324--13391362 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
13391314 TTTTTAGTTT
*
13391324 TGTTTTTAGTAATTTTTTTA
1 TGTTTTTAGTAATTGTTTTA
13391344 TGTTTTT-GTAATTGTTTTA
1 TGTTTTTAGTAATTGTTTTA
13391363 GCTTAATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.69
Consensus pattern (20 bp):
TGTTTTTAGTAATTGTTTTA
Found at i:13393174 original size:21 final size:21
Alignment explanation
Indices: 13393148--13393193 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
13393138 AGCAAGGGCT
* * *
13393148 TGTGGAGTGGCCATACGAGCA
1 TGTGGAATAGCCATACGAACA
13393169 TGTGGAATAGCCATACGAACA
1 TGTGGAATAGCCATACGAACA
13393190 TGTG
1 TGTG
13393194 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (21 bp):
TGTGGAATAGCCATACGAACA
Found at i:13393425 original size:20 final size:19
Alignment explanation
Indices: 13393380--13393426 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
13393370 GTGACCCCTG
*
13393380 TTTTCAAAATTTTCAAGTT
1 TTTTCAAAATTATCAAGTT
* *
13393399 TTTTCAAAATTATCTATTT
1 TTTTCAAAATTATCAAGTT
13393418 TGTTTCAAA
1 T-TTTCAAA
13393427 TTGATCCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.53
Consensus pattern (19 bp):
TTTTCAAAATTATCAAGTT
Found at i:13397292 original size:34 final size:34
Alignment explanation
Indices: 13397254--13397352 Score: 90
Period size: 34 Copynumber: 3.1 Consensus size: 34
13397244 TGTTGAAATG
13397254 GACTATGTATGATATATGGCTAAATTAATAATTT
1 GACTATGTATGATATATGGCTAAATTAATAATTT
* * * *
13397288 GAC----TA-G-TA-ATGG-TACATT-TTGAAATG
1 GACTATGTATGATATATGGCTAAATTAAT-AATTT
13397314 GACTATGTATGATATATGGCTAAATTAATAATTT
1 GACTATGTATGATATATGGCTAAATTAATAATTT
13397348 GACTA
1 GACTA
13397353 GTAATGGTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 20
0.63 0.11 0.27
Matches are distributed among these distances:
25 1 0.02
26 11 0.23
27 4 0.09
28 2 0.04
29 1 0.02
30 4 0.09
31 1 0.02
32 2 0.04
33 4 0.09
34 16 0.34
35 1 0.02
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.38
Consensus pattern (34 bp):
GACTATGTATGATATATGGCTAAATTAATAATTT
Found at i:13397339 original size:60 final size:60
Alignment explanation
Indices: 13397246--13397367 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
13397236 TATAAATATG
13397246 TTGAAATGGACTATGTATGATATATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
1 TTGAAATGGACTATGTATGATATATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
13397306 TTGAAATGGACTATGTATGATATATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
1 TTGAAATGGACTATGTATGATATATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
13397366 TT
1 TT
13397368 CGCTGTTAAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (60 bp):
TTGAAATGGACTATGTATGATATATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
Found at i:13401650 original size:93 final size:93
Alignment explanation
Indices: 13401537--13401708 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
13401527 CGCCCATAAG
* *
13401537 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
13401602 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
13401630 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
13401695 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
13401709 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:13401705 original size:46 final size:46
Alignment explanation
Indices: 13401530--13401705 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
13401520 TGTAACCCGC
* * *
13401530 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
13401576 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
13401626 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
13401669 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
13401706 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:13404895 original size:22 final size:22
Alignment explanation
Indices: 13404870--13404914 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
13404860 GGGGAAAAAA
13404870 TGAAAAATTGTAAATAAGAAGT
1 TGAAAAATTGTAAATAAGAAGT
13404892 TGAAAAATTGTAAATAAGAAGT
1 TGAAAAATTGTAAATAAGAAGT
13404914 T
1 T
13404915 ATATGTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (22 bp):
TGAAAAATTGTAAATAAGAAGT
Found at i:13408303 original size:7 final size:7
Alignment explanation
Indices: 13408291--13408318 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
13408281 CATGGGTCTT
13408291 ATATATA
1 ATATATA
13408298 ATATATA
1 ATATATA
13408305 ATATATA
1 ATATATA
13408312 ATATATA
1 ATATATA
13408319 TTTACGTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATATATA
Found at i:13415123 original size:32 final size:32
Alignment explanation
Indices: 13415078--13415157 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
13415068 TTTTGTTATT
* *
13415078 TATATATAATATATATATGCA-TGCATGGGTG
1 TATATATAGTATATATATGAAGTGCATGGGTG
*
13415109 TCATATATAGTATATAT-TTAAGTGCATGGGTG
1 T-ATATATAGTATATATATGAAGTGCATGGGTG
13415141 T-TATAT-GTATAATATAT
1 TATATATAGTAT-ATATAT
13415158 TTGTGTGGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 4 0.10
30 9 0.21
31 4 0.10
32 25 0.60
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.42
Consensus pattern (32 bp):
TATATATAGTATATATATGAAGTGCATGGGTG
Found at i:13415158 original size:32 final size:32
Alignment explanation
Indices: 13415099--13415159 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
13415089 TATATATGCA
13415099 TGCATGGGTGTCATATATAGTATATATTTAAG
1 TGCATGGGTGTCATATATAGTATATATTTAAG
* *
13415131 TGCATGGGTGTTATATGTA-TAATATATTT
1 TGCATGGGTGTCATATATAGT-ATATATTT
13415160 GTGTGGGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (32 bp):
TGCATGGGTGTCATATATAGTATATATTTAAG
Found at i:13415174 original size:29 final size:28
Alignment explanation
Indices: 13415142--13415220 Score: 77
Period size: 33 Copynumber: 2.6 Consensus size: 28
13415132 GCATGGGTGT
* *
13415142 TATATGTATAATATATTTGTGTGGGTCTG
1 TATATATATAATATATATGTGTGGGT-TG
*
13415171 TATATACATAGTACATATATATGTGTGGGTTT
1 TATAT--ATA-TA-ATATATATGTGTGGGTTG
13415203 TATTATATATAATATATA
1 TA-TATATATAATATATA
13415221 CGTGGTTATA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
29 12 0.29
30 2 0.05
31 5 0.12
32 5 0.12
33 18 0.43
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (28 bp):
TATATATATAATATATATGTGTGGGTTG
Found at i:13416993 original size:29 final size:29
Alignment explanation
Indices: 13416945--13417002 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
13416935 TATTTGACTT
13416945 CAAAATATTGAAAATATTAAATATAAGTAG
1 CAAAATATTGAAAATATTAAATA-AAGTAG
* * *
13416975 CAAAAT-TTTAAAATTTTAATTAAAGTAG
1 CAAAATATTGAAAATATTAAATAAAGTAG
13417003 AGCGGGATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.24
29 13 0.52
30 6 0.24
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.34
Consensus pattern (29 bp):
CAAAATATTGAAAATATTAAATAAAGTAG
Found at i:13417931 original size:25 final size:24
Alignment explanation
Indices: 13417887--13417935 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
13417877 TTTCATCTTA
* *
13417887 TTTTTGTTATTATTATTTTTCTTTC
1 TTTTTGTAATTATTACTTTT-TTTC
*
13417912 TTTTTGTAATTATTCCTTTTTTTC
1 TTTTTGTAATTATTACTTTTTTTC
13417936 CCGGAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.12, C:0.10, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTTGTAATTATTACTTTTTTTC
Found at i:13422456 original size:30 final size:28
Alignment explanation
Indices: 13422398--13422457 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 28
13422388 TAATTAATTA
*
13422398 ATTTTTTTAAATTTTAATTTTATTAAAAT
1 ATTTTTTTAAATTTTAATTTCA-TAAAAT
13422427 ATTTTTTTATAATTTTTAATTTGCA-AAAAT
1 ATTTTTTTA-AA-TTTTAATTT-CATAAAAT
13422457 A
1 A
13422458 ACTTTCTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 9 0.33
30 8 0.30
31 9 0.33
32 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTTTTTAAATTTTAATTTCATAAAAT
Found at i:13425079 original size:23 final size:21
Alignment explanation
Indices: 13425036--13425087 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
13425026 TTATAGGAAA
*
13425036 ATATTTATTTTAATATTTTTTGT
1 ATATTT-TTTTAATATATTTT-T
*
13425059 ATATTTTTTGTATTATATTTTT
1 ATATTTTTT-TAATATATTTTT
13425081 A-ATTTTT
1 ATATTTTT
13425088 ATATAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 6 0.23
22 5 0.19
23 15 0.58
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (21 bp):
ATATTTTTTTAATATATTTTT
Found at i:13425536 original size:31 final size:30
Alignment explanation
Indices: 13425494--13425593 Score: 78
Period size: 31 Copynumber: 3.2 Consensus size: 30
13425484 GATGAGTCAG
*
13425494 TTTACACTTTGGTCACTCTTGTATTAGTAAA
1 TTTACAATTTGGTCA-TCTTGTATTAGTAAA
* **
13425525 TTTACAATTTGGACAAT-TAAATATTAGTAAA
1 TTTACAATTTGGTC-ATCT-TGTATTAGTAAA
* * *
13425556 ATTATAATTTGGTCA-CTTGACTATTAGCAAA
1 TTTACAATTTGGTCATCTTG--TATTAGTAAA
13425587 TTTACAA
1 TTTACAA
13425594 GTCATTCTGA
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
30 3 0.06
31 48 0.92
32 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (30 bp):
TTTACAATTTGGTCATCTTGTATTAGTAAA
Found at i:13430388 original size:243 final size:243
Alignment explanation
Indices: 13430049--13430531 Score: 813
Period size: 243 Copynumber: 2.0 Consensus size: 243
13430039 AGCAACCTAT
** *
13430049 CGTTGAAGTCGTGACACTAAGCATGGTATGTCATGACACCGATCCTCAAAGTCACAACTACAAAC
1 CGTTGAAGTCGCAACACTAAGCATGGTATGTCACGACACCGATCCTCAAAGTCACAACTACAAAC
* * *
13430114 CCTTGAGGTCGTAAATCCAAGAAAATTTTTGAAATGAAGAAACCTAATGGCTATTATCATCGAGG
66 CCTCGAGGTAGCAAATCCAAGAAAATTTTTGAAATGAAGAAACCTAATGGCTATTATCATCGAGG
* *
13430179 TTACAACACCAGCAAGGTTGTGTCGCGACACCAAGTGCCCCTAAGTCAAGCTCGTGCCCACTTTC
131 TTACAACACCAGCAAGGTTGTGTCGCGACACCAAGTGCCCCCAAGTCAAGCTCGTGCACACTTTC
* *
13430244 AAGAGTGTCACGACACTAAAGCTTGGGTGTTGCGACTTTGAAGTTAGC
196 AAGAATGTCACGACACTAAAGCTTGGGTGTTGCGACTTTAAAGTTAGC
* *
13430292 CGTTGAAGTCGCAACACTAAGCATGTTATGTCACGACACCGATCCTCAAATTCACAACTACAAAC
1 CGTTGAAGTCGCAACACTAAGCATGGTATGTCACGACACCGATCCTCAAAGTCACAACTACAAAC
*
13430357 CCTCGAGGTAGCAAATCCAAGAAAATTTTTGAAATGAAGAAACCTAATGGCTATTATCATTGAGG
66 CCTCGAGGTAGCAAATCCAAGAAAATTTTTGAAATGAAGAAACCTAATGGCTATTATCATCGAGG
*
13430422 TTACAACACCGGCAAGGTTGTGTCGCGACACCAAGTGCCCCCAAGTCAAGCTCGTGCACACTTTC
131 TTACAACACCAGCAAGGTTGTGTCGCGACACCAAGTGCCCCCAAGTCAAGCTCGTGCACACTTTC
* * *
13430487 ACGAATGTCACGTCACTAAAGCTTGGGTGTTGTGACTTTAAAGTT
196 AAGAATGTCACGACACTAAAGCTTGGGTGTTGCGACTTTAAAGTT
13430532 TGATAGGTGA
Statistics
Matches: 223, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
243 223 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (243 bp):
CGTTGAAGTCGCAACACTAAGCATGGTATGTCACGACACCGATCCTCAAAGTCACAACTACAAAC
CCTCGAGGTAGCAAATCCAAGAAAATTTTTGAAATGAAGAAACCTAATGGCTATTATCATCGAGG
TTACAACACCAGCAAGGTTGTGTCGCGACACCAAGTGCCCCCAAGTCAAGCTCGTGCACACTTTC
AAGAATGTCACGACACTAAAGCTTGGGTGTTGCGACTTTAAAGTTAGC
Found at i:13433305 original size:20 final size:22
Alignment explanation
Indices: 13433282--13433330 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
13433272 TACAAAATAA
*
13433282 TCAAAATAATTT-T-TAAAAAT
1 TCAAAATAATTTATAAAAAAAT
*
13433302 TCAAAAT-GTTTATAAAAAAAT
1 TCAAAATAATTTATAAAAAAAT
13433323 TCAAAATA
1 TCAAAATA
13433331 TATATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.12
20 8 0.33
21 13 0.54
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (22 bp):
TCAAAATAATTTATAAAAAAAT
Found at i:13433398 original size:17 final size:18
Alignment explanation
Indices: 13433353--13433398 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
13433343 AAAGTTATAA
*
13433353 AAAATTTAAAAAAATTCT
1 AAAATTTTAAAAAATTCT
*
13433371 -AAATATATAAAAAATT-T
1 AAAAT-TTTAAAAAATTCT
13433388 AAAATTTTAAA
1 AAAATTTTAAA
13433399 CATGTTCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATTTTAAAAAATTCT
Found at i:13444321 original size:9 final size:9
Alignment explanation
Indices: 13444307--13444337 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
13444297 GTTAAACGAA
13444307 TCGAGTTAT
1 TCGAGTTAT
*
13444316 TCGAGTTAA
1 TCGAGTTAT
13444325 TCGAGTTAT
1 TCGAGTTAT
13444334 TCGA
1 TCGA
13444338 ATCAACTCGA
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:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:13444414 original size:9 final size:9
Alignment explanation
Indices: 13444390--13444444 Score: 92
Period size: 9 Copynumber: 6.1 Consensus size: 9
13444380 TGAGTTTTCA
*
13444390 AATTCAAAT
1 AATTCGAAT
*
13444399 AACTCGAAT
1 AATTCGAAT
13444408 AATTCGAAT
1 AATTCGAAT
13444417 AATTCGAAT
1 AATTCGAAT
13444426 AATTCGAAT
1 AATTCGAAT
13444435 AATTCGAAT
1 AATTCGAAT
13444444 A
1 A
13444445 TCAAACTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (9 bp):
AATTCGAAT
Found at i:13448939 original size:44 final size:46
Alignment explanation
Indices: 13448849--13448940 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
13448839 TTTGGTTCGC
*
13448849 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
*
13448895 TGTAATGGAATAGAGGCGTAGT-GGT-ATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
13448939 TG
1 TG
13448941 GAATAGAGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 20 0.45
45 3 0.07
46 21 0.48
ACGTcount: A:0.25, C:0.04, G:0.32, T:0.39
Consensus pattern (46 bp):
TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
Found at i:13448941 original size:39 final size:44
Alignment explanation
Indices: 13448849--13448957 Score: 138
Period size: 46 Copynumber: 2.5 Consensus size: 44
13448839 TTTGGTTCGC
*
13448849 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--A
*
13448895 TGTAATGGAATAGAGGCGTAGT-GGT-ATTCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTA
*
13448935 TG-AATGGAATAGAGGTGTAATAG
1 TGTAATGGAATAGAGGCGTAATAG
13448958 CATAAGGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
39 17 0.29
40 3 0.05
43 1 0.02
44 13 0.22
45 3 0.05
46 21 0.36
ACGTcount: A:0.28, C:0.04, G:0.32, T:0.37
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTA
Found at i:13449119 original size:15 final size:15
Alignment explanation
Indices: 13449099--13449137 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
13449089 CATAATTGTT
13449099 ATAAAATATAATTTA
1 ATAAAATATAATTTA
13449114 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
13449131 ATAAAAT
1 ATAAAAT
13449138 TGTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:13449144 original size:17 final size:17
Alignment explanation
Indices: 13449104--13449137 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13449094 TTGTTATAAA
13449104 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
13449121 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
13449138 TGTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:13449209 original size:20 final size:21
Alignment explanation
Indices: 13449170--13449209 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
13449160 AATTTACTAA
*
13449170 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
13449191 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
13449210 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:13449251 original size:54 final size:54
Alignment explanation
Indices: 13449061--13449256 Score: 144
Period size: 54 Copynumber: 3.4 Consensus size: 54
13449051 TATTAATATA
* * * * * *
13449061 AATAATAAATAATTTAATCATATTTTAACATAATTGTTATAAAATATAATTTAAT
1 AATAATAAATAATTAAAT-AAAATTTAAAATAATTATTATTAAATATAATTTAAT
* * * **
13449116 AA-AATATATAATTTAATAAAATTGTTAATAA-ATATTCTTATATAAATTTACTAATAAAAT
1 AATAATAAATAATTAAATAAAA-T-TTAA-AATA-ATTATTAT-TAAA--TA-TAATTTAAT
* * *
13449176 CATAATATATAATACTAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
1 AATAATAAATAAT--T-AAATAAAATTTAAAATAATTATTATTAAATATAATTTAAT
13449233 AATAATAAATAATTAAATAAAATT
1 AATAATAAATAATTAAATAAAATT
13449257 CTTATTCTTA
Statistics
Matches: 111, Mismatches: 17, Indels: 27
0.72 0.11 0.17
Matches are distributed among these distances:
53 2 0.02
54 24 0.22
55 8 0.07
56 8 0.07
57 21 0.19
58 2 0.02
59 2 0.02
60 12 0.11
61 19 0.17
62 5 0.05
63 2 0.02
64 6 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (54 bp):
AATAATAAATAATTAAATAAAATTTAAAATAATTATTATTAAATATAATTTAAT
Found at i:13449335 original size:32 final size:32
Alignment explanation
Indices: 13449299--13449362 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
13449289 TATATAATAC
*
13449299 TATAAAATATAATTTAAATAATTATTATTAAA
1 TATAAAATATAATATAAATAATTATTATTAAA
** ** *
13449331 TATAATTTATAATATACTTTATTATTATTAAA
1 TATAAAATATAATATAAATAATTATTATTAAA
13449363 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAAAATATAATATAAATAATTATTATTAAA
Found at i:13450774 original size:49 final size:49
Alignment explanation
Indices: 13450702--13450805 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
13450692 GAAAAAAAAC
* * ** * *
13450702 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
*
13450751 AAATTAAAATTGAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
13450800 AAATTA
1 AAATTA
13450806 TAACACATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
Found at i:13452966 original size:12 final size:12
Alignment explanation
Indices: 13452942--13452975 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13452932 CCGCATTTTA
13452942 AGCAAAAGAACG
1 AGCAAAAGAACG
* *
13452954 AGCCAAAGCACG
1 AGCAAAAGAACG
13452966 AGCAAAAGAA
1 AGCAAAAGAA
13452976 AATAAATAAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.56, C:0.21, G:0.24, T:0.00
Consensus pattern (12 bp):
AGCAAAAGAACG
Found at i:13454082 original size:23 final size:22
Alignment explanation
Indices: 13454038--13454082 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
13454028 ATAAAAAATC
*
13454038 TATTTAAAAAAAGGTCAAATTT
1 TATTTAAAAAAAGGTAAAATTT
13454060 TATTTAAAATAAAGG-AAATATTT
1 TATTTAAAA-AAAGGTAAA-ATTT
13454083 CCACTTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (22 bp):
TATTTAAAAAAAGGTAAAATTT
Found at i:13454915 original size:13 final size:13
Alignment explanation
Indices: 13454897--13454921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13454887 AACATTCGGC
13454897 CGGTGGGAATAAT
1 CGGTGGGAATAAT
13454910 CGGTGGGAATAA
1 CGGTGGGAATAA
13454922 ACAAATAAAA
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:0.08, G:0.40, T:0.20
Consensus pattern (13 bp):
CGGTGGGAATAAT
Found at i:13461451 original size:22 final size:22
Alignment explanation
Indices: 13461412--13461466 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
13461402 ACAATATAAT
* *
13461412 AACAAAATAGTAGTAAAACAAC
1 AACAAAACAGTAGCAAAACAAC
* *
13461434 AACGAAACAGTAGCAAAATAAC
1 AACAAAACAGTAGCAAAACAAC
13461456 AACAAAACAGT
1 AACAAAACAGT
13461467 TGATTTGGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.62, C:0.16, G:0.11, T:0.11
Consensus pattern (22 bp):
AACAAAACAGTAGCAAAACAAC
Found at i:13463185 original size:71 final size:71
Alignment explanation
Indices: 13463110--13463325 Score: 159
Period size: 71 Copynumber: 3.1 Consensus size: 71
13463100 TATACAATTA
*
13463110 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTACATG
1 ATATTTTGTATGAATCAAATTAATATATTAATTATATTCTTTCCAAAAGAATATTAATTTACATG
13463175 TCTATT
66 TCTATT
** * * * * * * *
13463181 ATATTTTG-A-CCA--AAATTAAT-TAATATAACTGT-TTATATT--AATA-AAT-TTGA-TAAA
1 ATATTTTGTATGAATCAAATTAATAT-AT-TAATTATATTCT-TTCCAAAAGAATATTAATTTAC
* *
13463235 ATATATAAAATT
63 ATGTCT---ATT
*
13463247 ATATTTTGTATGAATCAAATTTATATATTAATTATATTCTTTCCAAAAGAATATTAATTT-CAAT
1 ATATTTTGTATGAATCAAATTAATATATTAATTATATTCTTTCCAAAAGAATATTAATTTAC-AT
*
13463311 GTCTTTT
65 GTCTATT
13463318 ATATTTTG
1 ATATTTTG
13463326 ACTGAAATTA
Statistics
Matches: 102, Mismatches: 25, Indels: 36
0.63 0.15 0.22
Matches are distributed among these distances:
63 6 0.06
64 3 0.03
65 3 0.03
66 15 0.15
67 13 0.13
68 8 0.08
69 8 0.08
70 13 0.13
71 22 0.22
72 3 0.03
73 3 0.03
74 5 0.05
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (71 bp):
ATATTTTGTATGAATCAAATTAATATATTAATTATATTCTTTCCAAAAGAATATTAATTTACATG
TCTATT
Found at i:13463314 original size:137 final size:136
Alignment explanation
Indices: 13463001--13463417 Score: 683
Period size: 138 Copynumber: 3.0 Consensus size: 136
13462991 AGAAAAAAAG
* * *
13463001 AATTATATTCTTTCCAAAATAATATTAATTTCCATGTATTGTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCAATGTCTT-TATATTTTGACCGAAATTAATTAA
*
13463066 TATAACTGTTTATATTAATAAATTTAATAAAATATATACAATTAATATTTTGTATGAATCAAATT
65 TATAACTGTTTATATTAATAAATTTGATAAAATATATACAATT-ATATTTTGTATGAATCAAATT
13463131 CATATATT
129 CATATATT
*
13463139 AATTATATTCTTTCCAAAAGAATATTAATTT-ACATGTCTATTATATTTTGACCAAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCA-ATGTCT-TTATATTTTGACCGAAATTAATTA
*
13463203 ATATAACTGTTTATATTAATAAATTTGATAAAATATATAAAATTATATTTTGTATGAATCAAATT
64 ATATAACTGTTTATATTAATAAATTTGATAAAATATATACAATTATATTTTGTATGAATCAAATT
*
13463268 TATATATT
129 CATATATT
*
13463276 AATTATATTCTTTCCAAAAGAATATTAATTTCAATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCAATGTC-TTTATATTTTGACCGAAATTAATTAA
* *
13463341 TATAACTGTTTATATTAATAAATTCGATAAAATATATACAATTAGTATTTTGTATGAATCAAATA
65 TATAACTGTTTATATTAATAAATTTGATAAAATATATACAATTA-TATTTTGTATGAATCAAATT
13463406 CATATATT
129 CATATATT
13463414 AATT
1 AATT
13463418 TTATCTATGT
Statistics
Matches: 261, Mismatches: 13, Indels: 10
0.92 0.05 0.04
Matches are distributed among these distances:
137 129 0.49
138 131 0.50
139 1 0.00
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (136 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCAATGTCTTTATATTTTGACCGAAATTAATTAAT
ATAACTGTTTATATTAATAAATTTGATAAAATATATACAATTATATTTTGTATGAATCAAATTCA
TATATT
Found at i:13466008 original size:3 final size:3
Alignment explanation
Indices: 13466000--13466048 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
13465990 ATGAATTAAA
* *
13466000 TAT TAT TAT TA- TAT TA- TAT TAT TAT AAT GTAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
13466044 TAT TA
1 TAT TA
13466049 ACTAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:13466019 original size:13 final size:13
Alignment explanation
Indices: 13466003--13466048 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
13465993 AATTAAATAT
13466003 TATTATTATATTA
1 TATTATTATATTA
* *
13466016 TATTATTATAATG
1 TATTATTATATTA
*
13466029 TATTATTAT-TAA
1 TATTATTATATTA
13466041 TATTATTA
1 TATTATTA
13466049 ACTAATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 8 0.29
13 20 0.71
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:13466020 original size:16 final size:16
Alignment explanation
Indices: 13465999--13466046 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
13465989 TATGAATTAA
13465999 ATATTATTATTATATT
1 ATATTATTATTATATT
13466015 ATATTATTA-TA-A-T
1 ATATTATTATTATATT
*
13466028 GTATTATTATTAATATT
1 ATATTATTATT-ATATT
13466045 AT
1 AT
13466047 TAACTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
13 9 0.35
14 2 0.08
15 3 0.12
16 10 0.38
17 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATATTATTATTATATT
Found at i:13466542 original size:17 final size:18
Alignment explanation
Indices: 13466520--13466553 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13466510 TAAATGAGTT
13466520 AATTA-GGATTAAATTGG
1 AATTAGGGATTAAATTGG
*
13466537 AATTAGGGTTTAAATTG
1 AATTAGGGATTAAATTG
13466554 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (18 bp):
AATTAGGGATTAAATTGG
Found at i:13484350 original size:10 final size:10
Alignment explanation
Indices: 13484335--13484364 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
13484325 TTATAGTTTC
13484335 CTTTTTCTTT
1 CTTTTTCTTT
*
13484345 CTTTTTTTTT
1 CTTTTTCTTT
13484355 CTTTTTCTTT
1 CTTTTTCTTT
13484365 TTTATTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:13501563 original size:20 final size:20
Alignment explanation
Indices: 13501540--13501610 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
13501530 CTTCGATGTT
13501540 TCTGTTTGCACTTTGGTGCC
1 TCTGTTTGCACTTTGGTGCC
* *
13501560 TCTGATCGCACATTT-GTGCC
1 TCTGTTTGCAC-TTTGGTGCC
* * * *
13501580 TTTGTTTGTACTTCGGTGCT
1 TCTGTTTGCACTTTGGTGCC
13501600 TCTGTTATGCA
1 TCTGTT-TGCA
13501611 TCTATGATGC
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
19 2 0.05
20 30 0.79
21 6 0.16
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (20 bp):
TCTGTTTGCACTTTGGTGCC
Found at i:13508122 original size:7 final size:7
Alignment explanation
Indices: 13508110--13508146 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
13508100 GCTAAGCTAC
13508110 CACTTAT
1 CACTTAT
13508117 CACTTAT
1 CACTTAT
13508124 CACTTAT
1 CACTTAT
*
13508131 CACTTGT
1 CACTTAT
*
13508138 CACTGAT
1 CACTTAT
13508145 CA
1 CA
13508147 GATAAGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (7 bp):
CACTTAT
Found at i:13508131 original size:57 final size:58
Alignment explanation
Indices: 13508058--13508319 Score: 203
Period size: 57 Copynumber: 4.3 Consensus size: 58
13508048 CTTCCATGGA
* * *
13508058 ATCACTTATCATTTATCTCTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
13508115 ATCACTTATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACTACTTATCACTT
1 ATCACTTGTCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAG---CTAC----CACTT
* * ** * *
13508179 ATCACTTGTCACTTATCACTTGTCACTTG-TCACTGATCAGAT-AAG-TGTAGCTA-AAGCTACC
1 ATCACTTGTCACTTATCACTTGTCAC-TGATCA--GATAAG-TGTAGCTAAAGCTACCA-CT--T
* *
13508240 ACTTATCACTTGTCACTTGTCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTACCACTT
1 A----TCACTTGTCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
13508302 ATCACTTGTCACTGATCA
1 ATCACTTGTCACTTATCA
13508320 GAAGTACTCA
Statistics
Matches: 165, Mismatches: 17, Indels: 45
0.73 0.07 0.20
Matches are distributed among these distances:
57 46 0.28
58 16 0.10
59 2 0.01
60 4 0.02
61 1 0.01
62 2 0.01
63 10 0.06
64 43 0.26
65 31 0.19
66 9 0.05
67 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (58 bp):
ATCACTTGTCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:13508180 original size:7 final size:7
Alignment explanation
Indices: 13508168--13508217 Score: 64
Period size: 7 Copynumber: 7.1 Consensus size: 7
13508158 CTAAGCTACT
13508168 ACTTATC
1 ACTTATC
13508175 ACTTATC
1 ACTTATC
*
13508182 ACTTGTC
1 ACTTATC
13508189 ACTTATC
1 ACTTATC
*
13508196 ACTTGTC
1 ACTTATC
*
13508203 ACTTGTC
1 ACTTATC
*
13508210 ACTGATC
1 ACTTATC
13508217 A
1 A
13508218 GATAAGTGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (7 bp):
ACTTATC
Found at i:13508190 original size:14 final size:14
Alignment explanation
Indices: 13508168--13508212 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
13508158 CTAAGCTACT
*
13508168 ACTTATCACTTATC
1 ACTTGTCACTTATC
13508182 ACTTGTCACTTATC
1 ACTTGTCACTTATC
*
13508196 ACTTGTCACTTGTC
1 ACTTGTCACTTATC
13508210 ACT
1 ACT
13508213 GATCAGATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.22, C:0.29, G:0.07, T:0.42
Consensus pattern (14 bp):
ACTTGTCACTTATC
Found at i:13508194 original size:21 final size:21
Alignment explanation
Indices: 13508168--13508217 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
13508158 CTAAGCTACT
13508168 ACTTATCACTTATCACTTGTC
1 ACTTATCACTTATCACTTGTC
*
13508189 ACTTATCACTTGTCACTTGTC
1 ACTTATCACTTATCACTTGTC
*
13508210 ACTGATCA
1 ACTTATCA
13508218 GATAAGTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (21 bp):
ACTTATCACTTATCACTTGTC
Done.