Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_pilon, whole genome shotgun sequence
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: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 18
Found at i:2981221 original size:113 final size:112
Alignment explanation
Indices: 2981097--2981473 Score: 539
Period size: 113 Copynumber: 3.4 Consensus size: 112
2981087 CAGAAAGAGT
*
2981097 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCTA
1 TCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCTA
*
2981162 TCACTTGATGGATTATCTTTTCCAGAAAGAGTTCATAATGAGAAGAAC
66 TCACTTGATGGATTAACTTTTCCAGAAA-AGTTCATAATGAGAAGAAC
*
2981210 TCATCTGAAGAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCTA
1 TCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCTA
* * ** *
2981272 TCACTTGATAGATTAGCTTTTCCAGTTCAAGTTCATAATAAGAAGAAC
66 TCACTTGATGGATTAACTTTTCCAG-AAAAGTTCATAATGAGAAGAAC
* * *
2981320 TCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTTCAGA-TTTTTGCTCAAATCC
1 TCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAACTTGTTCA-ACCTTTTGCTCAAATCT
* * *
2981384 ATCACTTGATGGATCAACTCTTCTAGAGAAAGTTCATAATGAGAAGAAC
65 ATCACTTGATGGATTAACTTTTCCAGA-AAAGTTCATAATGAGAAGAAC
*
2981433 TCATC-GAAAGAATGATGAAGAAGTTCATAATGAGAAGAACT
1 TCATCTG-AAGAAGGATGAAGAAGTTCATAATGAGAAGAACT
2981474 CATCAAGAGC
Statistics
Matches: 239, Mismatches: 18, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
110 101 0.42
111 2 0.01
112 2 0.01
113 133 0.56
114 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
TCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATCTA
TCACTTGATGGATTAACTTTTCCAGAAAAGTTCATAATGAGAAGAAC
Found at i:2981738 original size:3 final size:3
Alignment explanation
Indices: 2981730--2981825 Score: 174
Period size: 3 Copynumber: 32.0 Consensus size: 3
2981720 CCATATTGAT
*
2981730 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2981778 TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2981826 AATATATTAA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2989489 original size:134 final size:133
Alignment explanation
Indices: 2989182--2990250 Score: 1181
Period size: 134 Copynumber: 8.0 Consensus size: 133
2989172 TTTGCATATC
* * * *
2989182 TGATATTCCCTCCTA-AAGAAGCAGAACATATCCCTCTCTTTCAATATTTGATATTCTCTGAGTA
1 TGATATTCCCTTC-AGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAGTA
* * **
2989246 ACAGCGAAATAAGTCTACCCCGATTCAATCTTTCCC-GAGTAACAGGGGAATGGGATCAACTCCC
65 ACAGCG-AACAAGTCTACCCCGATTCAATC-TTCCCTGAGTGACAGTAGAAT-GGATCAACTCCC
* *
2989310 CTAGATT
127 CCAGATA
* * * *
2989317 TGATATTCTCTTCAGAAGAAGCGGAACAAATCCATCTCTTTCAAGATTTGATATTCTCTTAGTGA
1 TGATATTCCCTTCAGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAGTAA
* * *
2989382 TAGCAGAACAAGTCTGCACCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAACTCCCCCA
66 CAGC-GAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAACTCCCCCA
*
2989447 TATA
130 GATA
* * *
2989451 TGATATTCCCTTCAGAAGAAGCGGAACATATCCCTCTCTTTCAAGATTTGATACTCCCTGAGTAA
1 TGATATTCCCTTCAGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAGTAA
* ** *
2989516 CAGCTGAACAAGTCTA-CACGATTCAATCTT-CCTGAGTGACAGCGGAATGGATCAACTCCTCCA
66 CAGC-GAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAACTCCCCCA
*
2989579 AATA
130 GATA
* * *
2989583 TGATATTCCCTTCAGAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCTTTGAGTGA
1 TGATATTCCCTTCAGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAGTAA
* * * **
2989648 CAGTGGAACAAGTCTACCCCTATTCAATCTTCCTTGAGTGACAGCGGAATGGATCAACTCCCCCA
66 CAG-CGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAACTCCCCCA
*
2989713 TATA
130 GATA
* * * * * * *
2989717 TTATATTCCCTTTAGAAGAAGCGAAATATATCCCTCTCTTTCAATATTTGATATTCTCTGAGTGA
1 TGATATTCCCTTCAGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAGTAA
* * *
2989782 TAGCAGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAACTCCCCTA
66 CAGC-GAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAACTCCCCCA
*
2989847 GATC
130 GATA
* ** * * * *
2989851 TGATACTT-CATTCAGAAGAAGCGGAACATGTCTCTCCCTTTCAAGATTTGATATTCCCTGAGTG
1 TGATA-TTCCCTTCAGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAGTA
* * * * * *
2989915 ACAACGAAATAAGTTTACCCCAATTCAAT-TTCCCTGAGTGACAGCAGAATGGATCAACTCCCCT
65 ACAGCG-AACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAACTCCCCC
*
2989979 AGATC
129 AGATA
* ** * * * *
2989984 TGATATTCCCTCCAGAAGAAG-TAAAGCAAATACATCTCTTTCAAGATTTGATATTCCCTGAATA
1 TGATATTCCCTTCAGAAGAAGCGGAA-CAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAGTA
* * * *
2990048 ACATCGAAACAAGTCTGCCCCGATTCAATCTTCCCTAAGTGATAGT-GAAATGGATCAACAT-CC
65 ACAGCG-AACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGTAG-AATGGATCAAC-TCCC
2990111 CCAGAT-
127 CCAGATA
* * * * * *
2990117 TCGATATTCCCTCCAGAAGAAGCAGCATAAATCCCCCTCTTTCAAGATTTGATATTC-CTTGAGC
1 T-GATATTCCCTTCAGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCTC-TGAGT
* *
2990181 AACAGCGGAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAACAT-CC
64 AACAGC-GAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAAC-TCCC
2990245 CCAGAT
127 CCAGAT
2990251 CTACTATTCC
Statistics
Matches: 800, Mismatches: 115, Indels: 39
0.84 0.12 0.04
Matches are distributed among these distances:
132 110 0.14
133 137 0.17
134 456 0.57
135 96 0.12
136 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (133 bp):
TGATATTCCCTTCAGAAGAAGCGGAACAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAGTAA
CAGCGAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAACTCCCCCAG
ATA
Found at i:2990159 original size:401 final size:395
Alignment explanation
Indices: 2989179--2990260 Score: 1354
Period size: 401 Copynumber: 2.7 Consensus size: 395
2989169 TAATTTGCAT
* * *
2989179 ATCTGATATTCCCTCCTA-AAGAAGCAGAACATATCCCTCTCTTTCAATATTTGATATTCTCTGA
1 ATCTGATATTCCCTCC-AGAAGAAGTA-AACAAATCCCTCTCTTTCAAGATTTGATATTCTCTGA
* * * *
2989243 GTAACAGCGAAATAAGTCTACCCCGATTCAATCTTTCCC-GAGTAACAGGGGAATGGGATCAACT
64 GTAACATCGAAACAAGTCTACCCCGATTCAATC-TTCCCTGAGTGACAGCGGAAT-GGATCAACT
* * *
2989307 CCCCTAGATTTGATATTCTCTTCAGAAGAAGCGGAACAAATCCATCTCTTTCAAGATTTGATATT
127 CCCC-AGA-TTGATATTCCCTTCAGAAGAAGC-GAATAAATCCCTCTCTTTCAAGATTTGATATT
* *
2989372 CTCTTAGTGATAGCAGAACAAGTCTGCACCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATC
189 CTCTGAGTGATAGCAGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATC
* * * *
2989437 AACTCCCCCATATATGATATTCCCTTCAGAAGAAGCGGAACATATCCCTCTCTTTCAAGATTTGA
254 AACT-CCCCAGATCTGATATTCCATTCAGAAGAAGCGGAACATATCCCTCCCTTTCAAGATTTGA
* * *
2989502 TACTCCCTGAGTAACAGCTGAACAAGTCTACACGATTCAATCTTCCTGAGTGACAGCGGAATGGA
318 TACTCCCTGAGTAACAACTGAACAAGTCTACACAATTCAATCTTCCTGAGTGACAGCAGAATGGA
2989567 TCAACTCCTCCAA
383 TCAACTCCTCCAA
* * * *
2989580 ATATGATATTCCCTTCAGAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCTTTGAG
1 ATCTGATATTCCCTCCAGAAGAAGT-AAACAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAG
* * * *
2989645 TGACAGT-GGAACAAGTCTACCCCTATTCAATCTTCCTTGAGTGACAGCGGAATGGATCAACTCC
65 TAACA-TCGAAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACT-C
* * * * *
2989709 CCCATATATTATATTCCCTTTAGAAGAAGCGAAATATATCCCTCTCTTTCAATATTTGATATTCT
128 CCCAGAT-TGATATTCCCTTCAGAAGAAGCG-AATAAATCCCTCTCTTTCAAGATTTGATATTCT
2989774 CTGAGTGATAGCAGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAA
191 CTGAGTGATAGCAGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAA
* *
2989839 CTCCCCTAGATCTGATACTT-CATTCAGAAGAAGCGGAACATGTCTCTCCCTTTCAAGATTTGAT
256 CTCCCC-AGATCTGATA-TTCCATTCAGAAGAAGCGGAACATATCCCTCCCTTTCAAGATTTGAT
* * * * *
2989903 ATTCCCTGAGTGACAAC-GAAATAAGTTTACCCCAATTCAAT-TTCCCTGAGTGACAGCAGAATG
319 ACTCCCTGAGTAACAACTG-AACAAGTCTA-CACAATTCAATCTT-CCTGAGTGACAGCAGAATG
*
2989966 GATCAACTCC-CCTAG
381 GATCAACTCCTCC-AA
* * * *
2989981 ATCTGATATTCCCTCCAGAAGAAGTAAAGCAAATACATCTCTTTCAAGATTTGATATTCCCTGAA
1 ATCTGATATTCCCTCCAGAAGAAGTAAA-CAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAG
* * * * *
2990046 TAACATCGAAACAAGTCTGCCCCGATTCAATCTTCCCTAAGTGATAGTGAAATGGATCAACATCC
65 TAACATCGAAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAAC-TCC
* * *
2990111 CCAGATTCGATATTCCCTCCAGAAGAAGCAGCATAAATCCCCCTCTTTCAAGATTTGATATTC-C
129 CCAGATT-GATATTCCCTTCAGAAGAAGC-GAATAAATCCCTCTCTTTCAAGATTTGATATTCTC
** * * *
2990175 TTGAGCAACAGCGGAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAA
192 -TGAGTGATAGCAGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAA
2990240 CATCCCCAGATCT-ACTATTCC
256 C-TCCCCAGATCTGA-TATTCC
2990261 CTGAGTGACA
Statistics
Matches: 589, Mismatches: 70, Indels: 44
0.84 0.10 0.06
Matches are distributed among these distances:
399 7 0.01
400 211 0.36
401 364 0.62
402 7 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (395 bp):
ATCTGATATTCCCTCCAGAAGAAGTAAACAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAGT
AACATCGAAACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACTCCCC
AGATTGATATTCCCTTCAGAAGAAGCGAATAAATCCCTCTCTTTCAAGATTTGATATTCTCTGAG
TGATAGCAGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAACTCCC
CAGATCTGATATTCCATTCAGAAGAAGCGGAACATATCCCTCCCTTTCAAGATTTGATACTCCCT
GAGTAACAACTGAACAAGTCTACACAATTCAATCTTCCTGAGTGACAGCAGAATGGATCAACTCC
TCCAA
Found at i:2990193 original size:535 final size:536
Alignment explanation
Indices: 2989184--2990246 Score: 1382
Period size: 535 Copynumber: 2.0 Consensus size: 536
2989174 TGCATATCTG
2989184 ATATTCCCTCCTAAAGAAGCAGAACATATCCCTCTCTTTCAATATTTGATATTCTCTGAGTAACA
1 ATATTCCCTCCTAAAGAAGCAGAACATATCCCTCTCTTTCAATATTTGATATTCTCTGAGTAACA
* *
2989249 GCGAAATAAGTCTACCCCGATTCAATCTTTCCCGAGTAACAGGGGAATGGGATCAACTCCCCTAG
66 GCGAAACAAGTCTACCCCGATTCAATCTTTCCCGAGTAACAGGAGAATGGGATCAACTCCCCTAG
* * * * *
2989314 ATTTGATATTCTCTTCAGAAGAAGCGGAACAAATCCATCTCTTTCAAGATTTGATATTCTCTTAG
131 ATCTGATATTCTATTCAGAAGAAGCGGAACAAATCCATCCCTTTCAAGATTTGATATTCCCTGAG
* * * * *
2989379 TGATAGCAGAACAAGTCTGCACCGATTCAATCTTCCCTGAGTGACAGTAGAATGGATCAACTCCC
196 TGACAACAGAACAAGTCTACACCAATTCAATCTTCCCTGAGTGACAGCAGAATGGATCAACTCCC
* * * * * *
2989444 CCATATATGATATTCCCTTCAGAAGAAGCGGAACATATCCCTCTCTTTCAAGATTTGATACTCCC
261 CCAGATATGATATTCCCTCCAGAAGAAGCGAAACAAATACATCTCTTTCAAGATTTGATACTCCC
* * *
2989509 TGAGTAACAGCTGAACAAGTCTACACGATTCAATCTTCCTGAGTGACAGCGGAATGGATCAACTC
326 TGAATAACAGCTGAACAAGTCTACACGATTCAATCTTCCTAAGTGACAGCGAAATGGATCAACTC
* ** *
2989574 CTCCAAATATGATATTCCCTTCAGAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTC
391 CTCCAAATATGATATTCCCTCCAGAAGAAGCAGAACAAATCCCCCTCTTTCAAGATTTGATATTC
* ** * * *
2989639 TTTGAGTGACAGTGGAACAAGTCTACCCCT-ATTCAATCTTCCTTGAGTGACAGCGGAATGGATC
456 CTTGAGCAACAGCGGAACAAGTCT-CCCCTGATTCAATCTTCCCTGAGTGACAGCAGAATGGATC
2989703 AAC-TCCCCCATATATT
520 AACATCCCCCATATATT
* * *
2989719 ATATTCCCT-TTAGAAGAAGC-GAAATATATCCCTCTCTTTCAATATTTGATATTCTCTGAGTGA
1 ATATTCCCTCCTA-AAGAAGCAG-AACATATCCCTCTCTTTCAATATTTGATATTCTCTGAGTAA
* * * *
2989782 TAGC-AGAACAAGTCTGCCCCGATTCAATC-TTCCCTGAGTGACAGTAGAAT-GGATCAACTCCC
64 CAGCGA-AACAAGTCTACCCCGATTCAATCTTTCCC-GAGTAACAGGAGAATGGGATCAACTCCC
**
2989844 CTAGATCTGATACTTC-ATTCAGAAGAAGCGGAACATGTCTC-TCCCTTTCAAGATTTGATATTC
127 CTAGATCTGATA-TTCTATTCAGAAGAAGCGGAACAAATC-CATCCCTTTCAAGATTTGATATTC
* * *
2989907 CCTGAGTGACAAC-GAAATAAGTTTACCCCAATTCAAT-TTCCCTGAGTGACAGCAGAATGGATC
190 CCTGAGTGACAACAG-AACAAGTCTACACCAATTCAATCTTCCCTGAGTGACAGCAGAATGGATC
* * *
2989970 AACTCCCCTAGATCTGATATTCCCTCCAGAAGAAG-TAAAGCAAATACATCTCTTTCAAGATTTG
254 AACTCCCCCAGATATGATATTCCCTCCAGAAGAAGCGAAA-CAAATACATCTCTTTCAAGATTTG
* * * * * *
2990034 ATATTCCCTGAATAACATC-GAAACAAGTCTGCCCCGATTCAATCTTCCCTAAGTGATAGTGAAA
318 ATACTCCCTGAATAACAGCTG-AACAAGTCT-ACACGATTCAATCTT-CCTAAGTGACAGCGAAA
* * *
2990098 TGGATCAACATCC-CCAGAT-TCGATATTCCCTCCAGAAGAAGCAGCATAAATCCCCCTCTTTCA
380 TGGATCAAC-TCCTCCAAATAT-GATATTCCCTCCAGAAGAAGCAGAACAAATCCCCCTCTTTCA
*
2990161 AGATTTGATATTCCTTGAGCAACAGCGGAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGACA
443 AGATTTGATATTCCTTGAGCAACAGCGGAACAAGTCTCCCCTGATTCAATCTTCCCTGAGTGACA
*
2990226 GTAGAATGGATCAACATCCCC
508 GCAGAATGGATCAACATCCCC
2990247 AGATCTACTA
Statistics
Matches: 456, Mismatches: 57, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
532 3 0.01
533 103 0.23
534 117 0.26
535 225 0.49
536 8 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (536 bp):
ATATTCCCTCCTAAAGAAGCAGAACATATCCCTCTCTTTCAATATTTGATATTCTCTGAGTAACA
GCGAAACAAGTCTACCCCGATTCAATCTTTCCCGAGTAACAGGAGAATGGGATCAACTCCCCTAG
ATCTGATATTCTATTCAGAAGAAGCGGAACAAATCCATCCCTTTCAAGATTTGATATTCCCTGAG
TGACAACAGAACAAGTCTACACCAATTCAATCTTCCCTGAGTGACAGCAGAATGGATCAACTCCC
CCAGATATGATATTCCCTCCAGAAGAAGCGAAACAAATACATCTCTTTCAAGATTTGATACTCCC
TGAATAACAGCTGAACAAGTCTACACGATTCAATCTTCCTAAGTGACAGCGAAATGGATCAACTC
CTCCAAATATGATATTCCCTCCAGAAGAAGCAGAACAAATCCCCCTCTTTCAAGATTTGATATTC
CTTGAGCAACAGCGGAACAAGTCTCCCCTGATTCAATCTTCCCTGAGTGACAGCAGAATGGATCA
ACATCCCCCATATATT
Found at i:2993299 original size:3 final size:3
Alignment explanation
Indices: 2993291--2993333 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
2993281 ATTCGAGATG
*
2993291 ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2993334 ATATTACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2993906 original size:35 final size:35
Alignment explanation
Indices: 2993867--2993964 Score: 153
Period size: 35 Copynumber: 2.8 Consensus size: 35
2993857 AAATAAGTCC
2993867 ATTCACCAAGTGACCTGAGTTATTATAATAAATAT
1 ATTCACCAAGTGACCTGAGTTATTATAATAAATAT
2993902 ATTCACCAAGTGACAC-GAGTTATTATAATAAATAT
1 ATTCACCAAGTGAC-CTGAGTTATTATAATAAATAT
* * *
2993937 ATTCACCAAGTGACATTACTTATTATAA
1 ATTCACCAAGTGACCTGAGTTATTATAA
2993965 ATAGCATCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
35 57 0.98
36 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (35 bp):
ATTCACCAAGTGACCTGAGTTATTATAATAAATAT
Found at i:2994748 original size:30 final size:27
Alignment explanation
Indices: 2994694--2994760 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 27
2994684 GTCAAGGAGT
2994694 AGGAGGAGGAGAAGAAGGAAGAGAAAGCTA
1 AGGAGGAGGAGAAGAAGGAAGAG-AAG--A
* *
2994724 AGGAGGAGGAGAA-ATATGAGGAGAAGA
1 AGGAGGAGGAGAAGA-AGGAAGAGAAGA
2994751 AGGAGGAGGA
1 AGGAGGAGGA
2994761 TGAGAGAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 11 0.32
29 4 0.12
30 19 0.56
ACGTcount: A:0.48, C:0.01, G:0.46, T:0.04
Consensus pattern (27 bp):
AGGAGGAGGAGAAGAAGGAAGAGAAGA
Found at i:3001041 original size:33 final size:33
Alignment explanation
Indices: 3001004--3001085 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
3000994 GAATAAGGGT
*
3001004 TAATGGGAGGTAACGTGTCACGTTAGATAAAAA
1 TAATGGGAGGTAACGTGCCACGTTAGATAAAAA
*
3001037 TAATGGGAGGTAACATGCCACGTTAGATAAAAA
1 TAATGGGAGGTAACGTGCCACGTTAGATAAAAA
3001070 TAATGGGAGGTAACGT
1 TAATGGGAGGTAACGT
3001086 CAGGGACCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.39, C:0.10, G:0.28, T:0.23
Consensus pattern (33 bp):
TAATGGGAGGTAACGTGCCACGTTAGATAAAAA
Found at i:3001450 original size:206 final size:208
Alignment explanation
Indices: 3001095--3001509 Score: 816
Period size: 206 Copynumber: 2.0 Consensus size: 208
3001085 TCAGGGACCT
3001095 TACTGAAACTAAATTAAAAGTTCAATGACTATATTGCATGTTTTGAAAGTTAGGTGACCAAAAAT
1 TACTGAAACTAAATTAAAAGTTCAATGACTATATTGCATGTTTTGAAAGTTAGGTGACCAAAAAT
3001160 AAAAATATCCTAAAAGTTTGATGACTATTTATATAGTTTACCCTTAAAATATATGAGGATCAAGG
66 AAAAATATCCTAAAAGTTTGATGACTATTTATATAGTTTACCCTTAAAATATATGAGGATCAAGG
3001225 CTTGTAAGTTCCCGATAAAA-AAAAAAAAATCATGTTAAATTCAAATCGAATAAGGTTTAAGTAC
131 CTTGTAAGTTCCCGATAAAAGAAAAAAAAATCATGTTAAATTCAAATCGAATAAGGTTTAAGTAC
3001289 AAATTTAAGTTAA
196 AAATTTAAGTTAA
3001302 TACTGAAACTAAATTAAAAGTTCAATGACTAT-TTGCATGTTTTGAAAGTTAGGTGACCAAAAAT
1 TACTGAAACTAAATTAAAAGTTCAATGACTATATTGCATGTTTTGAAAGTTAGGTGACCAAAAAT
3001366 AAAAATATCCTAAAAGTTTGATGACTATTTATATAGTTTACCCTTAAAATATATGAGGATCAAGG
66 AAAAATATCCTAAAAGTTTGATGACTATTTATATAGTTTACCCTTAAAATATATGAGGATCAAGG
3001431 CTTGTAAGTTCCCGATAAAAGAAAAAAAAATCATGTTAAATTCAAATCGAATAAGGTTTAAGTAC
131 CTTGTAAGTTCCCGATAAAAGAAAAAAAAATCATGTTAAATTCAAATCGAATAAGGTTTAAGTAC
3001496 AAATTTAAGTTAA
196 AAATTTAAGTTAA
3001509 T
1 T
3001510 TTCAAATCAA
Statistics
Matches: 207, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
206 117 0.57
207 90 0.43
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (208 bp):
TACTGAAACTAAATTAAAAGTTCAATGACTATATTGCATGTTTTGAAAGTTAGGTGACCAAAAAT
AAAAATATCCTAAAAGTTTGATGACTATTTATATAGTTTACCCTTAAAATATATGAGGATCAAGG
CTTGTAAGTTCCCGATAAAAGAAAAAAAAATCATGTTAAATTCAAATCGAATAAGGTTTAAGTAC
AAATTTAAGTTAA
Found at i:3001826 original size:23 final size:23
Alignment explanation
Indices: 3001794--3001849 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
3001784 ATCAAAATAT
* * *
3001794 TATTTATTAAAAAT-ATTTTTTAA
1 TATTTTTTAAAAATAATATATT-A
*
3001817 TATTTTTTAATAATAATATATTA
1 TATTTTTTAAAAATAATATATTA
3001840 TATTTTTTAA
1 TATTTTTTAA
3001850 TATTATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTTTTAAAAATAATATATTA
Found at i:3001850 original size:23 final size:24
Alignment explanation
Indices: 3001816--3001899 Score: 82
Period size: 28 Copynumber: 3.3 Consensus size: 24
3001806 ATATTTTTTA
3001816 ATATTTTTTAATA-ATAATATATT
1 ATATTTTTTAATATATAATATATT
*
3001839 ATATTTTTTAATATTATAATATACTC
1 ATATTTTTTAATA-TATAATATA-TT
*
3001865 A-ATTATATTATAATAATATAAAATATT
1 ATATT-T-TT-TAAT-ATATAATATATT
3001892 ATATTTTT
1 ATATTTTT
3001900 ATTTCAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
23 13 0.26
25 11 0.22
26 5 0.10
27 5 0.10
28 15 0.30
29 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
ATATTTTTTAATATATAATATATT
Found at i:3002718 original size:14 final size:14
Alignment explanation
Indices: 3002701--3002730 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3002691 AAATCTGCAG
3002701 ACGTAAATGGTTAA
1 ACGTAAATGGTTAA
*
3002715 ACGTAGATGGTTAA
1 ACGTAAATGGTTAA
3002729 AC
1 AC
3002731 ATGTTATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (14 bp):
ACGTAAATGGTTAA
Found at i:3008189 original size:23 final size:24
Alignment explanation
Indices: 3008144--3008193 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
3008134 TAAGCGAACA
*
3008144 ATAAAATATATTTAATAAGTTAAT
1 ATAAAAAATATTTAATAAGTTAAT
*
3008168 ATAAAAAATATTT-TTAAGTTAAT
1 ATAAAAAATATTTAATAAGTTAAT
3008191 ATA
1 ATA
3008194 TATAATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
ATAAAAAATATTTAATAAGTTAAT
Found at i:3008393 original size:35 final size:36
Alignment explanation
Indices: 3008324--3008393 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
3008314 CACACATAAG
* * * *
3008324 TTTAAAAATTCAAATTACATAATTGAAATAAATTTT
1 TTTAAAAATTCAAAATAAATAAATAAAATAAATTTT
3008360 TTTAAAAATT-AAAATAAATAAATAAAATAAATTT
1 TTTAAAAATTCAAAATAAATAAATAAAATAAATTT
3008394 GAAATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (36 bp):
TTTAAAAATTCAAAATAAATAAATAAAATAAATTTT
Found at i:3008561 original size:13 final size:13
Alignment explanation
Indices: 3008539--3008572 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
3008529 GAGAATTATG
3008539 AATA-AAAAATTT
1 AATATAAAAATTT
3008551 AATATAAAAATTT
1 AATATAAAAATTT
3008564 AATATAAAA
1 AATATAAAA
3008573 TATTGATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATATAAAAATTT
Found at i:3008946 original size:31 final size:31
Alignment explanation
Indices: 3008906--3008976 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
3008896 ACCCGTGATA
*
3008906 ATCACATCTTAATTAAATAAAAACGAAAGTG
1 ATCATATCTTAATTAAATAAAAACGAAAGTG
*
3008937 ATCATATCTTAATTAAATAAAAATGAAAGTG
1 ATCATATCTTAATTAAATAAAAACGAAAGTG
3008968 A-CTATATCT
1 ATC-ATATCT
3008977 CATATTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 1 0.03
31 36 0.97
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.31
Consensus pattern (31 bp):
ATCATATCTTAATTAAATAAAAACGAAAGTG
Found at i:3016968 original size:63 final size:63
Alignment explanation
Indices: 3016895--3017020 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
3016885 CTTCTTTCTG
3016895 AGACAGTTCTTCACTAATGGTTACGAAGTTCAGATTGTTGGTTGGGGTTATGCCCGTAATTCC
1 AGACAGTTCTTCACTAATGGTTACGAAGTTCAGATTGTTGGTTGGGGTTATGCCCGTAATTCC
3016958 AGACAGTTCTTCACTAATGGTTACGAAGTTCAGATTGTTGGTTGGGGTTATGCCCGTAATTCC
1 AGACAGTTCTTCACTAATGGTTACGAAGTTCAGATTGTTGGTTGGGGTTATGCCCGTAATTCC
3017021 TGTGTTATCA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.35
Consensus pattern (63 bp):
AGACAGTTCTTCACTAATGGTTACGAAGTTCAGATTGTTGGTTGGGGTTATGCCCGTAATTCC
Found at i:3029841 original size:18 final size:18
Alignment explanation
Indices: 3029818--3029853 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3029808 TTTTGGTGCA
*
3029818 GAGGGAATCGATCCCCCT
1 GAGGGAACCGATCCCCCT
*
3029836 GAGGGAACCGATTCCCCT
1 GAGGGAACCGATCCCCCT
3029854 TTGAAGGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (18 bp):
GAGGGAACCGATCCCCCT
Found at i:3029883 original size:20 final size:20
Alignment explanation
Indices: 3029858--3029895 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3029848 TCCCCTTTGA
*
3029858 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
3029878 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
3029896 TGTGGTTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:3030291 original size:25 final size:24
Alignment explanation
Indices: 3030263--3030312 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 24
3030253 AATTTTCCAA
3030263 AAAAAAAAT-TTAAATTTTCGAAATT
1 AAAAAAAATGTT-AATTTTC-AAATT
3030288 AAAAAAAATGTTAATTTTCAAATT
1 AAAAAAAATGTTAATTTTCAAATT
3030312 A
1 A
3030313 TTGTGTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.25
25 16 0.67
26 2 0.08
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (24 bp):
AAAAAAAATGTTAATTTTCAAATT
Found at i:3034454 original size:24 final size:24
Alignment explanation
Indices: 3034425--3034475 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3034415 TTGGAAATGG
3034425 GGTTAGGGATTTTAATTAAGGGGA
1 GGTTAGGGATTTTAATTAAGGGGA
3034449 GGTTAGGGATTTTAATTAAGGGGA
1 GGTTAGGGATTTTAATTAAGGGGA
3034473 GGT
1 GGT
3034476 GTACTGCCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.39, T:0.33
Consensus pattern (24 bp):
GGTTAGGGATTTTAATTAAGGGGA
Found at i:3037424 original size:24 final size:24
Alignment explanation
Indices: 3037397--3037445 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3037387 TTGGAAATAG
3037397 GGTTAGAGATTTCAATTAAGGGGA
1 GGTTAGAGATTTCAATTAAGGGGA
* *
3037421 GGTTAGGGATTTTAATTAAGGGGA
1 GGTTAGAGATTTCAATTAAGGGGA
3037445 G
1 G
3037446 TTGTACTGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.02, G:0.37, T:0.31
Consensus pattern (24 bp):
GGTTAGAGATTTCAATTAAGGGGA
Found at i:3040088 original size:42 final size:42
Alignment explanation
Indices: 3040036--3040123 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
3040026 CTGCAAGGAA
* *
3040036 GAAAAACAGAAACTTGAAGCATCTTTGCATGAATGTAATGAG
1 GAAAAACAGAAACTTGAAGCATCTTTGCAAGAATGTAACGAG
* *
3040078 GAAAAACAGAAACTTGAAGCGTTTTTGCAAGAATGTAACGAG
1 GAAAAACAGAAACTTGAAGCATCTTTGCAAGAATGTAACGAG
3040120 GAAA
1 GAAA
3040124 TATCTAGAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (42 bp):
GAAAAACAGAAACTTGAAGCATCTTTGCAAGAATGTAACGAG
Found at i:3045694 original size:20 final size:20
Alignment explanation
Indices: 3045660--3045706 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3045650 GAGAGAGCAC
3045660 AGTAGAAAGTAAATGTAAAAG
1 AGTA-AAAGTAAATGTAAAAG
* *
3045681 AGTAAAAGTGAATGTGAAAG
1 AGTAAAAGTAAATGTAAAAG
*
3045701 ATTAAA
1 AGTAAA
3045707 TTTAGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.21
Consensus pattern (20 bp):
AGTAAAAGTAAATGTAAAAG
Found at i:3054074 original size:20 final size:20
Alignment explanation
Indices: 3054051--3054090 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3054041 ACTAATAACC
3054051 TTAACAGTCAGCTAACAGCT
1 TTAACAGTCAGCTAACAGCT
3054071 TTAACAGTCAGCTAACAGCT
1 TTAACAGTCAGCTAACAGCT
3054091 AAGACCAACA
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:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
TTAACAGTCAGCTAACAGCT
Found at i:3058600 original size:25 final size:25
Alignment explanation
Indices: 3058564--3058613 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3058554 GTATTGGTCT
3058564 TCCGTCTCCGTCCCCGTTTAAAAAA
1 TCCGTCTCCGTCCCCGTTTAAAAAA
*
3058589 TCCGTACT-CGTCTCCGTTTAAAAAA
1 TCCGT-CTCCGTCCCCGTTTAAAAAA
3058614 ATACAGGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (25 bp):
TCCGTCTCCGTCCCCGTTTAAAAAA
Found at i:3058946 original size:16 final size:16
Alignment explanation
Indices: 3058925--3058958 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3058915 ATTTTTTTGT
3058925 CATCCCTAATTATGGC
1 CATCCCTAATTATGGC
3058941 CATCCCTAATTATGGC
1 CATCCCTAATTATGGC
3058957 CA
1 CA
3058959 AGTATTTGGT
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:0.26, C:0.32, G:0.12, T:0.29
Consensus pattern (16 bp):
CATCCCTAATTATGGC
Found at i:3059255 original size:28 final size:28
Alignment explanation
Indices: 3059199--3059260 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
3059189 CAAAGTATTT
*
3059199 TTTTTTGTTAAAATAAATATTTAAAGTA
1 TTTTTTGTTAAAATAAATACTTAAAGTA
** **
3059227 TTTTTTGTTAAAATTGATACTTATTGTA
1 TTTTTTGTTAAAATAAATACTTAAAGTA
3059255 TTTTTT
1 TTTTTT
3059261 TTTTATCAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (28 bp):
TTTTTTGTTAAAATAAATACTTAAAGTA
Found at i:3071011 original size:21 final size:21
Alignment explanation
Indices: 3070982--3071024 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3070972 AATATGTAAA
3070982 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
3071003 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
3071024 T
1 T
3071025 TGCAACGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:3071066 original size:40 final size:40
Alignment explanation
Indices: 3071019--3071152 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 40
3071009 TGCGATTTTC
*
3071019 CAAATTTGCAACGCTAAT-CTGTAAA-TCACAACGCGATAGT
1 CAAATTTGCAACGC-AATAGT-TAAATTCACAACGCGATAGT
* * *
3071059 CAAATTTGCAATGCGATAGTTAAATTCGCAACGCGATAGT
1 CAAATTTGCAACGCAATAGTTAAATTCACAACGCGATAGT
* * * ** * * *
3071099 CAAATTCGCAACGCGATAGTCAAATTGGCAACACAAAAGT
1 CAAATTTGCAACGCAATAGTTAAATTCACAACGCGATAGT
*
3071139 CAAATTCGCAACGC
1 CAAATTTGCAACGC
3071153 GAATTTAATT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
39 6 0.07
40 75 0.93
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (40 bp):
CAAATTTGCAACGCAATAGTTAAATTCACAACGCGATAGT
Found at i:3071076 original size:20 final size:20
Alignment explanation
Indices: 3071047--3071154 Score: 153
Period size: 20 Copynumber: 5.4 Consensus size: 20
3071037 CTGTAAATCA
*
3071047 CAACGCGATAGTCAAATTTG
1 CAACGCGATAGTCAAATTCG
* *
3071067 CAATGCGATAGTTAAATTCG
1 CAACGCGATAGTCAAATTCG
3071087 CAACGCGATAGTCAAATTCG
1 CAACGCGATAGTCAAATTCG
*
3071107 CAACGCGATAGTCAAATTGG
1 CAACGCGATAGTCAAATTCG
* * *
3071127 CAACACAAAAGTCAAATTCG
1 CAACGCGATAGTCAAATTCG
3071147 CAACGCGA
1 CAACGCGA
3071155 ATTTAATTTC
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (20 bp):
CAACGCGATAGTCAAATTCG
Found at i:3072092 original size:23 final size:23
Alignment explanation
Indices: 3072043--3072094 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3072033 GTATTCAAAA
*
3072043 TTTGATCTTAGTCAATACCCGAC
1 TTTGATCTTAGTCAATACCAGAC
* *
3072066 TTTGATCTTGGTC-ATACTCAGAT
1 TTTGATCTTAGTCAATAC-CAGAC
3072089 TTTGAT
1 TTTGAT
3072095 GATGTATGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (23 bp):
TTTGATCTTAGTCAATACCAGAC
Found at i:3074155 original size:18 final size:18
Alignment explanation
Indices: 3074132--3074167 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3074122 AAGCAAAAGG
*
3074132 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
3074150 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
3074168 CAACCAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:3075010 original size:18 final size:18
Alignment explanation
Indices: 3074989--3075025 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3074979 GTAATTGGAG
3074989 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
3075007 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
3075025 T
1 T
3075026 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:3075032 original size:24 final size:24
Alignment explanation
Indices: 3074981--3075033 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3074971 TTTCATATGT
* * *
3074981 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
3075005 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
3075029 AATTT
1 AATTT
3075034 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:3075380 original size:39 final size:39
Alignment explanation
Indices: 3075337--3075462 Score: 243
Period size: 39 Copynumber: 3.2 Consensus size: 39
3075327 TCCGATGCTC
*
3075337 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
3075376 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
3075415 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
3075454 ATCAAAATC
1 ATCAAAATC
3075463 TACAACTTGA
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 86 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
Found at i:3075760 original size:20 final size:20
Alignment explanation
Indices: 3075735--3075781 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
3075725 GCAACGCTTA
3075735 TTTCGCATTGCGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
*
3075755 TTTCGCGTTGCGAATTTGAC
1 TTTCGCATTGCGAATTTGAC
*
3075775 TATCGCA
1 TTTCGCA
3075782 ACGCTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TTTCGCATTGCGAATTTGAC
Found at i:3075785 original size:54 final size:54
Alignment explanation
Indices: 3075703--3075826 Score: 212
Period size: 54 Copynumber: 2.3 Consensus size: 54
3075693 AAACCGAAAA
* *
3075703 TCGCGTTGCGAATTTGACTATTGCAACGCTTATTTCGCATTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTATCGCAACGCTTATTTCGCATTGCGAATTTAACTT
*
3075757 TCGCGTTGCGAATTTGACTATCGCAACGCTTATTTCGCGTTGCGAATTTAACTT
1 TCGCGTTGCGAATTTGACTATCGCAACGCTTATTTCGCATTGCGAATTTAACTT
*
3075811 TTGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
3075827 TACCTTCAAC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (54 bp):
TCGCGTTGCGAATTTGACTATCGCAACGCTTATTTCGCATTGCGAATTTAACTT
Found at i:3075965 original size:66 final size:60
Alignment explanation
Indices: 3075883--3076023 Score: 192
Period size: 66 Copynumber: 2.2 Consensus size: 60
3075873 TTTTTTAGAA
3075883 AAACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAAT
1 AAACAAATCAACTTTTACAAATCAATT-AACAA--AAAAAAA-AATT-TTATTTACACATC-AAT
3075948 T
60 T
* * * *
3075949 AAACAAATCAACTTTTACAAATCAATTAATAAAAAAATAAATTTTATTTCCTCATCAATT
1 AAACAAATCAACTTTTACAAATCAATTAACAAAAAAAAAAATTTTATTTACACATCAATT
3076009 AAACAAATCAACTTT
1 AAACAAATCAACTTT
3076024 CAATGTAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
60 19 0.27
61 11 0.15
62 4 0.06
63 6 0.08
65 4 0.06
66 27 0.38
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.31
Consensus pattern (60 bp):
AAACAAATCAACTTTTACAAATCAATTAACAAAAAAAAAAATTTTATTTACACATCAATT
Found at i:3077441 original size:21 final size:20
Alignment explanation
Indices: 3077381--3077448 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
3077371 GTGAATCGGG
*
3077381 CTCTTGAACGGCGG-GCGGGAC
1 CTCTTGAACGGTGGAG-GGG-C
* *
3077402 CTCTTGAACGATGATAGGGGC
1 CTCTTGAACGGTG-GAGGGGC
3077423 CTCTTGAACGGTAGGAGGGGC
1 CTCTTGAACGGT-GGAGGGGC
*
3077444 TTCTT
1 CTCTT
3077449 CGATGATGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 33 0.87
22 4 0.11
23 1 0.03
ACGTcount: A:0.18, C:0.22, G:0.37, T:0.24
Consensus pattern (20 bp):
CTCTTGAACGGTGGAGGGGC
Found at i:3077457 original size:42 final size:42
Alignment explanation
Indices: 3077401--3077503 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
3077391 GCGGGCGGGA
* * *
3077401 CCTCTTGAACGATGATAGGGGCCTCTTGAACGGTAGGAGGGG
1 CCTCTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGAGG
* * * * *
3077443 CTTCTTCG-ATGATGAGAGAGGCCTCTTGAATGATAGGAGATG
1 CCTCTT-GAATGATGATAGGGGCCTCTTGAACGATAGGAGAGG
3077485 CCTCTTGAATGATGATAGG
1 CCTCTTGAATGATGATAGG
3077504 TGTATCGGGC
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (42 bp):
CCTCTTGAATGATGATAGGGGCCTCTTGAACGATAGGAGAGG
Found at i:3077469 original size:21 final size:22
Alignment explanation
Indices: 3077401--3077499 Score: 82
Period size: 21 Copynumber: 4.7 Consensus size: 22
3077391 GCGGGCGGGA
* * *
3077401 CCTCTTGAACGATGA-TAGGGG
1 CCTCTTGAATGATGAGGAGAGG
* * *
3077422 CCTCTTGAACGGT-AGGAGGGG
1 CCTCTTGAATGATGAGGAGAGG
*
3077443 CTTCTTCG-ATGATGA-GAGAGG
1 CCTCTT-GAATGATGAGGAGAGG
*
3077464 CCTCTTGAATGAT-AGGAGATG
1 CCTCTTGAATGATGAGGAGAGG
3077485 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
3077500 TAGGTGTATC
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.05
21 58 0.91
22 3 0.05
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.26
Consensus pattern (22 bp):
CCTCTTGAATGATGAGGAGAGG
Found at i:3077939 original size:21 final size:21
Alignment explanation
Indices: 3077913--3077957 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
3077903 ATCTTCACGT
* *
3077913 AAAGTATCGAACTCATGATGC
1 AAAGTACCGAACTCATGACGC
3077934 AAAGTACCGAACTCATGACGC
1 AAAGTACCGAACTCATGACGC
3077955 AAA
1 AAA
3077958 ACACCGACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (21 bp):
AAAGTACCGAACTCATGACGC
Found at i:3077963 original size:21 final size:21
Alignment explanation
Indices: 3077920--3077970 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3077910 CGTAAAGTAT
* **
3077920 CGAACTCATGATGCAAAGTAC
1 CGAACTCATGACGCAAAACAC
3077941 CGAACTCATGACGCAAAACAC
1 CGAACTCATGACGCAAAACAC
*
3077962 CGACCTCAT
1 CGAACTCAT
3077971 CACGTAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.31, G:0.16, T:0.16
Consensus pattern (21 bp):
CGAACTCATGACGCAAAACAC
Found at i:3079669 original size:19 final size:19
Alignment explanation
Indices: 3079618--3079671 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
3079608 AGAAGTTTCT
*
3079618 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
3079638 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
3079658 GAAACTAAAATCGC
1 GAAACTAAAATCGC
3079672 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:3080192 original size:20 final size:20
Alignment explanation
Indices: 3080167--3080314 Score: 126
Period size: 20 Copynumber: 7.5 Consensus size: 20
3080157 GCGTAAAAAC
*
3080167 ATTTGACTTTCGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
3080187 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
3080207 ATTTGACTTAT-GTGTTGC-T
1 ATTTGACTT-TCGCGTTGCGA
* ***
3080226 ATTT-ACAAATTCGC-ACACGA
1 ATTTGAC--TTTCGCGTTGCGA
*
3080246 ATTTGAC-TTCTGTGTTGCGA
1 ATTTGACTTTC-GCGTTGCGA
*
3080266 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
3080286 ATTTGACTTTCGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
3080306 ATTTGACTT
1 ATTTGACTT
3080315 CTGTGTTGCG
Statistics
Matches: 100, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
18 5 0.05
19 7 0.07
20 83 0.83
21 5 0.05
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:3080212 original size:40 final size:40
Alignment explanation
Indices: 3080167--3080313 Score: 160
Period size: 40 Copynumber: 3.7 Consensus size: 40
3080157 GCGTAAAAAC
* *
3080167 ATTTGACTTTCGCGTTACGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGTGTTGCGAATTTGACTATCGCGTTGCGA
* * ***
3080207 ATTTGACTTAT-GTGTTGC-TATTT-ACAAATTCGC-ACACGA
1 ATTTGACTT-TCGTGTTGCGAATTTGAC-TA-TCGCGTTGCGA
3080246 ATTTGAC-TTCTGTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTC-GTGTTGCGAATTTGACTATCGCGTTGCGA
3080286 ATTTGACTTTCGTGTTGCGAATTTGACT
1 ATTTGACTTTCGTGTTGCGAATTTGACT
3080314 TCTGTGTTGC
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
37 1 0.01
38 3 0.03
39 26 0.30
40 50 0.58
41 6 0.07
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (40 bp):
ATTTGACTTTCGTGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:3080320 original size:20 final size:20
Alignment explanation
Indices: 3080243--3080325 Score: 125
Period size: 20 Copynumber: 4.2 Consensus size: 20
3080233 AATTCGCACA
3080243 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTCTGTGTTG
*
3080263 CGAATTTGACTATC-GCGTTG
1 CGAATTTGACT-TCTGTGTTG
3080283 CGAATTTGACTT-TCGTGTTG
1 CGAATTTGACTTCT-GTGTTG
3080303 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTCTGTGTTG
3080323 CGA
1 CGA
3080326 TTTACAAATT
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.02
20 53 0.93
21 3 0.05
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (20 bp):
CGAATTTGACTTCTGTGTTG
Found at i:3080343 original size:40 final size:40
Alignment explanation
Indices: 3080167--3080346 Score: 124
Period size: 40 Copynumber: 4.5 Consensus size: 40
3080157 GCGTAAAAAC
* *
3080167 ATTTGACTTTCGCGTTACGAATTTGACTATCGCGTTGCGA
1 ATTTGACATTCGCGTTGCGAATTTGACTATCGCGTTGCGA
* * * * ***
3080207 ATTTGAC-TTATGTGTTGC-TATTT-ACAAATTCGC-ACACGA
1 ATTTGACATT-CGCGTTGCGAATTTGAC-TA-TCGCGTTGCGA
*
3080246 ATTTGAC-TTCTGTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGACATTC-GCGTTGCGAATTTGACTATCGCGTTGCGA
* * *
3080286 ATTTGACTTTCGTGTTGCGAATTTGACT-TCTGTGTTGCG-
1 ATTTGACATTCGCGTTGCGAATTTGACTATC-GCGTTGCGA
3080325 ATTT-ACAAATTCGCGTTGCGAA
1 ATTTGAC--ATTCGCGTTGCGAA
3080347 ATTGGAAACT
Statistics
Matches: 112, Mismatches: 17, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
38 4 0.04
39 36 0.32
40 67 0.60
41 5 0.04
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (40 bp):
ATTTGACATTCGCGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:3080363 original size:60 final size:60
Alignment explanation
Indices: 3080243--3080390 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 60
3080233 AATTCGCACA
* * *** *
3080243 CGAATTTGACTTCTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTCGTGTTG
1 CGAATTTGACTTCTGTGTTGCGAATTTGACAATCGCGTTGCGAATTGGAAACTCGAGTTG
3080303 CGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGAAATTGGAAACT-GAGTTG
1 CGAATTTGACTTCTGTGTTGCGAATTTGAC-AA-TCGCGTTGCG-AATTGGAAACTCGAGTTG
* * *
3080363 CGAAATTGGAGTTC-GCGTTGCGAATTTG
1 CG-AATTTGACTTCTGTGTTGCGAATTTG
3080391 TTGGTCATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
58 2 0.03
59 5 0.07
60 46 0.63
61 20 0.27
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (60 bp):
CGAATTTGACTTCTGTGTTGCGAATTTGACAATCGCGTTGCGAATTGGAAACTCGAGTTG
Found at i:3080382 original size:20 final size:19
Alignment explanation
Indices: 3080333--3080386 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
3080323 CGATTTACAA
3080333 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
3080352 AAACTGAGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
3080372 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
3080387 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:3081123 original size:30 final size:28
Alignment explanation
Indices: 3081089--3081156 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
3081079 ATTAATTTTA
*
3081089 TGAAAAATGATTTACATAAACCGAATTAT
1 TGAAAAAT-ATTTACATAAAACGAATTAT
* * *
3081118 CTGAAAACTAGTTTACGTAAAATGAATTAT
1 -TGAAAAATA-TTTACATAAAACGAATTAT
3081148 TGAAAAATA
1 TGAAAAATA
3081157 ATTTTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.31
Consensus pattern (28 bp):
TGAAAAATATTTACATAAAACGAATTAT
Found at i:3081422 original size:44 final size:48
Alignment explanation
Indices: 3081333--3081422 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 48
3081323 TAATATTAAA
*
3081333 TATATAAAATAATAATATTCATCATTAATAATTTAATAATATTATTTT
1 TATATAAAATAATAATATTAATCATTAATAATTTAATAATATTATTTT
* *
3081381 TATA-AAAATAAT-ATA-TAAT-ATTAATTATATTAGTAAT-TTATT
1 TATATAAAATAATAATATTAATCATTAATAAT-TTAATAATATTATT
3081423 ATATATTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
44 13 0.34
45 10 0.26
46 3 0.08
47 8 0.21
48 4 0.11
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (48 bp):
TATATAAAATAATAATATTAATCATTAATAATTTAATAATATTATTTT
Found at i:3081609 original size:19 final size:19
Alignment explanation
Indices: 3081560--3081613 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
3081550 ATTAATATTT
*
3081560 TATTAAAATGATATTAAAA
1 TATTAAAATAATATTAAAA
* *
3081579 TATTATATTAATATT-AAA
1 TATTAAAATAATATTAAAA
3081597 TATATAAAATAATATTA
1 TAT-TAAAATAATATTA
3081614 TTTTAAGTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TATTAAAATAATATTAAAA
Found at i:3088015 original size:21 final size:21
Alignment explanation
Indices: 3087976--3088016 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3087966 ATAAAAAAAT
* *
3087976 TACTTAAAACATTATTATTTC
1 TACTTAAAACATCAATATTTC
3087997 TACTTAAAACATCAATATTT
1 TACTTAAAACATCAATATTT
3088017 TTTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (21 bp):
TACTTAAAACATCAATATTTC
Found at i:3088406 original size:19 final size:18
Alignment explanation
Indices: 3088382--3088419 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
3088372 TAATAATGAG
*
3088382 TAATATTAATTTATATATT
1 TAATATTAATATA-ATATT
3088401 TAATATTAATATAATATT
1 TAATATTAATATAATATT
3088419 T
1 T
3088420 TTAGTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATATTAATATAATATT
Found at i:3104662 original size:3 final size:3
Alignment explanation
Indices: 3104642--3104712 Score: 76
Period size: 3 Copynumber: 23.7 Consensus size: 3
3104632 ATTGGGCCTG
*
3104642 TAA T-A TAA TAA -AA TTAA TAA TAAA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
*
3104687 TTA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TA
3104713 TTTAAATGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
2 6 0.10
3 45 0.78
4 7 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3105191 original size:124 final size:123
Alignment explanation
Indices: 3104854--3105936 Score: 527
Period size: 116 Copynumber: 9.3 Consensus size: 123
3104844 AATAAATTCT
*
3104854 TTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCT-G---GG--GATGATAA-TATC
1 TTTC-TTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGTTGATGATAACTATC
* * * * *
3104912 TCCTTCTGTGAT-GTAATT-TGGAAAATGGTTGAACAAGTTCTTCTTATTATAAAATT-TTC
64 TCCTTCTGTGATAG-AATTATGCAAAA-GGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* * * * * * *
3104971 TTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCCCTGGAAAAAGTTGATGTTGACCTATT
1 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAGGTTGATGAT-AACTATC
* * * * *
3105036 TCCTTCTGTGATAGAGTCATTCAAAATGTTGAATAAGCTCTTCTCATTATGAACTTCTTC
64 TCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* *
3105096 TTTATTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAATCTATCT
1 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGATAA-CTATCT
*
3105161 CCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC
65 CCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* * *
3105220 -TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA---AGCTGAT--CCA--T-
1 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGATAACTATCTC
** * * ** *
3105276 C--AAGTGATGGATTTGA-GCAAAAGGTTGAACAAATTTTTCTCATTATGAA--T-TTC
66 CTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* * * *
3105329 -TTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGTAA---TGTTGAT--CCA
1 TTTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAGGTTGATGATAACTA
*** ** **
3105387 --T-C--AAATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
62 TCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* * *
3105444 TTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTTCTCTGGAAA-----A-G----CTA-ATC
1 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGATAACTATCTC
* * * * * * **
3105498 CATCAAGTGGTGGATTTGA-GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
66 CTTC-TGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* * * * * *
3105557 TTTATTCTTCAGATGACGAGTTCTTTTCATTATGAACTCTAC-CTGGCAA---TGTTGAT--CCA
1 TTTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGGAAAGGTTGATGATAACTA
*** ** **
3105616 --T-C--AAATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
62 TCTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* * *
3105673 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTATCTGGAAA-----A-G----CTA-ATC
1 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGATAACTATCTC
* * * * * **
3105727 CATCAAGTGATGGATTTGA-GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
66 CTTC-TGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
* * * * * *
3105786 TTTATTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTATCTGGCAA---TGTTGAT--CCA-
1 TTTCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGATAACTAT
*** ** **
3105845 -T-C--AAATGAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
63 CTCCTTCTGTGATAGAATT-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
*
3105902 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACT
3105937 CGAACTGTCA
Statistics
Matches: 801, Mismatches: 109, Indels: 116
0.78 0.11 0.11
Matches are distributed among these distances:
108 4 0.00
109 18 0.02
110 5 0.01
111 5 0.01
112 115 0.14
113 185 0.23
114 12 0.01
115 17 0.02
116 209 0.26
117 7 0.01
119 4 0.00
120 7 0.01
121 4 0.00
122 5 0.01
123 46 0.06
124 110 0.14
125 48 0.06
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (123 bp):
TTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGATAACTATCTC
CTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
Found at i:3105529 original size:113 final size:113
Alignment explanation
Indices: 3105181--3105936 Score: 968
Period size: 113 Copynumber: 6.7 Consensus size: 113
3105171 TAGAATTATG
** *
3105181 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * ** *
3105245 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
*
3105293 CAAAAGGTTGAACAAATTTTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* * * *
3105354 TCATTATGAACTCTAC-CTGGTAATGTTGATCCATCAAATGATGAATTCAAA
63 TCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
*
3105405 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * ** *
3105470 TTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGGTGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
* ** *
3105518 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTATTCTTCAGATGACGAGTTCTTT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* * * *
3105583 TCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAA
63 TCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
3105634 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * ** *
3105699 TTATGAACTTTATCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
* **
3105747 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTATTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* * * * *
3105812 TCATTATGAACTCTATCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
63 TCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
3105863 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
3105928 TTATGAACT
66 TTATGAACT
3105937 CGAACTGTCA
Statistics
Matches: 554, Mismatches: 73, Indels: 33
0.84 0.11 0.05
Matches are distributed among these distances:
109 16 0.03
110 1 0.00
112 110 0.20
113 214 0.39
114 1 0.00
115 5 0.01
116 205 0.37
117 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAAA
Found at i:3105668 original size:229 final size:229
Alignment explanation
Indices: 3105181--3105936 Score: 1360
Period size: 229 Copynumber: 3.3 Consensus size: 229
3105171 TAGAATTATG
** *
3105181 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
3105245 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGTAAAAGGTTGAACAAAT
* *
3105310 TTTTCTCATTATGAA--T-TTC-TTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACC
131 TCTTCTCATTATGAACTTCTTCTTTATTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACC
*
3105371 TGGTAATGTTGATCCATCAAATGATGAATTCAAA
196 TGGCAATGTTGATCCATCAAATGATGAATTCAAA
*
3105405 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
3105470 TTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGGTGGATTTGAGTAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGTAAAAGGTTGAACAAAT
*
3105535 TCTTCTCATTATGAACTTCTTCTTTATTCTTCAGATGACGAGTTCTTTTCATTATGAACTCTACC
131 TCTTCTCATTATGAACTTCTTCTTTATTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACC
3105600 TGGCAATGTTGATCCATCAAATGATGAATTCAAA
196 TGGCAATGTTGATCCATCAAATGATGAATTCAAA
3105634 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
3105699 TTATGAACTTTATCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGTAAAAGGTTGAACAAAT
66 TTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGTAAAAGGTTGAACAAAT
*
3105764 TCTTCTCATTATGAACTTCTTCTTTATTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTATC
131 TCTTCTCATTATGAACTTCTTCTTTATTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACC
3105829 TGGCAATGTTGATCCATCAAATGATGAATTCAAA
196 TGGCAATGTTGATCCATCAAATGATGAATTCAAA
3105863 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
3105928 TTATGAACT
66 TTATGAACT
3105937 CGAACTGTCA
Statistics
Matches: 511, Mismatches: 16, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
224 38 0.07
225 98 0.19
227 1 0.00
228 3 0.01
229 371 0.73
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (229 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGTAAAAGGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCTTTATTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACC
TGGCAATGTTGATCCATCAAATGATGAATTCAAA
Found at i:3106880 original size:114 final size:114
Alignment explanation
Indices: 3106675--3107122 Score: 734
Period size: 114 Copynumber: 3.9 Consensus size: 114
3106665 AATCATGCAG
* * * ** * *
3106675 TTCATCTTTCAATTCTAATGATTGGTTTTGTGGTTCCTACCGAACCAGATCAAATAACTCAAAGA
1 TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
* * *
3106740 ACACTTCCAGACGATGTTATTAGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
3106789 TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACAAAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
*
3106854 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTATTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
*
3106903 TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCCGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
* * *
3106968 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTACGAGAAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
3107017 TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
*
3107082 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
3107123 CGAGAACGTG
Statistics
Matches: 313, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 313 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCTAATAATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:3107482 original size:19 final size:17
Alignment explanation
Indices: 3107454--3107502 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
3107444 AAAATAAAAG
*
3107454 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
3107473 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
3107489 AATAAATTGAATTT
1 AATAAATTGAATTT
3107503 AGAGAAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:3107918 original size:23 final size:25
Alignment explanation
Indices: 3107888--3107936 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3107878 TTCTTCTCTT
3107888 TTTTCA-TTTTTCATTTTTT-TTCA
1 TTTTCATTTTTTCATTTTTTCTTCA
3107911 TTTTCATTTTTTTCATTTTTTCTTCA
1 TTTTCA-TTTTTTCATTTTTTCTTCA
3107937 AGCATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.26
25 13 0.57
26 4 0.17
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTCATTTTTTCATTTTTTCTTCA
Found at i:3107922 original size:32 final size:33
Alignment explanation
Indices: 3107852--3107930 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 33
3107842 CATCTTGACC
*
3107852 CTCTTTTTT--TTTTTCCTTTTTTCTTCTTCTT
1 CTCTTTTTTCATTTTTCATTTTTTCTTCTTCTT
3107883 CTCTTTTTTCATTTTTCATTTTTT-TTCATT-TT
1 CTCTTTTTTCATTTTTCATTTTTTCTTC-TTCTT
3107915 CAT-TTTTTTCATTTTT
1 C-TCTTTTTTCATTTTT
3107931 TCTTCAAGCA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
31 9 0.21
32 19 0.44
33 15 0.35
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (33 bp):
CTCTTTTTTCATTTTTCATTTTTTCTTCTTCTT
Found at i:3107932 original size:17 final size:17
Alignment explanation
Indices: 3107886--3107930 Score: 76
Period size: 16 Copynumber: 2.8 Consensus size: 17
3107876 TCTTCTTCTC
3107886 TTTTTTCATTTTTCATT
1 TTTTTTCATTTTTCATT
3107903 TTTTTTCA-TTTTCA-T
1 TTTTTTCATTTTTCATT
3107918 TTTTTTCATTTTT
1 TTTTTTCATTTTT
3107931 TCTTCAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.33
16 10 0.37
17 8 0.30
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTCATTTTTCATT
Found at i:3118658 original size:26 final size:29
Alignment explanation
Indices: 3118610--3118665 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 29
3118600 AAAGAAAGAA
3118610 TTATAAATTAAATATATGAATTTT-TAAT
1 TTATAAATTAAATATATGAATTTTATAAT
3118638 TTAT-AATT-AATATA-GACATTTTATAAT
1 TTATAAATTAAATATATGA-ATTTTATAAT
3118665 T
1 T
3118666 GATTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 2 0.08
26 11 0.42
27 9 0.35
28 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (29 bp):
TTATAAATTAAATATATGAATTTTATAAT
Found at i:3119538 original size:40 final size:40
Alignment explanation
Indices: 3119450--3119538 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
3119440 AGATATTTCA
** *
3119450 GCCACCGCCTCCAAGTGGTCCACTCCGACGTTGCCACGCC
1 GCCACCGCCTCCAAGTGGTCCACTCCGACGCCGCCACGAC
* * * *
3119490 GCCGCCGCCTCCAAGTGGTCTACTCCGATGCCGCCATGAC
1 GCCACCGCCTCCAAGTGGTCCACTCCGACGCCGCCACGAC
*
3119530 GTCACCGCC
1 GCCACCGCC
3119539 GTACAGAAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.15, C:0.46, G:0.24, T:0.16
Consensus pattern (40 bp):
GCCACCGCCTCCAAGTGGTCCACTCCGACGCCGCCACGAC
Found at i:3132958 original size:127 final size:128
Alignment explanation
Indices: 3132732--3133433 Score: 762
Period size: 137 Copynumber: 5.3 Consensus size: 128
3132722 GGAAACAAAA
* *
3132732 ATCCTAAGATAACCAGACGTCCTCATCACGAAGGAACCGTGT-TATCTCAAAGATGGTCAGATGT
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTATATCTTAAAGATGGTCAGATGT
* * *
3132796 CCTCATCACGAATGAACAATACCATCTACCAATCAGAACTCTTCATCACGAAGGAGTCACATC
66 CCTCATCACGAAGGAACAATATCATCTACCAATCAGAACTCCTCATCACGAAGGAGTCACATC
3132859 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGT-TATCTTAAAGATGGTCAGATGT
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTATATCTTAAAGATGGTCAGATGT
* * * *
3132923 CCTCATCACGAATGAACAATACCATCTACCAATCAGAACTCTTCATCACGAATGAGTCACATC
66 CCTCATCACGAAGGAACAATATCATCTACCAATCAGAACTCCTCATCACGAAGGAGTCACATC
* ** * *
3132986 ATCCTTAGATAACCAGACGTCCTTATCATTAAGGAACTATGTTATCTCAAATATCTTTAAAGATG
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAAC--CG---TGT---ATATC-TTAAAGATG
* *
3133051 GCCAGATGTCCTCATCACGAAGGAACAATATCATCTACCAATCAAAACTCCTCATCACGAAGGAG
57 GTCAGATGTCCTCATCACGAAGGAACAATATCATCTACCAATCAGAACTCCTCATCACGAAGGAG
***
3133116 TCGTGTC
122 TCACATC
* * * * * * *
3133123 AGCTTTTGATAACCATACATTCTCATCATGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATG
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTG-----T---ATATC-TTAAAGATG
* * * *
3133188 GTCAGATGTCCTCATCACGAAGGAACGATGTCATCTACCAATCAGAACTCCTCATCATGAAAGAG
57 GTCAGATGTCCTCATCACGAAGGAACAATATCATCTACCAATCAGAACTCCTCATCACGAAGGAG
*
3133253 TCACGTC
122 TCACATC
* * * *
3133260 ATCCTTAGATAACCAGACGTCCTCATCATGAAGGAACTATGTTACCTCAAATATCTTCAAAAATG
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAAC--CG-T--GT---ATATCTT-AAAGATG
* * * * *
3133325 G-CTAGATGTTCTCATCACGAAGGAGCAATTTCAACTACCAATCAGAACTCCTCATCATGAAGGA
57 GTC-AGATGTCCTCATCACGAAGGAACAATATCATCTACCAATCAGAACTCCTCATCACGAAGGA
3133389 GTCACATC
121 GTCACATC
*
3133397 ATCCTTAGACAACCAGACGTCCTCATCACGAAGGAAC
1 ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAAC
3133434 AATGTCATAC
Statistics
Matches: 500, Mismatches: 53, Indels: 34
0.85 0.09 0.06
Matches are distributed among these distances:
127 158 0.32
129 1 0.00
132 3 0.01
135 1 0.00
136 7 0.01
137 328 0.66
139 1 0.00
140 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (128 bp):
ATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTATATCTTAAAGATGGTCAGATGT
CCTCATCACGAAGGAACAATATCATCTACCAATCAGAACTCCTCATCACGAAGGAGTCACATC
Found at i:3133311 original size:274 final size:264
Alignment explanation
Indices: 3132774--3133433 Score: 890
Period size: 274 Copynumber: 2.5 Consensus size: 264
3132764 GGAACCGTGT
* * * *
3132774 TATC-TCAAAGATGGTCAGATGTCCTCATCACGAATGAACAATACCATCTACCAATCAGAACTCT
1 TATCTTCAAAGATGGCCAGATGTCCTCATCACGAAGGAACAATATCATCTACCAATCAGAACTCC
* *
3132838 TCATCACGAAGGAGTCACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTA
66 TCATCACGAAGGAGTCACATCAGCCTTAGATAACCAGACATCCTCATCACGAAGGAACCGTGTTA
* *
3132903 TCTTAAAGATGGTCAGATGTCCTCATCACGAATGAACAATACCATCTACCAATCAGAACTCTTCA
131 TCTTAAAGATGGTCAGATGTCCTCATCACGAAGGAACAATACCATCTACCAATCAGAACTCCTCA
* * * *
3132968 TCACGAATGAGTCACATCATCCTTAGATAACCAGACGTCCTTATCATTAAGGAACTATGTTATCT
196 TCACGAAAGAGTCACATCATCCTTAGATAACCAGACGTCCTCATCATGAAGGAACTATGTTACCT
3133033 CAAA
261 CAAA
* *
3133037 TATCTTTAAAGATGGCCAGATGTCCTCATCACGAAGGAACAATATCATCTACCAATCAAAACTCC
1 TATCTTCAAAGATGGCCAGATGTCCTCATCACGAAGGAACAATATCATCTACCAATCAGAACTCC
*** * * * * *
3133102 TCATCACGAAGGAGTCGTGTCAGCTTTTGATAACCATACATTCTCATCATGAAGGAACCGTGTTA
66 TCATCACGAAGGAGTCACATCAGCCTTAGATAACCAGACATCCTCATCACGAAGGAACCGTG---
* **
3133167 TCTCAAATATCTTTAAAGATGGTCAGATGTCCTCATCACGAAGGAACGATGTCATCTACCAATCA
128 --T----TATC-TTAAAGATGGTCAGATGTCCTCATCACGAAGGAACAATACCATCTACCAATCA
* *
3133232 GAACTCCTCATCATGAAAGAGTCACGTCATCCTTAGATAACCAGACGTCCTCATCATGAAGGAAC
186 GAACTCCTCATCACGAAAGAGTCACATCATCCTTAGATAACCAGACGTCCTCATCATGAAGGAAC
3133297 TATGTTACCTCAAA
251 TATGTTACCTCAAA
* * * * * *
3133311 TATCTTCAAAAATGGCTAGATGTTCTCATCACGAAGGAGCAATTTCAACTACCAATCAGAACTCC
1 TATCTTCAAAGATGGCCAGATGTCCTCATCACGAAGGAACAATATCATCTACCAATCAGAACTCC
* * * *
3133376 TCATCATGAAGGAGTCACATCATCCTTAGACAACCAGACGTCCTCATCACGAAGGAAC
66 TCATCACGAAGGAGTCACATCAGCCTTAGATAACCAGACATCCTCATCACGAAGGAAC
3133434 AATGTCATAC
Statistics
Matches: 339, Mismatches: 47, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
263 4 0.01
264 106 0.31
269 1 0.00
273 4 0.01
274 224 0.66
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (264 bp):
TATCTTCAAAGATGGCCAGATGTCCTCATCACGAAGGAACAATATCATCTACCAATCAGAACTCC
TCATCACGAAGGAGTCACATCAGCCTTAGATAACCAGACATCCTCATCACGAAGGAACCGTGTTA
TCTTAAAGATGGTCAGATGTCCTCATCACGAAGGAACAATACCATCTACCAATCAGAACTCCTCA
TCACGAAAGAGTCACATCATCCTTAGATAACCAGACGTCCTCATCATGAAGGAACTATGTTACCT
CAAA
Found at i:3135035 original size:3 final size:3
Alignment explanation
Indices: 3135027--3135055 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3135017 TACCGTCTCG
3135027 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
3135056 AACCCTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3138851 original size:3 final size:3
Alignment explanation
Indices: 3138831--3138904 Score: 73
Period size: 3 Copynumber: 24.7 Consensus size: 3
3138821 ATTGGGCCTG
* *
3138831 TAA T-A TAA TAA -AA TTAA TAA TAAA TAA TAA TAT TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
*
3138876 TTA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
3138905 TTTAAATGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
2 6 0.10
3 48 0.79
4 7 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3140790 original size:17 final size:17
Alignment explanation
Indices: 3140770--3140803 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3140760 TCGCGTATCC
3140770 AAATAAAT-ATAATTAAA
1 AAATAAATGA-AATTAAA
3140787 AAATAAATGAAATTAAA
1 AAATAAATGAAATTAAA
3140804 GGTCAAACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATAAATGAAATTAAA
Found at i:3141000 original size:2 final size:2
Alignment explanation
Indices: 3140993--3141041 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3140983 ATCTAGTTTC
3140993 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3141035 AT AT AT A
1 AT AT AT A
3141042 CACGATTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3144267 original size:17 final size:17
Alignment explanation
Indices: 3144247--3144282 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3144237 GGAGAAAGGA
3144247 GATACATTTTTCCTTCG
1 GATACATTTTTCCTTCG
3144264 GATACATTTTTCCTTCG
1 GATACATTTTTCCTTCG
3144281 GA
1 GA
3144283 ATTTTTATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.44
Consensus pattern (17 bp):
GATACATTTTTCCTTCG
Found at i:3146219 original size:24 final size:24
Alignment explanation
Indices: 3146192--3146238 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3146182 TCAGTTGGTT
3146192 CCTCCTCATCGGCTGG-CTGGTGAA
1 CCTCCTCATCGG-TGGACTGGTGAA
* *
3146216 CCTCTTCATTGGTGGACTGGTGA
1 CCTCCTCATCGGTGGACTGGTGA
3146239 GCATCTTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.13, C:0.28, G:0.30, T:0.30
Consensus pattern (24 bp):
CCTCCTCATCGGTGGACTGGTGAA
Found at i:3155625 original size:21 final size:21
Alignment explanation
Indices: 3155599--3155638 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3155589 AAGACTTTAT
3155599 TTTCAAAATACAAAAATGATG
1 TTTCAAAATACAAAAATGATG
**
3155620 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
3155639 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATG
Found at i:3158867 original size:23 final size:24
Alignment explanation
Indices: 3158840--3158898 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
3158830 TTGACGATAT
* *
3158840 GTATCGATACCCCT-TTTGCATGG
1 GTATCGATACCCCTCCTTGAATGG
3158863 GTATCGATA-CCCTCCTTGAATGG
1 GTATCGATACCCCTCCTTGAATGG
*
3158886 GTACCGATACCCC
1 GTATCGATACCCC
3158899 CACATGAGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.13
23 24 0.77
24 3 0.10
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (24 bp):
GTATCGATACCCCTCCTTGAATGG
Found at i:3160920 original size:2 final size:2
Alignment explanation
Indices: 3160913--3160939 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3160903 CTTAAATGTT
3160913 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3160940 GTTTGCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3167334 original size:2 final size:2
Alignment explanation
Indices: 3167327--3167354 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3167317 TTTCGAAATA
3167327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3167355 TTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3169220 original size:13 final size:13
Alignment explanation
Indices: 3169190--3169223 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3169180 AAGAGGAGTA
*
3169190 ATTTTCAAAAATT
1 ATTTTCAAAAATG
3169203 A-TTTCAAAAATG
1 ATTTTCAAAAATG
3169215 ATTTTCAAA
1 ATTTTCAAA
3169224 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:3173708 original size:20 final size:20
Alignment explanation
Indices: 3173679--3173721 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3173669 ATTCCACCAC
*
3173679 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
3173699 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
3173719 ATG
1 ATG
3173722 AGCTCTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:3185654 original size:80 final size:80
Alignment explanation
Indices: 3185550--3185710 Score: 277
Period size: 80 Copynumber: 2.0 Consensus size: 80
3185540 TTGTATATTT
* * * *
3185550 TATAAAACCTTTTTAGTGGGATTAAGGGTGCTTAACGAGCGTTTGAACATACGGGACATGTCATG
1 TATAAAACCTTTTTAGTAGGATTAAGGGTGCTTAACGAGCATTTGAACATACGAGACAAGTCATG
3185615 CTAAGATAGCTTGCG
66 CTAAGATAGCTTGCG
3185630 TATAAAACCTTTTTAGTAGGATTAAGGGTGCTTAACGAGCATTTGAACATACGAGACAAGTCATG
1 TATAAAACCTTTTTAGTAGGATTAAGGGTGCTTAACGAGCATTTGAACATACGAGACAAGTCATG
*
3185695 CTAAGCTAGCTTGCG
66 CTAAGATAGCTTGCG
3185710 T
1 T
3185711 TTGATCATAC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (80 bp):
TATAAAACCTTTTTAGTAGGATTAAGGGTGCTTAACGAGCATTTGAACATACGAGACAAGTCATG
CTAAGATAGCTTGCG
Found at i:3188760 original size:30 final size:30
Alignment explanation
Indices: 3188726--3188784 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
3188716 TGTTCTGATG
3188726 GATTTAGTAGATGTTTCCACCGTCGGATTC
1 GATTTAGTAGATGTTTCCACCGTCGGATTC
3188756 GATTTAGTAGATGTTTCCACCGTCGGATT
1 GATTTAGTAGATGTTTCCACCGTCGGATT
3188785 AATGTCGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (30 bp):
GATTTAGTAGATGTTTCCACCGTCGGATTC
Found at i:3193920 original size:19 final size:18
Alignment explanation
Indices: 3193898--3193945 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
3193888 AAAAATTTCA
3193898 TTTTTAAAATTAAAAATAT
1 TTTTTAAAATT-AAAATAT
* **
3193917 TTTTAAAAACTTAATTTAT
1 TTTTTAAAA-TTAAAATAT
3193936 TTTTTAAAAT
1 TTTTTAAAAT
3193946 AATGCTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 21 0.88
20 2 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTTTAAAATTAAAATAT
Found at i:3203941 original size:19 final size:19
Alignment explanation
Indices: 3203917--3204003 Score: 68
Period size: 19 Copynumber: 4.4 Consensus size: 19
3203907 AGAACTTGTT
3203917 TTTCCAAACTAAAATCATG
1 TTTCCAAACTAAAATCATG
* *
3203936 TTTCCAACCTAAAA-CTTG
1 TTTCCAAACTAAAATCATG
*
3203954 TTTTTTTTCCAAACTAAAATCAGG
1 -----TTTCCAAACTAAAATCATG
* * *
3203978 TTCCCAACCTAAAATCACG
1 TTTCCAAACTAAAATCATG
3203997 TTTCCAA
1 TTTCCAA
3204004 TTTAACCACC
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
18 3 0.06
19 35 0.66
23 13 0.25
24 2 0.04
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (19 bp):
TTTCCAAACTAAAATCATG
Found at i:3203945 original size:39 final size:39
Alignment explanation
Indices: 3203887--3203991 Score: 131
Period size: 42 Copynumber: 2.6 Consensus size: 39
3203877 GTTTTCAATG
* *
3203887 TAAAATCAGTTTTCTAACCTAGAACTTG-TTTTTCCAAAC
1 TAAAATCAG-TTTCCAACCTAAAACTTGTTTTTTCCAAAC
3203926 TAAAATCATGTTTCCAACCTAAAACTTGTTTTTTTTCCAAAC
1 TAAAATCA-GTTTCCAACCTAAAACTTG--TTTTTTCCAAAC
*
3203968 TAAAATCAGGTTCCCAACCTAAAA
1 TAAAATCA-GTTTCCAACCTAAAA
3203992 TCACGTTTCC
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
39 24 0.41
40 1 0.02
42 33 0.57
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.35
Consensus pattern (39 bp):
TAAAATCAGTTTCCAACCTAAAACTTGTTTTTTCCAAAC
Found at i:3205677 original size:64 final size:64
Alignment explanation
Indices: 3205602--3205724 Score: 187
Period size: 64 Copynumber: 1.9 Consensus size: 64
3205592 AATGCATTTT
* *
3205602 ATGCATCGATGCACTCATG-TT-TTATGAAAACATCTAATACATTTTATGCATCGATGCACAGAC
1 ATGCATCGATGCACTCAGGCTTGTT-T-AAAACATCGAATACATTTTATGCATCGATGCACAGAC
3205665 C
64 C
*
3205666 ATGCATCGATGCACTCAGGCTTGTTTAAAACATCGAATGCATTTTATGCATCGATGCAC
1 ATGCATCGATGCACTCAGGCTTGTTTAAAACATCGAATACATTTTATGCATCGATGCAC
3205725 GCTTAGTGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
64 49 0.91
65 3 0.06
66 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTCAGGCTTGTTTAAAACATCGAATACATTTTATGCATCGATGCACAGACC
Found at i:3211111 original size:21 final size:21
Alignment explanation
Indices: 3211085--3211141 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
3211075 TTGTGCATAA
3211085 TGCATCGATACACTATGAAAG
1 TGCATCGATACACTATGAAAG
* * *
3211106 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAAAG
3211130 TGCATCGATACA
1 TGCATCGATACA
3211142 TCATGAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 10 0.34
22 1 0.03
23 1 0.03
24 17 0.59
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (21 bp):
TGCATCGATACACTATGAAAG
Found at i:3211160 original size:45 final size:44
Alignment explanation
Indices: 3211085--3211182 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 44
3211075 TTGTGCATAA
*
3211085 TGCATCGATACACTATGAAAGTGCATCGATGCATC-CCTTTGAATG
1 TGCATCGATACACTATGAAAGTGCACCGATGCA-CGCC-TTGAATG
3211130 TGCATCGATACA-TCATG-AAGATGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACT-ATGAAAG-TGCACCGATGCACGCCTTGAATG
3211174 TGCATCGAT
1 TGCATCGAT
3211183 GCACAAGGCC
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
44 21 0.43
45 28 0.57
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:3217571 original size:65 final size:65
Alignment explanation
Indices: 3217456--3217621 Score: 162
Period size: 65 Copynumber: 2.6 Consensus size: 65
3217446 GAAAAAGCCT
* * * * * *
3217456 GGGTGCATCGATGCA-TGTCTTGTGCATCGGTGCA-TAAAATCAATTTGATGTTTTAA-TAATAC
1 GGGTGCATCGATGCATTG-CATGTGCATCGGTACACTAAAAGCAATTCGATG-TTCAATTAAAAC
*
3217518 AT
64 AA
*
3217520 GGAGTGCATCGATGCATTGCATGTGCATCGGTACACT-AAAGCTATTCGATGTTCAATTAAAACA
1 GG-GTGCATCGATGCATTGCATGTGCATCGGTACACTAAAAGCAATTCGATGTTCAATTAAAACA
3217584 A
65 A
* *
3217585 GGGTGCATCGATGTATTG-ATTTATGCATCGGTACACT
1 GGGTGCATCGATGCATTGCA--TGTGCATCGGTACACT
3217622 TACCTGAAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
63 1 0.01
64 21 0.24
65 61 0.71
66 3 0.03
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (65 bp):
GGGTGCATCGATGCATTGCATGTGCATCGGTACACTAAAAGCAATTCGATGTTCAATTAAAACAA
Found at i:3220403 original size:30 final size:30
Alignment explanation
Indices: 3220369--3220452 Score: 159
Period size: 30 Copynumber: 2.8 Consensus size: 30
3220359 CCCGAAGGAC
*
3220369 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCCGTAA
3220399 CTATCCAGAGGTCATAAAGATCCTCCGTAA
1 CTATCCAGAGGTCATAAAGATCCTCCGTAA
3220429 CTATCCAGAGGTCATAAAGATCCT
1 CTATCCAGAGGTCATAAAGATCCT
3220453 AGTTAATTGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCCGTAA
Found at i:3220471 original size:30 final size:30
Alignment explanation
Indices: 3220369--3220488 Score: 150
Period size: 30 Copynumber: 4.0 Consensus size: 30
3220359 CCCGAAGGAC
*
3220369 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTAGGTAA
**
3220399 CTATCCAGAGGTCATAAAGATCCTCCGTAA
1 CTATCCAGAGGTCATAAAGATCCTAGGTAA
*
3220429 CTATCCAGAGGTCATAAAGATCCTAGTTAA
1 CTATCCAGAGGTCATAAAGATCCTAGGTAA
* * * * * *
3220459 TTGTCCATAGGTCCTGAAGAACCTAGGTAA
1 CTATCCAGAGGTCATAAAGATCCTAGGTAA
3220489 TCTGTCCATA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 79 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTAGGTAA
Found at i:3221263 original size:164 final size:164
Alignment explanation
Indices: 3220992--3221320 Score: 658
Period size: 164 Copynumber: 2.0 Consensus size: 164
3220982 CTATAACATA
3220992 AGTACAATGAAATTGCACTCACCTTAGCCTTGCTTGCTTTGATTTGATTCTAATTCTTCAATTGT
1 AGTACAATGAAATTGCACTCACCTTAGCCTTGCTTGCTTTGATTTGATTCTAATTCTTCAATTGT
3221057 TTCGGAACAAGCTTTCATTCTATATCTACATAATAATAACACATTGATACATATCAATATACTAA
66 TTCGGAACAAGCTTTCATTCTATATCTACATAATAATAACACATTGATACATATCAATATACTAA
3221122 TTGATATATTCTAAGCTATCACTTCATAGGCTAG
131 TTGATATATTCTAAGCTATCACTTCATAGGCTAG
3221156 AGTACAATGAAATTGCACTCACCTTAGCCTTGCTTGCTTTGATTTGATTCTAATTCTTCAATTGT
1 AGTACAATGAAATTGCACTCACCTTAGCCTTGCTTGCTTTGATTTGATTCTAATTCTTCAATTGT
3221221 TTCGGAACAAGCTTTCATTCTATATCTACATAATAATAACACATTGATACATATCAATATACTAA
66 TTCGGAACAAGCTTTCATTCTATATCTACATAATAATAACACATTGATACATATCAATATACTAA
3221286 TTGATATATTCTAAGCTATCACTTCATAGGCTAG
131 TTGATATATTCTAAGCTATCACTTCATAGGCTAG
3221320 A
1 A
3221321 AGAAAGCCAT
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 165 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (164 bp):
AGTACAATGAAATTGCACTCACCTTAGCCTTGCTTGCTTTGATTTGATTCTAATTCTTCAATTGT
TTCGGAACAAGCTTTCATTCTATATCTACATAATAATAACACATTGATACATATCAATATACTAA
TTGATATATTCTAAGCTATCACTTCATAGGCTAG
Found at i:3228297 original size:201 final size:201
Alignment explanation
Indices: 3227946--3228347 Score: 741
Period size: 201 Copynumber: 2.0 Consensus size: 201
3227936 GCGATTCAAG
*
3227946 AACCGTTGGAAAGATAAGAGACAGACGGTCGTATCTCCAGAAGACATCTTGACTAAATAAGATCA
1 AACCGTTGGAAAGATAAGAGAAAGACGGTCGTATCTCCAGAAGACATCTTGACTAAATAAGATCA
3228011 GGATACCATTCAAAAAGTCGTCGTAAGTCTTCTTCTGTTCTGATCTTCTTTTCCAATGCTTGGAC
66 GGATACCATTCAAAAAGTCGTCGTAAGTCTTCTTCTGTTCTGATCTTCTTTTCCAATGCTTGGAC
*
3228076 GAGTGGATCAATTGGAAGAGTTATTACTTCTTCCTTTGATGTGATCCTTGTGATGCATGTATCAT
131 GAGTGGATCAATTAGAAGAGTTATTACTTCTTCCTTTGATGTGATCCTTGTGATGCATGTATCAT
3228141 CCTCCC
196 CCTCCC
* *
3228147 AACCGTTGGAAAGATAAGAGAAATACGGTCGTATCTCTAGAAGACATCTTGACTAAATAAGATCA
1 AACCGTTGGAAAGATAAGAGAAAGACGGTCGTATCTCCAGAAGACATCTTGACTAAATAAGATCA
*
3228212 GGATCCCATTCAAAAAGTCGTCGTAAGTCTTCTTCTGTTCTGATCTTCTTTTCCAATGCTTGGAC
66 GGATACCATTCAAAAAGTCGTCGTAAGTCTTCTTCTGTTCTGATCTTCTTTTCCAATGCTTGGAC
* *
3228277 GAGTGGATCATTTAGAAGAGTTATTATTTCTTCCTTTGATGTGATCCTTGTGATGCATGTATCAT
131 GAGTGGATCAATTAGAAGAGTTATTACTTCTTCCTTTGATGTGATCCTTGTGATGCATGTATCAT
3228342 CCTCCC
196 CCTCCC
3228348 TTTCTTCAAA
Statistics
Matches: 194, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
201 194 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (201 bp):
AACCGTTGGAAAGATAAGAGAAAGACGGTCGTATCTCCAGAAGACATCTTGACTAAATAAGATCA
GGATACCATTCAAAAAGTCGTCGTAAGTCTTCTTCTGTTCTGATCTTCTTTTCCAATGCTTGGAC
GAGTGGATCAATTAGAAGAGTTATTACTTCTTCCTTTGATGTGATCCTTGTGATGCATGTATCAT
CCTCCC
Found at i:3231777 original size:19 final size:21
Alignment explanation
Indices: 3231755--3231798 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
3231745 TTTTTTGAAA
3231755 TTTTGGC-TTTTTTGTTTT-T
1 TTTTGGCTTTTTTTGTTTTGT
3231774 TTTTGGCTTTTTTTGTTTTGT
1 TTTTGGCTTTTTTTGTTTTGT
3231795 TTTT
1 TTTT
3231799 TTTAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.30
20 11 0.48
21 5 0.22
ACGTcount: A:0.00, C:0.05, G:0.16, T:0.80
Consensus pattern (21 bp):
TTTTGGCTTTTTTTGTTTTGT
Found at i:3238029 original size:31 final size:32
Alignment explanation
Indices: 3237958--3238031 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
3237948 GGTGTTTTCA
* *
3237958 TACGAGACACTTTAATCCTTTGGGGCTCTCTCG
1 TACGAGTCACTCTAATCCTTTGGGGC-CTCTCG
*
3237991 TATGAGTCACTCTAATCCTTTGGGG-CTCTCG
1 TACGAGTCACTCTAATCCTTTGGGGCCTCTCG
*
3238022 TGCGAGTCAC
1 TACGAGTCAC
3238032 CCAAAATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 14 0.39
33 22 0.61
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (32 bp):
TACGAGTCACTCTAATCCTTTGGGGCCTCTCG
Found at i:3238123 original size:19 final size:19
Alignment explanation
Indices: 3238089--3238146 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
3238079 CGTAGAATTT
3238089 GGTTTCCAATCTCAAAATCA
1 GGTTTCCAA-CTCAAAATCA
3238109 GGTTTCCAACTCAAAATCA
1 GGTTTCCAACTCAAAATCA
* *
3238128 AGTTTTCAAC-CTAAAATCA
1 GGTTTCCAACTC-AAAATCA
3238147 ATTTTTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
18 1 0.03
19 25 0.71
20 9 0.26
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (19 bp):
GGTTTCCAACTCAAAATCA
Found at i:3238147 original size:19 final size:19
Alignment explanation
Indices: 3238099--3238155 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
3238089 GGTTTCCAAT
* *
3238099 CTCAAAATCAGGTTTCCAA
1 CTCAAAATCAAGTTTTCAA
3238118 CTCAAAATCAAGTTTTCAA
1 CTCAAAATCAAGTTTTCAA
*
3238137 C-CTAAAATCAATTTTTCAA
1 CTC-AAAATCAAGTTTTCAA
3238156 TCGAAAACCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 1 0.03
19 33 0.97
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (19 bp):
CTCAAAATCAAGTTTTCAA
Found at i:3238191 original size:19 final size:19
Alignment explanation
Indices: 3238089--3238193 Score: 68
Period size: 19 Copynumber: 5.4 Consensus size: 19
3238079 CGTAGAATTT
*
3238089 GGTTTCCAATCTCAAAATCA
1 GGTTTCCAAACT-AAAATCA
3238109 GGTTTCC-AACTCAAAATCA
1 GGTTTCCAAACT-AAAATCA
* * *
3238128 AGTTTTCAACCTAAAATCA
1 GGTTTCCAAACTAAAATCA
** * * * *
3238147 ATTTTTCAATCGAAAACCTA
1 GGTTTCCAAACTAAAATC-A
**
3238167 CTTTTCCAAACTAAAATCA
1 GGTTTCCAAACTAAAATCA
3238186 GGTTTCCA
1 GGTTTCCA
3238194 CGTTAACCAG
Statistics
Matches: 68, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
19 44 0.65
20 24 0.35
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (19 bp):
GGTTTCCAAACTAAAATCA
Found at i:3240474 original size:2 final size:2
Alignment explanation
Indices: 3240467--3240494 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3240457 CCTGATGGGT
3240467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3240495 GCTCATATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3241874 original size:20 final size:21
Alignment explanation
Indices: 3241841--3241982 Score: 170
Period size: 21 Copynumber: 7.0 Consensus size: 21
3241831 AAATTAGGAT
3241841 GAAACCTG-ATTTTTAAGTTG
1 GAAACCTGAATTTTTAAGTTG
* *
3241861 GAAACTTGGATTTTTAAGTTG
1 GAAACCTGAATTTTTAAGTTG
*
3241882 GAAACCTGAATTTTTAGGTTG
1 GAAACCTGAATTTTTAAGTTG
* *
3241903 G-AACCTGAATTTTTAGGTTT
1 GAAACCTGAATTTTTAAGTTG
*
3241923 G-AATCTG-ATTTTTAAGTTG
1 GAAACCTGAATTTTTAAGTTG
3241942 GAAACCTGAATTTTTAAGGTT-
1 GAAACCTGAATTTTTAA-GTTG
*
3241963 GAAGCCTG-ATTTTTAAGTTG
1 GAAACCTGAATTTTTAAGTTG
3241983 CAATCCAGAT
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.13
20 44 0.41
21 46 0.43
22 3 0.03
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (21 bp):
GAAACCTGAATTTTTAAGTTG
Found at i:3241915 original size:41 final size:40
Alignment explanation
Indices: 3241840--3241982 Score: 182
Period size: 41 Copynumber: 3.5 Consensus size: 40
3241830 GAAATTAGGA
* *
3241840 TGAAACCTGATTTTTAAGTTGGAAACTTGGATTTTTAAGT
1 TGAAACCTGATTTTTAAGTTGGAAACCTGAATTTTTAAGT
* *
3241880 TGGAAACCTGAATTTTTAGGTTGG-AACCTGAATTTTTAGGTT
1 T-GAAACCTG-ATTTTTAAGTTGGAAACCTGAATTTTTAAG-T
*
3241922 TG-AATCTGATTTTTAAGTTGGAAACCTGAATTTTTAAGGT
1 TGAAACCTGATTTTTAAGTTGGAAACCTGAATTTTTAA-GT
*
3241962 TGAAGCCTGATTTTTAAGTTG
1 TGAAACCTGATTTTTAAGTTG
3241983 CAATCCAGAT
Statistics
Matches: 88, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
39 12 0.14
40 23 0.26
41 39 0.44
42 14 0.16
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (40 bp):
TGAAACCTGATTTTTAAGTTGGAAACCTGAATTTTTAAGT
Found at i:3241993 original size:20 final size:20
Alignment explanation
Indices: 3241842--3242017 Score: 92
Period size: 20 Copynumber: 8.8 Consensus size: 20
3241832 AATTAGGATG
* *
3241842 AAACCTGATTTTTAAGTTGG
1 AAACCAGATTTTTAAGTTGC
** *
3241862 AAACTTGGATTTTTAAGTTGG
1 AAAC-CAGATTTTTAAGTTGC
* *
3241883 AAACCTGAATTTTTAGGTTG-
1 AAACCAG-ATTTTTAAGTTGC
* * *
3241903 GAACCTGAATTTTTAGGTTTG-
1 AAACCAG-ATTTTTAAG-TTGC
* * *
3241924 -AATCTGATTTTTAAGTTGG
1 AAACCAGATTTTTAAGTTGC
*
3241943 AAACCTGAATTTTTAAGGTTG-
1 AAACCAG-ATTTTTAA-GTTGC
* *
3241964 AAGCCTGATTTTTAAGTTGC
1 AAACCAGATTTTTAAGTTGC
* *
3241984 AATCCAGA-TTTTAGGTTGC
1 AAACCAGATTTTTAAGTTGC
*
3242003 AAACCATATTTTTAA
1 AAACCAGATTTTTAA
3242018 ATTACAAGCA
Statistics
Matches: 131, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
18 3 0.02
19 28 0.21
20 50 0.38
21 46 0.35
22 4 0.03
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (20 bp):
AAACCAGATTTTTAAGTTGC
Found at i:3241995 original size:19 final size:19
Alignment explanation
Indices: 3241932--3242014 Score: 60
Period size: 19 Copynumber: 4.2 Consensus size: 19
3241922 TGAATCTGAT
* *
3241932 TTTTAAGTTGGAAACCTGAA
1 TTTTAAGTTGCAAACCAG-A
* *
3241952 TTTTTAAGGTTG-AAGCCTGA
1 -TTTTAA-GTTGCAAACCAGA
*
3241972 TTTTTAAGTTGCAATCCAGA
1 -TTTTAAGTTGCAAACCAGA
* *
3241992 TTTTAGGTTGCAAACCATA
1 TTTTAAGTTGCAAACCAGA
3242011 TTTT
1 TTTT
3242015 TAAATTACAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
19 24 0.44
20 14 0.26
21 12 0.22
22 4 0.07
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (19 bp):
TTTTAAGTTGCAAACCAGA
Found at i:3242007 original size:60 final size:58
Alignment explanation
Indices: 3241834--3241995 Score: 182
Period size: 60 Copynumber: 2.7 Consensus size: 58
3241824 AATATTGAAA
* * **
3241834 TTAGGATGAAACCTGATTTTTAAGTTGGAAACTTGGATTTTTAAGTTGGAAACCTGAATTT
1 TTAGGTTG-AACCTGATTTTTAAGTT-GAATC-CAGATTTTTAAGTTGGAAACCTGAATTT
* *
3241895 TTAGGTTGGAACCTGAATTTTTAGGTTTGAAT-CTGATTTTTAAGTTGGAAACCTGAATTT
1 TTAGGTT-GAACCTG-ATTTTTAAG-TTGAATCCAGATTTTTAAGTTGGAAACCTGAATTT
3241955 TTAAGGTTGAAGCCTGATTTTTAAGTTGCAATCCAGATTTT
1 TT-AGGTTGAA-CCTGATTTTTAAGTTG-AATCCAGATTTT
3241996 AGGTTGCAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
59 3 0.03
60 42 0.48
61 28 0.32
62 12 0.14
63 2 0.02
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.41
Consensus pattern (58 bp):
TTAGGTTGAACCTGATTTTTAAGTTGAATCCAGATTTTTAAGTTGGAAACCTGAATTT
Found at i:3242085 original size:40 final size:40
Alignment explanation
Indices: 3242048--3242168 Score: 120
Period size: 40 Copynumber: 3.0 Consensus size: 40
3242038 TCGTACACTT
3242048 CTAAATATTAAAGCGGTGATGTATTGTACAAGATACACAC
1 CTAAATATTAAAGCGGTGATGTATTGTACAAGATACACAC
* * * * *
3242088 CCAATTA-T-AAGCAATGTGATGTATTGTACAGGGTACACAC
1 CTAAATATTAAAGC--GGTGATGTATTGTACAAGATACACAC
* * * * *
3242128 CTAAATATGAAAGTGGTGATATATTATACGAGATACACAC
1 CTAAATATTAAAGCGGTGATGTATTGTACAAGATACACAC
3242168 C
1 C
3242169 CAATTACAAG
Statistics
Matches: 62, Mismatches: 15, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
38 4 0.06
39 1 0.02
40 54 0.87
42 3 0.05
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (40 bp):
CTAAATATTAAAGCGGTGATGTATTGTACAAGATACACAC
Found at i:3242173 original size:80 final size:80
Alignment explanation
Indices: 3242048--3242276 Score: 341
Period size: 80 Copynumber: 2.9 Consensus size: 80
3242038 TCGTACACTT
* * * * * *
3242048 CTAAATATTAAAGCGGTGATGTATTGTACAAGATACACACCCAATTATAAGCAATGTGATGTATT
1 CTAAATATGAAAGTGGTGATATATTATACGAGATACACACCCAATTACAAGCAATGTGATGTATT
*
3242113 GTACAGGGTACACAC
66 GTACAGGGAACACAC
*
3242128 CTAAATATGAAAGTGGTGATATATTATACGAGATACACACCCAATTACAAGAAATGTGATGTATT
1 CTAAATATGAAAGTGGTGATATATTATACGAGATACACACCCAATTACAAGCAATGTGATGTATT
**
3242193 GTATGGGGAACACAC
66 GTACAGGGAACACAC
* * *
3242208 CTAAATATGAAAGTGGTGATATATTATATGGGATACACACCCAATTACAAGCAAGGTGATGTATT
1 CTAAATATGAAAGTGGTGATATATTATACGAGATACACACCCAATTACAAGCAATGTGATGTATT
3242273 GTAC
66 GTAC
3242277 GTGATACACA
Statistics
Matches: 134, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 134 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (80 bp):
CTAAATATGAAAGTGGTGATATATTATACGAGATACACACCCAATTACAAGCAATGTGATGTATT
GTACAGGGAACACAC
Found at i:3242187 original size:40 final size:40
Alignment explanation
Indices: 3242063--3242297 Score: 194
Period size: 40 Copynumber: 5.9 Consensus size: 40
3242053 TATTAAAGCG
* *
3242063 GTGATGTATTGTACAAGATACACACCCAATTATAAGCAAT
1 GTGATGTATTGTACGAGATACACACCCAATTATAAGAAAT
* * *
3242103 GTGATGTATTGTAC-AGGGTACACACCTAA--ATATGAAAGT
1 GTGATGTATTGTACGA-GATACACACCCAATTATAAGAAA-T
* * *
3242142 GGTGATATATTATACGAGATACACACCCAATTACAAGAAAT
1 -GTGATGTATTGTACGAGATACACACCCAATTATAAGAAAT
* * * *
3242183 GTGATGTATTGTATGGGGA-ACACACCTAA--ATATGAAAGT
1 GTGATGTATTGTA-CGAGATACACACCCAATTATAAGAAA-T
* * * * * * *
3242222 GGTGATATATTATATGGGATACACACCCAATTACAAGCAAG
1 -GTGATGTATTGTACGAGATACACACCCAATTATAAGAAAT
*
3242263 GTGATGTATTGTACGTGATACACACCCAATTATAA
1 GTGATGTATTGTACGAGATACACACCCAATTATAA
3242298 ACAAGAATAA
Statistics
Matches: 153, Mismatches: 30, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
38 12 0.08
39 7 0.05
40 118 0.77
41 5 0.03
42 11 0.07
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (40 bp):
GTGATGTATTGTACGAGATACACACCCAATTATAAGAAAT
Found at i:3244385 original size:14 final size:14
Alignment explanation
Indices: 3244366--3244392 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3244356 TGTAGACAAC
3244366 TATTTTTAACAAAT
1 TATTTTTAACAAAT
3244380 TATTTTTAACAAA
1 TATTTTTAACAAA
3244393 AAATTCTTTG
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:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
TATTTTTAACAAAT
Found at i:3250897 original size:29 final size:30
Alignment explanation
Indices: 3250865--3250924 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
3250855 CATAATACAT
*
3250865 AAAAAA-TATTTCAAAA-AATAATATATATA
1 AAAAAATTATTT-AAAATAATAAAATATATA
3250894 AAAAAATTATTTAAAATTAATAAAATATATA
1 AAAAAATTATTTAAAA-TAATAAAATATATA
3250925 TTTAATTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 10 0.37
30 5 0.19
31 12 0.44
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAAAATTATTTAAAATAATAAAATATATA
Found at i:3251315 original size:2 final size:2
Alignment explanation
Indices: 3251308--3251346 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3251298 AAAGGAAAAG
*
3251308 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3251347 TTGACCTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3253391 original size:24 final size:24
Alignment explanation
Indices: 3253359--3253416 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
3253349 GTTGACGACC
3253359 TTGTTTCTTCATGATAAGGACACA
1 TTGTTTCTTCATGATAAGGACACA
* *
3253383 TTGTTTCTTCATGATAAGGATACC
1 TTGTTTCTTCATGATAAGGACACA
*
3253407 TTGTTCCTTC
1 TTGTTTCTTC
3253417 TAAAGAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (24 bp):
TTGTTTCTTCATGATAAGGACACA
Found at i:3254870 original size:16 final size:15
Alignment explanation
Indices: 3254849--3254882 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3254839 TTTTATTTTA
3254849 TTTTCTTTCTTTCCTT
1 TTTTCTTT-TTTCCTT
*
3254865 TTTTCTTTTTTTCTT
1 TTTTCTTTTTTCCTT
3254880 TTT
1 TTT
3254883 CTATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTTCCTT
Found at i:3254889 original size:16 final size:15
Alignment explanation
Indices: 3254849--3254891 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
3254839 TTTTATTTTA
*
3254849 TTTTCTTTCTTTCCTT
1 TTTTCTTTTTTTCC-T
3254865 TTTTCTTTTTTT-CT
1 TTTTCTTTTTTTCCT
3254879 TTTTCTATTTTTT
1 TTTTCT-TTTTTT
3254892 ATTTTTCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 7 0.28
15 7 0.28
16 11 0.44
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTTTCCT
Found at i:3254905 original size:17 final size:15
Alignment explanation
Indices: 3254864--3254922 Score: 66
Period size: 15 Copynumber: 3.8 Consensus size: 15
3254854 TTTCTTTCCT
*
3254864 TTTTTCT-TTTTTTC
1 TTTTTCTATTTTTTA
3254878 TTTTTCTATTTTTTA
1 TTTTTCTATTTTTTA
3254893 TTTTTCATCATTTTTTA
1 TTTTTC-T-ATTTTTTA
*
3254910 TTTCTTTTATTTT
1 TTT-TTCTATTTT
3254923 CTTCATGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
14 7 0.18
15 12 0.31
16 6 0.15
17 12 0.31
18 2 0.05
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTCTATTTTTTA
Found at i:3258880 original size:20 final size:18
Alignment explanation
Indices: 3258833--3258905 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
3258823 ACTGAATATT
* *
3258833 TGTCCTGAATGACCACTA
1 TGTCCCGAAGGACCACTA
3258851 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
3258870 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
3258889 TGTCCCAAAGGACCACT
1 TGTCCCGAAGGACCACT
3258906 GATTATCCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 29 0.63
19 2 0.04
20 15 0.33
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3260893 original size:10 final size:10
Alignment explanation
Indices: 3260878--3260903 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3260868 TTTAGAAATC
3260878 ATTTAAGTAA
1 ATTTAAGTAA
3260888 ATTTAAGTAA
1 ATTTAAGTAA
3260898 ATTTAA
1 ATTTAA
3260904 AAACATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (10 bp):
ATTTAAGTAA
Found at i:3263566 original size:971 final size:971
Alignment explanation
Indices: 3261685--3263628 Score: 3888
Period size: 971 Copynumber: 2.0 Consensus size: 971
3261675 CTGAGCTTTC
3261685 CAATAAATTCATATCATTATAAATCCATCATCTCCATTTAGTAGTATATTCACACATCATTTATC
1 CAATAAATTCATATCATTATAAATCCATCATCTCCATTTAGTAGTATATTCACACATCATTTATC
3261750 AAAAAATAGTATTATGGGCAGTTCATACCCTAATTAAAATCATAAATCAATTCAGTAAACATAAT
66 AAAAAATAGTATTATGGGCAGTTCATACCCTAATTAAAATCATAAATCAATTCAGTAAACATAAT
3261815 GGAAATGTTCCATAATTTAATTCAAATCATTATTTAAAAATCATACGAGGTTGACTTATCGCAAG
131 GGAAATGTTCCATAATTTAATTCAAATCATTATTTAAAAATCATACGAGGTTGACTTATCGCAAG
3261880 TCATAATCAATCAATTAAAATTATAATTAAATAAATAAAATACAGTCACCCTTACCTCATTACCG
196 TCATAATCAATCAATTAAAATTATAATTAAATAAATAAAATACAGTCACCCTTACCTCATTACCG
3261945 AACCTTGTATATGATATCTTTTTACTCACGTACATTGTTTTTCGCTTTCGAATCGCTAGAATCGT
261 AACCTTGTATATGATATCTTTTTACTCACGTACATTGTTTTTCGCTTTCGAATCGCTAGAATCGT
3262010 AAGATTTATCATGGTATGGACAACATCATATAAATAATACAATAGTCAAAATATATGTTAGTAAT
326 AAGATTTATCATGGTATGGACAACATCATATAAATAATACAATAGTCAAAATATATGTTAGTAAT
3262075 ATATTAATATAATCTAATTCCAATAATAAAAATTCTATAAAACATAATTGATACTTAATCGATAT
391 ATATTAATATAATCTAATTCCAATAATAAAAATTCTATAAAACATAATTGATACTTAATCGATAT
3262140 AAAAATCAAATCACTAATCCATAACAAGCTTCATGAAAATTTCAATCCTTACAAAATAACTCTTC
456 AAAAATCAAATCACTAATCCATAACAAGCTTCATGAAAATTTCAATCCTTACAAAATAACTCTTC
3262205 AATTCTATAATTATTCAATTTCATCATTACCCCCTCAACTTTCATAAACTTTGCATTTAAGTCAC
521 AATTCTATAATTATTCAATTTCATCATTACCCCCTCAACTTTCATAAACTTTGCATTTAAGTCAC
3262270 CATTTACAAATTCTTTTTAGAATTCACATCAACCTTTCTAATTTACTCAAAATGGTCCTTTATCA
586 CATTTACAAATTCTTTTTAGAATTCACATCAACCTTTCTAATTTACTCAAAATGGTCCTTTATCA
3262335 TTTTTAATTATCTCAAATCAAACACTAAAATTTCCAACATTGCAGTAATATACTAAATTAATATC
651 TTTTTAATTATCTCAAATCAAACACTAAAATTTCCAACATTGCAGTAATATACTAAATTAATATC
3262400 CTCACATTTACAAACTTGTAATTTAGTCACTGAATTTTCTAGTTTCTTCTTAACATAGAAAATTG
716 CTCACATTTACAAACTTGTAATTTAGTCACTGAATTTTCTAGTTTCTTCTTAACATAGAAAATTG
3262465 AACATAATTCTAATGATCCATGCTAAATTTCACTGTTCTAAATTATGGAAAAATATTTCTAGCCC
781 AACATAATTCTAATGATCCATGCTAAATTTCACTGTTCTAAATTATGGAAAAATATTTCTAGCCC
3262530 TTCTCTATCATCCTTCAAATTTTTGTGAAATTTCGATTCGATCTGGTTATTTGATTCCTTGTCGG
846 TTCTCTATCATCCTTCAAATTTTTGTGAAATTTCGATTCGATCTGGTTATTTGATTCCTTGTCGG
3262595 ACTTTACTACTTTATATCTTTTAATACAAATCCCGAATGAAATTTTTGATTCCCATGAAAA
911 ACTTTACTACTTTATATCTTTTAATACAAATCCCGAATGAAATTTTTGATTCCCATGAAAA
3262656 CAATAAATTCATATCATTATAAATCCATCATCTCCATTTAGTAGTATATTCACACATCATTTATC
1 CAATAAATTCATATCATTATAAATCCATCATCTCCATTTAGTAGTATATTCACACATCATTTATC
3262721 AAAAAATAGTATTATGGGCAGTTCATACCCTAATTAAAATCATAAATCAATTCAGTAAACATAAT
66 AAAAAATAGTATTATGGGCAGTTCATACCCTAATTAAAATCATAAATCAATTCAGTAAACATAAT
3262786 GGAAATGTTCCATAATTTAATTCAAATCATTATTTAAAAATCATACGAGGTTGACTTATCGCAAG
131 GGAAATGTTCCATAATTTAATTCAAATCATTATTTAAAAATCATACGAGGTTGACTTATCGCAAG
3262851 TCATAATCAATCAATTAAAATTATAATTAAATAAATAAAATACAGTCACCCTTACCTCATTACCG
196 TCATAATCAATCAATTAAAATTATAATTAAATAAATAAAATACAGTCACCCTTACCTCATTACCG
3262916 AACCTTGTATATGATATCTTTTTACTCACGTACATTGTTTTTCGCTTTCGAATCGCTAGAATCGT
261 AACCTTGTATATGATATCTTTTTACTCACGTACATTGTTTTTCGCTTTCGAATCGCTAGAATCGT
3262981 AAGATTTATCATGGTATGGACAACATCATATAAATAATACAATAGTCAAAATATATGTTAGTAAT
326 AAGATTTATCATGGTATGGACAACATCATATAAATAATACAATAGTCAAAATATATGTTAGTAAT
3263046 ATATTAATATAATCTAATTCCAATAATAAAAATTCTATAAAACATAATTGATACTTAATCGATAT
391 ATATTAATATAATCTAATTCCAATAATAAAAATTCTATAAAACATAATTGATACTTAATCGATAT
3263111 AAAAATCAAATCACTAATCCATAACAAGCTTCATGAAAATTTCAATCCTTACAAAATAACTCTTC
456 AAAAATCAAATCACTAATCCATAACAAGCTTCATGAAAATTTCAATCCTTACAAAATAACTCTTC
3263176 AATTCTATAATTATTCAATTTCATCATTACCCCCTCAACTTTCATAAACTTTGCATTTAAGTCAC
521 AATTCTATAATTATTCAATTTCATCATTACCCCCTCAACTTTCATAAACTTTGCATTTAAGTCAC
3263241 CATTTACAAATTCTTTTTAGAATTCACATCAACCTTTCTAATTTACTCAAAATGGTCCTTTATCA
586 CATTTACAAATTCTTTTTAGAATTCACATCAACCTTTCTAATTTACTCAAAATGGTCCTTTATCA
3263306 TTTTTAATTATCTCAAATCAAACACTAAAATTTCCAACATTGCAGTAATATACTAAATTAATATC
651 TTTTTAATTATCTCAAATCAAACACTAAAATTTCCAACATTGCAGTAATATACTAAATTAATATC
3263371 CTCACATTTACAAACTTGTAATTTAGTCACTGAATTTTCTAGTTTCTTCTTAACATAGAAAATTG
716 CTCACATTTACAAACTTGTAATTTAGTCACTGAATTTTCTAGTTTCTTCTTAACATAGAAAATTG
3263436 AACATAATTCTAATGATCCATGCTAAATTTCACTGTTCTAAATTATGGAAAAATATTTCTAGCCC
781 AACATAATTCTAATGATCCATGCTAAATTTCACTGTTCTAAATTATGGAAAAATATTTCTAGCCC
3263501 TTCTCTATCATCCTTCAAATTTTTGTGAAATTTCGATTCGATCTGGTTATTTGATTCCTTGTCGG
846 TTCTCTATCATCCTTCAAATTTTTGTGAAATTTCGATTCGATCTGGTTATTTGATTCCTTGTCGG
3263566 ACTTTACTACTTTATATCTTTTAATACAAATCCCGAATGAAATTTTTGATTCCCATGAAAA
911 ACTTTACTACTTTATATCTTTTAATACAAATCCCGAATGAAATTTTTGATTCCCATGAAAA
3263627 CA
1 CA
3263629 TTAATTTCTT
Statistics
Matches: 973, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
971 973 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.37
Consensus pattern (971 bp):
CAATAAATTCATATCATTATAAATCCATCATCTCCATTTAGTAGTATATTCACACATCATTTATC
AAAAAATAGTATTATGGGCAGTTCATACCCTAATTAAAATCATAAATCAATTCAGTAAACATAAT
GGAAATGTTCCATAATTTAATTCAAATCATTATTTAAAAATCATACGAGGTTGACTTATCGCAAG
TCATAATCAATCAATTAAAATTATAATTAAATAAATAAAATACAGTCACCCTTACCTCATTACCG
AACCTTGTATATGATATCTTTTTACTCACGTACATTGTTTTTCGCTTTCGAATCGCTAGAATCGT
AAGATTTATCATGGTATGGACAACATCATATAAATAATACAATAGTCAAAATATATGTTAGTAAT
ATATTAATATAATCTAATTCCAATAATAAAAATTCTATAAAACATAATTGATACTTAATCGATAT
AAAAATCAAATCACTAATCCATAACAAGCTTCATGAAAATTTCAATCCTTACAAAATAACTCTTC
AATTCTATAATTATTCAATTTCATCATTACCCCCTCAACTTTCATAAACTTTGCATTTAAGTCAC
CATTTACAAATTCTTTTTAGAATTCACATCAACCTTTCTAATTTACTCAAAATGGTCCTTTATCA
TTTTTAATTATCTCAAATCAAACACTAAAATTTCCAACATTGCAGTAATATACTAAATTAATATC
CTCACATTTACAAACTTGTAATTTAGTCACTGAATTTTCTAGTTTCTTCTTAACATAGAAAATTG
AACATAATTCTAATGATCCATGCTAAATTTCACTGTTCTAAATTATGGAAAAATATTTCTAGCCC
TTCTCTATCATCCTTCAAATTTTTGTGAAATTTCGATTCGATCTGGTTATTTGATTCCTTGTCGG
ACTTTACTACTTTATATCTTTTAATACAAATCCCGAATGAAATTTTTGATTCCCATGAAAA
Found at i:3270952 original size:28 final size:27
Alignment explanation
Indices: 3270933--3271007 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 27
3270923 AATAATTATG
*
3270933 TAAAACATAATATATA-AAAAATATTT
1 TAAAAAATAATATATATAAAAATATTT
3270959 TAAAAAATAATATATATAAAAAAAATATTT
1 TAAAAAATAATATATAT---AAAAATATTT
* *
3270989 AAAAAGAATAAAATATATA
1 TAAAA-AATAATATATATA
3271008 TTTAATTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
26 15 0.37
28 1 0.02
30 14 0.34
31 11 0.27
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (27 bp):
TAAAAAATAATATATATAAAAATATTT
Done.