Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 69 of 106
Found at i:12497519 original size:25 final size:24
Alignment explanation
Indices: 12497421--12497506 Score: 93
Period size: 26 Copynumber: 3.3 Consensus size: 24
12497411 AATTACTTTT
12497421 TAATATTAATAATTTTAATAATAAA
1 TAATATTAAT-ATTTTAATAATAAA
12497446 TAAT-TTCAATATATTTTAATAATAAA
1 TAATATT--A-ATATTTTAATAATAAA
*
12497472 TAATTTTTAATATTTTAATAATAATA
1 TAA-TATTAATATTTTAATAATAA-A
12497498 TTAATATTA
1 -TAATATTA
12497507 TTTGAAATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
24 2 0.04
25 19 0.36
26 24 0.45
27 6 0.11
28 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATATTAATATTTTAATAATAAA
Found at i:12498191 original size:14 final size:15
Alignment explanation
Indices: 12498168--12498197 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12498158 CATAATAAAC
12498168 ATATCTTAATCTAAT
1 ATATCTTAATCTAAT
12498183 ATATC-TAATCTAAT
1 ATATCTTAATCTAAT
12498197 A
1 A
12498198 CATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATCTTAATCTAAT
Found at i:12498389 original size:28 final size:27
Alignment explanation
Indices: 12498341--12498399 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
12498331 ATTAAATAAT
*
12498341 TTTAAATTTATTCAAATATCAAATTAA
1 TTTAAATTTATTCAAATATCAAATCAA
*
12498368 TTTAAATTATAATTGAAA-ATCAAATCAA
1 TTTAAATT-T-ATTCAAATATCAAATCAA
12498396 TTTA
1 TTTA
12498400 GAGATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 14 0.50
29 6 0.21
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (27 bp):
TTTAAATTTATTCAAATATCAAATCAA
Found at i:12499507 original size:23 final size:23
Alignment explanation
Indices: 12499480--12499524 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
12499470 TCGGAGGTTT
* *
12499480 TTTTTATTTCATTTTTATTTTAGA
1 TTTTGATTT-ATTTTGATTTTAGA
12499504 TTTTGATTTATTTTGATTTTA
1 TTTTGATTTATTTTGATTTTA
12499525 TTTTTAACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.71
Consensus pattern (23 bp):
TTTTGATTTATTTTGATTTTAGA
Found at i:12509407 original size:24 final size:24
Alignment explanation
Indices: 12509342--12509407 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
12509332 TGCTTGATTT
12509342 AAAA-AAATAAA-AAATAAAAATA
1 AAAATAAATAAATAAATAAAAATA
* * * *
12509364 AAATTAATTAATTAATTAAAAATA
1 AAAATAAATAAATAAATAAAAATA
12509388 AAAATAAATAAATAAATAAA
1 AAAATAAATAAATAAATAAA
12509408 TAAAAAGGGA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 3 0.09
23 5 0.15
24 26 0.76
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAATAAATAAATAAATAAAAATA
Found at i:12510705 original size:236 final size:236
Alignment explanation
Indices: 12510255--12511138 Score: 903
Period size: 236 Copynumber: 3.7 Consensus size: 236
12510245 TTATTTTCAC
* * * * ** *
12510255 TCACTTGATTTTGGCTCAGTCCAGATCATTTCTTATGATTCGTGATTTCA-TCCTAATCATTTAT
1 TCACTTGATCTTGACTCAGTCTAGATCATTTCTCATGATTTATGATTTCATTCC-GATCATTTAT
* * *
12510319 TTTTTACCTTGACTCTATCCTGGTTGCCTCATTTGACTCATGGTTTCATCCCGATCGCTTGATCT
65 TTTTTACCTTGACTCGATCCTGGTTGTCTCATTTGACTCATGGTTTCATCCCGATCACTTGATCT
* * * * * *
12510384 TAGTTC-GATCCAGATCATTTCTTATGATTCGTAGTTTCATCTCGATCATTTATTTTTAACCTTA
130 TGGCTCAG-TCCAGATCATTTCTTATGATTCGTGGTTTTATCCCGATCATTTATTTTTAACCTTG
* *
12510448 ACTCGATCCTAGTTACCTCATTTGACTCATAGTTTTATCTCGA
194 ACTCGGTCCTAGTTACCTCATTTGACTCATAGTTTTATCCCGA
** * * * *
12510491 TTTCTTGATCTTGACTCAATCTAGATCATTTCTCATGATTTGTGATTTTATTTCGATCATTTATT
1 TCACTTGATCTTGACTCAGTCTAGATCATTTCTCATGATTTATGATTTCATTCCGATCATTTATT
* * * * * *
12510556 TTTTACCTTAACCCGGTCCTGGTCGTCTCATTTGACTCGTAGTTTCATCCCGATCACTTGATCTT
66 TTTTACCTTGACTCGATCCTGGTTGTCTCATTTGACTCATGGTTTCATCCCGATCACTTGATCTT
* * * * * *
12510621 GGCTCAGTCTATATCATTTCTTATGATTCGTGGTTTTGTCCCAATCATTTATTTTTTATCTTGAC
131 GGCTCAGTCCAGATCATTTCTTATGATTCGTGGTTTTATCCCGATCATTTATTTTTAACCTTGAC
* * * * *
12510686 TCGGTCCTGGTTGCCTCATTTGACTCGTGGTTTCATCCCGA
196 TCGGTCCTAGTTACCTCATTTGACTCATAGTTTTATCCCGA
** * *
12510727 TGGCTTGATCTTGACTCAGTCTAGATCATTTTTCATGATTTATGATTTCATCCCGATCATTTATT
1 TCACTTGATCTTGACTCAGTCTAGATCATTTCTCATGATTTATGATTTCATTCCGATCATTTATT
* * *
12510792 TTTTACCTTGACTCGATCCTGATTATCTTATTTGACTCATGGTTTCATCCCGAT-AGCTTGATCT
66 TTTTACCTTGACTCGATCCTGGTTGTCTCATTTGACTCATGGTTTCATCCCGATCA-CTTGATCT
* * * * * * **
12510856 TGGCTTAGTCCAGATCATTTCTCATGATTCGTGATTCTATCCTGATTATTTATTTTCGACCTTGA
130 TGGCTCAGTCCAGATCATTTCTTATGATTCGTGGTTTTATCCCGATCATTTATTTTTAACCTTGA
* * * * * *
12510921 CTCAGTTCTAGTCACTTTATTTGACTCATTGTTTTATCCCGA
195 CTCGGTCCTAGTTACCTCATTTGACTCATAGTTTTATCCCGA
** * * * * *
12510963 TCACTTGATCTTGGTTTAGTCTATATCATTTCTCATGATTTATGATTTCGTCCCGATCATTCA-T
1 TCACTTGATCTTGACTCAGTCTAGATCATTTCTCATGATTTATGATTTCATTCCGATCATTTATT
** ** * * * * ** **
12511027 TTGGACCTTGACTTAATCCTAGCTGTTTCATTTCGTATCACTCATGGTTTCATCCCGGTTGCTCA
66 TTTTACCTTGACTCGATCCTGGTTGTCTCATTT-G----ACTCATGGTTTCATCCCGATCACTTG
* * * *
12511092 ATCTTGGCTAAGTCCAGATCATTGCTTATGATTTGTGGTTTCATCCC
126 ATCTTGGCTCAGTCCAGATCATTTCTTATGATTCGTGGTTTTATCCC
12511139 AATTATCATT
Statistics
Matches: 529, Mismatches: 110, Indels: 14
0.81 0.17 0.02
Matches are distributed among these distances:
235 25 0.05
236 441 0.83
237 3 0.01
240 60 0.11
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.44
Consensus pattern (236 bp):
TCACTTGATCTTGACTCAGTCTAGATCATTTCTCATGATTTATGATTTCATTCCGATCATTTATT
TTTTACCTTGACTCGATCCTGGTTGTCTCATTTGACTCATGGTTTCATCCCGATCACTTGATCTT
GGCTCAGTCCAGATCATTTCTTATGATTCGTGGTTTTATCCCGATCATTTATTTTTAACCTTGAC
TCGGTCCTAGTTACCTCATTTGACTCATAGTTTTATCCCGA
Found at i:12510909 original size:354 final size:353
Alignment explanation
Indices: 12510255--12511028 Score: 950
Period size: 354 Copynumber: 2.2 Consensus size: 353
12510245 TTATTTTCAC
* * * *
12510255 TCACTTGATTTTGGCTCAGTCCAGATCATTTCTTATGATTCGTGATTTCATCCTAATCATTTATT
1 TCACTTGATCTTGGCTCAGTCTATATCATTTCTTATGATTCGTGATTTCATCCCAATCATTTATT
*
12510320 TTTTACCTTGACTCTATCCTGGTTGCCTCATTTGACTCATGGTTTCATCCCGATCGCTTGATCTT
66 TTTTACCTTGACTCGATCCTGGTTGCCTCATTTGACTCATGGTTTCATCCCGATCGCTTGATCTT
* *
12510385 AGTTCGATCCAGATCATTTCTTATGATTCGTAGTTTCATCTCGATCATTTATTTTTAACCTTAAC
131 AGCTCGATCCAGATCATTTCTTATGATTC-TAGTTTCATCCCGATCATTTATTTTTAACCTTAAC
* * ** *
12510450 TCGATCCTAGTTACCTCATTTGACTCATAGTTTTATCTCGATTTCTTGATCTTGACTCAATCTAG
195 TCGATCCTAGTTACCTCATTTGACTCATAGTTTCATCCCGATAGCTTGATCTTGACTCAATCCAG
* * * ** * *
12510515 ATCATTTCTCATGATTTGTGATTTTATTTCGATCATTTATTTTTTACCTTAACCCGGTCCTGGTC
260 ATCATTTCTCATGATTCGTGATTCTATCTCGATCATTTATTTTCGACCTTAACCCAGTCCTAGTC
* *
12510580 -GTCTCATTTGACTCGTAGTTTCATCCCGA
325 ACT-TCATTTGACTCATAGTTTCATCCCGA
* **
12510609 TCACTTGATCTTGGCTCAGTCTATATCATTTCTTATGATTCGTGGTTTTGTCCCAATCATTTATT
1 TCACTTGATCTTGGCTCAGTCTATATCATTTCTTATGATTCGTGATTTCATCCCAATCATTTATT
* * * *
12510674 TTTTATCTTGACTCGGTCCTGGTTGCCTCATTTGACTCGTGGTTTCATCCCGATGGCTTGATCTT
66 TTTTACCTTGACTCGATCCTGGTTGCCTCATTTGACTCATGGTTTCATCCCGATCGCTTGATCTT
* *
12510739 -GACTC-AGTCTAGATCATTT-TTCATGATT-TATGATTTCATCCCGATCATTTATTTTTTACCT
131 AG-CTCGA-TCCAGATCATTTCTT-ATGATTCTA-G-TTTCATCCCGATCATTTATTTTTAACCT
* * * * * * *
12510800 TGACTCGATCCT-GATTATCTTATTTGACTCATGGTTTCATCCCGATAGCTTGATCTTGGCTTAG
191 TAACTCGATCCTAG-TTACCTCATTTGACTCATAGTTTCATCCCGATAGCTTGATCTTGACTCAA
* * * *
12510864 TCCAGATCATTTCTCATGATTCGTGATTCTATC-CTGATTATTTATTTTCGACCTTGACTCAGTT
255 TCCAGATCATTTCTCATGATTCGTGATTCTATCTC-GATCATTTATTTTCGACCTTAACCCAGTC
* * *
12510928 CTAGTCACTTTATTTGACTCATTGTTTTATCCCGA
319 CTAGTCACTTCATTTGACTCATAGTTTCATCCCGA
* * * ** * * *
12510963 TCACTTGATCTTGGTTTAGTCTATATCATTTCTCATGATTTATGATTTCGTCCCGATCATTCATT
1 TCACTTGATCTTGGCTCAGTCTATATCATTTCTTATGATTCGTGATTTCATCCCAATCATTTATT
12511028 T
66 T
12511029 GGACCTTGAC
Statistics
Matches: 359, Mismatches: 53, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
352 2 0.01
353 7 0.02
354 349 0.97
355 1 0.00
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (353 bp):
TCACTTGATCTTGGCTCAGTCTATATCATTTCTTATGATTCGTGATTTCATCCCAATCATTTATT
TTTTACCTTGACTCGATCCTGGTTGCCTCATTTGACTCATGGTTTCATCCCGATCGCTTGATCTT
AGCTCGATCCAGATCATTTCTTATGATTCTAGTTTCATCCCGATCATTTATTTTTAACCTTAACT
CGATCCTAGTTACCTCATTTGACTCATAGTTTCATCCCGATAGCTTGATCTTGACTCAATCCAGA
TCATTTCTCATGATTCGTGATTCTATCTCGATCATTTATTTTCGACCTTAACCCAGTCCTAGTCA
CTTCATTTGACTCATAGTTTCATCCCGA
Found at i:12510976 original size:118 final size:116
Alignment explanation
Indices: 12510255--12511002 Score: 732
Period size: 118 Copynumber: 6.3 Consensus size: 116
12510245 TTATTTTCAC
* * * *
12510255 TCACTTGATTTTGGCTCAGTCCAGATCATTTCTTATGATTCGTGATTTCATCCTAATCATTTATT
1 TCACTTGATCTTGGCTCAGTCTAGATCATTTCTCATGATTCGTGATTT-ATCCTGATCATTTATT
* *
12510320 TTTTACCTTGACTCTATCCTGGTTGCCTCATTTGACTCATGGTTTCATCCCGA
65 TTTTACCTTGACTC-GTCCTGGTTACCTCATTTGACTCATGGTTTCATCCCGA
* * * * *
12510373 TCGCTTGATCTTAGTTC-GATCCAGATCATTTCTTATGATTCGT-AGTTTCAT-CTCGATCATTT
1 TCACTTGATCTTGGCTCAG-TCTAGATCATTTCTCATGATTCGTGA-TTT-ATCCT-GATCATTT
* * * * * *
12510435 ATTTTTAACCTTAACTCGATCCTAGTTACCTCATTTGACTCATAGTTTTATCTCGA
62 ATTTTTTACCTTGACTCG-TCCTGGTTACCTCATTTGACTCATGGTTTCATCCCGA
** * * * *
12510491 TTTCTTGATCTTGACTCAATCTAGATCATTTCTCATGATTTGTGATTTTAT-TTCGATCATTTAT
1 TCACTTGATCTTGGCTCAGTCTAGATCATTTCTCATGATTCGTGA-TTTATCCT-GATCATTTAT
* * *** * *
12510555 TTTTTACCTTAACCCGGTCCTGGTCGTCTCATTTGACTCGTAGTTTCATCCCGA
64 TTTTTACCTTGACTC-GTCCTGGTTACCTCATTTGACTCATGGTTTCATCCCGA
* * * * **
12510609 TCACTTGATCTTGGCTCAGTCTATATCATTTCTTATGATTCGTGGTTTTGTCCCAATCATTTATT
1 TCACTTGATCTTGGCTCAGTCTAGATCATTTCTCATGATTCGT-GATTTATCCTGATCATTTATT
* * *
12510674 TTTTATCTTGACTCGGTCCTGGTTGCCTCATTTGACTCGTGGTTTCATCCCGA
65 TTTTACCTTGACTC-GTCCTGGTTACCTCATTTGACTCATGGTTTCATCCCGA
** * * ** *
12510727 TGGCTTGATCTTGACTCAGTCTAGATCATTTTTCATGATTTATGATTTCATCCCGATCATTTATT
1 TCACTTGATCTTGGCTCAGTCTAGATCATTTCTCATGATTCGTGATTT-ATCCTGATCATTTATT
* * *
12510792 TTTTACCTTGACTCGATCCTGATTATCTTATTTGACTCATGGTTTCATCCCGA
65 TTTTACCTTGACTCG-TCCTGGTTACCTCATTTGACTCATGGTTTCATCCCGA
* * *
12510845 T-AGCTTGATCTTGGCTTAGTCCAGATCATTTCTCATGATTCGTGATTCTATCCTGATTATTTAT
1 TCA-CTTGATCTTGGCTCAGTCTAGATCATTTCTCATGATTCGTGATT-TATCCTGATCATTTAT
** * * * * * * *
12510909 TTTCGACCTTGACTCAGTTCTAGTCACTTTATTTGACTCATTGTTTTATCCCGA
64 TTTTTACCTTGACTC-GTCCTGGTTACCTCATTTGACTCATGGTTTCATCCCGA
* * *
12510963 TCACTTGATCTTGGTTTAGTCTATATCATTTCTCATGATT
1 TCACTTGATCTTGGCTCAGTCTAGATCATTTCTCATGATT
12511003 TATGATTTCG
Statistics
Matches: 525, Mismatches: 90, Indels: 30
0.81 0.14 0.05
Matches are distributed among these distances:
117 9 0.02
118 507 0.97
119 9 0.02
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (116 bp):
TCACTTGATCTTGGCTCAGTCTAGATCATTTCTCATGATTCGTGATTTATCCTGATCATTTATTT
TTTACCTTGACTCGTCCTGGTTACCTCATTTGACTCATGGTTTCATCCCGA
Found at i:12511476 original size:3 final size:3
Alignment explanation
Indices: 12511457--12511510 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
12511447 TTTAATTAAA
* *
12511457 TAT T-T TAT TAT TTT TAT TAT TAT TAT TAT T-C TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
*
12511501 TTT TAT TAT T
1 TAT TAT TAT T
12511511 TATTTATTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 37 0.88
4 2 0.05
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:12511509 original size:27 final size:27
Alignment explanation
Indices: 12511460--12511522 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
12511450 AATTAAATAT
*
12511460 TTTA-TTATTTTTATTATTATTA-TTA
1 TTTATTTATTATTATTATTATTATTTA
*
12511485 TTCTATTTATTATTATTTTTATTATTTA
1 TT-TATTTATTATTATTATTATTATTTA
12511513 TTTATTTATT
1 TTTATTTATT
12511523 TTGGTCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 2 0.06
26 2 0.06
27 24 0.73
28 5 0.15
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTATTTATTATTATTATTATTATTTA
Found at i:12511781 original size:20 final size:23
Alignment explanation
Indices: 12511758--12511799 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
12511748 TATCTTTAAC
12511758 AGATA-AG-AACACACA-AAAAA
1 AGATACAGAAACACACAGAAAAA
12511778 AGATACAGAAACACACAGAAAA
1 AGATACAGAAACACACAGAAAA
12511800 TAAAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 8 0.42
23 4 0.21
ACGTcount: A:0.67, C:0.17, G:0.12, T:0.05
Consensus pattern (23 bp):
AGATACAGAAACACACAGAAAAA
Found at i:12512431 original size:18 final size:18
Alignment explanation
Indices: 12512404--12512462 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
12512394 CAATCGCAGG
*
12512404 TTTTTTTTTTCTATTTTA
1 TTTTTATTTTCTATTTTA
12512422 TTTTTATTTTCATATTTTGA
1 TTTTTATTTTC-TATTTT-A
*
12512442 --TTTATTTT-TATTTTG
1 TTTTTATTTTCTATTTTA
12512457 TTTTTA
1 TTTTTA
12512463 ACCTTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 6 0.17
17 4 0.11
18 18 0.51
19 6 0.17
20 1 0.03
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.78
Consensus pattern (18 bp):
TTTTTATTTTCTATTTTA
Found at i:12512431 original size:19 final size:19
Alignment explanation
Indices: 12512405--12512450 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
12512395 AATCGCAGGT
12512405 TTTTTTTTTC-TATTTT-A
1 TTTTTTTTTCATATTTTGA
12512422 TTTTTATTTTCATATTTTGA
1 TTTTT-TTTTCATATTTTGA
*
12512442 TTTATTTTT
1 TTTTTTTTT
12512451 ATTTTGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 5 0.20
18 5 0.20
19 10 0.40
20 5 0.20
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTTTTTCATATTTTGA
Found at i:12520147 original size:21 final size:19
Alignment explanation
Indices: 12520123--12520170 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
12520113 TTTTTTTAAT
12520123 AAATATATTATTTAAACAAAA
1 AAATATATT-TTT-AACAAAA
*
12520144 AAATGATTATTTTTAATAAAA
1 AAAT-A-TATTTTTAACAAAA
12520165 AAATAT
1 AAATAT
12520171 TTGTAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 1 0.04
21 14 0.58
22 4 0.17
23 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AAATATATTTTTAACAAAA
Found at i:12525694 original size:2 final size:2
Alignment explanation
Indices: 12525689--12525716 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12525679 TATATATATA
12525689 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
12525717 GAAGGGGATG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:12527945 original size:10 final size:11
Alignment explanation
Indices: 12527918--12527947 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12527908 AAAATGTTTG
12527918 ATAAATAATTT
1 ATAAATAATTT
12527929 ATAAATAATTT
1 ATAAATAATTT
12527940 -TAAATAAT
1 ATAAATAAT
12527948 ATTTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATAAATAATTT
Found at i:12528242 original size:166 final size:158
Alignment explanation
Indices: 12527941--12528335 Score: 395
Period size: 159 Copynumber: 2.4 Consensus size: 158
12527931 AAATAATTTT
* * * *
12527941 AAATAATATTTTA-ATATTTATTAATTAAAAAATATATCATAAATATAATAAAAATTT-TT-ATT
1 AAATAATATTTTATA-ATTTATTAATTAATAAATAAATTACAAATATAAT-AAAATTTATTAATT
* * * *
12528003 TTTTATTTATTTATAATTTAAATATAAATATATAAATTATTCAATAAATAATTTATAAACATATT
64 TTTAATTTATTTATAATTTAAATATAAATATATAAATTATTCAACAAACAATTTATAAACAAATT
* * **
12528068 TAATTTTTATTTATTTATTAAATTTAACAATCGATC
129 AAATTTTTATTTATTTAAT-AA---AA-AAT-GAAA
* *
12528104 ACATATATATTTTATAATTTATTAATTATATAAATAGATTACAAATATAATAAAATTTATTAATT
1 AAATA-ATATTTTATAATTTATTAATTA-ATAAATAAATTACAAATATAATAAAATTTATTAATT
* * * * * * *
12528169 TTTAATTTATTTATATTTATAAATATAAATGA-A-AAATTATTTAACGAACACTTTGTGAATAAA
64 TTTAATTTATTTATAATT-TAAATATAAAT-ATATAAATTATTCAACAAACAATTTATAAACAAA
* *
12528232 TTAAATTTTTATTTGTTTAATAAAAAATTAAA
127 TTAAATTTTTATTTATTTAATAAAAAATGAAA
* * *
12528264 AAATAATATTTTATAATTTATTAATTAAATAAATAAACTACAAAAATAATAAAATTTATTAATAT
1 AAATAATATTTTATAATTTATTAATT-AATAAATAAATTACAAATATAATAAAATTTATTAATTT
*
12528329 TCAATTT
65 TTAATTT
12528336 TGGGATAAAT
Statistics
Matches: 196, Mismatches: 28, Indels: 20
0.80 0.11 0.08
Matches are distributed among these distances:
159 60 0.31
160 6 0.03
161 3 0.02
162 2 0.01
163 4 0.02
164 27 0.14
165 23 0.12
166 58 0.30
167 12 0.06
168 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (158 bp):
AAATAATATTTTATAATTTATTAATTAATAAATAAATTACAAATATAATAAAATTTATTAATTTT
TAATTTATTTATAATTTAAATATAAATATATAAATTATTCAACAAACAATTTATAAACAAATTAA
ATTTTTATTTATTTAATAAAAAATGAAA
Found at i:12529953 original size:28 final size:28
Alignment explanation
Indices: 12529913--12529969 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
12529903 TTTTTGGTTG
12529913 TTGTTGTAGAAGATATCCTCATGTCTGA
1 TTGTTGTAGAAGATATCCTCATGTCTGA
12529941 TTGTTGTAGAAGATATCCTCATGTCTGA
1 TTGTTGTAGAAGATATCCTCATGTCTGA
12529969 T
1 T
12529970 GGATTTATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (28 bp):
TTGTTGTAGAAGATATCCTCATGTCTGA
Found at i:12546268 original size:2 final size:2
Alignment explanation
Indices: 12546261--12546300 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
12546251 CCAGTATTTG
12546261 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12546301 TTGCATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12554355 original size:18 final size:18
Alignment explanation
Indices: 12554332--12554366 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12554322 ACTTTTATTA
12554332 TTTTATTATTTCTTTTAT
1 TTTTATTATTTCTTTTAT
* *
12554350 TTTTATTTTTTGTTTTA
1 TTTTATTATTTCTTTTA
12554367 AAAATAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTATTATTTCTTTTAT
Found at i:12554748 original size:2 final size:2
Alignment explanation
Indices: 12554743--12554768 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12554733 CGTATGTGTG
12554743 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
12554769 AGAATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12555315 original size:17 final size:18
Alignment explanation
Indices: 12555283--12555319 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
12555273 GTAAATGAAT
12555283 TGAAAAAAATAATTTTTTA
1 TGAAAAAAAT-ATTTTTTA
12555302 TGAAAAAAAT-TTTTTTA
1 TGAAAAAAATATTTTTTA
12555319 T
1 T
12555320 AATTCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
TGAAAAAAATATTTTTTA
Found at i:12555488 original size:23 final size:21
Alignment explanation
Indices: 12555462--12555516 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
12555452 AATAATATAA
12555462 AATTTTAAAGTTAATAAAAAAAT
1 AATTTTAAAGTT-AT-AAAAAAT
*
12555485 AATTTTTAA-TTATAAAAAAT
1 AATTTTAAAGTTATAAAAAAT
**
12555505 AATAATAAAGTT
1 AATTTTAAAGTT
12555517 TCGCGCATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 13 0.48
21 4 0.15
22 2 0.07
23 8 0.30
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
AATTTTAAAGTTATAAAAAAT
Found at i:12555630 original size:4 final size:4
Alignment explanation
Indices: 12555614--12555655 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
12555604 TTTTGCTTTC
*
12555614 TCTT TCCT TCTT TC-T T-TT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
12555656 AGTTATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 4 0.12
4 30 0.88
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:12555635 original size:18 final size:18
Alignment explanation
Indices: 12555609--12555650 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
12555599 TTTATTTTTG
12555609 CTTTCTCTTTCCTTCTTT
1 CTTTCTCTTTCCTTCTTT
* *
12555627 CTTTTTCTTTCTTTCTTT
1 CTTTCTCTTTCCTTCTTT
12555645 CTTTCT
1 CTTTCT
12555651 TTCTTAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTCTCTTTCCTTCTTT
Found at i:12555884 original size:16 final size:14
Alignment explanation
Indices: 12555863--12555915 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
12555853 GGCAACTCAA
12555863 CTTTTTTTCTTTTTT
1 CTTTTTTT-TTTTTT
* *
12555878 GCTTTTTGTATTTTT
1 -CTTTTTTTTTTTTT
*
12555893 CTTTTTTTGTATTTT
1 CTTTTTTT-TTTTTT
12555908 CTTTTTTT
1 CTTTTTTT
12555916 AATTAAATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 7 0.23
15 17 0.55
16 7 0.23
ACGTcount: A:0.04, C:0.09, G:0.06, T:0.81
Consensus pattern (14 bp):
CTTTTTTTTTTTTT
Found at i:12555899 original size:15 final size:15
Alignment explanation
Indices: 12555880--12555915 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
12555870 TCTTTTTTGC
12555880 TTTTTGTATTTTTCTT
1 TTTTTGTA-TTTTCTT
12555896 TTTTTGTATTTTCTT
1 TTTTTGTATTTTCTT
12555911 TTTTT
1 TTTTT
12555916 AATTAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.83
Consensus pattern (15 bp):
TTTTTGTATTTTCTT
Found at i:12557534 original size:2 final size:2
Alignment explanation
Indices: 12557522--12557554 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12557512 TAGCTTTATG
*
12557522 TA TA TA CA 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 TA TA TA T
12557555 CTTGCACATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12558581 original size:7 final size:6
Alignment explanation
Indices: 12558573--12558616 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
12558563 TATTGGTTTG
*
12558573 AAAAAT GAAATAT AAAAAAT AAAAAT AAAAAT AAAAAAT AAAAA
1 AAAAAT -AAAAAT -AAAAAT AAAAAT AAAAAT -AAAAAT AAAAA
12558617 AAACTCAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
6 17 0.52
7 16 0.48
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:12558600 original size:13 final size:14
Alignment explanation
Indices: 12558573--12558617 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 14
12558563 TATTGGTTTG
* *
12558573 AAAAATGAAATATA
1 AAAAATAAAAAATA
12558587 AAAAAT-AAAAAT-
1 AAAAATAAAAAATA
12558599 AAAAATAAAAAATA
1 AAAAATAAAAAATA
12558613 AAAAA
1 AAAAA
12558618 AACTCAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 6 0.21
13 11 0.39
14 11 0.39
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAAATAAAAAATA
Found at i:12558617 original size:7 final size:7
Alignment explanation
Indices: 12558573--12558617 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
12558563 TATTGGTTTG
*
12558573 AAAAATG
1 AAAAATA
*
12558580 AAATATA
1 AAAAATA
12558587 AAAAAT-
1 AAAAATA
12558593 AAAAAT-
1 AAAAATA
12558599 AAAAATA
1 AAAAATA
12558606 AAAAATA
1 AAAAATA
12558613 AAAAA
1 AAAAA
12558618 AACTCAACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (7 bp):
AAAAATA
Found at i:12559038 original size:7 final size:7
Alignment explanation
Indices: 12559022--12559053 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
12559012 AAGCTTTTTT
*
12559022 TTTTCTC
1 TTTTCCC
12559029 TTTTCCC
1 TTTTCCC
12559036 TTTTCCC
1 TTTTCCC
12559043 TTTTCCC
1 TTTTCCC
12559050 TTTT
1 TTTT
12559054 ATCTTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (7 bp):
TTTTCCC
Found at i:12559059 original size:14 final size:14
Alignment explanation
Indices: 12559022--12559060 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
12559012 AAGCTTTTTT
12559022 TTTTCTCTTTTCCC
1 TTTTCTCTTTTCCC
*
12559036 TTTTCCCTTTTCCC
1 TTTTCTCTTTTCCC
*
12559050 TTTTATCTTTT
1 TTTTCTCTTTT
12559061 TTCTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTCTCTTTTCCC
Found at i:12572629 original size:2 final size:2
Alignment explanation
Indices: 12572622--12572656 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
12572612 ATGTCACCAA
12572622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12572657 ACTGCTCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12579536 original size:19 final size:19
Alignment explanation
Indices: 12579512--12579548 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
12579502 TTATTTTATA
12579512 AAAATTTAAA-ATATATATT
1 AAAA-TTAAATATATATATT
12579531 AAAATTAAATATATATAT
1 AAAATTAAATATATATAT
12579549 AATTCGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTAAATATATATATT
Found at i:12581898 original size:21 final size:21
Alignment explanation
Indices: 12581864--12581907 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12581854 AAAATATAGA
*
12581864 TTTTATCCAAATAATTTTAATT
1 TTTTATCCAAATAATCTT-ATT
*
12581886 TTTTAT-CAGATAATCTTATT
1 TTTTATCCAAATAATCTTATT
12581906 TT
1 TT
12581908 ATAAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTATCCAAATAATCTTATT
Found at i:12582294 original size:2 final size:2
Alignment explanation
Indices: 12582287--12582333 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
12582277 TGTTATGTGT
12582287 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
12582329 TA TA T
1 TA TA T
12582334 TGGTTTGTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12583438 original size:1 final size:1
Alignment explanation
Indices: 12583432--12583461 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
12583422 GATTACCATG
*
12583432 AAAAAAAAAAAAAAACAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12583462 CAGGAGATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12583453 original size:15 final size:15
Alignment explanation
Indices: 12583433--12583463 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12583423 ATTACCATGA
12583433 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
12583448 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
12583463 A
1 A
12583464 GGAGATCAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:12595461 original size:19 final size:20
Alignment explanation
Indices: 12595437--12595475 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
12595427 TTTTTACTTT
12595437 ATAAAAATT-TAAAATATAC
1 ATAAAAATTATAAAATATAC
12595456 ATAAAAATTAATAAAATATA
1 ATAAAAATT-ATAAAATATA
12595476 TAATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAAAATTATAAAATATAC
Found at i:12596139 original size:20 final size:20
Alignment explanation
Indices: 12596114--12596166 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
12596104 ATAATTTTTA
12596114 AATATTTATATTTAAAAAAT
1 AATATTTATATTTAAAAAAT
*
12596134 AATATTTTATATTTTAAAATAT
1 AATA-TTTATA-TTTAAAAAAT
12596156 AATATTT-TATT
1 AATATTTATATT
12596167 AATTTCGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 6 0.20
21 9 0.30
22 13 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTATATTTAAAAAAT
Found at i:12596673 original size:17 final size:17
Alignment explanation
Indices: 12596627--12596681 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
12596617 GCAAATTCAA
*
12596627 TAAATAACAAAAATTAT
1 TAAATAACAAAAAATAT
*
12596644 T--ATTACTATAAAAATAT
1 TAAATAAC-A-AAAAATAT
12596661 TAAATAACAAAAAATA-
1 TAAATAACAAAAAATAT
12596677 TAAAT
1 TAAAT
12596682 TTTCAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
15 4 0.13
16 6 0.19
17 16 0.52
18 1 0.03
19 4 0.13
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAATAACAAAAAATAT
Found at i:12599361 original size:38 final size:39
Alignment explanation
Indices: 12599303--12599384 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 39
12599293 GGATAGATTG
* * *
12599303 AATAAGATTAGATAAGAATTATTTTATATTTTT-ATA-AA
1 AATAAGATTAGAAAAAAATTA-ATTATATTTTTAATATAA
* *
12599341 AATAAGATTATAAAAAAATTAATTATTTTTTTAATATAA
1 AATAAGATTAGAAAAAAATTAATTATATTTTTAATATAA
12599380 AATAA
1 AATAA
12599385 TTTAATCTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 9 0.24
38 21 0.57
39 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (39 bp):
AATAAGATTAGAAAAAAATTAATTATATTTTTAATATAA
Found at i:12605271 original size:15 final size:16
Alignment explanation
Indices: 12605242--12605271 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12605232 GTTGGATTTA
12605242 AAAAAATTTTGAGATT
1 AAAAAATTTTGAGATT
12605258 AAAAAATTTT-AGAT
1 AAAAAATTTTGAGAT
12605272 CAGACTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (16 bp):
AAAAAATTTTGAGATT
Found at i:12608025 original size:16 final size:16
Alignment explanation
Indices: 12608004--12608036 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12607994 ATGGACTTCG
12608004 TTTTAGTGGTTGAATT
1 TTTTAGTGGTTGAATT
12608020 TTTTAGTGGTTGAATT
1 TTTTAGTGGTTGAATT
12608036 T
1 T
12608037 GTTAAGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.58
Consensus pattern (16 bp):
TTTTAGTGGTTGAATT
Found at i:12609972 original size:17 final size:17
Alignment explanation
Indices: 12609950--12609987 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12609940 TTAGAAACTT
*
12609950 AAAAATTAA-AATTTTG
1 AAAAAATAATAATTTTG
*
12609966 AAAAAATAATATTTTTG
1 AAAAAATAATAATTTTG
12609983 AAAAA
1 AAAAA
12609988 TAAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
AAAAAATAATAATTTTG
Found at i:12609979 original size:16 final size:17
Alignment explanation
Indices: 12609950--12609992 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
12609940 TTAGAAACTT
*
12609950 AAAAATTAAAA-TTTTG
1 AAAAAATAAAATTTTTG
*
12609966 AAAAAATAATATTTTTG
1 AAAAAATAAAATTTTTG
12609983 -AAAAATAAAA
1 AAAAAATAAAA
12609993 ATAAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
AAAAAATAAAATTTTTG
Found at i:12614574 original size:14 final size:15
Alignment explanation
Indices: 12614551--12614579 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12614541 TCACATATTG
12614551 AAAAATAATAAAATT
1 AAAAATAATAAAATT
12614566 AAAAA-AATAAAATT
1 AAAAATAATAAAATT
12614580 CTCCTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAATAAAATT
Found at i:12617902 original size:20 final size:20
Alignment explanation
Indices: 12617877--12617920 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
12617867 ATAAGTATAT
12617877 AGCATGAACATTCTTGTAAA
1 AGCATGAACATTCTTGTAAA
12617897 AGCATGAACATTCTTGTAAA
1 AGCATGAACATTCTTGTAAA
12617917 AGCA
1 AGCA
12617921 AAGAACTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (20 bp):
AGCATGAACATTCTTGTAAA
Found at i:12634412 original size:109 final size:108
Alignment explanation
Indices: 12634221--12634437 Score: 353
Period size: 109 Copynumber: 2.0 Consensus size: 108
12634211 TTGAGTATAC
*
12634221 TTCCATGATTGCTCATTAATTTCGGAAAGCCTCGTCTTGTACCTAAATTAGGTTTAGCAGATGGT
1 TTCCATGATTGCTCATTAATTTCGGAAAGCCTCGTCTTGTACCTAAATTAGGTTTAGCAGAAGGT
* *
12634286 TGTGTTAGACCTTTTTTTTTAGTTCCTCTAAAGTTGTTTATGTT
66 TGTGTTAGACC-TATTTTTAAGTTCCTCTAAAGTTGTTTATGTT
* * **
12634330 TTCCATGATTGCTCATTAATTTCGTAAAGCCTCGTCTTTTACCTATTTTAGGTTTAGCAGAAGGT
1 TTCCATGATTGCTCATTAATTTCGGAAAGCCTCGTCTTGTACCTAAATTAGGTTTAGCAGAAGGT
*
12634395 TGTGTTAGACCTATTTTTAAGTTTCTCTAAAGTTGTTTATGTT
66 TGTGTTAGACCTATTTTTAAGTTCCTCTAAAGTTGTTTATGTT
12634438 GCTGAGTATA
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 29 0.29
109 71 0.71
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.46
Consensus pattern (108 bp):
TTCCATGATTGCTCATTAATTTCGGAAAGCCTCGTCTTGTACCTAAATTAGGTTTAGCAGAAGGT
TGTGTTAGACCTATTTTTAAGTTCCTCTAAAGTTGTTTATGTT
Found at i:12640357 original size:24 final size:23
Alignment explanation
Indices: 12640300--12640376 Score: 84
Period size: 25 Copynumber: 3.3 Consensus size: 23
12640290 TTTAAATAAA
* *
12640300 ATAAATT-TTAATTTTTAATAAT
1 ATAAATTAATAATTTTTAATTAT
12640322 ATCAAATATAATAATTTTTAATTTAT
1 AT-AAAT-TAATAATTTTTAA-TTAT
* *
12640348 ATAAATTAATAATTGTTAATTAA
1 ATAAATTAATAATTTTTAATTAT
12640371 ATAAAT
1 ATAAAT
12640377 ATTAAAATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
22 2 0.04
23 13 0.28
24 13 0.28
25 14 0.30
26 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (23 bp):
ATAAATTAATAATTTTTAATTAT
Found at i:12640718 original size:20 final size:21
Alignment explanation
Indices: 12640681--12640754 Score: 134
Period size: 21 Copynumber: 3.6 Consensus size: 21
12640671 ATTCGAAATT
12640681 AATA-AAAATATTATTTTTTA
1 AATATAAAATATTATTTTTTA
12640701 AATATAAAATATTATTTTTTA
1 AATATAAAATATTATTTTTTA
12640722 AATATAAAATATTATTTTTTA
1 AATATAAAATATTATTTTTTA
12640743 AATAT-AAATATT
1 AATATAAAATATT
12640755 TAAAAATATC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 11 0.21
21 42 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATAAAATATTATTTTTTA
Found at i:12640763 original size:30 final size:30
Alignment explanation
Indices: 12640727--12640787 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
12640717 TTTTAAATAT
* * * *
12640727 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATAATTA
*
12640757 AAAATATCATTATATAAATATATATAATTA
1 AAAATATCATTATATAAATATAAATAATTA
12640787 A
1 A
12640788 TTAATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATAATTA
Found at i:12642432 original size:33 final size:34
Alignment explanation
Indices: 12642395--12642468 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 34
12642385 ATTATTTTTT
*
12642395 TTATAAATATTCTGA-AAATAAATTTCCTAAAAA-
1 TTATAAAT-TTCTGAGAAATAAATTTCCAAAAAAG
* * * *
12642428 TTATATATTTTTTAGAAATAAATTTTCAAAAAAG
1 TTATAAATTTCTGAGAAATAAATTTCCAAAAAAG
12642462 TTATAAA
1 TTATAAA
12642469 CTTTTTTCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
32 4 0.12
33 23 0.70
34 6 0.18
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (34 bp):
TTATAAATTTCTGAGAAATAAATTTCCAAAAAAG
Found at i:12642474 original size:34 final size:33
Alignment explanation
Indices: 12642410--12642474 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
12642400 AATATTCTGA
* * *
12642410 AAATAAATTTCCTAAAAATTATATATTTTTTAG
1 AAATAAATTTCCAAAAAATTATAAACTTTTTAG
*
12642443 AAATAAATTTTCAAAAAAGTTATAAACTTTTT
1 AAATAAATTTCCAAAAAA-TTATAAACTTTTT
12642475 TCTTAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 16 0.59
34 11 0.41
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (33 bp):
AAATAAATTTCCAAAAAATTATAAACTTTTTAG
Found at i:12643643 original size:26 final size:25
Alignment explanation
Indices: 12643614--12643663 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
12643604 AATTATAAAT
12643614 TTTTTTTCATTTTTATTTTTTTTAAG
1 TTTTTTTC-TTTTTATTTTTTTTAAG
*
12643640 TTTTTTTCTTTTTTTTTTTTTTAA
1 TTTTTTTCTTTTTATTTTTTTTAA
12643664 ATTCGAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.82
Consensus pattern (25 bp):
TTTTTTTCTTTTTATTTTTTTTAAG
Found at i:12644164 original size:3 final size:3
Alignment explanation
Indices: 12644158--12644186 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12644148 GATGATGATG
12644158 ATC ATC ATC ATC AT- ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
12644187 GAAATGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:12644177 original size:14 final size:14
Alignment explanation
Indices: 12644158--12644185 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12644148 GATGATGATG
12644158 ATCATCATCATCAT
1 ATCATCATCATCAT
12644172 ATCATCATCATCAT
1 ATCATCATCATCAT
12644186 CGAAATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (14 bp):
ATCATCATCATCAT
Found at i:12652410 original size:3 final size:3
Alignment explanation
Indices: 12652402--12652441 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
12652392 CAAGCTGCCA
* * *
12652402 CTG CTG CTG CTA CTG CTA CTG CTA CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C
12652442 AATTGGAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.07, C:0.35, G:0.25, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:12652411 original size:6 final size:6
Alignment explanation
Indices: 12652396--12652441 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
12652386 ACCAGGCAAG
* * * *
12652396 CTGCCA CTGCTG CTGCTA CTGCTA CTGCTA CTGCTG CTGCTG CTGC
1 CTGCTA CTGCTA CTGCTA CTGCTA CTGCTA CTGCTA CTGCTA CTGC
12652442 AATTGGAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.09, C:0.37, G:0.24, T:0.30
Consensus pattern (6 bp):
CTGCTA
Found at i:12652416 original size:12 final size:12
Alignment explanation
Indices: 12652395--12652441 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
12652385 CACCAGGCAA
*
12652395 GCTGCCACTGCT
1 GCTGCTACTGCT
12652407 GCTGCTACTGCT
1 GCTGCTACTGCT
*
12652419 ACTGCTACTGCT
1 GCTGCTACTGCT
*
12652431 GCTGCTGCTGC
1 GCTGCTACTGC
12652442 AATTGGAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.09, C:0.36, G:0.26, T:0.30
Consensus pattern (12 bp):
GCTGCTACTGCT
Found at i:12664068 original size:64 final size:64
Alignment explanation
Indices: 12663987--12664115 Score: 163
Period size: 64 Copynumber: 2.0 Consensus size: 64
12663977 GTTTTAAATG
* * * *
12663987 TTAAAAGAATAGAAATAAATAATAAAATG-TTTTATTAACTTGCTTTGTAGGTAATTAAATTTTT
1 TTAAAAGAATAGAAATAAATAATAAAA-GATATTATTAACTTGCTCTGTAAGTAATCAAATTTTT
* * *
12664051 TTAAAAG-ATTGAGAATAAATTATGAAAGATATTATTAACTTGCTCTGTAAGTAATCAAATTTTT
1 TTAAAAGAATAGA-AATAAATAATAAAAGATATTATTAACTTGCTCTGTAAGTAATCAAATTTTT
12664115 T
1 T
12664116 GGTTTGACTC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 5 0.09
64 51 0.91
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.41
Consensus pattern (64 bp):
TTAAAAGAATAGAAATAAATAATAAAAGATATTATTAACTTGCTCTGTAAGTAATCAAATTTTT
Found at i:12666341 original size:18 final size:18
Alignment explanation
Indices: 12666245--12666373 Score: 102
Period size: 18 Copynumber: 7.2 Consensus size: 18
12666235 TTTGTTCTTC
* *
12666245 ATACATTTGAGATGGAGT
1 ATACATTTGAGGTGGAGG
* *
12666263 ATATATTTGA---GGATG
1 ATACATTTGAGGTGGAGG
* *
12666278 ATACATTTGTGGTGGGGG
1 ATACATTTGAGGTGGAGG
* ** *
12666296 ATACATTTGTGGTAAATG
1 ATACATTTGAGGTGGAGG
*
12666314 ATACATTTGAGGTGGATG
1 ATACATTTGAGGTGGAGG
12666332 ATACATTTGAGGAGGTGGAGG
1 ATACATTT---GAGGTGGAGG
*
12666353 ATACATTTGAGTTGGAGG
1 ATACATTTGAGGTGGAGG
12666371 ATA
1 ATA
12666374 ACCATATGGA
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
15 11 0.12
18 61 0.69
21 17 0.19
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (18 bp):
ATACATTTGAGGTGGAGG
Found at i:12666346 original size:21 final size:21
Alignment explanation
Indices: 12666311--12666363 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
12666301 TTTGTGGTAA
12666311 ATGATACATTT---GAGGTGG
1 ATGATACATTTGAGGAGGTGG
12666329 ATGATACATTTGAGGAGGTGG
1 ATGATACATTTGAGGAGGTGG
*
12666350 AGGATACATTTGAG
1 ATGATACATTTGAG
12666364 TTGGAGGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 11 0.35
21 20 0.65
ACGTcount: A:0.30, C:0.06, G:0.34, T:0.30
Consensus pattern (21 bp):
ATGATACATTTGAGGAGGTGG
Found at i:12668070 original size:15 final size:13
Alignment explanation
Indices: 12668043--12668084 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
12668033 TATATTTATC
12668043 AATAAAT-TTTTA
1 AATAAATATTTTA
12668055 AAGTAACATATTTTA
1 AA-TAA-ATATTTTA
*
12668070 AATTAATATTTTA
1 AATAAATATTTTA
12668083 AA
1 AA
12668085 CAATGATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 2 0.08
13 13 0.50
14 4 0.15
15 7 0.27
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (13 bp):
AATAAATATTTTA
Found at i:12670431 original size:19 final size:20
Alignment explanation
Indices: 12670397--12670436 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12670387 AAAAGAATTG
*
12670397 ACAACAATATAAATATCAAA
1 ACAACAATAAAAATATCAAA
*
12670417 ACAACAA-AAAAATATTAAA
1 ACAACAATAAAAATATCAAA
12670436 A
1 A
12670437 TTCAAATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.17
Consensus pattern (20 bp):
ACAACAATAAAAATATCAAA
Found at i:12674185 original size:23 final size:24
Alignment explanation
Indices: 12674155--12674202 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
12674145 TTTATATTCA
* *
12674155 AATTTTAATTTTACAATTT-TTTT
1 AATTTTAAATCTACAATTTCTTTT
12674178 AATTTTAAATCTACAATTTCTTTT
1 AATTTTAAATCTACAATTTCTTTT
12674202 A
1 A
12674203 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (24 bp):
AATTTTAAATCTACAATTTCTTTT
Found at i:12674777 original size:3 final size:3
Alignment explanation
Indices: 12674763--12674803 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
12674753 TTTTGAAAGA
12674763 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12674804 AAGGTTTCTG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12676068 original size:18 final size:18
Alignment explanation
Indices: 12676045--12676337 Score: 142
Period size: 18 Copynumber: 16.6 Consensus size: 18
12676035 TTGTTATTAA
12676045 TAATATAATAATATTTAT
1 TAATATAATAATATTTAT
12676063 TAATATATTATAATA-TTAT
1 TAATATA--ATAATATTTAT
*
12676082 CT-ATAAATATAATATTTTAT
1 -TAATATA-ATAATA-TTTAT
*
12676102 TAATATTATAATATATTA-
1 TAATATAATAATAT-TTAT
* * *
12676120 AAATATTATATTATTTAT
1 TAATATAATAATATTTAT
*
12676138 TAATATAATATTATTTAT
1 TAATATAATAATATTTAT
* *
12676156 T-TTTTAATATATTATTT-T
1 TAATATAATA-A-TATTTAT
12676174 TAATAT-AT--TATTTAT
1 TAATATAATAATATTTAT
*
12676189 T-A-GTAAT-ATA-TTAT
1 TAATATAATAATATTTAT
*
12676203 TAATA-AATAATATCTAT
1 TAATATAATAATATTTAT
*
12676220 TAATAT-AT--TATTTAC
1 TAATATAATAATATTTAT
*
12676235 TAATAT-AT--TATTAAT
1 TAATATAATAATATTTAT
* * *
12676250 ATCATAT-ATTATA-TTAA
1 -TAATATAATAATATTTAT
12676267 TAATATAATACATTATTTAT
1 TAATATAATA-A-TATTTAT
* *
12676287 TTATATAATATTATTTATAT
1 TAATATAATAATA-TT-TAT
12676307 AATAAATATAATAATATTTAT
1 --T-AATATAATAATATTTAT
12676328 TAATATAATA
1 TAATATAATA
12676338 TTTACATAAT
Statistics
Matches: 215, Mismatches: 29, Indels: 62
0.70 0.09 0.20
Matches are distributed among these distances:
13 1 0.00
14 13 0.06
15 26 0.12
16 15 0.07
17 23 0.11
18 62 0.29
19 30 0.14
20 29 0.13
21 3 0.01
22 3 0.01
23 10 0.05
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATATAATAATATTTAT
Found at i:12676090 original size:23 final size:23
Alignment explanation
Indices: 12676048--12676130 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 23
12676038 TTATTAATAA
* * *
12676048 TATAATAATATTTATTAATATAT
1 TATAATATTATATATAAATATAT
* *
12676071 TATAATATTATCTATAAATATAA
1 TATAATATTATATATAAATATAT
**
12676094 TATTTTATTA-ATATTATAATATAT
1 TATAATATTATATA-TA-AATATAT
*
12676118 TAAAATATTATAT
1 TATAATATTATAT
12676131 TATTTATTAA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 2 0.04
23 29 0.63
24 13 0.28
25 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (23 bp):
TATAATATTATATATAAATATAT
Found at i:12676340 original size:52 final size:52
Alignment explanation
Indices: 12676048--12676348 Score: 149
Period size: 55 Copynumber: 5.7 Consensus size: 52
12676038 TTATTAATAA
* * ** *
12676048 TATAATAATATTTATTAATATATTA--TA-ATATTATCTATAAATATAAT-AT
1 TATAATAATATATATTAATATATTATTTATATAATAT-TATTTATATAATAAA
* * ** *
12676097 TTTATTAATAT-TA-TAATATATTA-AAATATTATATTATTTAT-TAATATAA
1 TATAATAATATATATTAATATATTATTTATATAATATTATTTATATAATA-AA
* * * * *
12676146 TATTAT-TTATTTTTTAATATATTATTTTTA-ATATATTATTTATTAGTAATATATTA
1 TATAATAATATATATTAATATATTATTTATATA-ATATTATTTA-TA-TAATA-A--A
* * * *
12676202 TTAATAAATAATATCTATTAATATATTATTTACTA-ATATATTATTAATATCATATAT
1 -T-AT-AATAATATATATTAATATATTATTTA-TATA-ATATTATTTATATAATA-AA
* *
12676259 TATATTAATAATATAATACAT-TATTTATTTATATAATATTATTTATATAATAAA
1 TATAATAAT-ATATATTA-ATATA-TTATTTATATAATATTATTTATATAATAAA
* * *
12676313 TATAATAATATTTATTAATATAATATTTACATAATA
1 TATAATAATATATATTAATATATTATTTATATAATA
12676349 AAATATTATT
Statistics
Matches: 193, Mismatches: 36, Indels: 43
0.71 0.13 0.16
Matches are distributed among these distances:
47 14 0.07
48 11 0.06
49 19 0.10
50 10 0.05
51 12 0.06
52 15 0.08
53 8 0.04
54 21 0.11
55 27 0.14
56 12 0.06
57 1 0.01
58 2 0.01
59 8 0.04
60 20 0.10
61 13 0.07
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (52 bp):
TATAATAATATATATTAATATATTATTTATATAATATTATTTATATAATAAA
Found at i:12676348 original size:98 final size:99
Alignment explanation
Indices: 12676174--12676367 Score: 213
Period size: 98 Copynumber: 2.0 Consensus size: 99
12676164 ATATTATTTT
* * *
12676174 TAATATATTATTTATTAGTAATATATTATTAATAAATAATATCTATTAATATATTATTTACTAAT
1 TAATACATTATTTATTAGTAATATATTATTAATAAATAATATATAATAATATATTATTTACTAAT
* **
12676239 ATATTATTAATATCATA-TATTATATTAATAATA
66 ATATTAATAATAAAATATTATTATATTAATAATA
*
12676272 TAATACATTATTTATT--TATATAATATTATTTATATAATAA-ATATAATAATAT-TTATTAATA
1 TAATACATTATTTATTAGTA-AT-ATATTATTAATA-AATAATATATAATAATATATTATT--TA
*
12676333 -TAATAT-TTACATAATAAAATATTATTTTATTAATA
61 CTAATATATTA-ATAATAAAATATTATTATATTAATA
12676368 TAGTAATTGT
Statistics
Matches: 81, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
96 2 0.02
97 10 0.12
98 50 0.62
99 19 0.23
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.50
Consensus pattern (99 bp):
TAATACATTATTTATTAGTAATATATTATTAATAAATAATATATAATAATATATTATTTACTAAT
ATATTAATAATAAAATATTATTATATTAATAATA
Found at i:12679400 original size:120 final size:120
Alignment explanation
Indices: 12679184--12679423 Score: 372
Period size: 120 Copynumber: 2.0 Consensus size: 120
12679174 AATACTTGCT
** * * *
12679184 ATGATGGTGCGAGATGTATTAGTCATTCTTGTGTTCACTGTAGCCTCTGAATTTGCTTTTAGCAC
1 ATGATGGTGCGAGATGTATTAACCATTCTGGTGTCCACTGTAGCCTCTGAATTTGCTTTTAACAC
*
12679249 TGGAGGATGTGTTCTTGATCCATTTTATAGTTCCTTAACTCCAAAAATGGTCAAG
66 TGGAGGATATGTTCTTGATCCATTTTATAGTTCCTTAACTCCAAAAATGGTCAAG
* * *
12679304 ATGATGGTGTGAGATGTATTAACCATTCTGGTGTCCACTGTTGTCTCTGAATTTGCTTTTAACAC
1 ATGATGGTGCGAGATGTATTAACCATTCTGGTGTCCACTGTAGCCTCTGAATTTGCTTTTAACAC
* * *
12679369 TTGAGGATATGTTTTTGATCCATTTTGTAGTTCCTTAACTCCAAAAATGGTCAAG
66 TGGAGGATATGTTCTTGATCCATTTTATAGTTCCTTAACTCCAAAAATGGTCAAG
12679424 GCCCTTATAT
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (120 bp):
ATGATGGTGCGAGATGTATTAACCATTCTGGTGTCCACTGTAGCCTCTGAATTTGCTTTTAACAC
TGGAGGATATGTTCTTGATCCATTTTATAGTTCCTTAACTCCAAAAATGGTCAAG
Found at i:12691924 original size:21 final size:22
Alignment explanation
Indices: 12691900--12691959 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 22
12691890 TATAATATTG
12691900 ATAAAAAATATTATTTTTAA-T
1 ATAAAAAATATTATTTTTAATT
*
12691921 AT--AAATTA-TA-TTTTAATT
1 ATAAAAAATATTATTTTTAATT
12691939 ATAAATAAATATATATTTTTA
1 ATAAA-AAATAT-TATTTTTA
12691960 TAAATACTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 11
0.70 0.05 0.26
Matches are distributed among these distances:
17 6 0.20
18 5 0.17
19 5 0.17
20 1 0.03
21 6 0.20
23 2 0.07
24 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAAAATATTATTTTTAATT
Found at i:12691936 original size:17 final size:17
Alignment explanation
Indices: 12691909--12691944 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
12691899 GATAAAAAAT
12691909 ATTATTTTTAA-TATAA
1 ATTATTTTTAATTATAA
12691925 ATTATATTTTAATTATAA
1 ATTAT-TTTTAATTATAA
12691943 AT
1 AT
12691945 AAATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 6 0.33
18 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATTTTTAATTATAA
Found at i:12692881 original size:16 final size:16
Alignment explanation
Indices: 12692862--12692893 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12692852 AAATTTATTT
12692862 AATTAAAAAAATTAAA
1 AATTAAAAAAATTAAA
*
12692878 AATTAAAAAATTTAAA
1 AATTAAAAAAATTAAA
12692894 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATTAAAAAAATTAAA
Found at i:12692894 original size:14 final size:14
Alignment explanation
Indices: 12692858--12692900 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
12692848 TACAAAATTT
12692858 ATTT-AATTAAAAAA
1 ATTTAAATT-AAAAA
*
12692872 ATTAAAAATTAAAAA
1 ATT-TAAATTAAAAA
12692887 ATTTAAATTAAAAA
1 ATTTAAATTAAAAA
12692901 TATCAAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 13 0.52
15 8 0.32
16 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTTAAATTAAAAA
Found at i:12693153 original size:24 final size:24
Alignment explanation
Indices: 12693126--12693211 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 24
12693116 TTACATCTTA
12693126 ATTATATAAAAATATAATATTTTT
1 ATTATATAAAAATATAATATTTTT
* * *
12693150 ATTAAATTAATATATTAAATAATAATTTT
1 ATTATA-TAA-A-A--ATATAATATTTTT
* *
12693179 ATTAATATAAATATATTATATTTTT
1 ATT-ATATAAAAATATAATATTTTT
12693204 ATATATAT
1 AT-TATAT
12693212 CCTGGGTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
24 5 0.11
25 19 0.40
26 2 0.04
27 1 0.02
28 1 0.02
29 17 0.36
30 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATTATATAAAAATATAATATTTTT
Found at i:12693157 original size:29 final size:29
Alignment explanation
Indices: 12693125--12693193 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
12693115 ATTACATCTT
*
12693125 AATT-ATATAAAAATATAATATTTTTATTA
1 AATTAATATAAAAA-ATAATAATTTTATTA
**
12693154 AATTAATATATTAAATAATAATTTTATTA
1 AATTAATATAAAAAATAATAATTTTATTA
*
12693183 ATATAAATATA
1 A-ATTAATATA
12693194 TTATATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
AATTAATATAAAAAATAATAATTTTATTA
Found at i:12693178 original size:30 final size:29
Alignment explanation
Indices: 12693139--12693196 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
12693129 ATATAAAAAT
*
12693139 ATAATATTTTTATTAA-ATTAATATATTAA
1 ATAATA-TTTTATTAATATAAATATATTAA
12693168 ATAATAATTTTATTAATATAAATATATTA
1 ATAAT-ATTTTATTAATATAAATATATTA
12693197 TATTTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATAATATTTTATTAATATAAATATATTAA
Found at i:12693535 original size:13 final size:12
Alignment explanation
Indices: 12693517--12693555 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
12693507 TATTTAATTT
12693517 AAAAAAATATATA
1 AAAAAAATAT-TA
12693530 AAAAAAA-ATTA
1 AAAAAAATATTA
12693541 ATAAAAAATATTA
1 A-AAAAAATATTA
12693554 AA
1 AA
12693556 CAAACCTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.12
12 9 0.38
13 12 0.50
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAAAATATTA
Found at i:12694708 original size:22 final size:23
Alignment explanation
Indices: 12694683--12694727 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
12694673 CCGAACTTTA
*
12694683 AAAAAAAATTTATAGAT-TTTTT
1 AAAAAAAATTTATAAATATTTTT
12694705 AAAAAAAATTTATAAATATTTTT
1 AAAAAAAATTTATAAATATTTTT
12694728 TTAAAGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AAAAAAAATTTATAAATATTTTT
Found at i:12695211 original size:18 final size:19
Alignment explanation
Indices: 12695190--12695231 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
12695180 TTTTCTTTCC
12695190 TTTTTAT-TTTTTTATTTA
1 TTTTTATCTTTTTTATTTA
*
12695208 -TTTTATCTTTTTTTTTTA
1 TTTTTATCTTTTTTATTTA
*
12695226 TATTTA
1 TTTTTA
12695232 ATAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.30
18 10 0.50
19 4 0.20
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTATCTTTTTTATTTA
Found at i:12696108 original size:8 final size:8
Alignment explanation
Indices: 12696097--12696139 Score: 77
Period size: 8 Copynumber: 5.2 Consensus size: 8
12696087 TTTTTTCTCT
12696097 TTTTTTTA
1 TTTTTTTA
12696105 TTTTTTTA
1 TTTTTTTA
12696113 TTTTTTTA
1 TTTTTTTA
12696121 TTTTTTTA
1 TTTTTTTA
12696129 TTTTTTATA
1 TTTTTT-TA
12696138 TT
1 TT
12696140 ATAATTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 30 0.88
9 4 0.12
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTTA
Found at i:12696108 original size:9 final size:9
Alignment explanation
Indices: 12696086--12696139 Score: 60
Period size: 8 Copynumber: 6.2 Consensus size: 9
12696076 CCTTAATGAT
*
12696086 TTTTTTTCTC
1 TTTTTTT-TA
12696096 TTTTTTTTA
1 TTTTTTTTA
12696105 -TTTTTTTA
1 TTTTTTTTA
12696113 -TTTTTTTA
1 TTTTTTTTA
12696121 -TTTTTTTA
1 TTTTTTTTA
*
12696129 TTTTTTATA
1 TTTTTTTTA
12696138 TT
1 TT
12696140 ATAATTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
8 24 0.59
9 10 0.24
10 7 0.17
ACGTcount: A:0.11, C:0.04, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:12697446 original size:21 final size:19
Alignment explanation
Indices: 12697422--12697461 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
12697412 CGAAAATCTA
*
12697422 TTTTATTTTTCTTTTCTTTTC
1 TTTTATTCTT-TTTT-TTTTC
12697443 TTTTATTCTTTTTTTTTTC
1 TTTTATTCTTTTTTTTTTC
12697462 CCCCAAGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTATTCTTTTTTTTTTC
Found at i:12700792 original size:18 final size:18
Alignment explanation
Indices: 12700765--12700809 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
12700755 CATAAATATG
* *
12700765 GTTGTGATTAGCTTTTTA
1 GTTGTAATTAACTTTTTA
12700783 GTTGTAATTAACTTTTTA
1 GTTGTAATTAACTTTTTA
*
12700801 GTTGCAATT
1 GTTGTAATT
12700810 CTTTTAGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.22, C:0.07, G:0.18, T:0.53
Consensus pattern (18 bp):
GTTGTAATTAACTTTTTA
Found at i:12705648 original size:18 final size:18
Alignment explanation
Indices: 12705625--12705660 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12705615 TACTCGATGG
12705625 TTGCAGCGTCTTTAAGTT
1 TTGCAGCGTCTTTAAGTT
*
12705643 TTGCAGCTTCTTTAAGTT
1 TTGCAGCGTCTTTAAGTT
12705661 CGTATCTTCG
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:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (18 bp):
TTGCAGCGTCTTTAAGTT
Found at i:12712739 original size:52 final size:51
Alignment explanation
Indices: 12712653--12712806 Score: 177
Period size: 52 Copynumber: 3.0 Consensus size: 51
12712643 TATAACCATA
* *
12712653 CAAACTTGCCCATTAAGAATCTCTCTCCTCTTAGAAATT-TTCTCTTGTAAGT
1 CAAACTTGCCTATTAAGAATC-CTCTCCTCTTAG-AATTCTTCTCTTGCAAGT
* * *
12712705 CAAACTTGCCTATTAAAAATCCATTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCC-TCTCCTCTTAGAATTCTTCTCTTGCAAGT
* * *
12712757 CAAACTTACCTATTAAGAATCCTCTTTCTCTT-GAAATTCTTCTTTTGCAA
1 CAAACTTGCCTATTAAGAATCCTC-TCCTCTTAG-AATTCTTCTCTTGCAA
12712807 ATCTTCTTGT
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
51 7 0.08
52 80 0.92
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCTCTCCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:12713765 original size:15 final size:15
Alignment explanation
Indices: 12713745--12713775 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12713735 TTCTGCTTTC
12713745 TTAATGAAACATTTA
1 TTAATGAAACATTTA
12713760 TTAATGAAACATTTA
1 TTAATGAAACATTTA
12713775 T
1 T
12713776 GTATACCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
TTAATGAAACATTTA
Found at i:12718860 original size:2 final size:2
Alignment explanation
Indices: 12718853--12718878 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12718843 TAACTAAGAT
12718853 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
12718879 AATGTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12719776 original size:24 final size:25
Alignment explanation
Indices: 12719749--12719796 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
12719739 ATTTTTATAT
* *
12719749 TTAAAATTTCATAA-AAAATATAAA
1 TTAAAATTTAAAAATAAAATATAAA
*
12719773 TTAATATTTAAAAATAAAATATAA
1 TTAAAATTTAAAAATAAAATATAA
12719797 TTTATATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
TTAAAATTTAAAAATAAAATATAAA
Found at i:12720432 original size:23 final size:25
Alignment explanation
Indices: 12720371--12720433 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
12720361 AATTAGATAC
*
12720371 TATATATAAAAATTAAATTAATAATAT
1 TATAT-TAAAAA-TAAAATAATAATAT
*
12720398 TATAATTTAAAATAAAATAA-AATAT
1 TAT-ATTAAAAATAAAATAATAATAT
12720423 TAT-TTAAAAAT
1 TATATTAAAAAT
12720434 TTAAGATCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 7 0.22
25 8 0.25
26 7 0.22
27 8 0.25
28 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TATATTAAAAATAAAATAATAATAT
Found at i:12724056 original size:13 final size:14
Alignment explanation
Indices: 12724040--12724073 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
12724030 CACAAAAAAG
12724040 AAAAAACCCA-CAA
1 AAAAAACCCACCAA
12724053 AAAAAACCCAGCCAA
1 AAAAAACCCA-CCAA
12724068 AAAAAA
1 AAAAAA
12724074 GAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
15 9 0.47
ACGTcount: A:0.71, C:0.26, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAACCCACCAA
Found at i:12726894 original size:21 final size:21
Alignment explanation
Indices: 12726859--12726899 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
12726849 AAAGAAAAAA
12726859 AAATTTTAAATTTGAATCTTTC
1 AAATTTTAAATTTG-ATCTTTC
*
12726881 AAATTTT-CATTTGATCTTT
1 AAATTTTAAATTTGATCTTT
12726900 TACATACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.54
Consensus pattern (21 bp):
AAATTTTAAATTTGATCTTTC
Found at i:12733436 original size:41 final size:41
Alignment explanation
Indices: 12733376--12733487 Score: 120
Period size: 41 Copynumber: 2.7 Consensus size: 41
12733366 CATCACAAAA
* * *
12733376 AAAAAAGATATTTGCATTTGCATCGCTTG-TATCTGCATCA-
1 AAAAAAGACATTCGCATTTGCATCGCTTGCT-TCTACATCAC
* * *
12733416 AAAAAGAGACATTCGTATTTGCACCGCTTGCTTCTATATCAC
1 AAAAA-AGACATTCGCATTTGCATCGCTTGCTTCTACATCAC
* *
12733458 AAGAAAGACATTCGCATTTGCATCACTTGC
1 AAAAAAGACATTCGCATTTGCATCGCTTGC
12733488 ATTTACACTT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
40 5 0.08
41 49 0.83
42 5 0.08
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (41 bp):
AAAAAAGACATTCGCATTTGCATCGCTTGCTTCTACATCAC
Found at i:12734111 original size:106 final size:106
Alignment explanation
Indices: 12733968--12734341 Score: 389
Period size: 107 Copynumber: 3.5 Consensus size: 106
12733958 GGCAAAATAT
* * * * * *
12733968 TTTTAAAATTTCAAATTTC-AACACCTCAAATGTATGAGGAGAATTCAAAGA-TTTTGGAATCCT
1 TTTTAAATTTTTAAAATTCTAACACCTCAAATGTATGAGAAGCATTCAAAGATTTTTGAAATCCT
* **
12734031 TAAAACCTTTAAGCACAATCTTTAAGACTTTCGGGTAAAACA
66 TAAGACCTTCGAGCACAATCTTTAAGAC-TTCGGGTAAAACA
* * * *
12734073 TTTTAAATTTTTAAACTTCTAATACCTCAAATGTATGAGAAGCGTTCAAAGATTTTTGAAATCCA
1 TTTTAAATTTTTAAAATTCTAACACCTCAAATGTATGAGAAGCATTCAAAGATTTTTGAAATCCT
* * * * *
12734138 TAAGACCTTCGAGCATAATTTTTAAGACCTCCGAGCAAAACA
66 TAAGACCTTCGAGCACAATCTTTAAGA-CTTCGGGTAAAACA
* * *** * *
12734180 TTTTAAATTTTTAAAGTTTTAACGTTTTAAATGTAT-AAAGAGCATTCAAAGATTTTTGAAATCC
1 TTTTAAATTTTTAAAATTCTAACACCTCAAATGTATGAGA-AGCATTCAAAGATTTTTGAAATCC
* * * *
12734244 TTAAGACC-TCGAGCACAATCTTTATGACCTCAAGATAAAACA
65 TTAAGACCTTCGAGCACAATCTTTAAGACTTC-GGGTAAAACA
* *
12734286 TTTTAAATTTTTAAAATT-TCAACACCTCTAATGTATGAGAAGCATTTAAAGATTTT
1 TTTTAAATTTTTAAAATTCT-AACACCTCAAATGTATGAGAAGCATTCAAAGATTTT
12734342 GAGATTTATA
Statistics
Matches: 218, Mismatches: 44, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
105 19 0.09
106 95 0.44
107 103 0.47
108 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (106 bp):
TTTTAAATTTTTAAAATTCTAACACCTCAAATGTATGAGAAGCATTCAAAGATTTTTGAAATCCT
TAAGACCTTCGAGCACAATCTTTAAGACTTCGGGTAAAACA
Found at i:12734321 original size:213 final size:212
Alignment explanation
Indices: 12733995--12734384 Score: 507
Period size: 213 Copynumber: 1.8 Consensus size: 212
12733985 TCAACACCTC
* * * *
12733995 AAATGTATGAGGAGAATTCAAAGATTTTGGAATCCTTAAAACCTTTAAGCACAATCTTTAAGACT
1 AAATGTATAAAGAGAATTCAAAGATTTTGAAATCCTTAAAACCTTCAAGCACAATCTTTAAGACT
* * * * *
12734060 TTCGGGTAAAACATTTTAAATTTTTAAACTTCTAATACCTCAAATGTATGAGAAGCGTTCAAAGA
66 CTCAGATAAAACATTTTAAATTTTTAAACTTCTAACACCTCAAATGTATGAGAAGCATTCAAAGA
* * *
12734125 TTTTTGAAATCCATAAGACCTTCGAGCATAATTTTTAAGACCTCCGAGCAAAACATTTTAAATTT
131 -TTTTGAAATCCATAAGACCTTCAAGCATAATCTCTAAGACCTCCGAGCAAAACATTTTAAATTT
12734190 TTAAAGTTTTAACGTTTT
195 TTAAAGTTTTAACGTTTT
* * * *
12734208 AAATGTATAAAGAGCATTCAAAGATTTTTGAAATCCTTAAGACC-TCGAGCACAATCTTTATGAC
1 AAATGTATAAAGAGAATTCAAAGA-TTTTGAAATCCTTAAAACCTTCAAGCACAATCTTTAAGAC
* * *
12734272 -CTCAAGATAAAACATTTTAAATTTTTAAAATT-TCAACACCTCTAATGTATGAGAAGCATTTAA
65 TCTC-AGATAAAACATTTTAAATTTTTAAACTTCT-AACACCTCAAATGTATGAGAAGCATTCAA
* ** * *
12734335 AGATTTTGAGATTTATAAGCCCTTCAAGCATAATCTCTATGACCTCCGAG
128 AGATTTTGAAATCCATAAGACCTTCAAGCATAATCTCTAAGACCTCCGAG
12734385 TACAATCCTT
Statistics
Matches: 150, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
212 42 0.28
213 91 0.61
214 17 0.11
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (212 bp):
AAATGTATAAAGAGAATTCAAAGATTTTGAAATCCTTAAAACCTTCAAGCACAATCTTTAAGACT
CTCAGATAAAACATTTTAAATTTTTAAACTTCTAACACCTCAAATGTATGAGAAGCATTCAAAGA
TTTTGAAATCCATAAGACCTTCAAGCATAATCTCTAAGACCTCCGAGCAAAACATTTTAAATTTT
TAAAGTTTTAACGTTTT
Found at i:12734370 original size:106 final size:107
Alignment explanation
Indices: 12733980--12734380 Score: 397
Period size: 106 Copynumber: 3.8 Consensus size: 107
12733970 TTAAAATTTC
* * * * *
12733980 AAATTTCAACACCTCAAATGTATGAGGAGAATTCAAAGA-TTTTGGAATCCT-TAAAACCTTTAA
1 AAATTTCAACACCTCAAATGTATGAGAAGCATTCAAAGATTTTTGAAATCCTATAAGACCTTCAA
* * *
12734043 GCACAATCTTTAAGACTTTCGGGTAAAACATTTTAAATTTTT-
66 GCACAATCTTTAAGAC-CTCAGATAAAACATTTTAAATTTTTA
* * * *
12734085 AAACTTCTAATACCTCAAATGTATGAGAAGCGTTCAAAGATTTTTGAAATCC-ATAAGACCTTCG
1 AAATTTC-AACACCTCAAATGTATGAGAAGCATTCAAAGATTTTTGAAATCCTATAAGACCTTCA
* * * *
12734149 AGCATAATTTTTAAGACCTCCGAGCAAAACATTTTAAATTTTTA
65 AGCACAATCTTTAAGACCTCAGA-TAAAACATTTTAAATTTTTA
* * *** * * *
12734193 AAGTTTTAACGTTTTAAATGTAT-AAAGAGCATTCAAAGATTTTTGAAATCCT-TAAGACC-TCG
1 AAATTTCAACACCTCAAATGTATGAGA-AGCATTCAAAGATTTTTGAAATCCTATAAGACCTTCA
*
12734255 AGCACAATCTTTATGACCTCAAGATAAAACATTTTAAATTTTTA
65 AGCACAATCTTTAAGACCTC-AGATAAAACATTTTAAATTTTTA
* * * * *
12734299 AAATTTCAACACCTCTAATGTATGAGAAGCATTTAAAGA-TTTTGAGAT-TTATAAGCCCTTCAA
1 AAATTTCAACACCTCAAATGTATGAGAAGCATTCAAAGATTTTTGAAATCCTATAAGACCTTCAA
* * *
12734362 GCATAATCTCTATGACCTC
66 GCACAATCTTTAAGACCTC
12734381 CGAGTACAAT
Statistics
Matches: 240, Mismatches: 45, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
104 1 0.00
105 20 0.08
106 119 0.50
107 96 0.40
108 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (107 bp):
AAATTTCAACACCTCAAATGTATGAGAAGCATTCAAAGATTTTTGAAATCCTATAAGACCTTCAA
GCACAATCTTTAAGACCTCAGATAAAACATTTTAAATTTTTA
Found at i:12735121 original size:19 final size:17
Alignment explanation
Indices: 12735081--12735124 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
12735071 AATTAATTGT
12735081 AAAAAAAATAAATTACA
1 AAAAAAAATAAATTACA
*
12735098 CAAAAGAAATTAAATTACA
1 -AAAA-AAAATAAATTACA
12735117 AAAAAAAA
1 AAAAAAAA
12735125 GAAAGAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 8 0.35
19 12 0.52
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAAAAAATAAATTACA
Found at i:12736851 original size:3 final size:3
Alignment explanation
Indices: 12736843--12736876 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12736833 TATTGTTTTT
12736843 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
12736877 TTTAAAGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12738775 original size:28 final size:29
Alignment explanation
Indices: 12738743--12738797 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
12738733 AATTTAAAAA
* *
12738743 TTTAAGATA-TAAATTATATATTTTATTT
1 TTTAAAATATTAAATTATACATTTTATTT
*
12738771 TTTAAAATATTAATTTATACATTTTAT
1 TTTAAAATATTAAATTATACATTTTAT
12738798 GAAAATGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (29 bp):
TTTAAAATATTAAATTATACATTTTATTT
Found at i:12744889 original size:2 final size:2
Alignment explanation
Indices: 12744874--12744933 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
12744864 TTTCCAGAAG
12744874 CT CT -T CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12744914 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
12744934 GGAAATTGCA
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12745463 original size:22 final size:22
Alignment explanation
Indices: 12745433--12745477 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12745423 GCGGTGTACG
12745433 ATTAAATTTAATAATTTATTTT
1 ATTAAATTTAATAATTTATTTT
* * *
12745455 ATTATATTTGATTATTTATTTT
1 ATTAAATTTAATAATTTATTTT
12745477 A
1 A
12745478 CATTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
ATTAAATTTAATAATTTATTTT
Found at i:12747222 original size:13 final size:13
Alignment explanation
Indices: 12747204--12747232 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12747194 CGCATTCATT
12747204 TTACCGCTATGGC
1 TTACCGCTATGGC
12747217 TTACCGCTATGGC
1 TTACCGCTATGGC
12747230 TTA
1 TTA
12747233 TTCTATACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (13 bp):
TTACCGCTATGGC
Found at i:12747430 original size:18 final size:18
Alignment explanation
Indices: 12747377--12747440 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 18
12747367 CATATTTATA
12747377 TTATATAAAATATTAATAATTT
1 TTATATAAAA-ATT-AT-A-TT
**
12747399 TTATATATTTAATTATATT
1 TTATATA-AAAATTATATT
12747418 TTATATAAAAATTATATT
1 TTATATAAAAATTATATT
12747436 TTATA
1 TTATA
12747441 ATTTATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 14 0.38
19 9 0.24
20 1 0.03
21 2 0.05
22 10 0.27
23 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATATAAAAATTATATT
Found at i:12747547 original size:10 final size:11
Alignment explanation
Indices: 12747524--12747556 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
12747514 AAATTTTAAA
12747524 TTATATTATTT
1 TTATATTATTT
12747535 TTATATT-TTT
1 TTATATTATTT
12747545 TTATATTATTT
1 TTATATTATTT
12747556 T
1 T
12747557 CATGTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATATTATTT
Found at i:12747569 original size:21 final size:21
Alignment explanation
Indices: 12747519--12747569 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
12747509 TATTAAAATT
*
12747519 TTAAATTATATTATTTTTATA
1 TTAAATTATATTATTTTCATA
*** *
12747540 TTTTTTTATATTATTTTCATG
1 TTAAATTATATTATTTTCATA
12747561 TTAAATTAT
1 TTAAATTAT
12747570 CATTTAGCCA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TTAAATTATATTATTTTCATA
Found at i:12749394 original size:2 final size:2
Alignment explanation
Indices: 12749382--12749411 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12749372 TAGGTTCTTA
12749382 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12749412 ATGATGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12753316 original size:2 final size:2
Alignment explanation
Indices: 12753309--12753333 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12753299 TAATCGGGAC
12753309 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12753334 CACATCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12753562 original size:26 final size:25
Alignment explanation
Indices: 12753525--12753582 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
12753515 TATTATGTTT
12753525 TAATATAA-ATATAAAATTAAATAAA
1 TAATA-AATATATAAAATTAAATAAA
* *
12753550 TATATAAATATATATAATTAAATAAT
1 TA-ATAAATATATAAAATTAAATAAA
12753576 TAATAAA
1 TAATAAA
12753583 AAATAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 9 0.31
26 20 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
TAATAAATATATAAAATTAAATAAA
Found at i:12756491 original size:3 final size:3
Alignment explanation
Indices: 12756485--12756572 Score: 131
Period size: 3 Copynumber: 29.0 Consensus size: 3
12756475 TTCATAGTAG
* * * *
12756485 TAA TAA TAA TAA TAT TCA CAT TAGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
12756531 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12756573 GATCACAAGT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
3 74 0.97
4 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12759869 original size:2 final size:2
Alignment explanation
Indices: 12759862--12759895 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12759852 AAGAAAACAA
12759862 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12759896 TTAATTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12776219 original size:27 final size:27
Alignment explanation
Indices: 12776166--12776221 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
12776156 TGACTAATCG
*
12776166 ATTAATTAAATTAAATCAATTTGATCA
1 ATTAATTAAATTAAATCAAATTGATCA
* *
12776193 ATTAATTTAATTATAATTAAATT-ATCA
1 ATTAATTAAATTA-AATCAAATTGATCA
12776220 AT
1 AT
12776222 ACCCTACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (27 bp):
ATTAATTAAATTAAATCAAATTGATCA
Found at i:12780778 original size:30 final size:30
Alignment explanation
Indices: 12780734--12780798 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
12780724 ATTAATTTAT
12780734 ATTAAAAGCTTATTTA-AGTACAAATTAAAG
1 ATTAAAAGCTTATTTAGA-TACAAATTAAAG
12780764 ATTACAAA-CTTATTTAGATACAAATTAAAG
1 ATTA-AAAGCTTATTTAGATACAAATTAAAG
12780794 ATTAA
1 ATTAA
12780799 GAATTTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 1 0.03
30 28 0.85
31 4 0.12
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (30 bp):
ATTAAAAGCTTATTTAGATACAAATTAAAG
Found at i:12780814 original size:25 final size:25
Alignment explanation
Indices: 12780785--12780832 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
12780775 ATTTAGATAC
*
12780785 AAATT-AAAGATTAAGAATTTATTGT
1 AAATTAAAAG-TTAAAAATTTATTGT
12780810 AAATTAAAAGTTAAAAATTTATT
1 AAATTAAAAGTTAAAAATTTATT
12780833 TGAATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (25 bp):
AAATTAAAAGTTAAAAATTTATTGT
Found at i:12780852 original size:28 final size:30
Alignment explanation
Indices: 12780814--12780892 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 30
12780804 TATTGTAAAT
* *
12780814 TAAAAGTTAAAAATTTATTTGAATATAATAA
1 TAAAA-TTAAAAATTTATTTAAATAAAATAA
* *
12780845 -AAAA-TAAATATTTCTTTAAATAAAATAA
1 TAAAATTAAAAATTTATTTAAATAAAATAA
12780873 TAAAATTCAAAAATTT-TTTA
1 TAAAATT-AAAAATTTATTTA
12780893 TTATTTTAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
28 20 0.50
29 4 0.10
30 9 0.22
31 7 0.17
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (30 bp):
TAAAATTAAAAATTTATTTAAATAAAATAA
Found at i:12784342 original size:51 final size:51
Alignment explanation
Indices: 12784237--12784342 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
12784227 AATAAAATTG
* *
12784237 TAATAATAATAAAATATATCTTGAAAAAAAGTTATAAACAAAAAACAAATA
1 TAATAATAATAAAATATACCTTGAAAAAAAGTTATAAACAAAAAACAAAAA
* *
12784288 TAATAGTAATAAAATATACCTTGAAGAAAA-TTACTGAAA-AAATAAA-AAAAA
1 TAATAATAATAAAATATACCTTGAAAAAAAGTTA-T-AAACAAA-AAACAAAAA
12784339 TAAT
1 TAAT
12784343 GTATAACATA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
50 3 0.06
51 39 0.81
52 6 0.12
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (51 bp):
TAATAATAATAAAATATACCTTGAAAAAAAGTTATAAACAAAAAACAAAAA
Found at i:12785060 original size:19 final size:19
Alignment explanation
Indices: 12785036--12785074 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
12785026 ATATATATAT
12785036 ATATATTAAATATTTAATTTA
1 ATAT-TTAAAT-TTTAATTTA
*
12785057 ATATTTTAATTTTAATTT
1 ATATTTAAATTTTAATTT
12785075 TTTTAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATTTAAATTTTAATTTA
Found at i:12785086 original size:28 final size:28
Alignment explanation
Indices: 12785046--12785126 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 28
12785036 ATATATTAAA
*
12785046 TATTTAATTTAATATTTTAATTTTAATT
1 TATTTAATATAATATTTTAATTTTAATT
* * ** *
12785074 TTTTTAATATAATATTTAAATTAAAAAT
1 TATTTAATATAATATTTTAATTTTAATT
*
12785102 TAATTAATATAATA-TTT-ATTTTAAT
1 TATTTAATATAATATTTTAATTTTAAT
12785127 ATAATTACAT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
26 5 0.12
27 2 0.05
28 34 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TATTTAATATAATATTTTAATTTTAATT
Done.