Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 130 of 133
Found at i:25512398 original size:4 final size:4
Alignment explanation
Indices: 25512391--25512430 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
25512381 ATAATATATA
25512391 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
25512431 AATATATCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:25521388 original size:12 final size:12
Alignment explanation
Indices: 25521371--25521395 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25521361 GCAGGCTTTG
25521371 CGCAAATGTATC
1 CGCAAATGTATC
25521383 CGCAAATGTATC
1 CGCAAATGTATC
25521395 C
1 C
25521396 TTATTAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (12 bp):
CGCAAATGTATC
Found at i:25526201 original size:13 final size:13
Alignment explanation
Indices: 25526183--25526228 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
25526173 AATCTATAAC
25526183 ATGATATAATGAT
1 ATGATATAATGAT
25526196 ATGATATAATGAT
1 ATGATATAATGAT
* *
25526209 ACGATACAA--AT
1 ATGATATAATGAT
25526220 ATGATATAA
1 ATGATATAA
25526229 ATAAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 9 0.31
13 20 0.69
ACGTcount: A:0.50, C:0.04, G:0.13, T:0.33
Consensus pattern (13 bp):
ATGATATAATGAT
Found at i:25526378 original size:32 final size:32
Alignment explanation
Indices: 25526342--25526414 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
25526332 TATAACACAT
* * *
25526342 AATTTTTATATAAAATATAATATAAATATATA
1 AATTTTAATATAAAACATAAAATAAATATATA
***
25526374 AATTTTAATATTTTACATAAAATAAATATATA
1 AATTTTAATATAAAACATAAAATAAATATATA
25526406 AATTATTAA
1 AATT-TTAA
25526415 ATTTACGCCG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 30 0.88
33 4 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (32 bp):
AATTTTAATATAAAACATAAAATAAATATATA
Found at i:25526405 original size:40 final size:38
Alignment explanation
Indices: 25526341--25526418 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 38
25526331 TTATAACACA
* *
25526341 TAATTTTTATATAAAATATAATATAAA-TATATAAATTT
1 TAATTTTTACATAAAATAAAATATAAATTAT-TAAATTT
25526379 TAATATTTTACATAAAATAAATATATAAATTATTAAATTT
1 TAAT-TTTTACATAAAATAAA-ATATAAATTATTAAATTT
25526419 ACGCCGAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 4 0.11
39 14 0.40
40 14 0.40
41 3 0.09
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (38 bp):
TAATTTTTACATAAAATAAAATATAAATTATTAAATTT
Found at i:25527321 original size:6 final size:6
Alignment explanation
Indices: 25527310--25527344 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
25527300 CCTGCATTCT
*
25527310 CACAAG CACAAG CACAAG CACAAG CACAGG CACAA
1 CACAAG CACAAG CACAAG CACAAG CACAAG CACAA
25527345 CTCAGTGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.49, C:0.34, G:0.17, T:0.00
Consensus pattern (6 bp):
CACAAG
Found at i:25534933 original size:16 final size:14
Alignment explanation
Indices: 25534909--25534946 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
25534899 AAAGAAATTT
*
25534909 AAAAAAAAGGGAAA
1 AAAAAAAAAGGAAA
25534923 AAAAGAAAAAGGAAA
1 AAAA-AAAAAGGAAA
25534938 AAAAAAAAA
1 AAAAAAAAA
25534947 CTTTCTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGGAAA
Found at i:25536395 original size:13 final size:11
Alignment explanation
Indices: 25536374--25536408 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
25536364 TGAGAATGTT
25536374 TATAATATAAA
1 TATAATATAAA
25536385 GTATGAATATAAA
1 -TAT-AATATAAA
25536398 TATAATATAAA
1 TATAATATAAA
25536409 AATTTAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.36
12 6 0.27
13 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (11 bp):
TATAATATAAA
Found at i:25538505 original size:22 final size:22
Alignment explanation
Indices: 25538480--25538521 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
25538470 ATTTTTTGTC
* *
25538480 CTTAATTCTAGGGATACAAATA
1 CTTAACTCTAGAGATACAAATA
*
25538502 CTTAACTCTCGAGATACAAA
1 CTTAACTCTAGAGATACAAA
25538522 AATAAATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (22 bp):
CTTAACTCTAGAGATACAAATA
Found at i:25542528 original size:22 final size:22
Alignment explanation
Indices: 25542503--25542544 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
25542493 ATTTTTTGTT
**
25542503 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAAATACAAATA
25542525 CTTAATTCTAGAAATACAAA
1 CTTAATTCTAGAAATACAAA
25542545 AACAAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (22 bp):
CTTAATTCTAGAAATACAAATA
Found at i:25544670 original size:28 final size:28
Alignment explanation
Indices: 25544638--25544692 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
25544628 CATTAAAAAG
* *
25544638 TTCTAATAAGTGTTAGCATGGAATATTT
1 TTCTAACAAGTGCTAGCATGGAATATTT
25544666 TTCTAACAAGTGCTAGCATGGAATATT
1 TTCTAACAAGTGCTAGCATGGAATATT
25544693 AAAAGAGCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (28 bp):
TTCTAACAAGTGCTAGCATGGAATATTT
Found at i:25557896 original size:27 final size:27
Alignment explanation
Indices: 25557845--25557897 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
25557835 ATAAATTAAG
*
25557845 ATAATATTATTTAATTTAATTCTATTT
1 ATAATATTATTTAATTTAATACTATTT
*
25557872 ATAATATTATTTTATCTT-ATACTATT
1 ATAATATTATTTAAT-TTAATACTATT
25557898 ATATTCTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (27 bp):
ATAATATTATTTAATTTAATACTATTT
Found at i:25558305 original size:2 final size:2
Alignment explanation
Indices: 25558300--25558334 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25558290 GACACACGAG
25558300 TA TA TA TA 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 TA TA TA TA T
25558335 TAGGTTTGGA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25558462 original size:12 final size:12
Alignment explanation
Indices: 25558445--25558482 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25558435 TTTCTTTAAA
25558445 TATATTAAAAAC
1 TATATTAAAAAC
*
25558457 TATATTAAAATAA
1 TATATTAAAA-AC
25558470 TAT-TTAAAAAC
1 TATATTAAAAAC
25558481 TA
1 TA
25558483 CAAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 3 0.13
12 16 0.70
13 4 0.17
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (12 bp):
TATATTAAAAAC
Found at i:25562298 original size:3 final size:3
Alignment explanation
Indices: 25562284--25562314 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
25562274 AGCTGGAAGT
25562284 TTC TTCC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC
25562315 CTAGCTTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:25570940 original size:27 final size:27
Alignment explanation
Indices: 25570899--25570951 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
25570889 CCCTTACCTT
*
25570899 TCATTTATAAGTAAGACCATTTATGTG
1 TCATTTATAAATAAGACCATTTATGTG
25570926 TCATTTATAAATAAGACCATTTATGT
1 TCATTTATAAATAAGACCATTTATGT
25570952 ACCATCTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (27 bp):
TCATTTATAAATAAGACCATTTATGTG
Found at i:25571904 original size:20 final size:20
Alignment explanation
Indices: 25571879--25571923 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
25571869 TATTAGGCAC
25571879 GTGGGGAGAGATTGGATGGG
1 GTGGGGAGAGATTGGATGGG
* * *
25571899 GTGGGGAGGGATTGGGTGTG
1 GTGGGGAGAGATTGGATGGG
25571919 GTGGG
1 GTGGG
25571924 ATGTTGGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.64, T:0.22
Consensus pattern (20 bp):
GTGGGGAGAGATTGGATGGG
Found at i:25572491 original size:26 final size:26
Alignment explanation
Indices: 25572463--25572511 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
25572453 TAAAAAATAA
*
25572463 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
25572488 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
25572512 ATTATTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:25589758 original size:2 final size:2
Alignment explanation
Indices: 25589685--25589740 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
25589675 AAATTGACGG
* * * * * *
25589685 TA TA TA TA AA TA TA AA CA TA TA TG TA TG TG 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
25589727 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
25589741 CACACACACG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:25590304 original size:2 final size:2
Alignment explanation
Indices: 25590297--25590324 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25590287 ATAATTTCTT
25590297 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
25590325 GATACACACA
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:25590461 original size:18 final size:18
Alignment explanation
Indices: 25590435--25590479 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
25590425 AATATTTAAC
*
25590435 AAAACAAACAAA-AAATAA
1 AAAAAAAACAAATAAA-AA
25590453 AAAAAAAACAAATAAAAA
1 AAAAAAAACAAATAAAAA
*
25590471 AAATAAAAC
1 AAAAAAAAC
25590480 GGAAATAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.07
Consensus pattern (18 bp):
AAAAAAAACAAATAAAAA
Found at i:25590610 original size:22 final size:22
Alignment explanation
Indices: 25590584--25590626 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25590574 CAGCCTCCCG
25590584 ACCAGCCACCCTACAGCCACCA
1 ACCAGCCACCCTACAGCCACCA
* * *
25590606 ACCAGCTACTCTACAGTCACC
1 ACCAGCCACCCTACAGCCACC
25590627 TAGATCCCCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.49, G:0.09, T:0.12
Consensus pattern (22 bp):
ACCAGCCACCCTACAGCCACCA
Found at i:25590742 original size:24 final size:24
Alignment explanation
Indices: 25590715--25590761 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
25590705 AAGAGGAAGC
*
25590715 TCTCTCGAAATCCCCTTCAATCTT
1 TCTCTAGAAATCCCCTTCAATCTT
* *
25590739 TCTCTAGGAATTCCCTTCAATCT
1 TCTCTAGAAATCCCCTTCAATCT
25590762 CCCTAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTCTAGAAATCCCCTTCAATCTT
Found at i:25591775 original size:16 final size:17
Alignment explanation
Indices: 25591743--25591778 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
25591733 ATAGGTTTCT
25591743 AAAATCCCTAAAAATCC
1 AAAATCCCTAAAAATCC
*
25591760 AAAATCCCT-TAAATCC
1 AAAATCCCTAAAAATCC
25591776 AAA
1 AAA
25591779 CCTCATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAATCCCTAAAAATCC
Found at i:25593062 original size:18 final size:18
Alignment explanation
Indices: 25593017--25593063 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
25593007 CACACCAATC
25593017 GAAAAAATAA-AAAAACAA
1 GAAAAAA-AACAAAAACAA
*
25593035 GAAGAAAAACAAAAACAA
1 GAAAAAAAACAAAAACAA
25593053 -AAAAACAAACA
1 GAAAAA-AAACA
25593064 CAGTCCTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.81, C:0.11, G:0.06, T:0.02
Consensus pattern (18 bp):
GAAAAAAAACAAAAACAA
Found at i:25593736 original size:20 final size:21
Alignment explanation
Indices: 25593684--25593737 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
25593674 CAGGTAAAAT
* *
25593684 TTTTTAT-TTTTATATTATTA
1 TTTTTATATTTTAAAATATTA
*
25593704 TTGTTATTATTTTAAAATA-TA
1 TTTTTA-TATTTTAAAATATTA
25593725 TTTTTATATTTTA
1 TTTTTATATTTTA
25593738 TGCATGATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 12 0.43
21 8 0.29
22 8 0.29
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTATATTTTAAAATATTA
Found at i:25594142 original size:16 final size:17
Alignment explanation
Indices: 25594110--25594180 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 17
25594100 ATAGGTTTTT
25594110 AAAATCCCTAAAAATCC
1 AAAATCCCTAAAAATCC
*
25594127 AAAATCCCT-TAAATCC
1 AAAATCCCTAAAAATCC
* *
25594143 -AAA-CCCCATAAAATCT
1 AAAATCCCTA-AAAATCC
**
25594159 AAAAT-CCTCGAAATCC
1 AAAATCCCTAAAAATCC
25594175 AAAATC
1 AAAATC
25594181 TTAAAAAATC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
14 3 0.07
15 3 0.07
16 21 0.51
17 14 0.34
ACGTcount: A:0.49, C:0.30, G:0.01, T:0.20
Consensus pattern (17 bp):
AAAATCCCTAAAAATCC
Found at i:25602435 original size:48 final size:48
Alignment explanation
Indices: 25602383--25602474 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
25602373 AAGTCCAAAG
*
25602383 ATAAAGTAAAATGCTTTCATTGTGGTAAAACAGGTCATATAAAGGTAT
1 ATAAAGTAAAATACTTTCATTGTGGTAAAACAGGTCATATAAAGGTAT
*
25602431 ATAAAGTGAAATACTTTCATTGTGGTAAAACAGGTCATATAAAG
1 ATAAAGTAAAATACTTTCATTGTGGTAAAACAGGTCATATAAAG
25602475 TGATACTGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.30
Consensus pattern (48 bp):
ATAAAGTAAAATACTTTCATTGTGGTAAAACAGGTCATATAAAGGTAT
Found at i:25623613 original size:12 final size:12
Alignment explanation
Indices: 25623596--25623625 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
25623586 TATTAGATTT
25623596 TCATAAATAATA
1 TCATAAATAATA
25623608 TCATAAATAATA
1 TCATAAATAATA
25623620 TCATAA
1 TCATAA
25623626 TGGTCATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (12 bp):
TCATAAATAATA
Found at i:25624020 original size:21 final size:21
Alignment explanation
Indices: 25623979--25624020 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25623969 TGGGTTGATC
*
25623979 TTTGATTTATTTATTTATTTA
1 TTTGATTTATCTATTTATTTA
* *
25624000 TTTGATTTATCTGTTTTTTTA
1 TTTGATTTATCTATTTATTTA
25624021 GATTTATCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.71
Consensus pattern (21 bp):
TTTGATTTATCTATTTATTTA
Found at i:25624769 original size:13 final size:13
Alignment explanation
Indices: 25624729--25624775 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
25624719 ATTTTTTTTG
25624729 GTATTTT-TTTAT
1 GTATTTTATTTAT
* *
25624741 -TATTTTATTAAA
1 GTATTTTATTTAT
25624753 GTATTTTATTTAT
1 GTATTTTATTTAT
25624766 GTA-TTTATTT
1 GTATTTTATTT
25624776 TTTTTCCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 6 0.21
12 10 0.34
13 13 0.45
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (13 bp):
GTATTTTATTTAT
Found at i:25624780 original size:21 final size:21
Alignment explanation
Indices: 25624754--25624802 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
25624744 TTTATTAAAG
25624754 TATTTT-ATTTATGTATTTATTT
1 TATTTTCATTTA-GTATTT-TTT
*
25624776 T-TTTTCCTTTAGTATTTTTT
1 TATTTTCATTTAGTATTTTTT
25624796 TATTTTC
1 TATTTTC
25624803 TATTAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.73
Consensus pattern (21 bp):
TATTTTCATTTAGTATTTTTT
Found at i:25624887 original size:24 final size:25
Alignment explanation
Indices: 25624863--25624910 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
25624853 TTAATTATTC
25624863 AATGATGAAATTTATA-AAAATTTCA
1 AATGAT-AAATTTATATAAAATTTCA
* *
25624888 AATGGTAAATTTTTATAAAATTT
1 AATGATAAATTTATATAAAATTT
25624911 TTAGGTGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (25 bp):
AATGATAAATTTATATAAAATTTCA
Found at i:25625187 original size:60 final size:59
Alignment explanation
Indices: 25625106--25625386 Score: 365
Period size: 60 Copynumber: 4.8 Consensus size: 59
25625096 AAAAGTTTCA
* *
25625106 AAAAAAATATTTTGA-GAAAAATTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTT
1 AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTT
* *
25625164 AAAAAAATATTTTTAAGGAAAAA-TTGAAAAGTATTAATTTTTTTTGAAAATAAAATTTTT
1 AAAAAAATATTTTT-AGGAAAAAGTTG-AAAGTATCAATTTTTCTTGAAAATAAAATTTTT
* *
25625224 -AAAAAATATTTTTAGG-AAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAA-TTTC
1 AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTT
* * * * **
25625280 AAAAAAAAATTATTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTGA
1 AAAAAAATATT-TTTAG-GAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTT
*
25625341 AGAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 A-AAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTG
25625387 TATGAAAAGC
Statistics
Matches: 194, Mismatches: 19, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
56 3 0.02
57 38 0.20
58 23 0.12
59 18 0.09
60 97 0.50
61 6 0.03
62 9 0.05
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (59 bp):
AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTTT
Found at i:25625249 original size:117 final size:118
Alignment explanation
Indices: 25625107--25625386 Score: 386
Period size: 117 Copynumber: 2.4 Consensus size: 118
25625097 AAAGTTTCAA
* * **
25625107 AAAAAATATTTTGAGAAAAATTTGAAAGTATCAATTTTTCTTGAAAATAAAATTT-TTAAAAAAA
1 AAAAAATATTTTTAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTCAAAAAAAAA
* * * * **
25625171 -TATTTTTAAGGAAAAATTGAAAAGTATTAATTTTTTTTGAAAATAAAATTT-TT
66 TTA-TTTTAAGAAAAAATTG-AAAGTATCAATTTTTCTTAAAAATAAAATTTAAG
* *
25625224 AAAAAATATTTTTAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAATTTCAAAAAAAAA
1 AAAAAATATTTTTAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTCAAAAAAAAA
*
25625289 TTATTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTGAAG
66 TTATTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTT-AAG
25625343 AAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAAAATATTTTT-AGAAAAAGTTGAAAGTATCAATTTTTCTTG
25625387 TATGAAAAGC
Statistics
Matches: 144, Mismatches: 14, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
117 79 0.55
118 21 0.15
119 15 0.10
120 29 0.20
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.39
Consensus pattern (118 bp):
AAAAAATATTTTTAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTCAAAAAAAAA
TTATTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTAAAAATAAAATTTAAG
Found at i:25628881 original size:1 final size:1
Alignment explanation
Indices: 25628877--25628914 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
25628867 TAAAAAGTCT
* *
25628877 AAAAAAAACAAAAAAAAAAAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25628915 TACCACGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.95, C:0.03, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:25629303 original size:12 final size:11
Alignment explanation
Indices: 25629269--25629358 Score: 58
Period size: 11 Copynumber: 7.9 Consensus size: 11
25629259 TTGAGAGATG
25629269 AGAAAAAAAAA
1 AGAAAAAAAAA
25629280 AGAGGAAGAAAAAA
1 AGA--AA-AAAAAA
**
25629294 TTAAAAAAAAA
1 AGAAAAAAAAA
25629305 AGAAAAAAAAGA
1 AGAAAAAAAA-A
*
25629317 A-AAAATGAAAA
1 AGAAAA-AAAAA
* *
25629328 ATAAAAAATAA
1 AGAAAAAAAAA
*
25629339 A-AAATAAAAA
1 AGAAAAAAAAA
*
25629349 TGAAAAAAAA
1 AGAAAAAAAA
25629359 GATGAAAATG
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 7 0.11
11 34 0.56
12 11 0.18
13 2 0.03
14 7 0.11
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:25629305 original size:14 final size:14
Alignment explanation
Indices: 25629266--25629358 Score: 77
Period size: 13 Copynumber: 6.8 Consensus size: 14
25629256 TGGTTGAGAG
*
25629266 ATGAGAAAAAAAAA
1 ATGAAAAAAAAAAA
** *
25629280 A-GAGGAAGAAAAA
1 ATGAAAAAAAAAAA
*
25629293 ATTAAAAAAAAAAGA
1 ATGAAAAAAAAAA-A
25629308 A--AAAAAAGAAAAA
1 ATGAAAAAA-AAAAA
*
25629321 ATGAAAAATAAAAA
1 ATGAAAAAAAAAAA
*
25629335 AT-AAAAAATAAAA
1 ATGAAAAAAAAAAA
25629348 ATGAAAAAAAA
1 ATGAAAAAAAA
25629359 GATGAAAATG
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
13 30 0.48
14 26 0.41
15 7 0.11
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.09
Consensus pattern (14 bp):
ATGAAAAAAAAAAA
Found at i:25629316 original size:28 final size:27
Alignment explanation
Indices: 25629266--25629358 Score: 98
Period size: 28 Copynumber: 3.4 Consensus size: 27
25629256 TGGTTGAGAG
* * **
25629266 ATGAGAAAAAAAAAAGAGGAAGAAAAA
1 ATGAAAAAAAAAAAAAAAAAAGAAAAA
*
25629293 ATTAAAAAAAAAAGAAAAAAAAGAAAAA
1 ATGAAAAAAAAAA-AAAAAAAAGAAAAA
* *
25629321 ATGAAAAATAAAAAATAAAAAA-TAAAA
1 ATGAAAAA-AAAAAAAAAAAAAGAAAAA
25629348 ATGAAAAAAAA
1 ATGAAAAAAAA
25629359 GATGAAAATG
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
26 3 0.05
27 23 0.41
28 25 0.45
29 5 0.09
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.09
Consensus pattern (27 bp):
ATGAAAAAAAAAAAAAAAAAAGAAAAA
Found at i:25629328 original size:35 final size:35
Alignment explanation
Indices: 25629289--25629356 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
25629279 AAGAGGAAGA
25629289 AAAAATTAAAAAA-AAAAGAA-AAAAAAGAAAAAATG
1 AAAAA-TAAAAAATAAAA-AATAAAAAAGAAAAAATG
*
25629324 AAAAATAAAAAATAAAAAATAAAAATGAAAAAA
1 AAAAATAAAAAATAAAAAATAAAAAAGAAAAAA
25629357 AAGATGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (35 bp):
AAAAATAAAAAATAAAAAATAAAAAAGAAAAAATG
Found at i:25630540 original size:46 final size:46
Alignment explanation
Indices: 25630488--25630680 Score: 196
Period size: 46 Copynumber: 4.3 Consensus size: 46
25630478 TTTTTAAAAT
* * * * *
25630488 TGAGAATTTTTAAAAAATTTTCAAATGAGAATTTTTTAGTCTTAAA
1 TGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTCTTAAA
* * *
25630534 TGAGAATCGTTAAGACATTTTCAAGTGAGAATCTTTGAGTTTTAAA
1 TGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTCTTAAA
* * * *
25630580 TTAAAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTGTCAAA
1 TGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTCTTAAA
* * * * *
25630626 TAAGAATCTTT--GA-ATTTT-AAATGAGAAACTTTAAGTGTCAAA
1 TGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTCTTAAA
*
25630668 TGAGAATATTTAA
1 TGAGAATCTTTAA
25630681 TGTTAAATGA
Statistics
Matches: 125, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
42 31 0.25
43 5 0.04
44 2 0.02
46 87 0.70
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (46 bp):
TGAGAATCTTTAAGACATTTTCAAATGAGAATCTTTGAGTCTTAAA
Found at i:25630612 original size:25 final size:24
Alignment explanation
Indices: 25630479--25630763 Score: 111
Period size: 21 Copynumber: 12.8 Consensus size: 24
25630469 ATCTTGATTT
* * *
25630479 TTTTAAAATTGAGAATTTTTAAAAAA
1 TTTTCAAA-TGAGAATCTTT-AAGAA
* *
25630505 TTTTCAAATGAGAATTTTTTAG--
1 TTTTCAAATGAGAATCTTTAAGAA
* *
25630527 TCTT-AAATGAGAATCGTTAAGACA
1 TTTTCAAATGAGAATCTTTAAGA-A
* *
25630551 TTTTCAAGTGAGAATCTTT--GAG
1 TTTTCAAATGAGAATCTTTAAGAA
* *
25630573 TTTT-AAATTAAAATCTTTAAGACA
1 TTTTCAAATGAGAATCTTTAAGA-A
25630597 TTTTCAAATGAGAATCTTT--G-A
1 TTTTCAAATGAGAATCTTTAAGAA
* * *
25630618 GTGTCAAATAAGAATCTTT--GAA
1 TTTTCAAATGAGAATCTTTAAGAA
*
25630640 TTTT-AAATGAGAAACTTTAAG--
1 TTTTCAAATGAGAATCTTTAAGAA
* *
25630661 -TGTCAAATGAGAATATTT---AA
1 TTTTCAAATGAGAATCTTTAAGAA
* * *
25630681 TGTT-AAATGAAAAT-TTT-TGAA
1 TTTTCAAATGAGAATCTTTAAGAA
*
25630702 TTTT-AAATGAGAAT-TTTGAG-A
1 TTTTCAAATGAGAATCTTTAAGAA
* * *
25630723 TATGTCGAATGTGAATCTTT--GAA
1 T-TTTCAAATGAGAATCTTTAAGAA
*
25630746 -TTACAAATGAGAATCTTT
1 TTTTCAAATGAGAATCTTT
25630764 GAAGTGTAAA
Statistics
Matches: 197, Mismatches: 40, Indels: 49
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.02
20 11 0.06
21 101 0.51
22 14 0.07
23 15 0.08
24 11 0.06
25 35 0.18
26 7 0.04
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (24 bp):
TTTTCAAATGAGAATCTTTAAGAA
Found at i:25630663 original size:42 final size:41
Alignment explanation
Indices: 25630596--25630690 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 41
25630586 TCTTTAAGAC
* * *
25630596 ATTTTCAAATGAGAATCTTTGAGTGTCAAATAAGAATCTTTGA
1 ATTTT-AAATGAGAAACTTTAAGTGTCAAATAAGAATATTT-A
*
25630639 ATTTTAAATGAGAAACTTTAAGTGTCAAATGAGAATATTTA
1 ATTTTAAATGAGAAACTTTAAGTGTCAAATAAGAATATTTA
*
25630680 ATGTTAAATGA
1 ATTTTAAATGA
25630691 AAATTTTTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 11 0.23
42 31 0.66
43 5 0.11
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (41 bp):
ATTTTAAATGAGAAACTTTAAGTGTCAAATAAGAATATTTA
Found at i:25630830 original size:79 final size:79
Alignment explanation
Indices: 25630730--25630902 Score: 222
Period size: 79 Copynumber: 2.2 Consensus size: 79
25630720 AGATATGTCG
* * * * * *
25630730 AATGTGAATCTTTGAATTACAAATGAGAATCTTTGAAGTGTAAAACTCAAAATTTGTC-AAGTGT
1 AATGAGAATCTTTGAATTACAAATAAAAATATTTGAAGTGTAAAACCCAAAATTTATCGAA-TGT
*
25630794 GAATATTCGAATTTA
65 GAATATTCGAATTCA
* * *
25630809 AATGAGAATTTTTGAATTACAAATAAAAATATTTGAGGTGTGAAACCCAAAATTTATCGAATGTG
1 AATGAGAATCTTTGAATTACAAATAAAAATATTTGAAGTGTAAAACCCAAAATTTATCGAATGTG
*
25630874 AATCTTCGAATTCA
66 AATATTCGAATTCA
*
25630888 AATGAAAATCTTTGA
1 AATGAGAATCTTTGA
25630903 GATGTGAAAC
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 78 0.98
80 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (79 bp):
AATGAGAATCTTTGAATTACAAATAAAAATATTTGAAGTGTAAAACCCAAAATTTATCGAATGTG
AATATTCGAATTCA
Found at i:25631146 original size:114 final size:114
Alignment explanation
Indices: 25630964--25631232 Score: 369
Period size: 114 Copynumber: 2.4 Consensus size: 114
25630954 TTTTGAACTG
* * * * * * *
25630964 TTGGATGTGAATATCTAAATTTCAAACAAAAAGCTTTGAACTCAACTTTTGGATGCGAATCTCTA
1 TTGGATGTGAATCTCTAAAATTCAAACGAAAAGCTTTGAACCCAACTTTTAGATGCAAATCTATA
*
25631029 AATTTTTAAATGAGAACCTTTGAACTTAGATATGAAACTCTAAGATTTT
66 AATTTTTAAATGAGAACCTTTGAACTTAGATATGAAACTCTAAGATTTA
* *
25631078 TTGGATGTGAATCTCTAAAATTCAAACGAAAAGCTTTGAACCCAATTTTTAGATGCAAATTTATA
1 TTGGATGTGAATCTCTAAAATTCAAACGAAAAGCTTTGAACCCAACTTTTAGATGCAAATCTATA
* * * *
25631143 AATTTTTGAGTGAGAACCTTTGGACTTAGATGTGAAACTCTAAGATTTA
66 AATTTTTAAATGAGAACCTTTGAACTTAGATATGAAACTCTAAGATTTA
* * *
25631192 TTGAATGTGAACCT-TCAAAATTCAAACGAAAAACTTTGAAC
1 TTGGATGTGAATCTCT-AAAATTCAAACGAAAAGCTTTGAAC
25631233 TTTTGGGATG
Statistics
Matches: 137, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
113 1 0.01
114 136 0.99
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (114 bp):
TTGGATGTGAATCTCTAAAATTCAAACGAAAAGCTTTGAACCCAACTTTTAGATGCAAATCTATA
AATTTTTAAATGAGAACCTTTGAACTTAGATATGAAACTCTAAGATTTA
Found at i:25632655 original size:16 final size:17
Alignment explanation
Indices: 25632615--25632655 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
25632605 TATTTAAATA
*
25632615 TTTTATTTATGTATTTT
1 TTTTCTTTATGTATTTT
*
25632632 TTTCCTTTA-GTATTTT
1 TTTTCTTTATGTATTTT
25632648 TTTTCTTT
1 TTTTCTTT
25632656 TCTATTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTCTTTATGTATTTT
Found at i:25632752 original size:24 final size:26
Alignment explanation
Indices: 25632716--25632765 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
25632706 TTAATTATCC
25632716 AATGATGAAA-TT-TATAGAAATTTTA
1 AATGATGAAATTTCTATA-AAATTTTA
25632741 AATGAT-AAATTTCTATAAAATTTTA
1 AATGATGAAATTTCTATAAAATTTTA
25632766 GGTGTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.13
25 16 0.70
26 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (26 bp):
AATGATGAAATTTCTATAAAATTTTA
Found at i:25632773 original size:24 final size:26
Alignment explanation
Indices: 25632716--25632778 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
25632706 TTAATTATCC
*
25632716 AATGATGAAATT-TATAGAAATTTTA
1 AATGATAAAATTCTATAGAAATTTTA
*
25632741 AATGATAAATTTCTATA-AAATTTTA
1 AATGATAAAATTCTATAGAAATTTTA
**
25632766 GGTG-TAAAATTCT
1 AATGATAAAATTCT
25632779 GTCTAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 8 0.25
25 20 0.62
26 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.41
Consensus pattern (26 bp):
AATGATAAAATTCTATAGAAATTTTA
Found at i:25632977 original size:59 final size:58
Alignment explanation
Indices: 25632876--25633037 Score: 156
Period size: 59 Copynumber: 2.8 Consensus size: 58
25632866 AATAATTTTT
* * * *
25632876 TTTTCAAAAAGTAT-TTTTGAGGAAAAGTTGAAAATATTAATTTTTCTTAAAAATAAAA
1 TTTTCAAAAA-TATATTTTAAGGAGAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAA
* *
25632934 TTTTCAAAAATATATATTTAAGGAGAAGTTGAAAGTATCAA-TTTTCTTTGAAATTAAAA
1 TTTTCAAAAATATAT-TTTAAGGAGAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAAA
** * *
25632993 TTTGAAGAAAAAATATTTTTA--AG--GTTGAAAGTATCAATTTTTCTT
1 TTTTCA-AAAATATATTTTAAGGAGAAGTTGAAAGTATCAATTTTTCTT
25633038 GTATAAAAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
55 16 0.18
56 5 0.06
57 5 0.06
58 16 0.18
59 39 0.44
60 8 0.09
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (58 bp):
TTTTCAAAAATATATTTTAAGGAGAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAA
Found at i:25634350 original size:4 final size:4
Alignment explanation
Indices: 25634341--25634368 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
25634331 CTCATTTTTC
25634341 TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT
25634369 CTCTAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:25639984 original size:2 final size:2
Alignment explanation
Indices: 25639968--25640006 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
25639958 TTATGTATGT
25639968 TA TA -A TA TA -A TA 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 TA TA TA TA TA TA TA T
25640007 GATTAAGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25643171 original size:10 final size:9
Alignment explanation
Indices: 25643156--25643226 Score: 56
Period size: 10 Copynumber: 7.6 Consensus size: 9
25643146 AATTCAATTT
25643156 TTATTTTGTA
1 TTATTTT-TA
25643166 TTATTTTTA
1 TTATTTTTA
*
25643175 TT-TTTTTT
1 TTATTTTTA
*
25643183 TTGTATTTTA
1 TTAT-TTTTA
25643193 TGTA-TTTTA
1 T-TATTTTTA
25643202 TTATTTATTA
1 TTATTT-TTA
*
25643212 TTATTATTA
1 TTATTTTTA
25643221 TGTATT
1 T-TATT
25643227 AATATATGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 9 0.18
9 17 0.33
10 24 0.47
11 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (9 bp):
TTATTTTTA
Found at i:25643173 original size:16 final size:15
Alignment explanation
Indices: 25643152--25643219 Score: 63
Period size: 16 Copynumber: 4.6 Consensus size: 15
25643142 GCCCAATTCA
25643152 ATTTTTATTTTGTATT
1 ATTTTTATTTT-TATT
25643168 ATTTTTATTTTT-TT
1 ATTTTTATTTTTATT
*
25643182 -TTTGTA-TTTTATGT
1 ATTTTTATTTTTAT-T
25643196 A-TTTTATTATTTATT
1 ATTTTTATT-TTTATT
*
25643211 ATTATTATT
1 ATTTTTATT
25643220 ATGTATTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
12 4 0.09
13 6 0.14
14 7 0.16
15 4 0.09
16 22 0.51
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (15 bp):
ATTTTTATTTTTATT
Found at i:25643184 original size:22 final size:22
Alignment explanation
Indices: 25643152--25643219 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
25643142 GCCCAATTCA
*
25643152 ATTTTTATTTTGTATTATTTTT
1 ATTTTTTTTTTGTATTATTTTT
*
25643174 ATTTTTTTTTTGTATT-TTATGT
1 ATTTTTTTTTTGTATTATT-TTT
* * *
25643196 ATTTTATTATT-TATTATTATT
1 ATTTTTTTTTTGTATTATTTTT
25643217 ATT
1 ATT
25643220 ATGTATTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 10 0.26
22 28 0.74
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (22 bp):
ATTTTTTTTTTGTATTATTTTT
Found at i:25643198 original size:28 final size:29
Alignment explanation
Indices: 25643167--25643226 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
25643157 TATTTTGTAT
* *
25643167 TATTTTTATT-TTTTTTTTGTATT-TTATG
1 TATTTTTATTATTTATTAT-TATTATTATG
25643195 TA-TTTTATTATTTATTATTATTATTATG
1 TATTTTTATTATTTATTATTATTATTATG
25643223 TATT
1 TATT
25643227 AATATATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
27 11 0.41
28 15 0.56
29 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (29 bp):
TATTTTTATTATTTATTATTATTATTATG
Found at i:25643450 original size:3 final size:3
Alignment explanation
Indices: 25643437--25643465 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
25643427 TGTTTATCTG
25643437 ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25643466 TGTTTTTTTT
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:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:25644341 original size:17 final size:17
Alignment explanation
Indices: 25644319--25644443 Score: 60
Period size: 19 Copynumber: 7.0 Consensus size: 17
25644309 TTTTTTAGAA
*
25644319 ATTTATTTATTTGTTTT
1 ATTTATTTATTTATTTT
25644336 ATTTATTTATTTATTTTT
1 ATTTATTTATTTA-TTTT
* *
25644354 ATTAGATTAGATTTATTTAAT
1 ATT-TATT-TATTTATTT--T
*
25644375 ATTT-TTTATCTTTATCTT
1 ATTTATTTA--TTTATTTT
* *
25644393 ATTT-TTATTTTTGTTTT
1 ATTTATT-TATTTATTTT
* *
25644410 ACTTTTCTTTATTTTTTTT
1 A--TTTATTTATTTATTTT
25644429 A-TT-TTTATTTATTTT
1 ATTTATTTATTTATTTT
25644444 TACTTTTATT
Statistics
Matches: 85, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
15 11 0.13
16 2 0.02
17 19 0.22
18 15 0.18
19 21 0.25
20 13 0.15
21 4 0.05
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTATTTT
Found at i:25644399 original size:27 final size:26
Alignment explanation
Indices: 25644369--25644434 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
25644359 ATTAGATTTA
*
25644369 TTTAATATTTTTTATCTTTATC-TTATT
1 TTTATTATTTTTTA-CTTT-TCTTTATT
*
25644396 TTTATTTTTGTTTTACTTTTCTTTATT
1 TTTATTATT-TTTTACTTTTCTTTATT
*
25644423 TTTTTTATTTTT
1 TTTATTATTTTT
25644435 ATTTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 5 0.15
27 23 0.70
28 5 0.15
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTATTATTTTTTACTTTTCTTTATT
Found at i:25644450 original size:7 final size:6
Alignment explanation
Indices: 25644377--25644455 Score: 58
Period size: 6 Copynumber: 13.7 Consensus size: 6
25644367 TATTTAATAT
* * * * * *
25644377 TTTTTA TCTTTA -TCTTA TTTTTA TTTTT- GTTTTA CTTTTC TTTATTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA
*
25644424 TTTTTA TTTTTA --TTTA TTTTTA CTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
25644456 GTTCTATTTT
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
4 4 0.07
5 7 0.12
6 40 0.71
7 5 0.09
ACGTcount: A:0.14, C:0.06, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:25644551 original size:58 final size:56
Alignment explanation
Indices: 25644470--25644689 Score: 211
Period size: 58 Copynumber: 3.9 Consensus size: 56
25644460 TATTTTCTTT
** * *
25644470 AAATAAAAATCAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTTCTTAA
1 AAATAAATTTCAAAAAAAGATTTTT-GGAAAAAGTTGAAAGTATCAATTTTCCTTAA
* **
25644527 AAATAAATTTTCAAAAAAAGATTTTTGAGAAAAAGTTGAAAGTATCAATTCTCCTTGG
1 AAATAAA-TTTCAAAAAAAGATTTTTG-GAAAAAGTTGAAAGTATCAATTTTCCTTAA
* *
25644585 AAATCAAAGTTTCAAAAAAAAATATTTTTGG----AG--AAAAG-ATCAATTTTCCTTAA
1 AAAT-AAA-TTTC--AAAAAAAGATTTTTGGAAAAAGTTGAAAGTATCAATTTTCCTTAA
* *
25644638 AAATAAATTTCCAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAATAAATTTCAAAAAAAG-ATTTTT-GGAAAAAGTTGAAAGTATCAATTTT
25644690 TTCTACACAA
Statistics
Matches: 133, Mismatches: 16, Indels: 27
0.76 0.09 0.15
Matches are distributed among these distances:
49 6 0.05
50 6 0.05
51 6 0.05
52 3 0.02
53 16 0.12
54 4 0.03
55 2 0.02
56 2 0.02
57 12 0.09
58 54 0.41
59 7 0.05
60 1 0.01
61 14 0.11
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (56 bp):
AAATAAATTTCAAAAAAAGATTTTTGGAAAAAGTTGAAAGTATCAATTTTCCTTAA
Found at i:25644635 original size:53 final size:51
Alignment explanation
Indices: 25644565--25644673 Score: 130
Period size: 50 Copynumber: 2.1 Consensus size: 51
25644555 GAAAAAGTTG
**
25644565 AAAGTATCAATTCTCCTTGGAAATCAAAGTTTCAAAAAAAAATATTTTTGGAGA
1 AAAGTATCAATTCTCCTTAAAAAT-AAA-TTTC-AAAAAAAATATTTTTGGAGA
* * * *
25644619 AAAG-ATCAATTTTCCTTAAAAATAAATTTCCAAAAAAGTATTTTTGGGGA
1 AAAGTATCAATTCTCCTTAAAAATAAATTTCAAAAAAAATATTTTTGGAGA
25644669 AAAGT
1 AAAGT
25644674 TGAAAGTATC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
50 21 0.44
51 4 0.08
52 3 0.06
53 16 0.33
54 4 0.08
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (51 bp):
AAAGTATCAATTCTCCTTAAAAATAAATTTCAAAAAAAATATTTTTGGAGA
Found at i:25648135 original size:17 final size:17
Alignment explanation
Indices: 25648113--25648157 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
25648103 GATGAAAAAT
* *
25648113 AAAAAAAAAGA-TGATG
1 AAAAAAAAAAACTAATG
25648129 AAAAAAAAAAACTAATG
1 AAAAAAAAAAACTAATG
25648146 AAAAAATAAAAA
1 AAAAAA-AAAAA
25648158 AAGAGATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
17 10 0.40
18 5 0.20
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (17 bp):
AAAAAAAAAAACTAATG
Found at i:25648136 original size:18 final size:17
Alignment explanation
Indices: 25648113--25648158 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
25648103 GATGAAAAAT
* *
25648113 AAAAAAAAAGATGATGA
1 AAAAAAAAAAATAATGA
*
25648130 AAAAAAAAAACTAATGA
1 AAAAAAAAAAATAATGA
25648147 AAAAATAAAAAA
1 AAAAA-AAAAAA
25648159 AGAGATTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (17 bp):
AAAAAAAAAAATAATGA
Found at i:25648159 original size:20 final size:21
Alignment explanation
Indices: 25648107--25648164 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 21
25648097 ACAATGGATG
25648107 AAAAATAAAAAAAAAGATGAT
1 AAAAATAAAAAAAAAGATGAT
**
25648128 GAAAAA-AAAAAACTA-ATGA-
1 -AAAAATAAAAAAAAAGATGAT
*
25648147 AAAAATAAAAAAAGAGAT
1 AAAAATAAAAAAAAAGAT
25648165 TCAAATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
18 5 0.17
19 7 0.23
20 6 0.20
21 7 0.23
22 5 0.17
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (21 bp):
AAAAATAAAAAAAAAGATGAT
Found at i:25649483 original size:41 final size:41
Alignment explanation
Indices: 25649407--25649947 Score: 811
Period size: 41 Copynumber: 13.1 Consensus size: 41
25649397 ATGATCGTCA
25649407 AGGAGCAATTTATTTTTCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
*
25649449 AGGAGCAATTTATTTTTCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
25649490 AGGAGCAATTTACTTTTCAAAGTCGTAGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
25649531 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
25649572 AGGAGCAATTTA-CTTTCAAAAGTCGTGATGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
25649613 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * *
25649654 AAGAGCAATTTA-TTTCCAAAGTCGTGGTGCCTCTATTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
25649694 AGGAGCAATTTATTTTCCAAAGTCGTGGTACCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* *
25649735 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
25649776 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
* * * * *
25649817 AGGAGTAATTTACTTTTCAAAATCGTGGTACCTTTGTTTAG
1 AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
25649858 AGGAGCAATTTA-TTTTCAAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTATTTTTC-AAAGTCGTGGTGCCTCTGTTTAG
* * * *
25649899 AGGAGCAATTT-TTGTTTCTTAAAGTCATTGAGCCTCTGTTTGG
1 AGGAGCAATTTATT-TTTC--AAAGTCGTGGTGCCTCTGTTTAG
25649942 AGGAGC
1 AGGAGC
25649948 TTTGGTCAAA
Statistics
Matches: 458, Mismatches: 34, Indels: 13
0.91 0.07 0.03
Matches are distributed among these distances:
40 46 0.10
41 361 0.79
42 26 0.06
43 25 0.05
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (41 bp):
AGGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAG
Found at i:25649857 original size:245 final size:246
Alignment explanation
Indices: 25649409--25649909 Score: 864
Period size: 245 Copynumber: 2.0 Consensus size: 246
25649399 GATCGTCAAG
* *
25649409 GAGCAATTTATTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCG
1 GAGCAATTTA-TTTTCAAAAGTCGTGGTGCCTCTATTTAGAGGAGCAATTTATTTTCCAAAGTCG
*
25649474 TGGTACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTAGTGCCTCTGTTTAGAGGAGCAA
65 TGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTAGTGCCTCTGTTTAGAGGAGCAA
*
25649539 TTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAAGTCGTGATGCC
130 TTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAAGTCGTGATACC
25649604 TCTGTTTAGAGGAGCAATTTATTTTTC-AAAGTCGTGGTGCCTCTGTTTAGAA
195 TCTGTTTAGAGGAGCAATTTA-TTTTCAAAAGTCGTGGTGCCTCTGTTTAGAA
*
25649656 GAGCAATTTA-TTTCCAAAGTCGTGGTGCCTCTATTTAGAGGAGCAATTTATTTTCCAAAGTCGT
1 GAGCAATTTATTTTCAAAAGTCGTGGTGCCTCTATTTAGAGGAGCAATTTATTTTCCAAAGTCGT
*
25649720 GGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAAT
66 GGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTAGTGCCTCTGTTTAGAGGAGCAAT
* *
25649785 TTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGTAATTTACTTTTCAAAA-TCGTGGTACC
131 TTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCAAAAGTCGTGATACC
* *
25649849 TTTGTTTAGAGGAGCAATTTATTTTCAAAAGTCGTGGTGCCTCTGTTTAGAG
195 TCTGTTTAGAGGAGCAATTTATTTTCAAAAGTCGTGGTGCCTCTGTTTAGAA
25649901 GAGCAATTT
1 GAGCAATTT
25649910 TTGTTTCTTA
Statistics
Matches: 242, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
244 5 0.02
245 219 0.90
246 8 0.03
247 10 0.04
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (246 bp):
GAGCAATTTATTTTCAAAAGTCGTGGTGCCTCTATTTAGAGGAGCAATTTATTTTCCAAAGTCGT
GGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTAGTGCCTCTGTTTAGAGGAGCAAT
TTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCAAAAGTCGTGATACCT
CTGTTTAGAGGAGCAATTTATTTTCAAAAGTCGTGGTGCCTCTGTTTAGAA
Found at i:25649961 original size:1 final size:1
Alignment explanation
Indices: 25649955--25650016 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
25649945 AGCTTTGGTC
* * * * * * * *
25649955 AAAAAAAAAATAAAAAACATAAAAAATAAAAAAAAACATAAAAAACAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25650017 TGACAATGTT
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:25649980 original size:19 final size:19
Alignment explanation
Indices: 25649955--25650016 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
25649945 AGCTTTGGTC
*
25649955 AAAAAAAAAATAAAAAACAT
1 AAAAAACAAA-AAAAAACAT
*
25649975 AAAAAATAAAAAAAAACAT
1 AAAAAACAAAAAAAAACAT
25649994 AAAAAACAAAAAAAAACA-
1 AAAAAACAAAAAAAAACAT
25650012 AAAAA
1 AAAAA
25650017 TGACAATGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.12
19 26 0.65
20 9 0.22
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (19 bp):
AAAAAACAAAAAAAAACAT
Found at i:25649995 original size:28 final size:25
Alignment explanation
Indices: 25649955--25650016 Score: 88
Period size: 27 Copynumber: 2.4 Consensus size: 25
25649945 AGCTTTGGTC
25649955 AAAAAAAAAATAAAAAACATAAAAAA
1 AAAAAAAAAATAAAAAACA-AAAAAA
25649981 TAAAAAAAAACATAAAAAACAAAAAAA
1 -AAAAAAAAA-ATAAAAAACAAAAAAA
*
25650008 AACAAAAAA
1 AAAAAAAAA
25650017 TGACAATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 8 0.24
27 15 0.45
28 10 0.30
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (25 bp):
AAAAAAAAAATAAAAAACAAAAAAA
Found at i:25650022 original size:10 final size:10
Alignment explanation
Indices: 25649955--25650016 Score: 67
Period size: 9 Copynumber: 6.5 Consensus size: 10
25649945 AGCTTTGGTC
25649955 AAAAAAAA-A
1 AAAAAAAACA
*
25649964 ATAAAAAAC-
1 AAAAAAAACA
* *
25649973 ATAAAAAATA
1 AAAAAAAACA
25649983 AAAAAAAAC-
1 AAAAAAAACA
*
25649992 ATAAAAAACA
1 AAAAAAAACA
25650002 AAAAAAAACA
1 AAAAAAAACA
25650012 AAAAA
1 AAAAA
25650017 TGACAATGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
9 23 0.52
10 21 0.48
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:25650462 original size:3 final size:3
Alignment explanation
Indices: 25650449--25650477 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
25650439 TGTTTATCTG
25650449 ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
25650478 TTTTATTTTT
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:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:25650848 original size:19 final size:19
Alignment explanation
Indices: 25650812--25650848 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
25650802 TAGATTCCGG
*
25650812 TTGAATTTTTTGACGAAGT
1 TTGAATTTTTCGACGAAGT
*
25650831 TTGAATTTTTCGATGAAG
1 TTGAATTTTTCGACGAAG
25650849 ATTCCGACCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.05, G:0.22, T:0.46
Consensus pattern (19 bp):
TTGAATTTTTCGACGAAGT
Found at i:25650966 original size:20 final size:20
Alignment explanation
Indices: 25650941--25650993 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
25650931 TCCGGTGAAC
25650941 TTTCGACGAAATTTTCCAGA
1 TTTCGACGAAATTTTCCAGA
* *
25650961 TTTCGATGATATTTTCCAGA
1 TTTCGACGAAATTTTCCAGA
*
25650981 ATTCGACGAAATT
1 TTTCGACGAAATT
25650994 CAACCGGAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTCGACGAAATTTTCCAGA
Found at i:25651387 original size:27 final size:27
Alignment explanation
Indices: 25651357--25651413 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
25651347 ATTAGATTTA
25651357 TTTAATATT-TTTTATCTTTATC-TTATT
1 TTTAATATTGTTTTA-CTTT-TCTTTATT
* *
25651384 TTTATTTTTGTTTTACTTTTCTTTATT
1 TTTAATATTGTTTTACTTTTCTTTATT
25651411 TTT
1 TTT
25651414 TTTATCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 2 0.08
27 19 0.73
28 5 0.19
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTAATATTGTTTTACTTTTCTTTATT
Found at i:25651421 original size:15 final size:15
Alignment explanation
Indices: 25651364--25651431 Score: 66
Period size: 15 Copynumber: 4.3 Consensus size: 15
25651354 TTATTTAATA
25651364 TTTTTTATCTTTATCT
1 TTTTTTATCTTTAT-T
* *
25651380 TATTTTTATTTTTGTT
1 T-TTTTTATCTTTATT
*
25651396 TTACTTT-TCTTTATT
1 TT-TTTTATCTTTATT
25651411 TTTTTTATCTTTATT
1 TTTTTTATCTTTATT
25651426 TATTTT
1 T-TTTT
25651432 CACTTTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
14 3 0.07
15 18 0.43
16 10 0.24
17 11 0.26
ACGTcount: A:0.13, C:0.07, G:0.01, T:0.78
Consensus pattern (15 bp):
TTTTTTATCTTTATT
Found at i:25651451 original size:22 final size:22
Alignment explanation
Indices: 25651413--25651454 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
25651403 TCTTTATTTT
25651413 TTTTATCTTTATTTATTTTCAC
1 TTTTATCTTTATTTATTTTCAC
*
25651435 TTTTAT-TTTGTTCTATTTTC
1 TTTTATCTTTATT-TATTTTC
25651455 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATCTTTATTTATTTTCAC
Found at i:25651537 original size:59 final size:58
Alignment explanation
Indices: 25651470--25651650 Score: 240
Period size: 59 Copynumber: 3.1 Consensus size: 58
25651460 ATAAAAATCA
*
25651470 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATTAATTTTCTTTGAAAATCAAAATTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATC-AAATTTTC
* * *
25651529 AAAAAATATTTTTCGGAAAAAGTTGAAAGTATCAATTTT-TCTTAAAAAT-AAATTTTC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCT-TTGAAAATCAAATTTTC
* * * * *
25651586 AAAAAAGAATTTTTGAGGAAAAGTTGAAAGTATCAATTCTCCTTGAAAATCAAAGTTTC
1 AAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATCAAATTTTC
25651645 AAAAAA
1 AAAAAA
25651651 AATATATTTT
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
57 14 0.13
58 36 0.34
59 56 0.53
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (58 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATCAAATTTTC
Found at i:25651619 original size:58 final size:58
Alignment explanation
Indices: 25651467--25651742 Score: 259
Period size: 58 Copynumber: 4.8 Consensus size: 58
25651457 TAAATAAAAA
* * *
25651467 TCAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATTAA-TTTTCTTTGAAAATCAAAATTT
1 TCAAAAAAA-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATC-AAATTT
* *
25651527 TCAAAAAATATTTTTCG-GAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAATTT
1 TCAAAAAAAATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAATTT
* * * *
25651584 TCAAAAAAGAATTTTTGAGGAAAAGTTGAAAGTATCAATTCTCCTTGAAAATCAAAGTT
1 TCAAAAAA-AATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAATTT
* *
25651643 TCAAAAAAAATATATTTTTAGG----G--AAAAG-ATCAATTTTTCTTAAAAAT-AAATTT
1 TC-AAAAAAA-AT-TTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAATTT
* * * *
25651696 TTAAAAAAGTATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTTA
1 TCAAAAAA-AATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTA
25651743 CACAAGAACA
Statistics
Matches: 180, Mismatches: 20, Indels: 34
0.77 0.09 0.15
Matches are distributed among these distances:
51 6 0.03
52 8 0.04
53 6 0.03
54 16 0.09
55 5 0.03
57 21 0.12
58 50 0.28
59 39 0.22
60 22 0.12
61 7 0.04
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (58 bp):
TCAAAAAAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATCAAATTT
Found at i:25655035 original size:11 final size:11
Alignment explanation
Indices: 25655014--25655055 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 11
25655004 AGTTGTAGAG
25655014 ATTTTTA-TTC
1 ATTTTTATTTC
25655024 ATTTTTATTTC
1 ATTTTTATTTC
25655035 AATTTTTTATTTC
1 -A-TTTTTATTTC
*
25655048 ATATTTAT
1 ATTTTTAT
25655056 CATTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 7 0.25
11 9 0.32
12 2 0.07
13 10 0.36
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (11 bp):
ATTTTTATTTC
Found at i:25655043 original size:13 final size:14
Alignment explanation
Indices: 25655025--25655053 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
25655015 TTTTTATTCA
25655025 TTTTTATTTCA-AT
1 TTTTTATTTCATAT
25655038 TTTTTATTTCATAT
1 TTTTTATTTCATAT
25655052 TT
1 TT
25655054 ATCATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTATTTCATAT
Found at i:25658127 original size:12 final size:12
Alignment explanation
Indices: 25658093--25658140 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
25658083 ATGAAAAATA
25658093 AGAAAAAAAAAG
1 AGAAAAAAAAAG
*
25658105 ATGATGGAAAAAAAG
1 A-GA--AAAAAAAAG
*
25658120 AGAAAAAAATAG
1 AGAAAAAAAAAG
25658132 AGAAAAAAA
1 AGAAAAAAA
25658141 TGAAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 17 0.57
13 2 0.07
14 2 0.07
15 9 0.30
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (12 bp):
AGAAAAAAAAAG
Found at i:25658141 original size:12 final size:12
Alignment explanation
Indices: 25658112--25658149 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
25658102 AAGATGATGG
25658112 AAAAAA-AGAGA
1 AAAAAATAGAGA
25658123 AAAAAATAGAGA
1 AAAAAATAGAGA
25658135 AAAAAAT-GA-A
1 AAAAAATAGAGA
25658145 AAAAA
1 AAAAA
25658150 TGAAAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 6 0.23
11 8 0.31
12 12 0.46
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (12 bp):
AAAAAATAGAGA
Found at i:25658155 original size:7 final size:8
Alignment explanation
Indices: 25658135--25658165 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
25658125 AAAATAGAGA
25658135 AAAAAATG
1 AAAAAATG
25658143 AAAAAAATG
1 -AAAAAATG
25658152 AAAAAATG
1 AAAAAATG
25658160 AAAAAA
1 AAAAAA
25658166 GAGATTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:25658156 original size:10 final size:10
Alignment explanation
Indices: 25658112--25658165 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
25658102 AAGATGATGG
25658112 AAAAAAA-GA
1 AAAAAAATGA
25658121 GAAAAAAATAGA
1 -AAAAAAAT-GA
25658133 GAAAAAAATG-
1 -AAAAAAATGA
25658143 AAAAAAATG-
1 AAAAAAATGA
25658152 -AAAAAATGA
1 AAAAAAATGA
25658161 AAAAA
1 AAAAA
25658166 GAGATTCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.20
9 9 0.22
10 11 0.28
11 1 0.03
12 11 0.28
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:25660125 original size:42 final size:41
Alignment explanation
Indices: 25660044--25660187 Score: 198
Period size: 42 Copynumber: 3.5 Consensus size: 41
25660034 GACTGTCAAA
* * *
25660044 AAGCAATTTATTTTTTCAAAGTTTTGTTGTCTCTGTTTAGAG
1 AAGCAATTTA-CTTTTCAAAGTTTCGTTGCCTCTGTTTAGAG
* * *
25660086 AAGCAATTTACTTTTCAAAGTCGTGGTTGCCTCTATTTAGAG
1 AAGCAATTTACTTTTCAAAGT-TTCGTTGCCTCTGTTTAGAG
*
25660128 AGGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAG
1 AAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAG
*
25660169 GAGCAATTTACTTTTCAAA
1 AAGCAATTTACTTTTCAAA
25660188 AGATAAGCCA
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
41 44 0.49
42 46 0.51
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (41 bp):
AAGCAATTTACTTTTCAAAGTTTCGTTGCCTCTGTTTAGAG
Found at i:25660353 original size:43 final size:43
Alignment explanation
Indices: 25660304--25660444 Score: 156
Period size: 43 Copynumber: 3.2 Consensus size: 43
25660294 CTCTGTTTAA
* * *
25660304 AGGAGCTTTGTTTAATCTTCAAAGTCATTAAACCTCTTATTAG
1 AGGAGCTTTGTTTAATTTTCAAAGTCATTGAACCTCTAATTAG
* * * *
25660347 AGGAGCTTTATTTAATTTTCAAAGTCGTTGAACCTCTAAATAT
1 AGGAGCTTTGTTTAATTTTCAAAGTCATTGAACCTCTAATTAG
* * **
25660390 AGGAGCTTTGTTTATGTTTCTCAAAGTCATTGAGCCTCTGCTTAG
1 AGGAGCTTTGTTTA-ATTT-TCAAAGTCATTGAACCTCTAATTAG
*
25660435 AAGAGCTTTG
1 AGGAGCTTTG
25660445 ATCAAAATTT
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 49 0.61
44 3 0.04
45 28 0.35
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.39
Consensus pattern (43 bp):
AGGAGCTTTGTTTAATTTTCAAAGTCATTGAACCTCTAATTAG
Found at i:25660479 original size:25 final size:25
Alignment explanation
Indices: 25660448--25660503 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 25
25660438 AGCTTTGATC
25660448 AAAATTT-AAAAAATAAAAACAAAAA
1 AAAATTTCAAAAAA-AAAAACAAAAA
25660473 AAAATTTTCAAAAAAAAAAACAAAAA
1 AAAA-TTTCAAAAAAAAAAACAAAAA
25660499 AAAAT
1 AAAAT
25660504 GGGTCAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 5 0.17
26 18 0.62
27 6 0.21
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (25 bp):
AAAATTTCAAAAAAAAAAACAAAAA
Found at i:25660510 original size:27 final size:27
Alignment explanation
Indices: 25660455--25660510 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
25660445 ATCAAAATTT
**
25660455 AAAAAATAAAAACAAAAAAAAATTTTC
1 AAAAAATAAAAACAAAAAAAAATGGTC
25660482 AAAAAA-AAAAACAAAAAAAAATGGGTC
1 AAAAAATAAAAACAAAAAAAAAT-GGTC
25660509 AA
1 AA
25660511 GTTGAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (27 bp):
AAAAAATAAAAACAAAAAAAAATGGTC
Found at i:25660948 original size:11 final size:11
Alignment explanation
Indices: 25660913--25660948 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
25660903 GAGGGGAGGT
25660913 AACCAAAGAAAA
1 AACC-AAGAAAA
*
25660925 AACCAAGCAAA
1 AACCAAGAAAA
25660936 AACCAAGAAAA
1 AACCAAGAAAA
25660947 AA
1 AA
25660949 GGTATGAGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.72, C:0.19, G:0.08, T:0.00
Consensus pattern (11 bp):
AACCAAGAAAA
Found at i:25662598 original size:59 final size:59
Alignment explanation
Indices: 25662525--25662684 Score: 180
Period size: 59 Copynumber: 2.7 Consensus size: 59
25662515 TAAAATTTTC
* * *
25662525 AAGAATAATATTTTTGAGAAAAAATTGAAAGTATCAATTTTTCTTACGAATAAAT-TTTAAAA
1 AAGAA-AAT-TTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTA--AAAAAATATTCAAAA
* *
25662587 AA-AAAATTTTTTTAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAATATTCAAAA
1 AAGAAAATTTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAAATATTCAAAA
**** *
25662645 AAGTTTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTT
1 AAGAAAATTTTTTGAGAAAAAGTTGAAAGTATCAATTTTT
25662685 TTTTGTACAA
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
57 6 0.07
58 8 0.10
59 63 0.75
60 3 0.04
61 2 0.02
62 2 0.02
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.39
Consensus pattern (59 bp):
AAGAAAATTTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAAAATATTCAAAA
Found at i:25663718 original size:14 final size:16
Alignment explanation
Indices: 25663687--25663721 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
25663677 TGATGAACTA
25663687 ATGATAATGATGATTT
1 ATGATAATGATGATTT
25663703 ATGATAAT-AT-ATTT
1 ATGATAATGATGATTT
25663717 ATGAT
1 ATGAT
25663722 TTTGAAGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 2 0.11
16 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (16 bp):
ATGATAATGATGATTT
Found at i:25663914 original size:91 final size:91
Alignment explanation
Indices: 25663801--25663987 Score: 349
Period size: 91 Copynumber: 2.1 Consensus size: 91
25663791 TGATATGTTT
25663801 TGATATGTTATTAATTCTTTGAATGCTTACTTAAATGTTTTAGAAGCATAATGCCAATAATGTTT
1 TGATATGTTATTAATTCTTTGAATGCTTACTTAAATGTTTTAGAAGCATAATGCCAATAATGTTT
25663866 CTGAATAAGCTATATATATATATATA
66 CTGAATAAGCTATATATATATATATA
*
25663892 TGATATGTTATTAATTCTTTGAATGCTTACTTAAATGTTTTGGAAGCATAATGCCAATAATGTTT
1 TGATATGTTATTAATTCTTTGAATGCTTACTTAAATGTTTTAGAAGCATAATGCCAATAATGTTT
*
25663957 TTGAATAAGCTATATATATATATATA
66 CTGAATAAGCTATATATATATATATA
25663983 T-ATAT
1 TGATAT
25663988 ATATGAAAAC
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
90 4 0.04
91 90 0.96
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (91 bp):
TGATATGTTATTAATTCTTTGAATGCTTACTTAAATGTTTTAGAAGCATAATGCCAATAATGTTT
CTGAATAAGCTATATATATATATATA
Found at i:25663974 original size:2 final size:2
Alignment explanation
Indices: 25663967--25663991 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25663957 TTGAATAAGC
25663967 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 T
25663992 GAAAACGATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25669663 original size:52 final size:52
Alignment explanation
Indices: 25669606--25669751 Score: 154
Period size: 52 Copynumber: 2.8 Consensus size: 52
25669596 AACCGTTATT
**
25669606 GAGAGATTTTTGGGATTTAATTTCAAAATCAATTGGCATTAAAAATGAT-GTG
1 GAGAGATTTTTGGGATTTAATTTCAAAATCAATTCACATTAAAAATGATAG-G
* * * * * *
25669658 GAGAGATTGTCGGAATTTAATTCCATAATCAATTCACATT-AAATTGATAGG
1 GAGAGATTTTTGGGATTTAATTTCAAAATCAATTCACATTAAAAATGATAGG
* * * *
25669709 GAAAGA-TTTTGGGATTTGATTTCAGAATCAATTCTCATTAAAA
1 GAGAGATTTTTGGGATTTAATTTCAAAATCAATTCACATTAAAA
25669752 CGAAAATCAA
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
50 26 0.34
51 16 0.21
52 34 0.45
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (52 bp):
GAGAGATTTTTGGGATTTAATTTCAAAATCAATTCACATTAAAAATGATAGG
Found at i:25669748 original size:50 final size:50
Alignment explanation
Indices: 25669613--25669751 Score: 145
Period size: 50 Copynumber: 2.7 Consensus size: 50
25669603 ATTGAGAGAT
** *
25669613 TTTTGGGATTTAATTTCAAAATCAATTGGCATTAAAAATGATGTGGAGAGA
1 TTTTGGGATTTAATTTCAAAATCAATTCACATT-AAAATGATGTGGAAAGA
* * * * *
25669664 TTGTCGGAATTTAATTCCATAATCAATTCACATTAAATTGATAG-GGAAAGA
1 TT-TTGGGATTTAATTTCAAAATCAATTCACATTAAAATGAT-GTGGAAAGA
* * *
25669715 TTTTGGGATTTGATTTCAGAATCAATTCTCATTAAAA
1 TTTTGGGATTTAATTTCAAAATCAATTCACATTAAAA
25669752 CGAAAATCAA
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
50 28 0.39
51 17 0.24
52 26 0.37
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (50 bp):
TTTTGGGATTTAATTTCAAAATCAATTCACATTAAAATGATGTGGAAAGA
Found at i:25672248 original size:48 final size:48
Alignment explanation
Indices: 25672182--25672275 Score: 125
Period size: 48 Copynumber: 2.0 Consensus size: 48
25672172 TTTGAATGTT
* **
25672182 TGTGAGTAAACTAGAAAAGATTGAGAGGATCTGCATAGGTATGGTGCA
1 TGTGAGTAAACTAAAAAAGATTGAGAGGATCCACATAGGTATGGTGCA
* * * *
25672230 TGTGAGTGAATTAAAAAAGTTTGAGAGGATCCACATATGTATGGTG
1 TGTGAGTAAACTAAAAAAGATTGAGAGGATCCACATAGGTATGGTG
25672276 TATAAGAGCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (48 bp):
TGTGAGTAAACTAAAAAAGATTGAGAGGATCCACATAGGTATGGTGCA
Found at i:25674225 original size:13 final size:13
Alignment explanation
Indices: 25674207--25674232 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25674197 TTTTTGTCGC
25674207 TGATCATGGCGAT
1 TGATCATGGCGAT
25674220 TGATCATGGCGAT
1 TGATCATGGCGAT
25674233 CATAGTGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
TGATCATGGCGAT
Found at i:25674944 original size:26 final size:27
Alignment explanation
Indices: 25674892--25674964 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 27
25674882 ATTTAAATAT
*
25674892 AATATAATAACAAAAATATGATATAAA
1 AATATAATAACAAAAATATAATATAAA
*
25674919 AATATATTAA-AAAAATATAACT-TAAA
1 AATATAATAACAAAAATATAA-TATAAA
* * * *
25674945 ATTTTAATAATAATAATATA
1 AATATAATAACAAAAATATA
25674965 TAACTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 20 0.53
27 18 0.47
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (27 bp):
AATATAATAACAAAAATATAATATAAA
Found at i:25675043 original size:23 final size:23
Alignment explanation
Indices: 25674944--25675054 Score: 63
Period size: 23 Copynumber: 5.0 Consensus size: 23
25674934 TATAACTTAA
* *
25674944 AATTTTAAT-AATAATAATATAT
1 AATTTTTATAAATTATAATATAT
* *
25674966 AACTTTTAATAAAATTA-AAAATAT
1 AA-TTTTTAT-AAATTATAATATAT
* *
25674990 -ATATTTTAT-ATTTTTAAT-TAT
1 AAT-TTTTATAAATTATAATATAT
**
25675011 -ATTAATATAAATTATAATATAT
1 AATTTTTATAAATTATAATATAT
**
25675033 AATTTTTATAAAAAATAATATA
1 AATTTTTATAAATTATAATATA
25675055 AATATATAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 15
0.70 0.15 0.16
Matches are distributed among these distances:
20 4 0.06
21 15 0.22
22 8 0.12
23 30 0.45
24 6 0.09
25 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTTTATAAATTATAATATAT
Found at i:25682929 original size:16 final size:15
Alignment explanation
Indices: 25682904--25682934 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
25682894 GTATCTAGAA
25682904 GCATAAAAATCAGAC
1 GCATAAAAATCAGAC
25682919 GCATCAAAAATCAGAC
1 GCAT-AAAAATCAGAC
25682935 CTTGATCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.23, G:0.13, T:0.13
Consensus pattern (15 bp):
GCATAAAAATCAGAC
Found at i:25689611 original size:19 final size:19
Alignment explanation
Indices: 25689587--25689630 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
25689577 TATCAATCAC
25689587 CAGTTGCCCAGTTGATAAA
1 CAGTTGCCCAGTTGATAAA
25689606 CAGTTGCCCAGTTGATAAA
1 CAGTTGCCCAGTTGATAAA
*
25689625 GAGTTG
1 CAGTTG
25689631 GGACTAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (19 bp):
CAGTTGCCCAGTTGATAAA
Found at i:25691270 original size:307 final size:307
Alignment explanation
Indices: 25690716--25691333 Score: 1211
Period size: 307 Copynumber: 2.0 Consensus size: 307
25690706 CCTTTGGATC
25690716 ACAAATTTCTTTCTCACTGATCATAAGCTTGTCGATTCTGTTAGCATGCCTTCTATTGGATGCGA
1 ACAAATTTCTTTCTCACTGATCATAAGCTTGTCGATTCTGTTAGCATGCCTTCTATTGGATGCGA
25690781 TTAGATGGAAGTACTTGGTGTTATAATCACCGAATTTGATCCATTGTGATCAAGATTTTTGGACC
66 TTAGATGGAAGTACTTGGTGTTATAATCACCGAATTTGATCCATTGTGATCAAGATTTTTGGACC
25690846 ATGAGTGCTCCTCATTTTTGTAAAGACACCACAATTCATTCCTTAGGTTGGCTAGCGTCGGATGC
131 ATGAGTGCTCCTCATTTTTGTAAAGACACCACAATTCATTCCTTAGGTTGGCTAGCGTCGGATGC
25690911 TAATCGTAAGATAGTCTGTGCTTCATCCTCATTCTCTAGTTTGTCGATATCTACTACCATTTTAT
196 TAATCGTAAGATAGTCTGTGCTTCATCCTCATTCTCTAGTTTGTCGATATCTACTACCATTTTAT
*
25690976 GGATTCTTTAGGCATCCTTATTGGCATGATCTTCTTGTTATTTTTTA
261 GGATTCTTTAGGCATCCTTATTGGCATGATCTTCTTGTCATTTTTTA
25691023 ACAAATTTCTTTCTCACTGATCATAAGCTTGTCGATTCTGTTAGCATGCCTTCTATTGGATGCGA
1 ACAAATTTCTTTCTCACTGATCATAAGCTTGTCGATTCTGTTAGCATGCCTTCTATTGGATGCGA
25691088 TTAGATGGAAGTA-TTCGGTGTTATAATCACCGAATTTGATCCATTGTGATCAAGATTTTTGGAC
66 TTAGATGGAAGTACTT-GGTGTTATAATCACCGAATTTGATCCATTGTGATCAAGATTTTTGGAC
25691152 CATGAGTGCTCCTCATTTTTGTAAAGACACCACAATTCATTCCTTAGGTTGGCTAGCGTCGGATG
130 CATGAGTGCTCCTCATTTTTGTAAAGACACCACAATTCATTCCTTAGGTTGGCTAGCGTCGGATG
25691217 CTAATCGTAAGATAGTCTGTGCTTCATCCTCATTCTCTAGTTTGTCGATATCTACTACCATTTTA
195 CTAATCGTAAGATAGTCTGTGCTTCATCCTCATTCTCTAGTTTGTCGATATCTACTACCATTTTA
25691282 TGGATTCTTTAGGCATCCTTATTGGCATGATCTTCTTGTCATTTTTTA
260 TGGATTCTTTAGGCATCCTTATTGGCATGATCTTCTTGTCATTTTTTA
25691330 ACAA
1 ACAA
25691334 GTTTGAAGGT
Statistics
Matches: 309, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
306 2 0.01
307 307 0.99
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (307 bp):
ACAAATTTCTTTCTCACTGATCATAAGCTTGTCGATTCTGTTAGCATGCCTTCTATTGGATGCGA
TTAGATGGAAGTACTTGGTGTTATAATCACCGAATTTGATCCATTGTGATCAAGATTTTTGGACC
ATGAGTGCTCCTCATTTTTGTAAAGACACCACAATTCATTCCTTAGGTTGGCTAGCGTCGGATGC
TAATCGTAAGATAGTCTGTGCTTCATCCTCATTCTCTAGTTTGTCGATATCTACTACCATTTTAT
GGATTCTTTAGGCATCCTTATTGGCATGATCTTCTTGTCATTTTTTA
Found at i:25694574 original size:18 final size:18
Alignment explanation
Indices: 25694547--25694587 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
25694537 GGTAATATAA
25694547 ATATCCTAGCTAGTAAAT
1 ATATCCTAGCTAGTAAAT
*
25694565 ATATCGTAGCTAGTAAAT
1 ATATCCTAGCTAGTAAAT
25694583 ATATC
1 ATATC
25694588 AGTTTCCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (18 bp):
ATATCCTAGCTAGTAAAT
Found at i:25698975 original size:13 final size:12
Alignment explanation
Indices: 25698950--25698989 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
25698940 TTTAAATTTA
*
25698950 ATAATTTAAAAT
1 ATAATATAAAAT
25698962 ATAATATAAAA-
1 ATAATATAAAAT
25698973 ATAATATAAAAAT
1 ATAATAT-AAAAT
25698986 ATAA
1 ATAA
25698990 AAGTGATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 7 0.28
12 14 0.56
13 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:25698978 original size:11 final size:11
Alignment explanation
Indices: 25698949--25698986 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
25698939 ATTTAAATTT
*
25698949 AATAATTTAAA
1 AATAATATAAA
25698960 ATATAATATAAA
1 A-ATAATATAAA
25698972 AATAATATAAA
1 AATAATATAAA
25698983 AATA
1 AATA
25698987 TAAAAGTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAATATAAA
Found at i:25699749 original size:26 final size:26
Alignment explanation
Indices: 25699713--25699768 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
25699703 TTTATTAAAA
* *
25699713 TTTTTTTCAATCATAATTATAATAAT
1 TTTTTTTCAATCACAATAATAATAAT
*
25699739 TTTTTTTCAATCACAATAATAATACT
1 TTTTTTTCAATCACAATAATAATAAT
25699765 TTTT
1 TTTT
25699769 ATTATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTTTTCAATCACAATAATAATAAT
Found at i:25701215 original size:2 final size:2
Alignment explanation
Indices: 25701208--25701243 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
25701198 ATATTATGCG
* *
25701208 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25701244 GGAGTAAGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25713310 original size:2 final size:2
Alignment explanation
Indices: 25713303--25713336 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
25713293 AGTGAGAAGA
* *
25713303 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25713337 GTAGTTGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25717254 original size:11 final size:11
Alignment explanation
Indices: 25717238--25717263 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25717228 TAAAAAATGA
25717238 ATACAATATAT
1 ATACAATATAT
25717249 ATACAATATAT
1 ATACAATATAT
25717260 ATAC
1 ATAC
25717264 CATTTTAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (11 bp):
ATACAATATAT
Found at i:25717698 original size:195 final size:195
Alignment explanation
Indices: 25717366--25717761 Score: 774
Period size: 195 Copynumber: 2.0 Consensus size: 195
25717356 TAATAGTTAA
25717366 TTTTGAATTGCTTAAAGATTTTTTTTAAACCTAATGAAGGGTTGAGTGAAAACCCCCTAGACAAA
1 TTTTGAATTGCTTAAAGATTTTTTTTAAACCTAATGAAGGGTTGAGTGAAAACCCCCTAGACAAA
* *
25717431 TGGATACTGAATTAACCATTCACCTAAACAGTTGGTTAATTTAGGTTTAAGTGGGTTTGAACTAT
66 AGGATACTGAATTAACCATTCACCTAAACAGGTGGTTAATTTAGGTTTAAGTGGGTTTGAACTAT
25717496 TCTCTCTAATATTACTTGTAACTTTAAACAAGACATTTTAGAAATTCATGCCTTAGAAATCTTGG
131 TCTCTCTAATATTACTTGTAACTTTAAACAAGACATTTTAGAAATTCATGCCTTAGAAATCTTGG
25717561 TTTTGAATTGCTTAAAGATTTTTTTTAAACCTAATGAAGGGTTGAGTGAAAACCCCCTAGACAAA
1 TTTTGAATTGCTTAAAGATTTTTTTTAAACCTAATGAAGGGTTGAGTGAAAACCCCCTAGACAAA
25717626 AGGATACTGAATTAACCATTCACCTAAACAGGTGGTTAATTTAGGTTTAAGTGGGTTTGAACTAT
66 AGGATACTGAATTAACCATTCACCTAAACAGGTGGTTAATTTAGGTTTAAGTGGGTTTGAACTAT
25717691 TCTCTCTAATATTACTTGTAACTTTAAACAAGACATTTTAGAAATTCATGCCTTAGAAATCTTGG
131 TCTCTCTAATATTACTTGTAACTTTAAACAAGACATTTTAGAAATTCATGCCTTAGAAATCTTGG
25717756 TTTTGA
1 TTTTGA
25717762 TCTTAAAATA
Statistics
Matches: 199, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
195 199 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (195 bp):
TTTTGAATTGCTTAAAGATTTTTTTTAAACCTAATGAAGGGTTGAGTGAAAACCCCCTAGACAAA
AGGATACTGAATTAACCATTCACCTAAACAGGTGGTTAATTTAGGTTTAAGTGGGTTTGAACTAT
TCTCTCTAATATTACTTGTAACTTTAAACAAGACATTTTAGAAATTCATGCCTTAGAAATCTTGG
Found at i:25720495 original size:58 final size:56
Alignment explanation
Indices: 25720296--25720640 Score: 205
Period size: 57 Copynumber: 6.1 Consensus size: 56
25720286 TTTTAAAAAA
* * * * *
25720296 TTTTACTTTAAGAAAAATTGATATTTTAACTTTATTC-TCAAA-TTCTTGAAAATTCTT
1 TTTTA-TTTAAGAAAAATTGATACTTCAACTTT-TCCTTAAAATTTTTTGAAAATT-TT
* * * * * * *
25720353 GTTTA---AGGAAAGATTGATATTTCAACTCTTCCCTCAAATCTTTTTG-AAATTATT
1 TTTTATTTAAGAAAAATTGATACTTCAACTTTTCCTTAAAAT-TTTTTGAAAATT-TT
**
25720407 TGCGT-TTTAA-AGAAAATTGATACTTCAACTTTTCCTTAAACATTTTTTGAAATATTTT
1 T-TTTATTTAAGA-AAAATTGATACTTCAACTTTTCCTTAAA-ATTTTTTGAAA-ATTTT
* * *
25720465 TTTTATTTAAGAAAAATTGATACTTTAACTTTT-TTTGAAAAATATTTTTTAAAATATTT
1 TTTTATTTAAGAAAAATTGATACTTCAACTTTTCCTT--AAAAT-TTTTTGAAAAT-TTT
* * * *
25720524 TTTTATTTAA-AGAAAATTAAATATTTCAACTTTTTCCTCAAAA--TTTTG-AAATTAT
1 TTTTATTTAAGA-AAAATT-GATACTTCAAC-TTTTCCTTAAAATTTTTTGAAAATTTT
* * * *
25720579 TTTTATTTAAGAAAAAATTGATACTTCAACTTTTTCTT-TATTTTTTTAAAAATTTT
1 TTTTATTTAAG-AAAAATTGATACTTCAACTTTTCCTTAAAATTTTTTGAAAATTTT
25720635 TGTTTA
1 T-TTTA
25720641 AAAAGAAAAT
Statistics
Matches: 224, Mismatches: 37, Indels: 54
0.71 0.12 0.17
Matches are distributed among these distances:
52 2 0.01
53 26 0.12
54 13 0.06
55 31 0.14
56 18 0.08
57 46 0.21
58 37 0.17
59 34 0.15
60 12 0.05
61 4 0.02
62 1 0.00
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.49
Consensus pattern (56 bp):
TTTTATTTAAGAAAAATTGATACTTCAACTTTTCCTTAAAATTTTTTGAAAATTTT
Found at i:25720539 original size:60 final size:59
Alignment explanation
Indices: 25720412--25720612 Score: 190
Period size: 60 Copynumber: 3.5 Consensus size: 59
25720402 TTATTTGCGT
*
25720412 TTTAAAG-AAAATTGATACTTCAACTTTTCCTTAAACATTTTTTGAAATATTTTTTTTA
1 TTTAAAGAAAAATTGATACTTCAACTTTTCCTTAAACATTTTTTAAAATATTTTTTTTA
* * *
25720470 TTT-AAGAAAAATTGATACTTTAACTTTT-TTTGAAAAATATTTTTTAAAATA-TTTTTTTA
1 TTTAAAGAAAAATTGATACTTCAACTTTTCCTT---AAACATTTTTTAAAATATTTTTTTTA
* * * * *
25720529 TTTAAAG-AAAATTAAATATTTCAACTTTTTCCTCAAA-A--TTTT-GAA-ATTATTTTTA
1 TTTAAAGAAAAATT-GATACTTCAAC-TTTTCCTTAAACATTTTTTAAAATATTTTTTTTA
25720584 TTT-AAGAAAAAATTGATACTTCAACTTTT
1 TTTAAAG-AAAAATTGATACTTCAACTTTT
25720613 TCTTTATTTT
Statistics
Matches: 119, Mismatches: 13, Indels: 26
0.75 0.08 0.16
Matches are distributed among these distances:
54 8 0.07
55 21 0.18
56 10 0.08
57 5 0.04
58 24 0.20
59 20 0.17
60 26 0.22
61 4 0.03
62 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (59 bp):
TTTAAAGAAAAATTGATACTTCAACTTTTCCTTAAACATTTTTTAAAATATTTTTTTTA
Found at i:25720694 original size:52 final size:53
Alignment explanation
Indices: 25720523--25720701 Score: 156
Period size: 53 Copynumber: 3.3 Consensus size: 53
25720513 TTAAAATATT
* ** *
25720523 TTTTTATTT--AAAGAAAATTAAATATTTCAACTTTTTCCTCAAAATTTTGAAATTA
1 TTTTTATTTAAAAAGAAAATT-AATACTTCAACTTTTT-CT--TTATTTTTAAATTA
* * *
25720578 TTTTTATTTAAGAA-AAAATTGATACTTCAACTTTTTCTTTATTTTTTTAAA-AA
1 TTTTTATTTAAAAAGAAAATTAATACTTCAACTTTTTCTTTA--TTTTTAAATTA
*
25720631 TTTTTGTTTAAAAAGAAAATTAATGA-TT-AACTTTTTC-TTATTTTTAAATTA
1 TTTTTATTTAAAAAGAAAATTAAT-ACTTCAACTTTTTCTTTATTTTTAAATTA
25720682 TTTTTATTTTAAAAATGAAA
1 TTTTTA-TTTAAAAA-GAAA
25720702 CCCACTCAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
50 8 0.08
51 6 0.06
52 12 0.12
53 26 0.25
54 19 0.18
55 24 0.23
56 6 0.06
57 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (53 bp):
TTTTTATTTAAAAAGAAAATTAATACTTCAACTTTTTCTTTATTTTTAAATTA
Found at i:25722838 original size:16 final size:15
Alignment explanation
Indices: 25722813--25722848 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
25722803 CATAATAAAA
25722813 AATAATTATAAAATT
1 AATAATTATAAAATT
25722828 AATAATATATAAAATT
1 AATAAT-TATAAAATT
25722844 AATAA
1 AATAA
25722849 AAATGATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AATAATTATAAAATT
Found at i:25723064 original size:24 final size:21
Alignment explanation
Indices: 25723037--25723086 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
25723027 TTTTTAGTAC
25723037 ATAAAGATTAATTATTATATATTA
1 ATAAAGATT-A-T-TTATATATTA
* *
25723061 ATAAATATTATTTATATTTTA
1 ATAAAGATTATTTATATATTA
25723082 ATAAA
1 ATAAA
25723087 TATAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 14 0.58
22 1 0.04
23 1 0.04
24 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATAAAGATTATTTATATATTA
Found at i:25723077 original size:21 final size:20
Alignment explanation
Indices: 25723047--25723089 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
25723037 ATAAAGATTA
25723047 ATTATTATATATTAATAAAT
1 ATTATTATATATTAATAAAT
*
25723067 ATTATTTATATTTTAATAAAT
1 ATTA-TTATATATTAATAAAT
25723088 AT
1 AT
25723090 AAATAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTATTATATATTAATAAAT
Found at i:25723934 original size:14 final size:15
Alignment explanation
Indices: 25723915--25723945 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
25723905 TTAACAAGAA
25723915 AAAGAA-GAAAAAAG
1 AAAGAAGGAAAAAAG
25723929 AAAGAAGGAAAAAAG
1 AAAGAAGGAAAAAAG
25723944 AA
1 AA
25723946 GGCTGATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAGAAGGAAAAAAG
Found at i:25732394 original size:26 final size:26
Alignment explanation
Indices: 25732344--25732395 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
25732334 GTTCCCTGAA
* *
25732344 ATCAGACACAGTTTAAGGAATAGGAC
1 ATCAGACACAGTTCAAAGAATAGGAC
25732370 ATCAGACACAGTTGCAAAGAA-AGGAC
1 ATCAGACACAGTT-CAAAGAATAGGAC
25732396 TTCATTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (26 bp):
ATCAGACACAGTTCAAAGAATAGGAC
Found at i:25737276 original size:14 final size:14
Alignment explanation
Indices: 25737257--25737288 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
25737247 TCATAAACGA
*
25737257 ATATATAGATAAAT
1 ATATATAAATAAAT
25737271 ATATATAAATAAAT
1 ATATATAAATAAAT
25737285 ATAT
1 ATAT
25737289 TCATAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
ATATATAAATAAAT
Found at i:25737332 original size:10 final size:10
Alignment explanation
Indices: 25737313--25737362 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
25737303 TAAATGATAA
*
25737313 TTAAACAAAT
1 TTAAATAAAT
25737323 TTAAATAAAT
1 TTAAATAAAT
*
25737333 ATAAATAAATT
1 TTAAATAAA-T
*
25737344 TTTAATAAAT
1 TTAAATAAAT
*
25737354 TAAAATAAA
1 TTAAATAAA
25737363 AGATAAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 25 0.76
11 8 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
TTAAATAAAT
Done.