Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001100.1 Kokia drynarioides strain JFW-HI SEQ_112372, 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: 338068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 45 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36 CACTTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:961 original size:23 final size:23
Alignment explanation
Indices: 913--961 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
903 TAGAGTAGGT
*
913 TATATATTATTTTTATAATATTA
1 TATATATTATTTTTATAATATCA
936 TATATTATTA-TTTTATTAAT-TCA
1 TATA-TATTATTTTTA-TAATATCA
959 TAT
1 TAT
962 TTTAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TATATATTATTTTTATAATATCA
Found at i:1083 original size:61 final size:58
Alignment explanation
Indices: 936--1100 Score: 165
Period size: 61 Copynumber: 2.8 Consensus size: 58
926 TATAATATTA
* * *
936 TATATTATTATTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATGTTATTAAAT
1 TATA-TATTATTTTATTAAAAT-ATA-TTTAATAATAATTATATTAAGAATATGATTAAAT
* * * *
996 TATATATTATTTTATTAAATTGTATTTAGTAATAATTATATT-ATAATATGATTAAAT
1 TATATATTATTTTATTAAAATATATTTAATAATAATTATATTAAGAATATGATTAAAT
*
1053 TATTTAATTTTATTATTATTAAAATATATTTAATAATAATCT-TATTAA
1 TA--T-ATATTATT-TTATTAAAATATATTTAATAATAAT-TATATTAA
1101 AATGTAATAA
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
57 14 0.16
58 17 0.19
59 15 0.17
60 15 0.17
61 26 0.29
62 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (58 bp):
TATATATTATTTTATTAAAATATATTTAATAATAATTATATTAAGAATATGATTAAAT
Found at i:3450 original size:16 final size:16
Alignment explanation
Indices: 3429--3468 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3419 TAAATTATTG
3429 ATTACAACTATATTCC
1 ATTACAACTATATTCC
* * *
3445 ATTACATCTCTATTTC
1 ATTACAACTATATTCC
3461 ATTACAAC
1 ATTACAAC
3469 CGTTTATTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTACAACTATATTCC
Found at i:3841 original size:26 final size:26
Alignment explanation
Indices: 3808--3857 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
3798 ATTAAGTAAC
3808 AATAAAATCAC-AAATAATTTAAATGT
1 AATAAAATCACGAAAT-ATTTAAATGT
3834 AATAAAATCACGAAATATTTAAAT
1 AATAAAATCACGAAATATTTAAAT
3858 TGTCATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.30
Consensus pattern (26 bp):
AATAAAATCACGAAATATTTAAATGT
Found at i:9735 original size:26 final size:26
Alignment explanation
Indices: 9692--9741 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
9682 CAAAATACTA
* *
9692 AAAAAAAAAACAACAAATTTCAAAGG
1 AAAAAAAAAACAAAAAATCTCAAAGG
*
9718 AAAAAAAAAATAAAAAATCTCAAA
1 AAAAAAAAAACAAAAAATCTCAAA
9742 AAATCTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.74, C:0.10, G:0.04, T:0.12
Consensus pattern (26 bp):
AAAAAAAAAACAAAAAATCTCAAAGG
Found at i:10563 original size:29 final size:29
Alignment explanation
Indices: 10481--10740 Score: 188
Period size: 30 Copynumber: 8.7 Consensus size: 29
10471 GAGGTCCTTG
* ** *
10481 AACTTTCCAAAAAAACATATTTAGACCCTTA
1 AACTTTTCAAAATTACAT-TTTA-ACCCCTA
** *
10512 AACTTTTCAAAAATTTGATTTTAACCCCAA
1 AACTTTTC-AAAATTACATTTTAACCCCTA
**
10542 AACTTTTCAAAATTACATTTTAACATCTA
1 AACTTTTCAAAATTACATTTTAACCCCTA
* *
10571 AACTTGTCCAAAATTGCATTTTAA-CCCTCA
1 AACTT-TTCAAAATTACATTTTAACCCCT-A
* *
10601 AACTTTTCCAAAATTACATTTTGATCCCTA
1 AACTTTT-CAAAATTACATTTTAACCCCTA
*
10631 AACTTTTTCTAAAATTGCATTTTAACCCCTA
1 AAC-TTTTC-AAAATTACATTTTAACCCCTA
* * *
10662 AA-TTTCTGTAAAATTACATTTTAACCCTTG
1 AACTTT-T-CAAAATTACATTTTAACCCCTA
* *
10692 AACTTCTCAAAATCT-TATTTTAA-CCCTCA
1 AACTTTTCAAAAT-TACATTTTAACCCCT-A
* *
10721 AAC-TTCCAAAATCACATTTT
1 AACTTTTCAAAATTACATTTT
10741 GATCCTCAAA
Statistics
Matches: 181, Mismatches: 35, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
28 15 0.08
29 42 0.23
30 77 0.43
31 41 0.23
32 6 0.03
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (29 bp):
AACTTTTCAAAATTACATTTTAACCCCTA
Found at i:10584 original size:59 final size:59
Alignment explanation
Indices: 10484--10800 Score: 231
Period size: 60 Copynumber: 5.3 Consensus size: 59
10474 GTCCTTGAAC
** *
10484 TTTCCAAAAAAACATATTTAGACCCTTAAACTTTTCAAAAATTTG-ATTTTAACCC-CAAAACT
1 TTTCCAAAATTACAT-TTTA-ACCC-TAAACTTTTCCAAAA-TTGCATTTTAACCCTC-AAACT
* *
10546 TTT-CAAAATTACATTTTAACATCTAAACTTGTCCAAAATTGCATTTTAACCCTCAAACT
1 TTTCCAAAATTACATTTTAAC-CCTAAACTTTTCCAAAATTGCATTTTAACCCTCAAACT
* *
10605 TTTCCAAAATTACATTTTGATCCCTAAACTTTTTCTAAAATTGCATTTTAACCC-CTAAA-T
1 TTTCCAAAATTACATTTT-AACCCTAAAC-TTTTCCAAAATTGCATTTTAACCCTC-AAACT
** * * *
10665 TTCTGTAAAATTACATTTTAACCCTTGAACTTCT-CAAAATCT-TATTTTAACCCTCAAAC-
1 TT-TCCAAAATTACATTTTAACCC-TAAACTTTTCCAAAAT-TGCATTTTAACCCTCAAACT
* * * * * *** * *
10724 -TTCCAAAATCACATTTTGATCCTCAAACCTTTCTAAAATCATATTTTGACACC-CGAACT
1 TTTCCAAAATTACATTTTAACCCT-AAACTTTTCCAAAATTGCATTTTAAC-CCTCAAACT
*
10783 TTTCCAAAATTACCTTTT
1 TTTCCAAAATTACATTTT
10801 GATCCCAATT
Statistics
Matches: 207, Mismatches: 30, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
56 1 0.00
57 21 0.10
58 21 0.10
59 53 0.26
60 54 0.26
61 54 0.26
62 3 0.01
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (59 bp):
TTTCCAAAATTACATTTTAACCCTAAACTTTTCCAAAATTGCATTTTAACCCTCAAACT
Found at i:10675 original size:61 final size:59
Alignment explanation
Indices: 10510--10740 Score: 201
Period size: 59 Copynumber: 3.9 Consensus size: 59
10500 TTTAGACCCT
* *
10510 TAAACTTTTCAAAAATTTG-ATTTTAACCCCAAAACTTTTCAAAATTACATTTTAACATC
1 TAAACTTTTCAAAAA-TTGCATTTTAACCCCTAAACTTTTCAAAATTACATTTTAACACC
* * *
10569 TAAACTTGTCCAAAATTGCATTTTAA-CCCTCAAACTTTTCCAAAATTACATTTTGATC-CC
1 TAAACTTTTCAAAAATTGCATTTTAACCCCT-AAACTTTT-CAAAATTACATTTT-AACACC
* *
10629 TAAACTTTTTCTAAAATTGCATTTTAACCCCTAAA-TTTCTGTAAAATTACATTTTAAC-CC
1 TAAAC-TTTTCAAAAATTGCATTTTAACCCCTAAACTTT-T-CAAAATTACATTTTAACACC
* * * * *
10689 TTGAACTTCTC-AAAATCT-TATTTTAA-CCCTCAAAC-TTCCAAAATCACATTTT
1 -TAAACTTTTCAAAAAT-TGCATTTTAACCCCT-AAACTTTTCAAAATTACATTTT
10741 GATCCTCAAA
Statistics
Matches: 145, Mismatches: 16, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
57 12 0.08
58 10 0.07
59 45 0.31
60 32 0.22
61 42 0.29
62 4 0.03
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (59 bp):
TAAACTTTTCAAAAATTGCATTTTAACCCCTAAACTTTTCAAAATTACATTTTAACACC
Found at i:10696 original size:91 final size:89
Alignment explanation
Indices: 10481--10740 Score: 233
Period size: 91 Copynumber: 2.9 Consensus size: 89
10471 GAGGTCCTTG
** * **
10481 AACTT-TCCAAAAAAACATATTTAGACCCTTAAACTTTTCAAAAATTTGATTTTAACCCCAAAAC
1 AACTTCTCCAAAATTACAT-TTTA-ACCCTTAAACTTTTCCAAAATTACATTTTAACCCCAAAAC
*
10545 TTTTCAAAATTACATTTTAACATCTA
64 TTTTCAAAATTACATTTTAACACCTA
* * * * * *
10571 AACTTGTCCAAAATTGCATTTTAACCCTCAAACTTTTCCAAAATTACATTTTGATCCCTAAACTT
1 AACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCCAAAAC-T
* *
10636 TTTCTAAAATTGCATTTTAACCCCTA
65 TTTC-AAAATTACATTTTAACACCTA
* ** * * *
10662 AATTTCTGTAAAATTACATTTTAACCCTTGAACTTCT-CAAAATCT-TATTTTAACCCTC-AAAC
1 AACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAAT-TACATTTTAACCC-CAAAAC
* *
10724 -TTCCAAAATCACATTTT
64 TTTTCAAAATTACATTTT
10741 GATCCTCAAA
Statistics
Matches: 138, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
87 11 0.08
88 3 0.02
89 33 0.24
90 32 0.23
91 59 0.43
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (89 bp):
AACTTCTCCAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCCAAAACTT
TTCAAAATTACATTTTAACACCTA
Found at i:10764 original size:30 final size:28
Alignment explanation
Indices: 10692--10772 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 28
10682 TTAACCCTTG
** * *
10692 AACTTCTCAAAATCTTATTTTAACCCTCA
1 AACTTC-CAAAATCACATTTTGATCCTCA
10721 AACTTCCAAAATCACATTTTGATCCTCA
1 AACTTCCAAAATCACATTTTGATCCTCA
* *
10749 AACCTTTCTAAAATCATATTTTGA
1 AA-C-TTCCAAAATCACATTTTGA
10773 CACCCGAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 20 0.45
29 7 0.16
30 17 0.39
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (28 bp):
AACTTCCAAAATCACATTTTGATCCTCA
Found at i:10792 original size:30 final size:30
Alignment explanation
Indices: 10724--10806 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
10714 ACCCTCAAAC
*
10724 TTCCAAAATCACATTTTGATCCTCAAACCT
1 TTCCAAAATCACATTTTGATCCCCAAACCT
* * * *
10754 TTCTAAAATCATATTTTGA-CACCCGAACTT
1 TTCCAAAATCACATTTTGATC-CCCAAACCT
* *
10784 TTCCAAAATTACCTTTTGATCCC
1 TTCCAAAATCACATTTTGATCCC
10807 AATTCCCCGA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
29 1 0.02
30 40 0.95
31 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (30 bp):
TTCCAAAATCACATTTTGATCCCCAAACCT
Found at i:14843 original size:15 final size:14
Alignment explanation
Indices: 14825--14863 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
14815 AATTAGTTTA
14825 TAATTAATTTAATCT
1 TAATTAATTTAAT-T
*
14840 TAATTAATCTAATT
1 TAATTAATTTAATT
14854 TAATATAATT
1 TAAT-TAATT
14864 AAGTTGACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (14 bp):
TAATTAATTTAATT
Found at i:17648 original size:16 final size:16
Alignment explanation
Indices: 17627--17658 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17617 CAAATTACAA
17627 TCATTAAGTTTAACTT
1 TCATTAAGTTTAACTT
17643 TCATTAAGTTTAACTT
1 TCATTAAGTTTAACTT
17659 ATGCCTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
TCATTAAGTTTAACTT
Found at i:19257 original size:3 final size:3
Alignment explanation
Indices: 19249--19283 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19239 TTCTTCAAGA
19249 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
19284 AGGATCTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:20213 original size:26 final size:25
Alignment explanation
Indices: 20184--20240 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
20174 TTAATTAGTA
*
20184 TAAAAAATTAACAATTCAAAATAAAT
1 TAAAAAATTAACAATT-AAAACAAAT
* * *
20210 TAAAAAGTTAATAATTTAAACAAAT
1 TAAAAAATTAACAATTAAAACAAAT
20235 TAAAAA
1 TAAAAA
20241 TTAGGAGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (25 bp):
TAAAAAATTAACAATTAAAACAAAT
Found at i:20214 original size:25 final size:24
Alignment explanation
Indices: 20186--20243 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
20176 AATTAGTATA
*
20186 AAAAATTAACAATTCAAAATAAATT
1 AAAAATTAACAATT-AAAACAAATT
* *
20211 AAAAAGTTAATAATTTAAACAAATT
1 AAAAA-TTAACAATTAAAACAAATT
20236 AAAAATTA
1 AAAAATTA
20244 GGAGAGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 3 0.10
25 18 0.62
26 8 0.28
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAAATTAACAATTAAAACAAATT
Found at i:20222 original size:16 final size:17
Alignment explanation
Indices: 20203--20243 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
20193 AACAATTCAA
*
20203 AATAAATTAAA-AAGTT
1 AATAAATTAAACAAATT
*
20219 AATAATTTAAACAAATT
1 AATAAATTAAACAAATT
20236 AA-AAATTA
1 AATAAATTA
20244 GGAGAGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
AATAAATTAAACAAATT
Found at i:31718 original size:52 final size:52
Alignment explanation
Indices: 31655--32203 Score: 719
Period size: 52 Copynumber: 10.6 Consensus size: 52
31645 TAAATGCAAT
* * *
31655 AGGTCCGATGACTTTGTTTCATCGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTACG
* * * * *
31707 AGGTCTGATGACTATGTTTCGTC-TGAGTATATGAATCATTTACGGATTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTACG
*
31758 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTACG
* *
31810 AGGTCCAATGATTATGTGTCATCGTGAGTATATGAATCCTTTA-AGGATTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACA-GATTACG
* * **
31862 AGGTCCGATGACTATGTGTCATCATGAGTATATGAATCTTTTATGGATTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTACG
* *
31914 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTACG
* * * * ** **
31966 AGGTCTGATGACTATGAGTCATCATGAGTATATGATTCCTTTATGGATTGTG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTACG
* ** *
32018 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATATTTTA-TGCATT-CG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAG-ATTACG
* *
32069 AGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTACG
* * * *
32121 AGGTCTGATGATTATGTGTCATTGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTACG
* *
32173 AGGTCCGATGATTATGTGTCATTGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
32204 TAAATGAGAA
Statistics
Matches: 439, Mismatches: 52, Indels: 12
0.87 0.10 0.02
Matches are distributed among these distances:
51 90 0.21
52 349 0.79
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTACG
Found at i:32174 original size:26 final size:26
Alignment explanation
Indices: 32093--32174 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
32083 TGTGTCATCG
32093 TGAGTATATGAATCCTTTACAGATTA
1 TGAGTATATGAATCCTTTACAGATTA
* * * *
32119 TGAGGTCTGATGATTAT-GTGT-C--ATTG
1 TGA-GTAT-ATGA--ATCCTTTACAGATTA
32145 TGAGTATATGAATCCTTTACAGATTA
1 TGAGTATATGAATCCTTTACAGATTA
32171 TGAG
1 TGAG
32175 GTCCGATGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 16
0.62 0.12 0.25
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 5 0.12
25 3 0.08
26 16 0.40
27 3 0.08
28 5 0.12
29 2 0.05
30 2 0.05
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (26 bp):
TGAGTATATGAATCCTTTACAGATTA
Found at i:36658 original size:16 final size:17
Alignment explanation
Indices: 36637--36668 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
36627 CTTGATCATC
36637 ATAAACACA-ATAATTT
1 ATAAACACATATAATTT
36653 ATAAACACATATAATT
1 ATAAACACATATAATT
36669 GAAGCAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAACACATATAATTT
Found at i:39357 original size:13 final size:13
Alignment explanation
Indices: 39339--39403 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
39329 TTTTTTAGAA
*
39339 AAAGTCAATAGTC
1 AAAGTCAATGGTC
* * *
39352 AAAGTCAACGATA
1 AAAGTCAATGGTC
39365 AAAGTCAATGGTC
1 AAAGTCAATGGTC
*
39378 AACAATCAATGGTC
1 AA-AGTCAATGGTC
39392 AAAGTCAATGGT
1 AAAGTCAATGGT
39404 TAACAGTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 30 0.71
14 12 0.29
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (13 bp):
AAAGTCAATGGTC
Found at i:39386 original size:27 final size:27
Alignment explanation
Indices: 39338--39408 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
39328 GTTTTTTAGA
* *
39338 AAAAGTCAATAGTCAA-AGTCAACGAT
1 AAAAGTCAATGGTCAACAATCAACGAT
* *
39364 AAAAGTCAATGGTCAACAATCAATGGT
1 AAAAGTCAATGGTCAACAATCAACGAT
* *
39391 CAAAGTCAATGGTTAACA
1 AAAAGTCAATGGTCAACA
39409 GTTAACAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
26 15 0.39
27 23 0.61
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.21
Consensus pattern (27 bp):
AAAAGTCAATGGTCAACAATCAACGAT
Found at i:39388 original size:14 final size:14
Alignment explanation
Indices: 39369--39436 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 14
39359 ACGATAAAAG
39369 TCAATGGTCAACAA
1 TCAATGGTCAACAA
*
39383 TCAATGGTCAA-AG
1 TCAATGGTCAACAA
*
39396 TCAATGGTTAACAGTTA
1 TCAATGGTCAACA---A
* *
39413 ACAATTGGTCAACGA
1 TCAA-TGGTCAACAA
39428 TCAATGGTC
1 TCAATGGTC
39437 GGTCAACAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
13 11 0.26
14 17 0.40
15 4 0.10
17 3 0.07
18 7 0.17
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (14 bp):
TCAATGGTCAACAA
Found at i:39464 original size:7 final size:7
Alignment explanation
Indices: 39454--39547 Score: 50
Period size: 7 Copynumber: 15.1 Consensus size: 7
39444 AGTCAATGGT
39454 CGGTCAA
1 CGGTCAA
39461 CGGTCAA
1 CGGTCAA
*
39468 TGGTC-A
1 CGGTCAA
39474 --GTCAA
1 CGGTCAA
39479 CGGTCAA
1 CGGTCAA
*
39486 TGGT---
1 CGGTCAA
39490 CGGTCAA
1 CGGTCAA
*
39497 CGATCAA
1 CGGTCAA
*
39504 TGGTCAA
1 CGGTCAA
*
39511 TGGT---
1 CGGTCAA
39515 CGGTCAA
1 CGGTCAA
39522 CGGTCAA
1 CGGTCAA
*
39529 TGGT---
1 CGGTCAA
39533 CGGTCAA
1 CGGTCAA
39540 CGGTCAA
1 CGGTCAA
39547 C
1 C
39548 TGTCGATTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 24
0.67 0.09 0.24
Matches are distributed among these distances:
4 12 0.18
5 1 0.02
6 1 0.02
7 52 0.79
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (7 bp):
CGGTCAA
Found at i:39490 original size:25 final size:24
Alignment explanation
Indices: 39454--39533 Score: 82
Period size: 25 Copynumber: 3.5 Consensus size: 24
39444 AGTCAATGGT
*
39454 CGGTCAACGGTCAATGGTCAGTCAA
1 CGGTCAATGGTCAATGGTC-GTCAA
39479 CGGTCAATGGTC----G--GTCAA
1 CGGTCAATGGTCAATGGTCGTCAA
*
39497 CGATCAATGGTCAATGGTCGGTCAA
1 CGGTCAATGGTCAATGGTC-GTCAA
39522 CGGTCAATGGTC
1 CGGTCAATGGTC
39534 GGTCAACGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
18 16 0.36
21 1 0.02
22 1 0.02
25 27 0.60
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (24 bp):
CGGTCAATGGTCAATGGTCGTCAA
Found at i:39552 original size:18 final size:18
Alignment explanation
Indices: 39419--39546 Score: 166
Period size: 18 Copynumber: 6.7 Consensus size: 18
39409 GTTAACAATT
*
39419 GGTCAACGATCAATGGTC
1 GGTCAACGGTCAATGGTC
*
39437 GGTCAACAGTCAATGGTC
1 GGTCAACGGTCAATGGTC
39455 GGTCAACGGTCAATGGTC
1 GGTCAACGGTCAATGGTC
*
39473 AGTCAACGGTCAATGGTC
1 GGTCAACGGTCAATGGTC
39491 GGTCAACGATCAATGGTCAATGGTC
1 GGTC-A--A-C---GGTCAATGGTC
39516 GGTCAACGGTCAATGGTC
1 GGTCAACGGTCAATGGTC
39534 GGTCAACGGTCAA
1 GGTCAACGGTCAA
39547 CTGTCGATTA
Statistics
Matches: 98, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
18 77 0.79
19 1 0.01
21 2 0.02
22 2 0.02
24 1 0.01
25 15 0.15
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (18 bp):
GGTCAACGGTCAATGGTC
Found at i:44446 original size:14 final size:13
Alignment explanation
Indices: 44427--44461 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
44417 TTTCTACTCT
44427 TTTTTATGACTATG
1 TTTTTATGA-TATG
*
44441 TTTTTAAGATATG
1 TTTTTATGATATG
44454 TTTTTATG
1 TTTTTATG
44462 CGAGCTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.23, C:0.03, G:0.14, T:0.60
Consensus pattern (13 bp):
TTTTTATGATATG
Found at i:51994 original size:13 final size:13
Alignment explanation
Indices: 51976--52001 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51966 TTACAAGTGA
51976 GGGATGTACTAAT
1 GGGATGTACTAAT
51989 GGGATGTACTAAT
1 GGGATGTACTAAT
52002 TGAGCAGCAA
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:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
GGGATGTACTAAT
Found at i:53010 original size:20 final size:21
Alignment explanation
Indices: 52964--53010 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
52954 TTTTGAAGTG
* *
52964 TTAAAATGATTTTGACTTAGT
1 TTAAAATGATTCTGACATAGT
*
52985 TT-AAATTATTCTGACAT-GT
1 TTAAAATGATTCTGACATAGT
53004 TTAAAAT
1 TTAAAAT
53011 CATTTTAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.18
20 16 0.73
21 2 0.09
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (21 bp):
TTAAAATGATTCTGACATAGT
Found at i:55221 original size:20 final size:20
Alignment explanation
Indices: 55193--55247 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
55183 AAGGCCTGTG
* *
55193 GTATCGATATTTTT-TCACAA
1 GTATTGATATTTTTAT-AAAA
55213 GTATTGATATTTTTATAAAA
1 GTATTGATATTTTTATAAAA
*
55233 GTATTGATAATTTTA
1 GTATTGATATTTTTA
55248 AATTGGTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (20 bp):
GTATTGATATTTTTATAAAA
Found at i:62332 original size:41 final size:41
Alignment explanation
Indices: 62275--62356 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
62265 TGAATGTTCT
62275 TAGTTGTTAAAGCCACTTCTTTTCA-GTCTTTCTAGTTTGTG
1 TAGTTGTTAAAGCCACTTCTTTT-ATGTCTTTCTAGTTTGTG
62316 TAGTTGTTAAAGCCACTTCTTTTATGTCTTTCTAGTTTGTG
1 TAGTTGTTAAAGCCACTTCTTTTATGTCTTTCTAGTTTGTG
62357 AACTTCACGG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 1 0.03
41 39 0.98
ACGTcount: A:0.17, C:0.16, G:0.17, T:0.50
Consensus pattern (41 bp):
TAGTTGTTAAAGCCACTTCTTTTATGTCTTTCTAGTTTGTG
Found at i:62873 original size:39 final size:39
Alignment explanation
Indices: 62817--62924 Score: 117
Period size: 39 Copynumber: 2.8 Consensus size: 39
62807 CCCGAAGTCC
** ** *
62817 TATTCTCGCTCAAGCAGTTTTCAGCAGGATGCATCTCCA
1 TATTCTCAATCAAGCAGTTTTCAGCAAAATCCATCTCCA
** * *
62856 TATTCTCAATCTGGCAGTTTTAAGCAAAATCCATCTCCC
1 TATTCTCAATCAAGCAGTTTTCAGCAAAATCCATCTCCA
**
62895 TATTCTCGCTCAAGCAGTTTTCAGCAAAAT
1 TATTCTCAATCAAGCAGTTTTCAGCAAAAT
62925 ATACCTCAGT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (39 bp):
TATTCTCAATCAAGCAGTTTTCAGCAAAATCCATCTCCA
Found at i:62938 original size:39 final size:38
Alignment explanation
Indices: 62817--62939 Score: 111
Period size: 39 Copynumber: 3.2 Consensus size: 38
62807 CCCGAAGTCC
** *
62817 TATTCTCGCTCAAGCAGTTTTCAGCAGGATGCATCTCCA
1 TATTCTCGCTCAAGCAGTTTTCAGCAAAATACATCT-CA
** ** * * *
62856 TATTCTCAATCTGGCAGTTTTAAGCAAAATCCATCTCCC
1 TATTCTCGCTCAAGCAGTTTTCAGCAAAATACATCT-CA
* *
62895 TATTCTCGCTCAAGCAGTTTTCAGCAAAATATACCTCA
1 TATTCTCGCTCAAGCAGTTTTCAGCAAAATACATCTCA
62933 GTATTCT
1 -TATTCT
62940 GGATATGATA
Statistics
Matches: 65, Mismatches: 18, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
38 1 0.02
39 64 0.98
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (38 bp):
TATTCTCGCTCAAGCAGTTTTCAGCAAAATACATCTCA
Found at i:63260 original size:22 final size:22
Alignment explanation
Indices: 63235--63284 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
63225 AAATAAAGTA
**
63235 TTTTCAGCTTTTCCTTTTTTTT
1 TTTTCAGCTTTTCCGGTTTTTT
* *
63257 TTTTCCAGTTTTTCGGGTTTTTT
1 TTTT-CAGCTTTTCCGGTTTTTT
63280 TTTTC
1 TTTTC
63285 TTTGCTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.04, C:0.16, G:0.10, T:0.70
Consensus pattern (22 bp):
TTTTCAGCTTTTCCGGTTTTTT
Found at i:84818 original size:3 final size:3
Alignment explanation
Indices: 84810--84861 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
84800 CTGGGAAACA
* * *
84810 TCT TCT TCT TTT TCT T-T CTCC TCT TCT TTT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT
84855 TCT TCT T
1 TCT TCT T
84862 TTTCAATACC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:84836 original size:18 final size:19
Alignment explanation
Indices: 84813--84862 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
84803 GGAAACATCT
84813 TCTTCTTTTTCTTTC-TCC
1 TCTTCTTTTTCTTTCTTCC
*
84831 TCTTCTTTTTC-TTCTTCT
1 TCTTCTTTTTCTTTCTTCC
*
84849 TCTTCTTCTTCTTT
1 TCTTCTTTTTCTTT
84863 TTCAATACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 3 0.11
18 23 0.82
19 2 0.07
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTCTTTTTCTTTCTTCC
Found at i:85607 original size:11 final size:11
Alignment explanation
Indices: 85591--85616 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
85581 ATTGCGTCGA
85591 CATCAGTACGT
1 CATCAGTACGT
85602 CATCAGTACGT
1 CATCAGTACGT
85613 CATC
1 CATC
85617 CTTTCAGTAT
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:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (11 bp):
CATCAGTACGT
Found at i:100229 original size:2 final size:2
Alignment explanation
Indices: 100222--100246 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
100212 TTGCATTTTC
100222 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
100247 ATGTTAGTGT
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:110459 original size:17 final size:17
Alignment explanation
Indices: 110424--110462 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
110414 ATTGTCATCA
*
110424 CATTTTAATTGTCCCTG
1 CATTTTAATTGTCCATG
* *
110441 CATTTTATTTGTCGATG
1 CATTTTAATTGTCCATG
110458 CATTT
1 CATTT
110463 GCATTGTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (17 bp):
CATTTTAATTGTCCATG
Found at i:113362 original size:18 final size:19
Alignment explanation
Indices: 113325--113364 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
113315 GAAAAATTAT
113325 TTTTATTTCTTAAGTAATA
1 TTTTATTTCTTAAGTAATA
**
113344 TTTTATTT-TTATTTAATA
1 TTTTATTTCTTAAGTAATA
113362 TTT
1 TTT
113365 AGTAAACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTATTTCTTAAGTAATA
Found at i:113387 original size:28 final size:26
Alignment explanation
Indices: 113348--113400 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
113338 GTAATATTTT
*
113348 ATTTTTATTTAATATTTAGTAAACTTAC
1 ATTTTTATTTAAAATTT--TAAACTTAC
113376 ATTTTT-TCTTAAAATTTTAAACTTA
1 ATTTTTAT-TTAAAATTTTAAACTTA
113401 AATAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 8 0.35
27 1 0.04
28 14 0.61
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.55
Consensus pattern (26 bp):
ATTTTTATTTAAAATTTTAAACTTAC
Found at i:115400 original size:26 final size:26
Alignment explanation
Indices: 115371--115430 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
115361 GGAACTTGTT
* *
115371 CAGAATTATTGCTGCATGAA-TATGTC
1 CAGAATTATCGCTGCAT-AAGTAGGTC
*
115397 CAGAGTTATCGCTGCATAAGTAGGTC
1 CAGAATTATCGCTGCATAAGTAGGTC
*
115423 TAGAATTA
1 CAGAATTA
115431 CGCCCAGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.32
Consensus pattern (26 bp):
CAGAATTATCGCTGCATAAGTAGGTC
Found at i:117713 original size:17 final size:17
Alignment explanation
Indices: 117683--117716 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
117673 GTACTCGAAA
*
117683 ACAATAATGCGTTGTGC
1 ACAATAATACGTTGTGC
*
117700 ACAATAATATGTTGTGC
1 ACAATAATACGTTGTGC
117717 TGATGAGTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (17 bp):
ACAATAATACGTTGTGC
Found at i:117910 original size:16 final size:15
Alignment explanation
Indices: 117877--117919 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
117867 TCTAAGTATT
*
117877 CTAAACTAAATTAAA
1 CTAAATTAAATTAAA
*
117892 CTAAGTTAAATTAAAA
1 CTAAATTAAATT-AAA
117908 CTAAATTAAATT
1 CTAAATTAAATT
117920 CTCTTGCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (15 bp):
CTAAATTAAATTAAA
Found at i:131367 original size:23 final size:23
Alignment explanation
Indices: 131340--131385 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
131330 CAATTATCTC
131340 AAAAATATAAAAATTACAAGATA
1 AAAAATATAAAAATTACAAGATA
131363 AAAAATATAAAAATTACAAGATA
1 AAAAATATAAAAATTACAAGATA
131386 TAAGCTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAAATATAAAAATTACAAGATA
Found at i:135337 original size:19 final size:19
Alignment explanation
Indices: 135310--135355 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
135300 ATGCCATAGG
135310 ATGCACTTCACGTGCCAGT
1 ATGCACTTCACGTGCCAGT
* **
135329 ATGCGCTTCGTGTGCCAGT
1 ATGCACTTCACGTGCCAGT
*
135348 TTGCACTT
1 ATGCACTT
135356 TATGTTCCAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.15, C:0.28, G:0.24, T:0.33
Consensus pattern (19 bp):
ATGCACTTCACGTGCCAGT
Found at i:160272 original size:52 final size:52
Alignment explanation
Indices: 160157--160491 Score: 354
Period size: 52 Copynumber: 6.5 Consensus size: 52
160147 TGCATATTTA
** * * * *
160157 ATACTCACGATGACACACAGTCATCGGACCT-TTAATCCGTAGAGGGA-TCAT
1 ATACTCACGATGACACGTAGTCATCAGACCTCATAATCCATA-AAGGATTCAT
* ** * *
160208 ATACTCATGATGACAAATAATCATCAGACCTCATAATCCATAAAGGACTT-TT
1 ATACTCACGATGACACGTAGTCATCAGACCTCATAATCCATAAAGGA-TTCAT
* ** *
160260 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCATAAAAGATTCAT
1 ATACTCACGATGACACGTAGTCATCAGACCTCATAATCCATAAAGGATTCAT
* * * **
160312 ATACTCACGATAACATGTAGTCATCAGACCTTATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCAGACCTCATAATCCATAAAGGATTCAT
* * * *
160364 ATACTCACAATGACACGTAGTCATCGGACCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCAGACCTCATAATCCATAAAGGATTCAT
* *
160416 ACACTCATGATGACACGTAGTCATC-GAACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACGTAGTCATCAG-ACCTCATAATCCATAAAGGATTCAT
* * *
160468 ATACTCACAATTACACATAGTCAT
1 ATACTCACGATGACACGTAGTCAT
160492 TGGACCTTTT
Statistics
Matches: 237, Mismatches: 42, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
51 33 0.14
52 203 0.86
53 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACGTAGTCATCAGACCTCATAATCCATAAAGGATTCAT
Found at i:160348 original size:104 final size:104
Alignment explanation
Indices: 160157--160498 Score: 422
Period size: 104 Copynumber: 3.3 Consensus size: 104
160147 TGCATATTTA
* * * *
160157 ATACTCACGATGACACACAGTCATCGGACCT-TTAATCCGTAGAGGGA-TCATATACTCATGATG
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTA-AAGGATTCATATACTCATGATG
* * *
160220 ACAAATAATCATCAGACCTCATAATCCATAAAGGACTT-TT
65 ACAAGTAGTCATCAGACCTCATAATCCATAAAGGA-TTCAT
* * * * * *
160260 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCATAAAAGATTCATATACTCACGATAA
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCATGATGA
* * **
160325 CATGTAGTCATCAGACCTTATAATCTGTAAAGGATTCAT
66 CAAGTAGTCATCAGACCTCATAATCCATAAAGGATTCAT
* * *
160364 ATACTCACAATGACACGTAGTCATCGGACCTCATAATTCGTAAAGGATTCATACACTCATGATGA
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCATGATGA
*
160429 CACGTAGTCATC-GAACCTCATAATCCATAAAGGATTCAT
66 CAAGTAGTCATCAG-ACCTCATAATCCATAAAGGATTCAT
* *
160468 ATACTCACAATTACACATAGTCATTGGACCT
1 ATACTCACAATGACACATAGTCATCGGACCT
160499 TTTTCATTTA
Statistics
Matches: 204, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
103 35 0.17
104 169 0.83
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.27
Consensus pattern (104 bp):
ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCATGATGA
CAAGTAGTCATCAGACCTCATAATCCATAAAGGATTCAT
Found at i:160447 original size:156 final size:155
Alignment explanation
Indices: 160157--160500 Score: 404
Period size: 156 Copynumber: 2.2 Consensus size: 155
160147 TGCATATTTA
* * * **
160157 ATACTCACGATGACACACAGTCATCGGACCTTTAATCCGTAGAGGGATCATATACTCATGATGAC
1 ATACTCACGATAACACACAGTCATCAGACCTTTAATCCGTAGAAGGATCATATACTCACAATGAC
* * * *
160222 AAATAATCATCAGACCTCATAATCCATAAAGGACTTTTATACTCACGATGACACATAGTCATTGG
66 AAATAATCATCAGACCTCATAATCCATAAAGGACTTATACACTCACGATGACACATAGTCATCGA
160287 ACCTCATAATCCATAAAAGATTCAT
131 ACCTCATAATCCATAAAAGATTCAT
*** *
160312 ATACTCACGATAACATGTAGTCATCAGACCTTATAATCTGTA-AAGGATTCATATACTCACAATG
1 ATACTCACGATAACACACAGTCATCAGACCTT-TAATCCGTAGAAGGA-TCATATACTCACAATG
** * * * * * *
160376 ACACGTAGTCATCGGACCTCATAATTCGTAAAGGA-TTCATACACTCATGATGACACGTAGTCAT
64 ACAAATAATCATCAGACCTCATAATCCATAAAGGACTT-ATACACTCACGATGACACATAGTCAT
*
160440 CGAACCTCATAATCCATAAAGGATTCAT
128 CGAACCTCATAATCCATAAAAGATTCAT
* * * **
160468 ATACTCACAATTACACATAGTCATTGGACCTTT
1 ATACTCACGATAACACACAGTCATCAGACCTTT
160501 TTCATTTACG
Statistics
Matches: 158, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
155 34 0.22
156 124 0.78
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (155 bp):
ATACTCACGATAACACACAGTCATCAGACCTTTAATCCGTAGAAGGATCATATACTCACAATGAC
AAATAATCATCAGACCTCATAATCCATAAAGGACTTATACACTCACGATGACACATAGTCATCGA
ACCTCATAATCCATAAAAGATTCAT
Found at i:178375 original size:44 final size:44
Alignment explanation
Indices: 178306--178393 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
178296 ATTATTGACA
* *
178306 TAGAAAGCATTCTCCGTGTGTTGTGGACAATCTTCATAACTGTG
1 TAGAAAGCATTCTCCATGTGCTGTGGACAATCTTCATAACTGTG
178350 TAGAAAGCATTCTCCATGTGCTGTGGACAATCTTCATAACTGTG
1 TAGAAAGCATTCTCCATGTGCTGTGGACAATCTTCATAACTGTG
178394 GTTGTCACCG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (44 bp):
TAGAAAGCATTCTCCATGTGCTGTGGACAATCTTCATAACTGTG
Found at i:186620 original size:23 final size:20
Alignment explanation
Indices: 186576--186620 Score: 54
Period size: 23 Copynumber: 2.1 Consensus size: 20
186566 AGTAGAAAAT
*
186576 TAAATAAATTAATGCACGAA
1 TAAATAAATTAATGCACAAA
186596 TAAATAAATTTAATATGCACAAA
1 TAAATAAA-TT-A-ATGCACAAA
186619 TA
1 TA
186621 CTAAAAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 2 0.10
22 1 0.05
23 10 0.48
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.29
Consensus pattern (20 bp):
TAAATAAATTAATGCACAAA
Found at i:187373 original size:20 final size:21
Alignment explanation
Indices: 187348--187389 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
187338 GAGCTTATGA
*
187348 TTTATCT-TACTTTAAAATTT
1 TTTATCTAAACTTTAAAATTT
*
187368 TTTATCTAAAGTTTAAAATTT
1 TTTATCTAAACTTTAAAATTT
187389 T
1 T
187390 CAAAATCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTATCTAAACTTTAAAATTT
Found at i:193944 original size:63 final size:63
Alignment explanation
Indices: 193841--193971 Score: 246
Period size: 63 Copynumber: 2.1 Consensus size: 63
193831 AAATGCAATA
*
193841 GAGT-TGCTCATAAACTCGGTAGGATTGCTAGTGATAATCGTTGTAATTTTACTTTCGATATG
1 GAGTATGCTCATAAACTCAGTAGGATTGCTAGTGATAATCGTTGTAATTTTACTTTCGATATG
193903 GAGTATGCTCATAAACTCAGTAGGATTGCTAGTGATAATCGTTGTAATTTTACTTTCGATATG
1 GAGTATGCTCATAAACTCAGTAGGATTGCTAGTGATAATCGTTGTAATTTTACTTTCGATATG
193966 GAGTAT
1 GAGTAT
193972 CCTAGCGATA
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 4 0.06
63 63 0.94
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (63 bp):
GAGTATGCTCATAAACTCAGTAGGATTGCTAGTGATAATCGTTGTAATTTTACTTTCGATATG
Found at i:195181 original size:144 final size:147
Alignment explanation
Indices: 194953--195310 Score: 503
Period size: 143 Copynumber: 2.4 Consensus size: 147
194943 TTTTCAAAAC
* * *
194953 AAAATCACTATTTTTCTTAAAAATTAAAACTTTTATTTTGAAATAATTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTTCTTAAAACTCAAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTTT
*
195018 GTTTAAAAATTTAAATTTTTTCTTTAAAATGACT-AAAAA-A-ATTTTTATTTTTAAAAATCTAA
66 GTTTAAAAATTTAAA-TTTTTCCTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATCTAA
*
195080 A-CTTTATTTTTTTAATG
130 ATCTTTATTTTTTTAAAG
* * * *
195097 AAAATCACTATTTTTCTTAAAACTCCAAATTTTTATTTCAAAATAATT-AAAAAATCAAATCTTT
1 AAAATCACTATTTTTCTTAAAACTCAAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTTT
195161 GTTTAAAAATTTAAACTTTTTCCTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATCTAA
66 GTTTAAAAATTTAAA-TTTTTCCTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATCTAA
*
195226 ACTTTCTTTTTTTTTTTAAAG
130 A---TCTTTATTTTTTTAAAG
* ** *
195247 AAAATCACAATTTTT-TTAAAACTCAAAACTTTTATTTCGAAATTGTTAAAAAAATCAATACTTT
1 AAAATCACTATTTTTCTTAAAACTCAAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTTT
195311 TCCCAAGATC
Statistics
Matches: 187, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
143 47 0.25
144 47 0.25
145 1 0.01
146 23 0.12
149 27 0.14
150 42 0.22
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (147 bp):
AAAATCACTATTTTTCTTAAAACTCAAAACTTTTATTTCGAAATAATTAAAAAAATCAAAACTTT
GTTTAAAAATTTAAATTTTTCCTTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATCTAAA
TCTTTATTTTTTTAAAG
Found at i:198156 original size:11 final size:11
Alignment explanation
Indices: 198142--198171 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
198132 AAAGATTACT
198142 AAAAAGAAAAG
1 AAAAAGAAAAG
198153 AAAAAGAAAAG
1 AAAAAGAAAAG
198164 AAAAAGAA
1 AAAAAGAA
198172 GTAGCCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:213898 original size:161 final size:161
Alignment explanation
Indices: 213708--214034 Score: 627
Period size: 161 Copynumber: 2.0 Consensus size: 161
213698 TTTACACCAC
*
213708 AAACCGTATGATCATAAAACTCATGTAGCCACTCTTCAAAGATGGCATTCAAATGATTCAGGTTC
1 AAACCGTATGATCATAAAACTCATGTAGCCACTCTTAAAAGATGGCATTCAAATGATTCAGGTTC
*
213773 AGGTCTAAATCTGAACATTTGCAATCCGTTCCTTTACTCGAACTATGGCCTATGTTTCCATAGTC
66 AGGTCTAAATCTGAACATTTGCAATCCGTTCCTTTACTCAAACTATGGCCTATGTTTCCATAGTC
213838 CGATCATCCAATGGTAGATCTAAGCCAACTA
131 CGATCATCCAATGGTAGATCTAAGCCAACTA
213869 AAACCGTATGATCATAAAACTCATGTAGCCACTCTTAAAAGATGGCATTCAAATGATTCAGGTTC
1 AAACCGTATGATCATAAAACTCATGTAGCCACTCTTAAAAGATGGCATTCAAATGATTCAGGTTC
213934 AGGTCTAAATCTGAACATTTGCAATCCGTTCCTTTACTCAAACTATGGCCTATGTTTCCATAGTC
66 AGGTCTAAATCTGAACATTTGCAATCCGTTCCTTTACTCAAACTATGGCCTATGTTTCCATAGTC
*
213999 CGATCATCCAATGGTTGATCTAAGCCAACTA
131 CGATCATCCAATGGTAGATCTAAGCCAACTA
214030 AAACC
1 AAACC
214035 AACAAGGTTG
Statistics
Matches: 163, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 163 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.30
Consensus pattern (161 bp):
AAACCGTATGATCATAAAACTCATGTAGCCACTCTTAAAAGATGGCATTCAAATGATTCAGGTTC
AGGTCTAAATCTGAACATTTGCAATCCGTTCCTTTACTCAAACTATGGCCTATGTTTCCATAGTC
CGATCATCCAATGGTAGATCTAAGCCAACTA
Found at i:217733 original size:15 final size:15
Alignment explanation
Indices: 217701--217734 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
217691 CAAAATTTTC
**
217701 TAAACCCTAAATCTT
1 TAAACCCTAAATAAT
217716 TAAACCCTAAATAAT
1 TAAACCCTAAATAAT
217731 TAAA
1 TAAA
217735 AACCTAAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAACCCTAAATAAT
Found at i:227084 original size:10 final size:10
Alignment explanation
Indices: 227069--227102 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
227059 ATTAAAAAGA
227069 ATCAAATAAG
1 ATCAAATAAG
227079 ATCAAAT-AG
1 ATCAAATAAG
227088 AATCAAATAAG
1 -ATCAAATAAG
227099 ATCA
1 ATCA
227103 GATATTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.21
Consensus pattern (10 bp):
ATCAAATAAG
Found at i:227328 original size:15 final size:15
Alignment explanation
Indices: 227308--227338 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
227298 AATTATTTAG
227308 TATACTAATTTAATT
1 TATACTAATTTAATT
*
227323 TATACTAATTTGATT
1 TATACTAATTTAATT
227338 T
1 T
227339 GATCCTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (15 bp):
TATACTAATTTAATT
Found at i:228310 original size:31 final size:30
Alignment explanation
Indices: 228272--228335 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
228262 TACATAATAG
* *
228272 AAAATAATATATACATAGAATACAATAAAAT
1 AAAATAATATACACATAGAATAAAAT-AAAT
* *
228303 AAAATAATATACATATAGGATAAAATAAAT
1 AAAATAATATACACATAGAATAAAATAAAT
228333 AAA
1 AAA
228336 GAAAAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (30 bp):
AAAATAATATACACATAGAATAAAATAAAT
Found at i:228460 original size:30 final size:30
Alignment explanation
Indices: 228397--228597 Score: 151
Period size: 30 Copynumber: 6.8 Consensus size: 30
228387 GGTTAAATCA
* * *
228397 GAATTTTTGGAAA-TTTGGGGGTTAAAGTT
1 GAATTTTTGGAAATTTTAGGGGTCAAATTT
*
228426 GAATTTTTGGAAATTTTAGGGATCAAATTT
1 GAATTTTTGGAAATTTTAGGGGTCAAATTT
* * * * *
228456 GAATTTTTAGAAA-ATTCGGGGTTAATTTT
1 GAATTTTTGGAAATTTTAGGGGTCAAATTT
* *
228485 GAATTTTTAGAAAATTTT-GGGGTCAAATTC
1 GAATTTTT-GGAAATTTTAGGGGTCAAATTT
* * * *
228515 AAATTTTTGGAAATTTT-GATGGTCGAATTC
1 GAATTTTTGGAAATTTTAG-GGGTCAAATTT
* * *
228545 AAATTTTTGGAAAGTTTAGGGGTCAAAATAT
1 GAATTTTTGGAAATTTTAGGGGTC-AAATTT
* * *
228576 -AATTTTTAGATAGTTTAGGGGT
1 GAATTTTTGGAAATTTTAGGGGT
228598 TAAAAAAATT
Statistics
Matches: 139, Mismatches: 27, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
29 41 0.29
30 92 0.66
31 6 0.04
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (30 bp):
GAATTTTTGGAAATTTTAGGGGTCAAATTT
Found at i:228478 original size:59 final size:59
Alignment explanation
Indices: 228397--228527 Score: 165
Period size: 59 Copynumber: 2.2 Consensus size: 59
228387 GGTTAAATCA
* * * *
228397 GAATTTTTGGAAATTTGGGGGTTAAAGTTGAATTTTT-GGAAATTTTAGGGATCAAATTT
1 GAATTTTTGGAAAATTCGGGGTTAAAGTTGAATTTTTAGAAAATTTT-GGGATCAAATTC
* ** *
228456 GAATTTTTAGAAAATTCGGGGTTAATTTTGAATTTTTAGAAAATTTTGGGGTCAAATTC
1 GAATTTTTGGAAAATTCGGGGTTAAAGTTGAATTTTTAGAAAATTTTGGGATCAAATTC
*
228515 AAATTTTTGGAAA
1 GAATTTTTGGAAA
228528 TTTTGATGGT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
59 53 0.87
60 8 0.13
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (59 bp):
GAATTTTTGGAAAATTCGGGGTTAAAGTTGAATTTTTAGAAAATTTTGGGATCAAATTC
Found at i:229828 original size:19 final size:19
Alignment explanation
Indices: 229803--229846 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
229793 TTACATTTAT
229803 AAAATAAATAAT-AAAATAA
1 AAAATAAA-AATGAAAATAA
*
229822 GAAATAAAAATGAAAATAA
1 AAAATAAAAATGAAAATAA
229841 AAAATA
1 AAAATA
229847 GTTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (19 bp):
AAAATAAAAATGAAAATAA
Found at i:230337 original size:40 final size:39
Alignment explanation
Indices: 230265--230402 Score: 161
Period size: 40 Copynumber: 3.5 Consensus size: 39
230255 ATAGCTTTAA
* *
230265 AGGTAAAAGATTAGATTG-CTTTAATCTGCCCCATGGTCG
1 AGGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGGTCG
* **
230304 AGGTAAGAGATTGACTGGTCTTCAATCTGCCCCATGGTTA
1 AGGTAAAAGATTGA-TGGTCTTCAATCTGCCCCATGGTCG
* *
230344 AGGTAAAAGATTGGATGGTCTTCAATCTGCCCAATGGCCG
1 AGGTAAAAGATT-GATGGTCTTCAATCTGCCCCATGGTCG
*
230384 GGGTAAAAGATTGGATGGT
1 AGGTAAAAGATT-GATGGT
230403 TGTAACTTCA
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.02
39 13 0.15
40 68 0.80
41 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (39 bp):
AGGTAAAAGATTGATGGTCTTCAATCTGCCCCATGGTCG
Found at i:230476 original size:50 final size:50
Alignment explanation
Indices: 230421--230526 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 50
230411 CACTCTACTT
* * *
230421 CAGCTTCAAGAGTATAAGATTCGTCC-TTGCGGCTTCAATTTGCCCCTCTA
1 CAGCTTCAAGAGAATAAGATTCG-CCATTGCAGCTTCAATCTGCCCCTCTA
* * * *
230471 CAGCTTTAGGTGAATGAGATTCGCCATTGCAGCTTCAATCTGCCCCTCTA
1 CAGCTTCAAGAGAATAAGATTCGCCATTGCAGCTTCAATCTGCCCCTCTA
230521 CAGCTT
1 CAGCTT
230527 TAGGTATATG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 2 0.04
50 46 0.96
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (50 bp):
CAGCTTCAAGAGAATAAGATTCGCCATTGCAGCTTCAATCTGCCCCTCTA
Found at i:230527 original size:50 final size:50
Alignment explanation
Indices: 230437--230578 Score: 173
Period size: 50 Copynumber: 2.8 Consensus size: 50
230427 CAAGAGTATA
* *
230437 AGATTCGTCC-TTGCGGCTTCAATTTGCCCCTCTACAGCTTTAGGTGA-ATG
1 AGATTCG-CCATTGCAGCTTCAATCTGCCCCTCTACAGCTTTAGGT-ATATG
230487 AGATTCGCCATTGCAGCTTCAATCTGCCCCTCTACAGCTTTAGGTATATG
1 AGATTCGCCATTGCAGCTTCAATCTGCCCCTCTACAGCTTTAGGTATATG
* * ** *
230537 AGATTTGCCATTG-TGACTTCAATCTGTTCCTCTACAACTTTA
1 AGATTCGCCATTGCAG-CTTCAATCTGCCCCTCTACAGCTTTA
230579 AGGGTATAGG
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
49 4 0.05
50 78 0.95
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (50 bp):
AGATTCGCCATTGCAGCTTCAATCTGCCCCTCTACAGCTTTAGGTATATG
Found at i:242950 original size:39 final size:37
Alignment explanation
Indices: 242830--242955 Score: 89
Period size: 39 Copynumber: 3.3 Consensus size: 37
242820 CCTGTCGCGG
* * *
242830 GGTAAGAGATTAGCTGATGGTGATCGGCCCCAAGG-TCGA
1 GGTAAAAGATT-GCAGATGGTGATCTG-CCC-AGGCTCGA
*
242869 GGTAAAAGA-T-CAGATGGCTGTAATCTACCCAGGCTC-A
1 GGTAAAAGATTGCAGATGG-TG--ATCTGCCCAGGCTCGA
* *
242906 GGGTAAGAGATTGGCCGATGGTGATCTGCCCTAGGCTCGA
1 -GGTAAAAGATT-GCAGATGGTGATCTGCCC-AGGCTCGA
242946 GGTAAAAGAT
1 GGTAAAAGAT
242956 CGGATGGCTG
Statistics
Matches: 69, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
36 6 0.09
37 6 0.09
38 21 0.30
39 27 0.39
40 3 0.04
41 6 0.09
ACGTcount: A:0.28, C:0.18, G:0.33, T:0.21
Consensus pattern (37 bp):
GGTAAAAGATTGCAGATGGTGATCTGCCCAGGCTCGA
Found at i:243060 original size:86 final size:86
Alignment explanation
Indices: 242924--243314 Score: 239
Period size: 78 Copynumber: 4.8 Consensus size: 86
242914 GATTGGCCGA
* * * * *
242924 TGGTGATCTGCCCTAGGCTCGAGGTAAAAGATCGGATGGCTGCAAACTACCTCAGGCTCGGGGTA
1 TGGTGATCTGCCCTAAGCTCGAGGTAAAAGATCGGATGACTGCAAACTACCCCAAGCTCGAGGTA
242989 AGAGATTAAAAGATTGACTGG
66 AGAGATTAAAAGATTGACTGG
* * *
243010 TGGTGATCTGTCCC-AAGCTCGGGGTAAAAGATCGGATGATTGCAATCTACCCCAAGCTCGAGGT
1 TGGTGATCTG-CCCTAAGCTCGAGGTAAAAGATCGGATGACTGCAAACTACCCCAAGCTCGAGGT
*
243074 AAGAGA-T------TT-ACTGA
65 AAGAGATTAAAAGATTGACTGG
* * * * * *
243088 TGGGGATCTG-CCTCAAGCTCG-GCATAAAAGATCAGATGGCTGCAATCTACCACAAGCTC-A-G
1 TGGTGATCTGCCCT-AAGCTCGAG-GTAAAAGATCGGATGACTGCAAACTACCCCAAGCTCGAGG
* *
243149 ---G-G--TAAGAGATTGACTGA
64 TAAGAGATTAAAAGATTGACTGG
* * * *
243166 TGGTGATCTG-CCTCAAGCTC-AGGGTAAAAGATTGGATTG-CTGCAATCTGCCCTAAGCTC---
1 TGGTGATCTGCCCT-AAGCTCGA-GGTAAAAGATCGGA-TGACTGCAAACTACCCCAAGCTCGAG
* *
243225 -T-AG-G--TAAGAGATTGACTGA
63 GTAAGAGATTAAAAGATTGACTGG
* * * * * * *
243244 TGGTGATTTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTACAATCTGCCCCAAGCTCGAGGTA
1 TGGTGATCTGCCCTAAGCTCGAGGTAAAAGATCGGATGACTGCAAACTACCCCAAGCTCGAGGTA
*
243309 AAAGAT
66 AGAGAT
243315 CGGATGACGA
Statistics
Matches: 249, Mismatches: 29, Indels: 54
0.75 0.09 0.16
Matches are distributed among these distances:
71 1 0.00
72 1 0.00
73 1 0.00
76 3 0.01
77 6 0.02
78 165 0.66
79 7 0.03
82 1 0.00
83 1 0.00
84 1 0.00
85 1 0.00
86 58 0.23
87 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (86 bp):
TGGTGATCTGCCCTAAGCTCGAGGTAAAAGATCGGATGACTGCAAACTACCCCAAGCTCGAGGTA
AGAGATTAAAAGATTGACTGG
Found at i:243064 original size:39 final size:39
Alignment explanation
Indices: 243015--243667 Score: 303
Period size: 39 Copynumber: 16.7 Consensus size: 39
243005 ACTGGTGGTG
* *
243015 ATCTGTCCCAAGCTCGGGGTAAAAGATCGGATGATTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATTGTA
* * * ** * **
243054 ATCTACCCCAAGCTCGAGGTAAGAGAT-TTACTGATGGGG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGA-TGATTGTA
* ** * ** *
243093 ATCTGCCTCAAGCTCGGCATAAAAGATCAGATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATTGTA
* * * * * * *
243132 ATCTACCACAAGCTCAGGGTAAGAGAT-TGACTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGA-TGATTGTA
* * * * *
243171 ATCTGCCTCAAGCTCAGGGTAAAAGATTGGATTG-CTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGA-TGATTGTA
* ** * * * *
243210 ATCTGCCCTAAGCTCTAGGTAAGAGAT-TGACTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGA-TGATTGTA
* ** **
243249 ATTTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTACA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATTGTA
* *
243288 ATCTGCCCCAAGCTCGAGGTAAAAGATCGGATGA-CGATA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATTG-TA
* * * * * ** *
243327 ATCTGCCTCAAGCTCGGAGTAAGAGATTGGCTGAAAGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATTGTA
* * * *
243366 ATCTGCCCCAAGCTCGCGGTAAAAGATCAGAAAGCTT-TA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATC-GGATGATTGTA
* * * * *
243405 ATCTGCCTCAAGCTCGGGGTAAGAGATTGGTTGATAGTA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATTGTA
* **
243444 ATCTTCCTTAAGCTCGGGGTAAAAGATCGGATGATTGTA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATTGTA
* * *** * * * * *
243483 ATCTGCCCTAGGCTCAAAGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATTGTA
* * * * ** ** *
243522 ATTTGCCCTAAGCTTGGGGTAAAATATTTGATGGCTGCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATTGTA
* * * * * * *
243561 ATCTGCCCTAAGCTCGAGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATTGTA
* * * * ** **
243600 ATCTG-TCCTAGTCTCAGAGTAAAAGATCGGATGGCTACA
1 ATCTGCCCCAAG-CTCGGGGTAAAAGATCGGATGATTGTA
* *
243639 ATCTGCCCCAGGCTCGGGGTAAGAGATCG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCG
243668 AAATCTTCAA
Statistics
Matches: 436, Mismatches: 166, Indels: 24
0.70 0.27 0.04
Matches are distributed among these distances:
38 13 0.03
39 410 0.94
40 13 0.03
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGATTGTA
Found at i:243132 original size:78 final size:78
Alignment explanation
Indices: 242999--243353 Score: 428
Period size: 78 Copynumber: 4.6 Consensus size: 78
242989 AGAGATTAAA
* **
242999 AGATTGACTGGTGGTGATCTGTCC-CAAGCTCGGGGTAAAAGATCGGATGATTGCAATCTACCCC
1 AGATTGACTGATGGTGATCTG-CCTCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCCC
243063 AAGCTCGAGGTAAG
65 AAGCTCGAGGTAAG
* * ** * *
243077 AGATTTACTGATGGGGATCTGCCTCAAGCTCGGCATAAAAGATCAGATGGCTGCAATCTACCACA
1 AGATTGACTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCCCA
243142 AGCTC-AGGGTAAG
66 AGCTCGA-GGTAAG
* * * * *
243155 AGATTGACTGATGGTGATCTGCCTCAAGCTCAGGGTAAAAGATTGGATTGCTGCAATCTGCCCTA
1 AGATTGACTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCCCA
*
243220 AGCTCTAGGTAAG
66 AGCTCGAGGTAAG
* * * *
243233 AGATTGACTGATGGTGATTTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTACAATCTGCCCCA
1 AGATTGACTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCCCA
*
243298 AGCTCGAGGTAAA
66 AGCTCGAGGTAAG
* * * * * *
243311 AGATCGGA-TGACGATAATCTGCCTCAAGCTCGGAGTAAGAGAT
1 AGAT-TGACTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGAT
243354 TGGCTGAAAG
Statistics
Matches: 236, Mismatches: 37, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
77 3 0.01
78 230 0.97
79 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (78 bp):
AGATTGACTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTACCCCA
AGCTCGAGGTAAG
Found at i:243354 original size:156 final size:155
Alignment explanation
Indices: 243015--243392 Score: 404
Period size: 156 Copynumber: 2.4 Consensus size: 155
243005 ACTGGTGGTG
* *
243015 ATCTGTCC-CAAGCTCGGGGTAAAAGATCGGATGATTGCAATCTACCCCAAGCTCGAGGTAAGAG
1 ATCTG-CCTCAAGCTC-GGGTAAAAGATTGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGAG
* * *
243079 ATTTACTGATGGGGATCTGCCTCAAGCTCGGCATAAAAGATCAGATGGCTGCAATCTACCACAAG
64 ATTGACTGATGGGGATCTGCCCCAAGCTCGGCATAAAAGATCAGATGGCTACAATCTACCACAAG
* * * * *
243144 CTCAGGGTAAGAGATTGACTGATGGTG
129 CTCAGGGTAAAAGATGGACTGACGATA
* * *
243171 ATCTGCCTCAAGCTCAGGGTAAAAGATTGGATTG-CTGCAATCTGCCCTAAGCTCTAGGTAAGAG
1 ATCTGCCTCAAGCTC-GGGTAAAAGATTGGA-TGACTGCAATCTACCCCAAGCTCGAGGTAAGAG
* * ** * * *
243235 ATTGACTGATGGTGATTTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTACAATCTGCCCCAAG
64 ATTGACTGATGGGGATCTGCCCCAAGCTCGGCATAAAAGATCAGATGGCTACAATCTACCACAAG
243300 CTC-GAGGTAAAAGATCGGA-TGACGATA
129 CTCAG-GGTAAAAGAT-GGACTGACGATA
* * ** ** * * *
243327 ATCTGCCTCAAGCTCGGAGTAAGAGATTGGCTGAAAGTGATCTGCCCCAAGCTCGCGGTAAAAGA
1 ATCTGCCTCAAGCTCGG-GTAAAAGATTGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGAGA
243392 T
65 T
243393 CAGAAAGCTT
Statistics
Matches: 185, Mismatches: 31, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
155 7 0.04
156 174 0.94
157 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.22
Consensus pattern (155 bp):
ATCTGCCTCAAGCTCGGGTAAAAGATTGGATGACTGCAATCTACCCCAAGCTCGAGGTAAGAGAT
TGACTGATGGGGATCTGCCCCAAGCTCGGCATAAAAGATCAGATGGCTACAATCTACCACAAGCT
CAGGGTAAAAGATGGACTGACGATA
Found at i:243646 original size:117 final size:117
Alignment explanation
Indices: 243171--243665 Score: 414
Period size: 117 Copynumber: 4.2 Consensus size: 117
243161 ACTGATGGTG
* * * *
243171 ATCTGCCTCAAGCTCAGGGTAAAAGATTGGATTGCTGCAATCTGCCCTAAGCTCTAGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGCTGCAATCTGCCCTAAGCTCGAGGTAAGAGA
* * * *
243236 TTGACTGATGGTGATTTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTACA
66 TTGGCTGATGGTGATCTGCCCCAAGCTCAGAGTAAAAGATCGGATGGCTACA
* * * *
243288 ATCTGCCCCAAGCTCGAGGTAAAAGATCGGATGAC-GATAATCTG-CCTCAAGCTCG-GAGTAAG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGCTG-CAATCTGCCCT-AAGCTCGAG-GTAAG
** * * ** **
243350 AGATTGGCTGAAAGTGATCTGCCCCAAGCTC-GCGGTAAAAGATCAGAAAGCTTTA
63 AGATTGGCTGATGGTGATCTGCCCCAAGCTCAG-AGTAAAAGATCGGATGGCTACA
* * * * * * * * *
243405 ATCTGCCTCAAGCTCGGGGTAAGAGATTGG-TTGATAGTAATCTTCCTTAAGCTCGGGGTAAAAG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGCT-GCAATCTGCCCTAAGCTCGAGGTAAGAG
* * * * * * * * * *
243469 ATCGGATGATTGTAATCTGCCCTAGGCTCAAAGTAAGAGATTGGCTGATGG-T--G
65 ATTGGCTGATGGTGATCTGCCCCAAGCTCAGAGTAAAAGA-T--CGGATGGCTACA
* * * * *
243522 ATTTGCCCTAAGCTTGGGGTAAAATATTTGATGGCTGCAATCTGCCCTAAGCTCGAGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGCTGCAATCTGCCCTAAGCTCGAGGTAAGAGA
* *
243587 TTGGCTGATGGTGATCTG-TCCTAGTCTCAGAGTAAAAGATCGGATGGCTACA
66 TTGGCTGATGGTGATCTGCCCCAAG-CTCAGAGTAAAAGATCGGATGGCTACA
* *
243639 ATCTGCCCCAGGCTCGGGGTAAGAGAT
1 ATCTGCCCCAAGCTCGGGGTAAAAGAT
243666 CGAAATCTTC
Statistics
Matches: 288, Mismatches: 73, Indels: 34
0.73 0.18 0.09
Matches are distributed among these distances:
114 6 0.02
115 1 0.00
116 10 0.03
117 258 0.90
118 8 0.03
119 1 0.00
120 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (117 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGGCTGCAATCTGCCCTAAGCTCGAGGTAAGAGA
TTGGCTGATGGTGATCTGCCCCAAGCTCAGAGTAAAAGATCGGATGGCTACA
Found at i:243661 original size:156 final size:156
Alignment explanation
Indices: 243297--243665 Score: 404
Period size: 156 Copynumber: 2.4 Consensus size: 156
243287 AATCTGCCCC
* * *
243297 AAGCTC-GAGGTAAAAGATCGGATGACGATAATCTGCCTCAAGCTCGGAGTAAGAGATTGGCTGA
1 AAGCTCAGA-GTAAAAGATCGGATGACTATAATCTGCCCCAGGCTCGGAGTAAGAGATTGGCTGA
** *
243361 AAGTGATCTGCCCCAAGCTCGCGGTAAAAGATCAGAAAGCTTTAATCTGCCTCAAGCTCGGGGTA
65 AAGTGATCTGCCCCAAGCTCGCGGTAAAAGATCAGAAAGCTGCAATCTGCCTCAAGCTCGAGGTA
*
243426 AGAGATTGGTTGATAGTAATCTTCCTT
130 AGAGATTGGCTGATAGTAATCTTCCTT
* * * * * ** *
243453 AAGCTCGGGGTAAAAGATCGGATGATTGTAATCTGCCCTAGGCTCAAAGTAAGAGATTGGCTGAT
1 AAGCTCAGAGTAAAAGATCGGATGACTATAATCTGCCCCAGGCTCGGAGTAAGAGATTGGCTGAA
* * * * * * ** **
243518 GGTGATTTGCCCTAAGCTTGGGGTAAAATATTTGATGGCTGCAATCTGCC-CTAAGCTCGAGGTA
66 AGTGATCTGCCCCAAGCTCGCGGTAAAAGATCAGAAAGCTGCAATCTGCCTC-AAGCTCGAGGTA
* *
243582 AGAGATTGGCTGATGGTGATCTGTCC-T
130 AGAGATTGGCTGATAGTAATCT-TCCTT
* * *
243609 -AGTCTCAGAGTAAAAGATCGGATGGCTACAATCTGCCCCAGGCTCGGGGTAAGAGAT
1 AAG-CTCAGAGTAAAAGATCGGATGACTATAATCTGCCCCAGGCTCGGAGTAAGAGAT
243666 CGAAATCTTC
Statistics
Matches: 173, Mismatches: 36, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
155 3 0.02
156 166 0.96
157 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (156 bp):
AAGCTCAGAGTAAAAGATCGGATGACTATAATCTGCCCCAGGCTCGGAGTAAGAGATTGGCTGAA
AGTGATCTGCCCCAAGCTCGCGGTAAAAGATCAGAAAGCTGCAATCTGCCTCAAGCTCGAGGTAA
GAGATTGGCTGATAGTAATCTTCCTT
Found at i:253662 original size:32 final size:30
Alignment explanation
Indices: 253626--253689 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
253616 TCAAAGAATG
253626 TAATAAATAAAAAATAAATATATATTAATATA
1 TAATAAATAAAAAAT-AA-ATATATTAATATA
**
253658 TAATAAATAGCAAATAAATATATTAATATA
1 TAATAAATAAAAAATAAATATATTAATATA
253688 TA
1 TA
253690 CTTGGATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 15 0.50
31 2 0.07
32 13 0.43
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (30 bp):
TAATAAATAAAAAATAAATATATTAATATA
Found at i:254089 original size:13 final size:13
Alignment explanation
Indices: 254073--254097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
254063 ATGTAATTGG
254073 GTTTTTGGGTTTA
1 GTTTTTGGGTTTA
254086 GTTTTTGGGTTT
1 GTTTTTGGGTTT
254098 TGTAATTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.00, G:0.32, T:0.64
Consensus pattern (13 bp):
GTTTTTGGGTTTA
Found at i:256467 original size:30 final size:30
Alignment explanation
Indices: 256422--256628 Score: 193
Period size: 30 Copynumber: 6.9 Consensus size: 30
256412 TTAAAATCGA
* *
256422 GTCAGATTTGAATTTTTGGAAACTTT-AGG
1 GTCAAATTTGAATTTTTGGAAAATTTAAGG
* * * *
256451 GATTAAATTGGAATTTTTGAAAAATTTAGGG
1 G-TCAAATTTGAATTTTTGGAAAATTTAAGG
* *
256482 GTCAAATTTAAATTTTTGGAAAGTTTAAGG
1 GTCAAATTTGAATTTTTGGAAAATTTAAGG
* * *
256512 GTCAAAATTGAATTTTTAGAAAATTTGAGG
1 GTCAAATTTGAATTTTTGGAAAATTTAAGG
* *
256542 GTCAAATTTGAATTTTTGAAAAATTTTAGTG
1 GTCAAATTTGAATTTTTGGAAAATTTAAG-G
* ** * **
256573 TTC-AATTCAAATTTTTAGAAAATTCGAGG
1 GTCAAATTTGAATTTTTGGAAAATTTAAGG
* *
256602 GTCAAATTTGAATTTTTAGAAAGTTTA
1 GTCAAATTTGAATTTTTGGAAAATTTA
256629 GGTGTTAATA
Statistics
Matches: 140, Mismatches: 34, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
29 4 0.03
30 130 0.93
31 6 0.04
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (30 bp):
GTCAAATTTGAATTTTTGGAAAATTTAAGG
Found at i:256500 original size:60 final size:58
Alignment explanation
Indices: 256422--256636 Score: 236
Period size: 60 Copynumber: 3.6 Consensus size: 58
256412 TTAAAATCGA
* *
256422 GTCAGATTTGAATTTTTGGAAACTTTAGGGATTAAATTGGAATTTTT-GAAAAATTT-AGGG
1 GTCAAATTTGAATTTTTGGAAAGTTTAGGG-TTAAATT-GAATTTTTAG-AAAATTTGA-GG
* *
256482 GTCAAATTTAAATTTTTGGAAAGTTTAAGGGTCAAAATTGAATTTTTAGAAAATTTGAGG
1 GTCAAATTTGAATTTTTGGAAAGTTT-AGGGT-TAAATTGAATTTTTAGAAAATTTGAGG
* * * * * *
256542 GTCAAATTTGAATTTTTGAAAAATTTTAGTGTTCAATTCAAATTTTTAGAAAATTCGAGG
1 GTCAAATTTGAATTTTTG-GAAAGTTTAGGGTTAAATT-GAATTTTTAGAAAATTTGAGG
*
256602 GTCAAATTTGAATTTTTAGAAAGTTTAGGTGTTAA
1 GTCAAATTTGAATTTTTGGAAAGTTTAGG-GTTAA
256637 TACATAATTT
Statistics
Matches: 131, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
59 12 0.09
60 102 0.78
61 17 0.13
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (58 bp):
GTCAAATTTGAATTTTTGGAAAGTTTAGGGTTAAATTGAATTTTTAGAAAATTTGAGG
Found at i:256585 original size:90 final size:90
Alignment explanation
Indices: 256429--256630 Score: 255
Period size: 90 Copynumber: 2.2 Consensus size: 90
256419 CGAGTCAGAT
* * * *
256429 TTGAATTTTTGGAAACTTTAGGGATTAAATTGGAATTTTTGAAAAATTTAGGGGTCAAATTTAAA
1 TTGAATTTTTAGAAAATTTAGGGATCAAATTGGAATTTTTGAAAAATTTAGGGGTCAAATTCAAA
* * *
256494 TTTTTGGAAAGTTTAAGGGTCAAAA
66 TTTTTAGAAAATTCAAGGGTCAAAA
* * *
256519 TTGAATTTTTAGAAAATTTGAGGG-TCAAATTTGAATTTTTGAAAAATTTTAGTGTTC-AATTCA
1 TTGAATTTTTAGAAAATTT-AGGGATCAAATTGGAATTTTTGAAAAA-TTTAGGGGTCAAATTCA
* *
256582 AATTTTTAGAAAATTCGAGGGTCAAAT
64 AATTTTTAGAAAATTCAAGGGTCAAAA
*
256609 TTGAATTTTTAGAAAGTTTAGG
1 TTGAATTTTTAGAAAATTTAGG
256631 TGTTAATACA
Statistics
Matches: 97, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
89 3 0.03
90 82 0.85
91 12 0.12
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.41
Consensus pattern (90 bp):
TTGAATTTTTAGAAAATTTAGGGATCAAATTGGAATTTTTGAAAAATTTAGGGGTCAAATTCAAA
TTTTTAGAAAATTCAAGGGTCAAAA
Found at i:256646 original size:30 final size:30
Alignment explanation
Indices: 256612--256677 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
256602 GTCAAATTTG
* * *
256612 AATTTTTAGAAAGTTTAGGTGTTAATACAT
1 AATTTTTAGAAAGTTTAGGGGTTAAAAAAT
*
256642 AATTTTTAGATAGTTTAGGGGTTAAAAAAT
1 AATTTTTAGAAAGTTTAGGGGTTAAAAAAT
256672 AATTTT
1 AATTTT
256678 AAAATGAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.44
Consensus pattern (30 bp):
AATTTTTAGAAAGTTTAGGGGTTAAAAAAT
Found at i:258556 original size:31 final size:31
Alignment explanation
Indices: 258440--258575 Score: 113
Period size: 31 Copynumber: 4.5 Consensus size: 31
258430 TTAATATAAC
* * *
258440 ATTTGATACTTGAACTTGACATTTTTTCTTA
1 ATTTGGTACTTAAACTTGACATTTTTTCCTA
* * *
258471 TTTTGGTACCTAAACTT---TTTTTTGTCC-A
1 ATTTGGTACTTAAACTTGACATTTTT-TCCTA
* * *
258499 ATTTAGTACTCAAACTTGACACTTTTTCCTA
1 ATTTGGTACTTAAACTTGACATTTTTTCCTA
**
258530 ATTTGGTACTTAAACTTG--ATTTTTTTTTA
1 ATTTGGTACTTAAACTTGACATTTTTTCCTA
*
258559 AGTTGGTACTTAAACTT
1 ATTTGGTACTTAAACTT
258576 TTTAGAGTCT
Statistics
Matches: 82, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
28 19 0.23
29 26 0.32
30 3 0.04
31 34 0.41
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTGACATTTTTTCCTA
Found at i:258603 original size:88 final size:89
Alignment explanation
Indices: 258440--258613 Score: 199
Period size: 88 Copynumber: 2.0 Consensus size: 89
258430 TTAATATAAC
* ** ***
258440 ATTTGATACTTGAACTTGACATTTTTTCTTATTTTGGTACCTAAACTTTTTTTTGTCCAATTTAG
1 ATTTGATACTTAAACTTGA-ATTTTTTCTTAAGTTGGTACCTAAACTTTTTAGAGTCCAATTTAG
258505 TACTCAAACTTGACACTTTTTCCTA
65 TACTCAAACTTGACACTTTTTCCTA
* * * * *
258530 ATTTGGTACTTAAACTTG-ATTTTTTTTTAAGTTGGTACTTAAACTTTTTAGAGTCTAATTTGGT
1 ATTTGATACTTAAACTTGAATTTTTTCTTAAGTTGGTACCTAAACTTTTTAGAGTCCAATTTAGT
* *
258594 A-TCCGAACTTGACTCTTTTT
66 ACT-CAAACTTGACACTTTTT
258614 TTTTTTAATT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
87 1 0.01
88 53 0.76
90 16 0.23
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.49
Consensus pattern (89 bp):
ATTTGATACTTAAACTTGAATTTTTTCTTAAGTTGGTACCTAAACTTTTTAGAGTCCAATTTAGT
ACTCAAACTTGACACTTTTTCCTA
Found at i:265528 original size:38 final size:39
Alignment explanation
Indices: 265460--265539 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 39
265450 ATTTTGACCC
* * * *
265460 TTTAATTTTTTAAAAATTTTAAATTAATAAA-TATTTAA
1 TTTAATTCTTTAAAAATTTAAAAATAATAAACAATTTAA
265498 TTTAATTCTTTAAAAATTATAAAAAT-ATAAACAATTTAA
1 TTTAATTCTTTAAAAATT-TAAAAATAATAAACAATTTAA
265537 TTT
1 TTT
265540 CGACATATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 22 0.61
39 14 0.39
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (39 bp):
TTTAATTCTTTAAAAATTTAAAAATAATAAACAATTTAA
Found at i:268469 original size:20 final size:20
Alignment explanation
Indices: 268433--268478 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
268423 TCATTAAGCT
*
268433 TTAATTAATCATTTTTA-ATC
1 TTAATTAATCATATTTATA-C
268453 TTAATTAAATC-TATTTATAC
1 TTAATT-AATCATATTTATAC
268473 TTAATT
1 TTAATT
268479 TAAACCATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTAATCATATTTATAC
Found at i:273787 original size:21 final size:22
Alignment explanation
Indices: 273763--273803 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
273753 CCTGTACTAG
273763 TTCTACC-AATACAAG-CATGAT
1 TTCTACCGAA-ACAAGTCATGAT
273784 TTCTACCGAAACAAGTCATG
1 TTCTACCGAAACAAGTCATG
273804 CAACTACCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (22 bp):
TTCTACCGAAACAAGTCATGAT
Found at i:275480 original size:20 final size:20
Alignment explanation
Indices: 275444--275489 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
275434 TCATTGAGCT
*
275444 TTAATTAATCATTTTTA-ATC
1 TTAATTAATCATATTTATA-C
275464 TTAATTAAATC-TATTTATAC
1 TTAATT-AATCATATTTATAC
275484 TTAATT
1 TTAATT
275490 TAAACCATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTAATCATATTTATAC
Found at i:277058 original size:19 final size:21
Alignment explanation
Indices: 277034--277072 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
277024 TTTTATAAGA
277034 AAAATTT-AAATAGA-AATTT
1 AAAATTTAAAATAGATAATTT
277053 AAAATTTAAAATAGATAATT
1 AAAATTTAAAATAGATAATT
277073 AAGTGGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAATTTAAAATAGATAATTT
Found at i:277944 original size:23 final size:23
Alignment explanation
Indices: 277918--277995 Score: 111
Period size: 23 Copynumber: 3.4 Consensus size: 23
277908 TGTATACTCG
277918 TAAATGTATCATGCTGACGAGCA
1 TAAATGTATCATGCTGACGAGCA
* * *
277941 TAAACGTATCATGCTGATGAGCT
1 TAAATGTATCATGCTGACGAGCA
* *
277964 TAAATGTATCACGCTGACGAGCG
1 TAAATGTATCATGCTGACGAGCA
277987 TAAATGTAT
1 TAAATGTAT
277996 TATATTAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (23 bp):
TAAATGTATCATGCTGACGAGCA
Found at i:278014 original size:46 final size:46
Alignment explanation
Indices: 277918--278015 Score: 115
Period size: 46 Copynumber: 2.1 Consensus size: 46
277908 TGTATACTCG
* * * * *
277918 TAAATGTATCATGCTGACGAGCATAAACGTATCATGCTGATGAGCT
1 TAAATGTATCACGCTGACGAGCATAAACGTATCATACTAATAAGCA
* * * *
277964 TAAATGTATCACGCTGACGAGCGTAAATGTATTATATTAATAAGCA
1 TAAATGTATCACGCTGACGAGCATAAACGTATCATACTAATAAGCA
278010 TAAATG
1 TAAATG
278016 AGCATGCAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (46 bp):
TAAATGTATCACGCTGACGAGCATAAACGTATCATACTAATAAGCA
Found at i:280473 original size:233 final size:233
Alignment explanation
Indices: 280066--280756 Score: 1229
Period size: 233 Copynumber: 3.0 Consensus size: 233
280056 AAGAAGATGA
*
280066 GTTTAACATATAATCAAACCATATGACATCTCAATCATATATCAAACCAAATCATTTTAAATTCA
1 GTTTAACATATAATCAAACCATATGACATCTCAATCATATATCAAACCAATTCATTTTAAATTCA
*
280131 ATATTTCAATACCTTACTCATGCTCAATTCAACATTTATCCATTTAAACATCGATCTCATACCAT
66 ATATTTCAATACCTTGCTCATGCTCAATTCAACATTTATCCATTTAAACATCGATCTCATACCAT
* *
280196 TTCATTTCAATTTTTCATTTTACATTAAACGTTTAGTGCAATGAACACTAGTAAACAGACTCGAA
131 TTCATTTCAATTTTTCATTTTACATTAAACGTTTAGTGCAATGAACTCTAGTAAACAGACTCGGA
*
280261 TACACAGGTAACTACATCATACCAGTTGCTCGTCCGAG
196 TACACAGGTAACTACATCACACCAGTTGCTCGTCCGAG
*
280299 GTTTAACATATAATCAAACCATATGACATCTCAATCATATATCAAACTAATTCATTTTAAATTCA
1 GTTTAACATATAATCAAACCATATGACATCTCAATCATATATCAAACCAATTCATTTTAAATTCA
** *
280364 ATATTTCAATAAATTGCTCATGCTCAATTCAACATTTATCCATTTAAACATTGATCTCATACCAT
66 ATATTTCAATACCTTGCTCATGCTCAATTCAACATTTATCCATTTAAACATCGATCTCATACCAT
* * *
280429 TTCATTTCAATTTTTCAATTTACATTAAACATTTAGTGCAATGAACTCTAGTAAATAGACTCGGA
131 TTCATTTCAATTTTTCATTTTACATTAAACGTTTAGTGCAATGAACTCTAGTAAACAGACTCGGA
* *
280494 TACACAGGTAACTACATCACACTAATTGCTCGTCCGAG
196 TACACAGGTAACTACATCACACCAGTTGCTCGTCCGAG
280532 GTTTAACATATAATCAAACCATATGACATCTCAATCATATATCAAACCAATTCATTTTAAATTCA
1 GTTTAACATATAATCAAACCATATGACATCTCAATCATATATCAAACCAATTCATTTTAAATTCA
280597 ATATTTCAATACCTTGCTCATGCTCAATTCAACATTTATCCATTTAAACATCGATCTCATACCAT
66 ATATTTCAATACCTTGCTCATGCTCAATTCAACATTTATCCATTTAAACATCGATCTCATACCAT
* *
280662 TTCATTTCAATTTTTCATTTTACATTAAACGTTTAGTGCAATGAACTTTAGTAAACATACTCGGA
131 TTCATTTCAATTTTTCATTTTACATTAAACGTTTAGTGCAATGAACTCTAGTAAACAGACTCGGA
*
280727 TACACAGGTAATTACATCACACCAGTTGCT
196 TACACAGGTAACTACATCACACCAGTTGCT
280757 TTTTCGAGCT
Statistics
Matches: 432, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
233 432 1.00
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (233 bp):
GTTTAACATATAATCAAACCATATGACATCTCAATCATATATCAAACCAATTCATTTTAAATTCA
ATATTTCAATACCTTGCTCATGCTCAATTCAACATTTATCCATTTAAACATCGATCTCATACCAT
TTCATTTCAATTTTTCATTTTACATTAAACGTTTAGTGCAATGAACTCTAGTAAACAGACTCGGA
TACACAGGTAACTACATCACACCAGTTGCTCGTCCGAG
Found at i:282739 original size:37 final size:36
Alignment explanation
Indices: 282689--282758 Score: 113
Period size: 37 Copynumber: 1.9 Consensus size: 36
282679 ATATTATATT
282689 GAAATAACTAGAAAAAGTTCCAAAAAATCCAATAAAA
1 GAAATAACTAGAAAAAGTTCCAAAAAA-CCAATAAAA
* *
282726 GAAATAACTAGAAAAAGTTCTAAAGAACCAATA
1 GAAATAACTAGAAAAAGTTCCAAAAAACCAATA
282759 TTTACACCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 6 0.19
37 25 0.81
ACGTcount: A:0.60, C:0.13, G:0.10, T:0.17
Consensus pattern (36 bp):
GAAATAACTAGAAAAAGTTCCAAAAAACCAATAAAA
Found at i:285383 original size:6 final size:6
Alignment explanation
Indices: 285369--285419 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
285359 TATTTTAACA
* * *
285369 TTTAAT TTTATT TTTATT TTT-TT GTTTATT TATATT GTTATT ATTTATT
1 TTTATT TTTATT TTTATT TTTATT -TTTATT TTTATT TTTATT -TTTATT
285418 TT
1 TT
285420 CATGTCATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
5 2 0.05
6 28 0.76
7 7 0.19
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:285424 original size:104 final size:101
Alignment explanation
Indices: 285230--285425 Score: 254
Period size: 101 Copynumber: 1.9 Consensus size: 101
285220 GTTTTCTTTT
*
285230 TTATTATTATTATTTATATTTAATTGTTTATTCTGACATTTAATTTATTAATTTTTTTGTTTATT
1 TTATTATTATTATTTATATTTAATTGTTTATTCTAACATTTAATTTATTAATTTTTTTGTTTATT
285295 TATTTATTTGTCATTTATTTTCATGTCTAATCCCAA
66 TATTTATTTGTCATTTATTTTCATGTCTAATCCCAA
* * * * *
285331 TTATTTTTATTGTTTATATTT-GTTAGTTTATTTTAACATTTAATTTTATTTTTATTTTTTTGTT
1 TTATTATTATTATTTATATTTAATT-GTTTATTCTAACATTTAA-TTTA--TTAATTTTTTTGTT
*
285395 TATTTATATTGTTAT-T-ATTTATTTTCATGTC
62 TATTTAT-TTATT-TGTCATTTATTTTCATGTC
285426 ATTTTATTGT
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
100 2 0.02
101 35 0.43
102 4 0.05
104 35 0.43
105 5 0.06
106 1 0.01
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (101 bp):
TTATTATTATTATTTATATTTAATTGTTTATTCTAACATTTAATTTATTAATTTTTTTGTTTATT
TATTTATTTGTCATTTATTTTCATGTCTAATCCCAA
Found at i:285518 original size:27 final size:26
Alignment explanation
Indices: 285467--285532 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
285457 TTTAATTTGC
**
285467 ATTTATTTTTATTATCTTGTTTATTT
1 ATTTATTTTTATTAAATTGTTTATTT
285493 ATTTATTTATTATTAAATT-TTATATTT
1 ATTTATTT-TTATTAAATTGTT-TATTT
*
285520 -TTTCTTTTT-TTAA
1 ATTTATTTTTATTAA
285533 TTACATGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 4 0.11
25 2 0.06
26 16 0.46
27 13 0.37
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (26 bp):
ATTTATTTTTATTAAATTGTTTATTT
Found at i:286593 original size:15 final size:14
Alignment explanation
Indices: 286568--286601 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
286558 ATTTACTTTG
286568 TTATTCTTTGCATT
1 TTATTCTTTGCATT
286582 TTATTGCTTTGCATT
1 TTATT-CTTTGCATT
286597 TTATT
1 TTATT
286602 TTATGTAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.15, C:0.12, G:0.09, T:0.65
Consensus pattern (14 bp):
TTATTCTTTGCATT
Found at i:299608 original size:14 final size:13
Alignment explanation
Indices: 299589--299652 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
299579 TGACTGGTCG
299589 TTGACCGTTGATCA
1 TTGACCGTTGA-CA
* *
299603 TTGACCATTGACT
1 TTGACCGTTGACA
* *
299616 TTGACTGTTGACTG
1 TTGACCGTTGAC-A
*
299630 TTGACCGTTGAAA
1 TTGACCGTTGACA
*
299643 TTGAACGTTG
1 TTGACCGTTG
299653 GCCGTTGACT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
13 20 0.50
14 20 0.50
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (13 bp):
TTGACCGTTGACA
Found at i:299626 original size:13 final size:14
Alignment explanation
Indices: 299588--299640 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
299578 TTGACTGGTC
299588 GTTGACCGTTGA-T
1 GTTGACCGTTGACT
* *
299601 CATTGACCATTGACT
1 -GTTGACCGTTGACT
*
299616 -TTGACTGTTGACT
1 GTTGACCGTTGACT
299629 GTTGACCGTTGA
1 GTTGACCGTTGA
299641 AATTGAACGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 11 0.34
14 20 0.62
15 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (14 bp):
GTTGACCGTTGACT
Found at i:302808 original size:6 final size:6
Alignment explanation
Indices: 302797--302837 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
302787 TCAAACTAAT
*
302797 AAAAGA AAAAGA AAAAGAA AAAAGA AAAAAA TAAAAGA AAA
1 AAAAGA AAAAGA AAAAG-A AAAAGA AAAAGA -AAAAGA AAA
302838 CAAAAAAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:302820 original size:13 final size:13
Alignment explanation
Indices: 302797--302837 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
302787 TCAAACTAAT
302797 AAAAG-AAAAAGA
1 AAAAGAAAAAAGA
302809 AAAAGAAAAAAGA
1 AAAAGAAAAAAGA
302822 AAAA-AATAAAAGA
1 AAAAGAA-AAAAGA
302835 AAA
1 AAA
302838 CAAAAAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Found at i:304049 original size:49 final size:49
Alignment explanation
Indices: 303898--304688 Score: 492
Period size: 49 Copynumber: 16.2 Consensus size: 49
303888 CATAGAGTTT
* * *** *
303898 GAAGAAGGATAGGTTCAAGCTATAACGGTGGACCTAACATCC-TAAAATC
1 GAAGAGGGATAGGTTGAAGCCGCAACGATGGACCTAACA-CCTTAAAATC
* * * **
303947 AAAGAGGGAAAGGTTGAAGCCGC-ACGACGGACCTTGCACCTTAAAA-C
1 GAAGAGGGATAGGTTGAAGCCGCAACGATGGACCTAACACCTTAAAATC
* * *
303994 TAAAGAGGGATAGGTTGAAGCCGTAACAATGGACCTAACACCTTAAAATC
1 -GAAGAGGGATAGGTTGAAGCCGCAACGATGGACCTAACACCTTAAAATC
* ** * * * * *
304044 GAAGAGGGAAACATTAAAGCCGCAAC-AGCGGATCTTACACCTTAAAATT
1 GAAGAGGGATAGGTTGAAGCCGCAACGA-TGGACCTAACACCTTAAAATC
* * * * *
304093 GAATAGGGATAGGTTGAAGTCGCAATGATGGACCTAATCACCCTAAAATT
1 GAAGAGGGATAGGTTGAAGCCGCAACGATGGACCTAA-CACCTTAAAATC
* * * * * * * *
304143 GAAAAGAGATAGATTAAAGTCACAACGGCT-GATCTAACA-CTCTAAAATC
1 GAAGAGGGATAGGTTGAAGCCGCAAC-GATGGACCTAACACCT-TAAAATC
* * * ** * *
304192 GAAGAGGGAAAGGCTAAAGCCATAACGATGGACCTTACACTTTAAAAT-
1 GAAGAGGGATAGGTTGAAGCCGCAACGATGGACCTAACACCTTAAAATC
* * ** ** *
304240 --TGAGGGATAGGTTGAAGCCGCAATGGCGGACCTAACACCCAAAAAAC
1 GAAGAGGGATAGGTTGAAGCCGCAACGATGGACCTAACACCTTAAAATC
* * * ** * * *
304287 TGAAG-GAGGAAAGGTCGAAGTCATAACGATGGATCTTACACCTTAAAATT
1 -GAAGAG-GGATAGGTTGAAGCCGCAACGATGGACCTAACACCTTAAAATC
* * *
304337 GAAGAGGGGTAGGTTGAAGTCGCAACGACGGACCTAACACCTTAAAATC
1 GAAGAGGGATAGGTTGAAGCCGCAACGATGGACCTAACACCTTAAAATC
* * ** * * * *
304386 GAAAAGGGATAGATTGAAGTTGTAACAGA-GGAACTAACACCATAAAACC
1 GAAGAGGGATAGGTTGAAGCCGCAAC-GATGGACCTAACACCTTAAAATC
* * * * *** * * * * *
304435 AAAAAGGGAAATGTTGAAGTTACAACGACGAACCTTACTCCTTAAAATT
1 GAAGAGGGATAGGTTGAAGCCGCAACGATGGACCTAACACCTTAAAATC
* ** * *
304484 GAAGAGGGATAGGTTGAAGCCGCAATGGCGGACATAACATCTTAAAATC
1 GAAGAGGGATAGGTTGAAGCCGCAACGATGGACCTAACACCTTAAAATC
* * *
304533 GAAGAGGGATAGGTTGAAGCCACAACGGTGGACCTAACACCCTAAAATC
1 GAAGAGGGATAGGTTGAAGCCGCAACGATGGACCTAACACCTTAAAATC
* * * * * * *
304582 GAAGAGGGAAAGATTGAAGTCGCAACGACT-AATCTTACACCTTAAAACC
1 GAAGAGGGATAGGTTGAAGCCGCAACGA-TGGACCTAACACCTTAAAATC
* * * *
304631 TAAGAGGGATAGGTTGAAGGCG-AGACGACGGACCTAACACCTTAAAACC
1 GAAGAGGGATAGGTTGAAGCCGCA-ACGATGGACCTAACACCTTAAAATC
*
304680 AAAGAGGGA
1 GAAGAGGGA
304689 ACAGATTGAA
Statistics
Matches: 562, Mismatches: 158, Indels: 44
0.74 0.21 0.06
Matches are distributed among these distances:
46 32 0.06
47 3 0.01
48 44 0.08
49 407 0.72
50 74 0.13
51 2 0.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.18
Consensus pattern (49 bp):
GAAGAGGGATAGGTTGAAGCCGCAACGATGGACCTAACACCTTAAAATC
Found at i:304200 original size:99 final size:98
Alignment explanation
Indices: 303983--304200 Score: 233
Period size: 99 Copynumber: 2.2 Consensus size: 98
303973 ACGGACCTTG
* * *
303983 CACCTTAAAA-CTAAAGAGGGATAGGTTGAAGCCGTAACAATGGACCTAACACCTTAAAATCGAA
1 CACCTTAAAATC-GAAGAGGGATAGGTTGAAGCCGCAACAATGGACCTAACACCCTAAAATCGAA
* * * *
304047 GAGGGAAACATTAAAGCCGCAACAGCGGATCTTA
65 AAGAGAAACATTAAAGCCACAACAGCGGATCTAA
* * * ** *
304081 CACCTTAAAATTGAATAGGGATAGGTTGAAGTCGCAATGATGGACCTAATCACCCTAAAATTGAA
1 CACCTTAAAATCGAAGAGGGATAGGTTGAAGCCGCAACAATGGACCTAA-CACCCTAAAATCGAA
* * * * *
304146 AAGAGATAGATTAAAGTCACAACGGCTGATCTAA
65 AAGAGAAACATTAAAGCCACAACAGCGGATCTAA
304180 CA-CTCTAAAATCGAAGAGGGA
1 CACCT-TAAAATCGAAGAGGGA
304201 AAGGCTAAAG
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
98 43 0.44
99 54 0.56
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (98 bp):
CACCTTAAAATCGAAGAGGGATAGGTTGAAGCCGCAACAATGGACCTAACACCCTAAAATCGAAA
AGAGAAACATTAAAGCCACAACAGCGGATCTAA
Found at i:304334 original size:145 final size:146
Alignment explanation
Indices: 304017--304344 Score: 335
Period size: 145 Copynumber: 2.2 Consensus size: 146
304007 GTTGAAGCCG
* * * * *
304017 TAACAATGGACCTAACACCTTAAAATCGAAGAGGGAAACATTAAAGCCGCAACAGCGGATCTTAC
1 TAACGATGGATCTAACACCTTAAAATCGAAGAGGGAAACACTAAAGCCACAACAGCGGACCTTAC
* * * *
304082 ACCTTAAAATTGAATAGGGATAGGTTGAAGTCGCAATGATGGACCTAATCACCCTAAAATTGAAA
66 ACCTTAAAATTG-A-AGGGATAGGTTGAAGCCGCAATGACGGACCTAATCACCCAAAAACTGAAA
* *
304147 AGAGATAGATTAAAGTCA
129 AGAGAAAGATCAAAGTCA
* * ** * *
304165 CAACGGCT-GATCTAACA-CTCTAAAATCGAAGAGGGAAAGGCTAAAGCCATAAC-GATGGACCT
1 TAAC-GATGGATCTAACACCT-TAAAATCGAAGAGGGAAACACTAAAGCCACAACAG-CGGACCT
* *
304227 TACACTTTAAAATTG-AGGGATAGGTTGAAGCCGCAATGGCGGACCTAA-CACCCAAAAAACTG-
63 TACACCTTAAAATTGAAGGGATAGGTTGAAGCCGCAATGACGGACCTAATCACCC-AAAAACTGA
* * *
304289 AAGGAGGAAAGGTCGAAGTCA
127 AAAGA-GAAAGATCAAAGTCA
* *
304310 TAACGATGGATCTTACACCTTAAAATTGAAGAGGG
1 TAACGATGGATCTAACACCTTAAAATCGAAGAGGG
304345 GTAGGTTGAA
Statistics
Matches: 147, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
144 11 0.07
145 72 0.49
146 2 0.01
147 3 0.02
148 58 0.39
149 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (146 bp):
TAACGATGGATCTAACACCTTAAAATCGAAGAGGGAAACACTAAAGCCACAACAGCGGACCTTAC
ACCTTAAAATTGAAGGGATAGGTTGAAGCCGCAATGACGGACCTAATCACCCAAAAACTGAAAAG
AGAAAGATCAAAGTCA
Found at i:305747 original size:25 final size:25
Alignment explanation
Indices: 305719--305816 Score: 67
Period size: 25 Copynumber: 3.8 Consensus size: 25
305709 AGTTATCTCT
*
305719 TTTATTATTTTTTATTTAATTTGTA
1 TTTATTATTTATTATTTAATTTGTA
*
305744 TTTATT-TTTATTATCTT-GTTTGTTTA
1 TTTATTATTTATTAT-TTAATTTG--TA
* *
305770 TTTATTTATTTATCATTAAATTT-TA
1 TTTA-TTATTTATTATTTAATTTGTA
* * *
305795 TTTTTTTTCTTTTTATTTAATT
1 TTTATTAT-TTATTATTTAATT
305817 ACATGTTGAT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
24 14 0.25
25 23 0.41
26 6 0.11
27 3 0.05
28 10 0.18
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.72
Consensus pattern (25 bp):
TTTATTATTTATTATTTAATTTGTA
Found at i:313094 original size:36 final size:31
Alignment explanation
Indices: 313031--313093 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
313021 TAAAGGGGGA
313031 AGACATTCCAAATGACTTTTCTTTCTACTCT
1 AGACATTCCAAATGACTTTTCTTTCTACTCT
313062 AGACATTCCAAATGACTTTTCTTTCTACTCT
1 AGACATTCCAAATGACTTTTCTTTCTACTCT
313093 A
1 A
313094 CATCATGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.41
Consensus pattern (31 bp):
AGACATTCCAAATGACTTTTCTTTCTACTCT
Found at i:320948 original size:23 final size:24
Alignment explanation
Indices: 320916--320961 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
320906 TTTAGGGTTT
*
320916 AATGTTACA-TATGATTAATATAAA
1 AATGTTACATTAT-AATAATATAAA
320940 AATG-TACATTATAATAATATAA
1 AATGTTACATTATAATAATATAA
320962 TTGTATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (24 bp):
AATGTTACATTATAATAATATAAA
Found at i:337669 original size:21 final size:21
Alignment explanation
Indices: 337645--337699 Score: 51
Period size: 21 Copynumber: 2.5 Consensus size: 21
337635 AGACCAACGA
*
337645 AAAATGAAGGAAA-AATGAAAG
1 AAAA-GAAGGAAAGAAAGAAAG
337666 AAAA-AAGAGAAAGAAAGAAAG
1 AAAAGAAG-GAAAGAAAGAAAG
337687 AAAGAAGAAGGAA
1 -AA-AAGAAGGAA
337700 GAAGGAGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 3 0.11
20 4 0.14
21 11 0.39
22 2 0.07
23 5 0.18
24 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (21 bp):
AAAAGAAGGAAAGAAAGAAAG
Found at i:337701 original size:18 final size:17
Alignment explanation
Indices: 337661--337721 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 17
337651 AAGGAAAAAT
337661 GAAAGAAAAAAGAGAAA
1 GAAAGAAAAAAGAGAAA
*
337678 GAAAGAAAGAA-AG-AA
1 GAAAGAAAAAAGAGAAA
* * * *
337693 GAAGGAAGAAGGAGAAG
1 GAAAGAAAAAAGAGAAA
337710 GAAA-AAAAAAGA
1 GAAAGAAAAAAGA
337722 TAATGTGTTT
Statistics
Matches: 33, Mismatches: 9, Indels: 5
0.70 0.19 0.11
Matches are distributed among these distances:
15 9 0.27
16 10 0.30
17 14 0.42
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAAAGAGAAA
Done.