Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 200 of 206
Found at i:60523539 original size:250 final size:250
Alignment explanation
Indices: 60523092--60523583 Score: 740
Period size: 250 Copynumber: 2.0 Consensus size: 250
60523082 GGCCAAACAT
** ** *
60523092 GAACTACTGTAGAAAAAGGGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGATAATACATC
1 GAACTACTGTAGAAAAAAAGAATCCACGTGGCAGCTTTTTTCAGTAATTTTGCTGATAATACATC
60523157 CTGCTTGAAGCGCTTTTAACACTATTTGTTCAGAAACGTCTTCTCAAAATTACTTTTTCAAGAAC
66 CTGCTTGAAGCGCTTTTAACACTATTTGTTCAGAAACGTCTTCTCAAAATTACTTTTTCAAGAAC
* * *
60523222 TACTGTAGAAAAATAGCGTCCACGTGGGAGCTTTTTTCATAAATTTTGCTGACAGTGCATCCTGC
131 TACTGTAGAAAAAGAGAGTCCACGTGGGAGCTTTTTTCATAAATATTGCTGACAGTGCATCCTGC
60523287 TTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTTTTTTTAA
196 TTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTTTTTTTAA
* *
60523342 GAACTACTGTAGAAAAAAAGAATCCACGTGGCAGCTTTTTTCATTAATTTTGCTG-TCAATGCAT
1 GAACTACTGTAGAAAAAAAGAATCCACGTGGCAGCTTTTTTCAGTAATTTTGCTGAT-AATACAT
* * * * * *
60523406 CCTGTTTGAAGCGTTTTTGACATTATTTGTTCAG-AACTGTCTTCTCAAAATTATTTTTTCAGGA
65 CCTGCTTGAAGCGCTTTTAACACTATTTGTTCAGAAAC-GTCTTCTCAAAATTACTTTTTCAAGA
* * *
60523470 ACTACTGTAGAAAAAGAGAGTCCACGTGGGAG-TTCTTTTCAGT-AATATTGTTGATAGTGCATT
129 ACTACTGTAGAAAAAGAGAGTCCACGTGGGAGCTT-TTTTCA-TAAATATTGCTGACAGTGCATC
*
60523533 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATT
192 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATT
60523584 AAAATTTAAT
Statistics
Matches: 218, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
249 6 0.03
250 211 0.97
251 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (250 bp):
GAACTACTGTAGAAAAAAAGAATCCACGTGGCAGCTTTTTTCAGTAATTTTGCTGATAATACATC
CTGCTTGAAGCGCTTTTAACACTATTTGTTCAGAAACGTCTTCTCAAAATTACTTTTTCAAGAAC
TACTGTAGAAAAAGAGAGTCCACGTGGGAGCTTTTTTCATAAATATTGCTGACAGTGCATCCTGC
TTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTTTTTTTAA
Found at i:60523631 original size:34 final size:33
Alignment explanation
Indices: 60523586--60523674 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 33
60523576 TCAAAATTAA
*
60523586 AATTTAATTAATTTTCTTAAAAAC-ACTTAACCC-
1 AATTTAATTAATTTT-TT-AAAACTACTAAACCCT
*
60523619 AAGTTTAATTAATTTATTTAAAACTCCTAAACCCT
1 AA-TTTAATTAATTT-TTTAAAACTACTAAACCCT
*
60523654 AATTTAATTAATTTTTAAAAA
1 AATTTAATTAATTTTTTAAAA
60523675 AGAACATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
33 13 0.27
34 33 0.67
35 3 0.06
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.42
Consensus pattern (33 bp):
AATTTAATTAATTTTTTAAAACTACTAAACCCT
Found at i:60523750 original size:21 final size:21
Alignment explanation
Indices: 60523725--60523790 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
60523715 CCTAGCACCT
60523725 TAAATTATTTTAACAAAACCC
1 TAAATTATTTTAACAAAACCC
* *** **
60523746 TAAATTCTACAAACCTAACCC
1 TAAATTATTTTAACAAAACCC
* *
60523767 TAAATCATTTTAACAAAACAC
1 TAAATTATTTTAACAAAACCC
60523788 TAA
1 TAA
60523791 CCCTAAAACC
Statistics
Matches: 31, Mismatches: 14, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAATTATTTTAACAAAACCC
Found at i:60523781 original size:42 final size:43
Alignment explanation
Indices: 60523703--60523790 Score: 117
Period size: 42 Copynumber: 2.0 Consensus size: 43
60523693 TTATTTTTAA
* * *
60523703 AAATTCTTAAAACCTAGCACCTTAAATTATTTTAACAAAACCCT
1 AAATTCTTAAAACCTA-CACCCTAAATCATTTTAACAAAACACT
60523747 AAATTC-TACAAACCTA-ACCCTAAATCATTTTAACAAAACACT
1 AAATTCTTA-AAACCTACACCCTAAATCATTTTAACAAAACACT
60523789 AA
1 AA
60523791 CCCTAAAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
42 25 0.62
43 2 0.05
44 13 0.32
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.28
Consensus pattern (43 bp):
AAATTCTTAAAACCTACACCCTAAATCATTTTAACAAAACACT
Found at i:60528113 original size:3 final size:3
Alignment explanation
Indices: 60528105--60528139 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
60528095 GAACCTCACC
*
60528105 ATG ATG ATG ATG GTG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
60528140 TTGATTCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:60528243 original size:2 final size:2
Alignment explanation
Indices: 60528226--60528258 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
60528216 GAAGAAGCTT
60528226 TA TA TA -A TA TA GTA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA T
60528259 TCCAAAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:60528793 original size:10 final size:10
Alignment explanation
Indices: 60528764--60528865 Score: 54
Period size: 10 Copynumber: 10.6 Consensus size: 10
60528754 GACATGTGGC
*
60528764 AAAAATAATT
1 AAAAATTATT
60528774 AAAAA--A-T
1 AAAAATTATT
60528781 AAAAATTATT
1 AAAAATTATT
** *
60528791 AAATTTTAAT
1 AAAAATTATT
*
60528801 AAAAAAT-TT
1 AAAAATTATT
*
60528810 AAAAGTTATT
1 AAAAATTATT
**
60528820 AAAAATTAGAA
1 AAAAATTA-TT
60528831 AAAAATTA-T
1 AAAAATTATT
**
60528840 AAAAA-TCGT
1 AAAAATTATT
60528849 AATAAATTATT
1 AA-AAATTATT
60528860 AAAAAT
1 AAAAAT
60528866 GTAAAGAAAT
Statistics
Matches: 68, Mismatches: 16, Indels: 16
0.68 0.16 0.16
Matches are distributed among these distances:
7 6 0.09
8 2 0.03
9 15 0.22
10 33 0.49
11 12 0.18
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (10 bp):
AAAAATTATT
Found at i:60528855 original size:19 final size:18
Alignment explanation
Indices: 60528831--60528902 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 18
60528821 AAAATTAGAA
60528831 AAAAATTATAAAAATCGT
1 AAAAATTATAAAAATCGT
60528849 AATAAATTATTAAAAAT-GT
1 AA-AAATTA-TAAAAATCGT
* * *
60528868 AAAGAAATACAAAATTCGT
1 AAA-AATTATAAAAATCGT
60528887 AAAAAGTTATAAAAAT
1 AAAAA-TTATAAAAAT
60528903 TATCTTAGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
18 10 0.23
19 26 0.60
20 7 0.16
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (18 bp):
AAAAATTATAAAAATCGT
Found at i:60528875 original size:20 final size:20
Alignment explanation
Indices: 60528810--60528875 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
60528800 TAAAAAATTT
*
60528810 AAAAGTTATTAAAAAT-TAGAA
1 AAAAATTATTAAAAATGT--AA
60528831 AAAAATTA-TAAAAATCGT-A
1 AAAAATTATTAAAAAT-GTAA
*
60528850 ATAAATTATTAAAAATGTAA
1 AAAAATTATTAAAAATGTAA
*
60528870 AGAAAT
1 AAAAAT
60528876 ACAAAATTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 10 0.26
20 20 0.53
21 7 0.18
22 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAAATTATTAAAAATGTAA
Found at i:60529422 original size:4 final size:4
Alignment explanation
Indices: 60529413--60529458 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
60529403 TCTGATTTCA
60529413 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
60529459 ACACTCCCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:60529661 original size:27 final size:27
Alignment explanation
Indices: 60529586--60529661 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 27
60529576 TATTTTTTAC
60529586 AATTTTATA-TTTTTACTATTCTATAA
1 AATTTTATATTTTTTACTATTCTATAA
**
60529612 AAAATTATAATTTTTT-CTATAT-TACTATA
1 AATTTTAT-ATTTTTTACTAT-TCTA-TA-A
*
60529641 TATTTTATATTTTTTACTATT
1 AATTTTATATTTTTTACTATT
60529662 TTTATAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
26 6 0.15
27 7 0.18
28 16 0.41
29 10 0.26
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (27 bp):
AATTTTATATTTTTTACTATTCTATAA
Found at i:60529673 original size:10 final size:10
Alignment explanation
Indices: 60529643--60529703 Score: 56
Period size: 10 Copynumber: 6.1 Consensus size: 10
60529633 TTACTATATA
60529643 TTTTAT-ATT
1 TTTTATAATT
60529652 TTTTACT-A-T
1 TTTTA-TAATT
60529661 TTTTATAATT
1 TTTTATAATT
60529671 TTTTATAAATT
1 TTTTAT-AATT
* *
60529682 CTTTACAATT
1 TTTTATAATT
60529692 TTTATATAATT
1 TTT-TATAATT
60529703 T
1 T
60529704 GTGGTTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 1 0.02
9 12 0.28
10 15 0.35
11 15 0.35
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:60529763 original size:21 final size:21
Alignment explanation
Indices: 60529734--60529782 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
60529724 TCTAGTTTTA
60529734 ATAAATTTTAAATATTTTTCT
1 ATAAATTTTAAATATTTTTCT
* *
60529755 ATAATTTTTTAATATTTTTCT
1 ATAAATTTTAAATATTTTTCT
*
60529776 ACAAATT
1 ATAAATT
60529783 GATTTTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (21 bp):
ATAAATTTTAAATATTTTTCT
Found at i:60537247 original size:31 final size:29
Alignment explanation
Indices: 60537206--60537269 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 29
60537196 CCACTCTCTT
*
60537206 TTTTTTTTTTATATATATTATCAGGGTAAAA
1 TTTTTCTTTTATATATA-TATCAGGGT-AAA
*
60537237 TTTTTCTTTTATATATATATTAGGGTAAA
1 TTTTTCTTTTATATATATATCAGGGTAAA
60537266 TTTT
1 TTTT
60537270 ATTTATATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 7 0.23
30 8 0.26
31 16 0.52
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (29 bp):
TTTTTCTTTTATATATATATCAGGGTAAA
Found at i:60537250 original size:29 final size:30
Alignment explanation
Indices: 60537207--60537277 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
60537197 CACTCTCTTT
*
60537207 TTTTTTTTTATATATAT-TATCAGGGTAAAA
1 TTTTTCTTTATATATATATATCAGGGT-AAA
*
60537237 TTTTTCTTT-TATATATATATTAGGGTAAA
1 TTTTTCTTTATATATATATATCAGGGTAAA
*
60537266 -TTTTATTTATAT
1 TTTTTCTTTATAT
60537278 GTTTTCAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.19
29 13 0.36
30 16 0.44
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (30 bp):
TTTTTCTTTATATATATATATCAGGGTAAA
Found at i:60543701 original size:4 final size:4
Alignment explanation
Indices: 60543692--60543737 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
60543682 AAAAAAGAGT
* *
60543692 AATA AATA AATA AGTA AATA AATA AATA GAT- AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT
60543738 GCCCGATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 2 0.05
4 35 0.95
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:60543707 original size:15 final size:15
Alignment explanation
Indices: 60543689--60543735 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
60543679 GTAAAAAAAG
60543689 AGTAATAAATAAATA
1 AGTAATAAATAAATA
60543704 AGTAAATAAATAAAT-
1 AGT-AATAAATAAATA
60543719 AGATAATAAATAAATA
1 AG-TAATAAATAAATA
60543735 A
1 A
60543736 ATGCCCGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
AGTAATAAATAAATA
Found at i:60547456 original size:285 final size:283
Alignment explanation
Indices: 60546935--60547509 Score: 927
Period size: 285 Copynumber: 2.0 Consensus size: 283
60546925 AGTTTTAGTG
*
60546935 GATGCATTACGATAGTGAAATTTATGTTGTTAAAGAAAACACCTAAATAAGCTAGTCTTGAAATT
1 GATGCATTACAATAGTGAAATTTATGTTGTTAAAGAAAACACCTAAATAAGCTAGTCTTGAAATT
* * *
60547000 TATTTTAATAGATCAGAGTGGCGCAGCGGAAGCGTGGTGGGCCCATAACCCACAGGTCCCAAGAT
66 TATTTTAACAAATCAGAGTGGCGCAGCGGAAGCATGGTGGGCCCATAACCCACAGGTCCCAAGAT
* * *
60547065 CGAAACTTGGCTCTGATAATTTTGAGCAAGTTTTTCTTGATTTTTTAAATTATTATCAAAATGTG
131 CGAAACTTGGCTCTCATAATTTTGAGAAAGGTTTTCTTGATTTTTTAAATTATTATCAAAATGTG
* *
60547130 GGTTGGCTTGATTTTTTAAATCAGAGTTGATGGATAATTAACTTGTGACGTATATATTAATATTA
196 GGCTGGCTTGATTTTTTAAATCAGAGTTGATGGATAATTAACTTGTGACATATATATTAATATTA
60547195 ATTTGAAAACGAAAAAAAAGTTATA
261 ATTTGAAAACG--AAAAAAGTTATA
* * * *
60547220 GATGCGTTACAATAGTGAAATTTGTGTTGTTAAATAAAACACCTAAATAAGTTAGTCTTGAAATT
1 GATGCATTACAATAGTGAAATTTATGTTGTTAAAGAAAACACCTAAATAAGCTAGTCTTGAAATT
* *
60547285 TATTTTAACAAATCAGAGTGGCGTAGCGGAAGCATGGTGGGCCCATAACCCATAGGTCCCAAGAT
66 TATTTTAACAAATCAGAGTGGCGCAGCGGAAGCATGGTGGGCCCATAACCCACAGGTCCCAAGAT
* * * * *
60547350 TGAAACTTGGCTTTCATAATTTTGAGAAAGGTTTTCTTGATTTTTTAAATTCTTGTCCAAATGTG
131 CGAAACTTGGCTCTCATAATTTTGAGAAAGGTTTTCTTGATTTTTTAAATTATTATCAAAATGTG
60547415 GGCTGGCTTGATTTTTTAAATCAGAGTTGATGGATAATTAACTTGTGACATATATATTAATATTA
196 GGCTGGCTTGATTTTTTAAATCAGAGTTGATGGATAATTAACTTGTGACATATATATTAATATTA
* *
60547480 ATTTGAAAATGTAAAAAGTTATA
261 ATTTGAAAACGAAAAAAGTTATA
60547503 GAT-CATT
1 GATGCATT
60547510 TGGTGAGTAA
Statistics
Matches: 267, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
282 3 0.01
283 14 0.05
285 250 0.94
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (283 bp):
GATGCATTACAATAGTGAAATTTATGTTGTTAAAGAAAACACCTAAATAAGCTAGTCTTGAAATT
TATTTTAACAAATCAGAGTGGCGCAGCGGAAGCATGGTGGGCCCATAACCCACAGGTCCCAAGAT
CGAAACTTGGCTCTCATAATTTTGAGAAAGGTTTTCTTGATTTTTTAAATTATTATCAAAATGTG
GGCTGGCTTGATTTTTTAAATCAGAGTTGATGGATAATTAACTTGTGACATATATATTAATATTA
ATTTGAAAACGAAAAAAGTTATA
Found at i:60548263 original size:10 final size:9
Alignment explanation
Indices: 60548227--60548290 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
60548217 TTCAAATAAA
60548227 TATTAAAA-
1 TATTAAAAT
60548235 TA-TAAAA-
1 TATTAAAAT
*
60548242 TATAAAAAT
1 TATTAAAAT
60548251 TATTAAGAAT
1 TATTAA-AAT
60548261 TA-TAAGCAAT
1 TATTAA--AAT
*
60548271 TATTAAATT
1 TATTAAAAT
60548280 TATTAAAAT
1 TATTAAAAT
60548289 TA
1 TA
60548291 ACAAAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
7 7 0.15
8 6 0.13
9 20 0.43
10 10 0.22
11 3 0.07
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (9 bp):
TATTAAAAT
Found at i:60548971 original size:47 final size:46
Alignment explanation
Indices: 60548891--60548979 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 46
60548881 TTTAATGTTC
* *
60548891 ACGAACATGTTCATTTAACTTAATTGAACATGTTTACGAACATTAG
1 ACGAACATGTTCATTGAACTTAATTGAACATGTTCACGAACATTAG
60548937 ACGAACATGTTCA-TGAACATATAATTGAACATGTTCACGAACA
1 ACGAACATGTTCATTGAAC-T-TAATTGAACATGTTCACGAACA
60548980 ATGTTAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
45 4 0.10
46 14 0.36
47 21 0.54
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (46 bp):
ACGAACATGTTCATTGAACTTAATTGAACATGTTCACGAACATTAG
Found at i:60551328 original size:15 final size:15
Alignment explanation
Indices: 60551308--60551339 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
60551298 CATTTTCTAG
60551308 TAAAAAGACAAATAC
1 TAAAAAGACAAATAC
*
60551323 TAAAAATACAAATAC
1 TAAAAAGACAAATAC
60551338 TA
1 TA
60551340 GATATTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.12, G:0.03, T:0.19
Consensus pattern (15 bp):
TAAAAAGACAAATAC
Found at i:60552042 original size:15 final size:15
Alignment explanation
Indices: 60552022--60552065 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
60552012 CCCAACTCCG
60552022 CAAAGAGAATGGCAA
1 CAAAGAGAATGGCAA
60552037 CAAAGAGAAT-G--A
1 CAAAGAGAATGGCAA
*
60552049 TAAAGAGAATGGCAA
1 CAAAGAGAATGGCAA
60552064 CA
1 CA
60552066 CGAATATCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 10 0.42
13 1 0.04
14 1 0.04
15 12 0.50
ACGTcount: A:0.55, C:0.11, G:0.25, T:0.09
Consensus pattern (15 bp):
CAAAGAGAATGGCAA
Found at i:60552151 original size:20 final size:20
Alignment explanation
Indices: 60552126--60552187 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
60552116 TTATTTAATT
60552126 AAATAATGACTTGGAATAAG
1 AAATAATGACTTGGAATAAG
* ** *
60552146 AAATAA-G-TTTTTAAT--T
1 AAATAATGACTTGGAATAAG
60552162 AAATAATGACTTGGAATAAG
1 AAATAATGACTTGGAATAAG
60552182 AAATAA
1 AAATAA
60552188 GTTTTTACAT
Statistics
Matches: 30, Mismatches: 8, Indels: 8
0.65 0.17 0.17
Matches are distributed among these distances:
16 6 0.20
17 1 0.03
18 10 0.33
19 1 0.03
20 12 0.40
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.31
Consensus pattern (20 bp):
AAATAATGACTTGGAATAAG
Found at i:60552159 original size:36 final size:36
Alignment explanation
Indices: 60552119--60552194 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
60552109 ACTCCTCTTA
60552119 TTTAATTAAATAATGACTTGGAATAAGAAATAAGTT
1 TTTAATTAAATAATGACTTGGAATAAGAAATAAGTT
60552155 TTTAATTAAATAATGACTTGGAATAAGAAATAAGTT
1 TTTAATTAAATAATGACTTGGAATAAGAAATAAGTT
60552191 TTTA
1 TTTA
60552195 CATATTTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (36 bp):
TTTAATTAAATAATGACTTGGAATAAGAAATAAGTT
Found at i:60559864 original size:17 final size:18
Alignment explanation
Indices: 60559832--60559874 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
60559822 TTTCATAGAT
*
60559832 TTAATAGTTTATATTA-AA
1 TTAATA-TTTACATTATAA
*
60559850 TTTATATTTACATTATAA
1 TTAATATTTACATTATAA
60559868 TTAATAT
1 TTAATAT
60559875 AAAAGCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTAATATTTACATTATAA
Found at i:60567357 original size:16 final size:17
Alignment explanation
Indices: 60567336--60567451 Score: 73
Period size: 16 Copynumber: 6.9 Consensus size: 17
60567326 ATATATTCAT
60567336 TTACATAAC-ACATAAC
1 TTACATAACTACATAAC
*
60567352 TTACATAACATACTTAA-
1 TTACATAAC-TACATAAC
*
60567369 -TACATAACTTGCATAAC
1 TTACATAAC-TACATAAC
*
60567386 TTACATAA-TACACAAC
1 TTACATAACTACATAAC
*** *
60567402 TTACATGTGTAAATAA-
1 TTACATAACTACATAAC
*
60567418 -TACAGAACTTACATAAC
1 TTACATAAC-TACATAAC
*
60567435 TTACATACCCTACATAA
1 TTACATA-ACTACATAA
60567452 ATTAAATAAG
Statistics
Matches: 74, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
15 4 0.05
16 40 0.54
17 5 0.07
18 24 0.32
19 1 0.01
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.29
Consensus pattern (17 bp):
TTACATAACTACATAAC
Found at i:60567359 original size:9 final size:9
Alignment explanation
Indices: 60567336--60567579 Score: 99
Period size: 9 Copynumber: 28.7 Consensus size: 9
60567326 ATATATTCAT
60567336 TTACATAAC
1 TTACATAAC
60567345 --ACATAAC
1 TTACATAAC
60567352 TTACATAAC
1 TTACATAAC
* *
60567361 ATACTTAA-
1 TTACATAAC
60567369 -TACATAAC
1 TTACATAAC
*
60567377 TTGCATAAC
1 TTACATAAC
60567386 TTACATAA-
1 TTACATAAC
*
60567394 -TACACAAC
1 TTACATAAC
*
60567402 TTACAT--G
1 TTACATAAC
*
60567409 TGTAAATAA-
1 T-TACATAAC
*
60567418 -TACAGAAC
1 TTACATAAC
60567426 TTACATAAC
1 TTACATAAC
*
60567435 TTACATACC
1 TTACATAAC
* *
60567444 CTACATAAA
1 TTACATAAC
* *
60567453 TTAAATAAG
1 TTACATAAC
60567462 TTACATAA-
1 TTACATAAC
*
60567470 TAATACATACC
1 T--TACATAAC
* *
60567481 CTACATAAA
1 TTACATAAC
* *
60567490 TTAAATAAG
1 TTACATAAC
60567499 TTACATAA-
1 TTACATAAC
*
60567507 -TACACAAC
1 TTACATAAC
**
60567515 TTACGCAAC
1 TTACATAAC
*
60567524 TTACATAAG
1 TTACATAAC
*
60567533 TTTCATAA-
1 TTACATAAC
*
60567541 -TACACAAC
1 TTACATAAC
***
60567549 TTATGCAAC
1 TTACATAAC
60567558 TTACATAA-
1 TTACATAAC
*
60567566 -GACATAAC
1 TTACATAAC
60567574 TTACAT
1 TTACAT
60567580 GTGTAAATAA
Statistics
Matches: 172, Mismatches: 43, Indels: 40
0.67 0.17 0.16
Matches are distributed among these distances:
7 42 0.24
8 5 0.03
9 119 0.69
10 6 0.03
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (9 bp):
TTACATAAC
Found at i:60567383 original size:25 final size:25
Alignment explanation
Indices: 60567337--60567441 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 25
60567327 TATATTCATT
*
60567337 TACATAACACATAACTTACATAACA
1 TACATAATACATAACTTACATAACA
* * *
60567362 TACTTAATACATAACTTGCATAACT
1 TACATAATACATAACTTACATAACA
* ***
60567387 TACATAATACACAACTTACAT-GTG
1 TACATAATACATAACTTACATAACA
* * *
60567411 TAAATAATACAGAACTTACATAACT
1 TACATAATACATAACTTACATAACA
60567436 TACATA
1 TACATA
60567442 CCCTACATAA
Statistics
Matches: 63, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
24 19 0.30
25 44 0.70
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.30
Consensus pattern (25 bp):
TACATAATACATAACTTACATAACA
Found at i:60567407 original size:34 final size:34
Alignment explanation
Indices: 60567369--60567551 Score: 123
Period size: 34 Copynumber: 5.1 Consensus size: 34
60567359 ACATACTTAA
* * *
60567369 TACATAACTTGCATAACTTACATAATACACAACT
1 TACATAAATTACATAAGTTACATAATACACAACT
* * * * *
60567403 TACATGTGTAAATAATACAGAACTTACATAACTTACATACCC
1 TACA----TAAAT--TACATAAGTTACATAA--TACACAACT
* * *
60567445 TACATAAATTAAATAAGTTACATAATAATACATACCC
1 TACATAAATTACATAAGTTACATAAT-ACACA-A-CT
*
60567482 TACATAAATTAAATAAGTTACATAATACACAACT
1 TACATAAATTACATAAGTTACATAATACACAACT
** * *
60567516 TACGCAACTTACATAAGTTTCATAATACACAACT
1 TACATAAATTACATAAGTTACATAATACACAACT
60567550 TA
1 TA
60567552 TGCAACTTAC
Statistics
Matches: 119, Mismatches: 19, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
34 37 0.31
35 4 0.03
36 17 0.14
37 28 0.24
38 9 0.08
40 14 0.12
42 10 0.08
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (34 bp):
TACATAAATTACATAAGTTACATAATACACAACT
Found at i:60567480 original size:37 final size:37
Alignment explanation
Indices: 60567436--60567508 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
60567426 TTACATAACT
60567436 TACATACCCTACATAAATTAAATAAGTTACATAATAA
1 TACATACCCTACATAAATTAAATAAGTTACATAATAA
60567473 TACATACCCTACATAAATTAAATAAGTTACATAATA
1 TACATACCCTACATAAATTAAATAAGTTACATAATA
60567509 CACAACTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (37 bp):
TACATACCCTACATAAATTAAATAAGTTACATAATAA
Found at i:60567557 original size:34 final size:34
Alignment explanation
Indices: 60567494--60567566 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
60567484 CATAAATTAA
60567494 ATAAGTTACATAATACACAACTTACGCAACTTAC
1 ATAAGTTACATAATACACAACTTACGCAACTTAC
* *
60567528 ATAAGTTTCATAATACACAACTTATGCAACTTAC
1 ATAAGTTACATAATACACAACTTACGCAACTTAC
60567562 ATAAG
1 ATAAG
60567567 ACATAACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.29
Consensus pattern (34 bp):
ATAAGTTACATAATACACAACTTACGCAACTTAC
Found at i:60567787 original size:34 final size:34
Alignment explanation
Indices: 60567742--60567821 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 34
60567732 TTGTCAAGGG
*
60567742 TAAGTTACATAATACACAACTTACGCAACTTACA
1 TAAGTTACATAATACACAACTTACACAACTTACA
* *
60567776 TAAGTTTCATAATACACAACTTACACAACTTTCA
1 TAAGTTACATAATACACAACTTACACAACTTACA
*
60567810 TAACTTACATAA
1 TAAGTTACATAA
60567822 CTTATAACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.30
Consensus pattern (34 bp):
TAAGTTACATAATACACAACTTACACAACTTACA
Found at i:60567830 original size:16 final size:18
Alignment explanation
Indices: 60567793--60567832 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
60567783 CATAATACAC
60567793 AACTTACACAACTTTCAT
1 AACTTACACAACTTTCAT
*
60567811 AACTTACATAAC-TT-AT
1 AACTTACACAACTTTCAT
60567827 AACTTA
1 AACTTA
60567833 TTCCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 2 0.10
18 11 0.52
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (18 bp):
AACTTACACAACTTTCAT
Found at i:60567967 original size:34 final size:34
Alignment explanation
Indices: 60567922--60568001 Score: 124
Period size: 34 Copynumber: 2.4 Consensus size: 34
60567912 TTGTCAAGGG
*
60567922 TAAGTTACATAATACACAACTTACGCAACTTACA
1 TAAGTTACATAATACACAACTTACACAACTTACA
* *
60567956 TAAGTTTCATAATACACAACTTACACAACTTTCA
1 TAAGTTACATAATACACAACTTACACAACTTACA
*
60567990 TAACTTACATAA
1 TAAGTTACATAA
60568002 CTTACATAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.30
Consensus pattern (34 bp):
TAAGTTACATAATACACAACTTACACAACTTACA
Found at i:60567975 original size:25 final size:26
Alignment explanation
Indices: 60567947--60568010 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
60567937 ACAACTTACG
*
60567947 CAACTTACATAAGTTTCATAA-TACA
1 CAACTTACATAACTTTCATAACTACA
*
60567972 CAACTTACACAACTTTCATAACTTACA
1 CAACTTACATAACTTTCATAAC-TACA
*
60567999 TAACTTACATAA
1 CAACTTACATAA
60568011 TGTATAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 19 0.58
27 14 0.42
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.31
Consensus pattern (26 bp):
CAACTTACATAACTTTCATAACTACA
Found at i:60568008 original size:9 final size:9
Alignment explanation
Indices: 60567926--60568010 Score: 70
Period size: 9 Copynumber: 9.9 Consensus size: 9
60567916 CAAGGGTAAG
60567926 TTACATAA-
1 TTACATAAC
*
60567934 -TACACAAC
1 TTACATAAC
**
60567942 TTACGCAAC
1 TTACATAAC
*
60567951 TTACATAAG
1 TTACATAAC
*
60567960 TTTCATAA-
1 TTACATAAC
*
60567968 -TACACAAC
1 TTACATAAC
*
60567976 TTACACAAC
1 TTACATAAC
*
60567985 TTTCATAAC
1 TTACATAAC
60567994 TTACATAAC
1 TTACATAAC
60568003 TTACATAA
1 TTACATAA
60568011 TGTATAACTT
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
7 11 0.18
9 51 0.82
ACGTcount: A:0.44, C:0.24, G:0.02, T:0.31
Consensus pattern (9 bp):
TTACATAAC
Found at i:60568077 original size:189 final size:180
Alignment explanation
Indices: 60567729--60568114 Score: 682
Period size: 189 Copynumber: 2.1 Consensus size: 180
60567719 ACATACCCTA
60567729 AATTTGTCAAGGGTAAGTTACATAATACACAACTTACGCAACTTACATAAGTTTCATAATACACA
1 AATTTGTCAAGGGTAAGTTACATAATACACAACTTACGCAACTTACATAAGTTTCATAATACACA
60567794 ACTTACACAACTTTCATAACTTACATAACTTATAACTTATTCCTAAATCCTAAACCCGTGCAATT
66 ACTTACACAACTTTCATAACTTACATAACTTATAACTTATTCCTAAATCCTAAACCCGTGCAATT
60567859 TATTGTCAATGTCAGACTTCAAGAATTAAGAAATGGACCATTCTTGGATG
131 TATTGTCAATGTCAGACTTCAAGAATTAAGAAATGGACCATTCTTGGATG
60567909 AATTTGTCAAGGGTAAGTTACATAATACACAACTTACGCAACTTACATAAGTTTCATAATACACA
1 AATTTGTCAAGGGTAAGTTACATAATACACAACTTACGCAACTTACATAAGTTTCATAATACACA
60567974 ACTTACACAACTTTCATAACTTACATAACTTACATAATGTATAACTTATTCCTAAATCCTAAACC
66 ACTTACACAACTTTCATAACTTACAT-A---AC----T-TATAACTTATTCCTAAATCCTAAACC
*
60568039 CGTGCAATTTATTGTCAATGTCAGACTTCAAGAATTAAGAAATGGACCGTTCTTGGATG
122 CGTGCAATTTATTGTCAATGTCAGACTTCAAGAATTAAGAAATGGACCATTCTTGGATG
60568098 AATTTGTCAAGGGTAAG
1 AATTTGTCAAGGGTAAG
60568115 CGACGGTTAT
Statistics
Matches: 196, Mismatches: 1, Indels: 9
0.95 0.00 0.04
Matches are distributed among these distances:
180 91 0.46
181 1 0.01
184 2 0.01
188 1 0.01
189 101 0.52
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (180 bp):
AATTTGTCAAGGGTAAGTTACATAATACACAACTTACGCAACTTACATAAGTTTCATAATACACA
ACTTACACAACTTTCATAACTTACATAACTTATAACTTATTCCTAAATCCTAAACCCGTGCAATT
TATTGTCAATGTCAGACTTCAAGAATTAAGAAATGGACCATTCTTGGATG
Found at i:60568997 original size:16 final size:16
Alignment explanation
Indices: 60568976--60569007 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
60568966 AAATGATGCA
*
60568976 CAGTCAAGAAAGAAGC
1 CAGTCAAGAAACAAGC
60568992 CAGTCAAGAAACAAGC
1 CAGTCAAGAAACAAGC
60569008 TTTTCATGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.50, C:0.22, G:0.22, T:0.06
Consensus pattern (16 bp):
CAGTCAAGAAACAAGC
Found at i:60573648 original size:21 final size:21
Alignment explanation
Indices: 60573622--60573671 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
60573612 CTACAACTTA
*
60573622 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
* *
60573643 AAGCAGAAGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
60573664 AAGCAGAG
1 AAGCAGAG
60573672 CAGGCCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.44, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:60574875 original size:2 final size:2
Alignment explanation
Indices: 60574868--60574903 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
60574858 NNNNNAATAG
60574868 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60574904 AATTCAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60578611 original size:2 final size:2
Alignment explanation
Indices: 60578606--60578657 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
60578596 TTATATATCG
* * *
60578606 TA TA TA TA TG CA TA TT TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60578647 TA TA TA TA TA T
1 TA TA TA TA TA T
60578658 TTTAAGCTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60579901 original size:3 final size:3
Alignment explanation
Indices: 60579893--60579965 Score: 132
Period size: 3 Copynumber: 25.0 Consensus size: 3
60579883 ACTAGATGGT
60579893 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
60579941 ATA ATA ATA ATA AT- ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
60579966 TTACAATGAA
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 64 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:60581048 original size:24 final size:24
Alignment explanation
Indices: 60581020--60581076 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
60581010 TGAAATTTGT
**
60581020 TTAGGTTTTGGTCTGTTTGGGCCA
1 TTAGGTTTTGGTAAGTTTGGGCCA
**
60581044 TTAGGTTTTTTTAAGTTTGGGCCA
1 TTAGGTTTTGGTAAGTTTGGGCCA
60581068 TTAGGTTTT
1 TTAGGTTTT
60581077 TTTGGGTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.12, C:0.09, G:0.28, T:0.51
Consensus pattern (24 bp):
TTAGGTTTTGGTAAGTTTGGGCCA
Found at i:60581085 original size:24 final size:24
Alignment explanation
Indices: 60581034--60581079 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
60581024 GTTTTGGTCT
60581034 GTTTGGGCCATTAGGTTTTTTTAA
1 GTTTGGGCCATTAGGTTTTTTTAA
60581058 GTTTGGGCCATTAGGTTTTTTT
1 GTTTGGGCCATTAGGTTTTTTT
60581080 GGGTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.13, C:0.09, G:0.26, T:0.52
Consensus pattern (24 bp):
GTTTGGGCCATTAGGTTTTTTTAA
Found at i:60581366 original size:3 final size:3
Alignment explanation
Indices: 60581317--60581346 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
60581307 ATTAACACAC
60581317 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
60581347 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:60583215 original size:29 final size:29
Alignment explanation
Indices: 60583173--60583248 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
60583163 GAAGAGGTAG
60583173 AGAACTTGTTCGTTGAGAGTTCGCGATGA
1 AGAACTTGTTCGTTGAGAGTTCGCGATGA
60583202 AGAACTTGTTCGTTGAGAGTTCGCGATGA
1 AGAACTTGTTCGTTGAGAGTTCGCGATGA
*
60583231 AGAACTTGTTCATTGAGA
1 AGAACTTGTTCGTTGAGA
60583249 AATTGTGTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (29 bp):
AGAACTTGTTCGTTGAGAGTTCGCGATGA
Found at i:60586102 original size:34 final size:34
Alignment explanation
Indices: 60586059--60586159 Score: 107
Period size: 34 Copynumber: 2.9 Consensus size: 34
60586049 ATGCTCAAAA
60586059 TGGACAACATTTATACATGCAAAGCAACCACATT
1 TGGACAACATTTATACATGCAAAGCAACCACATT
** *
60586093 TGGACAACA-TTATAACATATAAAATCAACCACATT
1 TGGACAACATTTAT-ACAT-GCAAAGCAACCACATT
* * *
60586128 TGGATATCATTGTA-ATATGCAAAGCAACCACA
1 TGGACAACATT-TATACATGCAAAGCAACCACA
60586160 CTTTAATACC
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
33 4 0.07
34 24 0.44
35 23 0.43
36 1 0.02
37 2 0.04
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.25
Consensus pattern (34 bp):
TGGACAACATTTATACATGCAAAGCAACCACATT
Found at i:60595467 original size:24 final size:25
Alignment explanation
Indices: 60595435--60595511 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 25
60595425 TGGCTCGAAA
* *
60595435 GAGCGTCCCGTTATTAGCT-TTCAT
1 GAGCTTCCCGTTAATAGCTCTTCAT
* * *
60595459 GAGCTTCCCATTAAATGGCTCTT-GT
1 GAGCTTCCCGTT-AATAGCTCTTCAT
60595484 GAGCTTCCCGTTAATAGCTCTTCA-
1 GAGCTTCCCGTTAATAGCTCTTCAT
60595508 GAGC
1 GAGC
60595512 ATCTCAATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 23 0.55
25 17 0.40
26 2 0.05
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (25 bp):
GAGCTTCCCGTTAATAGCTCTTCAT
Found at i:60595486 original size:25 final size:24
Alignment explanation
Indices: 60595458--60595505 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
60595448 TTAGCTTTCA
*
60595458 TGAGCTTCCCATTAAATGGCTCTTG
1 TGAGCTTCCCATT-AATAGCTCTTG
*
60595483 TGAGCTTCCCGTTAATAGCTCTT
1 TGAGCTTCCCATTAATAGCTCTT
60595506 CAGAGCATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (24 bp):
TGAGCTTCCCATTAATAGCTCTTG
Found at i:60596395 original size:20 final size:20
Alignment explanation
Indices: 60596370--60596411 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
60596360 TATTGGCTTG
60596370 TGAATGTGTTAAAGTGTTAA
1 TGAATGTGTTAAAGTGTTAA
*
60596390 TGAATGTGTTAATGTGTTAA
1 TGAATGTGTTAAAGTGTTAA
60596410 TG
1 TG
60596412 TGTTAATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (20 bp):
TGAATGTGTTAAAGTGTTAA
Found at i:60596418 original size:8 final size:8
Alignment explanation
Indices: 60596372--60596420 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
60596362 TTGGCTTGTG
60596372 AATGTGTT
1 AATGTGTT
*
60596380 AAAGTGTT
1 AATGTGTT
60596388 AA--TG--
1 AATGTGTT
60596392 AATGTGTT
1 AATGTGTT
60596400 AATGTGTT
1 AATGTGTT
60596408 AATGTGTT
1 AATGTGTT
60596416 AATGT
1 AATGT
60596421 AGAAATGTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
4 2 0.06
6 4 0.11
8 30 0.83
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.45
Consensus pattern (8 bp):
AATGTGTT
Found at i:60596427 original size:16 final size:16
Alignment explanation
Indices: 60596392--60596429 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
60596382 AGTGTTAATG
*
60596392 AATGTGTTAATGTGTT
1 AATGTGTTAATGTGTA
60596408 AATGTGTTAATGTAG-A
1 AATGTGTTAATGT-GTA
60596424 AATGTG
1 AATGTG
60596430 GCCTTGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (16 bp):
AATGTGTTAATGTGTA
Found at i:60600859 original size:22 final size:22
Alignment explanation
Indices: 60600799--60600856 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
60600789 AATCTTCAAG
60600799 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
60600818 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
60600840 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
60600857 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:60601243 original size:20 final size:19
Alignment explanation
Indices: 60601187--60601244 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
60601177 ACATGTGTAC
*
60601187 ATATATATTTATAATTTTA
1 ATATATATTTTTAATTTTA
*
60601206 ATACATATTTTGTAA-TTTA
1 ATATATATTTT-TAATTTTA
60601225 TATATATATTTTTATATTTT
1 -ATATATATTTTTA-ATTTT
60601245 TCTTATGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 15 0.47
20 14 0.44
21 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATATATTTTTAATTTTA
Found at i:60603004 original size:21 final size:20
Alignment explanation
Indices: 60602980--60603033 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
60602970 AATAAAAAGG
60602980 ATAAATTTTAAAACAATGTTA
1 ATAAATTTTAAAAC-ATGTTA
* *
60603001 ATAAACTCT-AAACATGTTA
1 ATAAATTTTAAAACATGTTA
60603020 ATAATAATTTTAAA
1 AT-A-AATTTTAAA
60603034 TAACGATGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 8 0.31
20 5 0.19
21 11 0.42
22 2 0.08
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (20 bp):
ATAAATTTTAAAACATGTTA
Found at i:60603394 original size:86 final size:86
Alignment explanation
Indices: 60603260--60603533 Score: 372
Period size: 86 Copynumber: 3.2 Consensus size: 86
60603250 AAGATCAGGG
* *** * *
60603260 TCTTTAGCGGCGTTTTTTTCTCAAATGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCAC
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGTGGCGCTTTGACCAC
*
60603325 AAACGCCACGAAAGAACCTAA
66 AAACGCCACTAAAGAACCTAA
* *
60603346 TCTTTAGTGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGTGGCGCTTCGACCAC
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGTGGCGCTTTGACCAC
60603411 AAACGCCACTAAAGAACCTAA
66 AAACGCCACTAAAGAACCTAA
* * * **
60603432 TCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAA-AGACCATGATCTTTAGTGGCGCTTTTTCCA
1 TCTTTAGCGGCGCTTTCCCCTCAAACGCCGC-AATAGACCCTGATCTATAGTGGCGCTTTGACCA
* *
60603496 CAAACGCCGCTAAA-AACCCTTA
65 CAAACGCCACTAAAGAA-CCTAA
60603518 TCTTTAGCGGCGCTTT
1 TCTTTAGCGGCGCTTT
60603534 GACCAAAAAC
Statistics
Matches: 168, Mismatches: 18, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
85 2 0.01
86 164 0.98
87 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (86 bp):
TCTTTAGCGGCGCTTTCCCCTCAAACGCCGCAATAGACCCTGATCTATAGTGGCGCTTTGACCAC
AAACGCCACTAAAGAACCTAA
Found at i:60603500 original size:129 final size:129
Alignment explanation
Indices: 60603302--60603552 Score: 335
Period size: 129 Copynumber: 1.9 Consensus size: 129
60603292 ATAGACCCTG
* *
60603302 ATCTATAGCGGCGCTTTGACCACAAACGCCACGAAAGAACCTAATCTTTAGTGGCGCTTTCCCCT
1 ATCTATAGCGGCGCTTTCACCACAAACGCCACGAAAGAACCTAATCTTTAGTGGCGCTTTCCCCA
* * *
60603367 CAAACGCCGC-AATAGACCCTGATCTATAGTGGCGCTTCGACCACAAACGCCACTAAAGAACCTA
66 CAAACGCCGCTAA-AAACCCTGATCTATAGCGGCGCTTCGACCAAAAACGCCACTAAAGAACCTA
* * * * * **
60603431 ATCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAG-ACCATGATCTTTAGTGGCGCTTTTTCC
1 ATCTATAGCGGCGCTTTCACCACAAACGCCACGAAAGAACC-TAATCTTTAGTGGCGCTTTCCCC
* * *
60603495 ACAAACGCCGCTAAAAACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAA
65 ACAAACGCCGCTAAAAACCCTGATCTATAGCGGCGCTTCGACCAAAAACGCCACTAAA
60603553 TTTGGCAGAT
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
128 3 0.03
129 100 0.95
130 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (129 bp):
ATCTATAGCGGCGCTTTCACCACAAACGCCACGAAAGAACCTAATCTTTAGTGGCGCTTTCCCCA
CAAACGCCGCTAAAAACCCTGATCTATAGCGGCGCTTCGACCAAAAACGCCACTAAAGAACCTA
Found at i:60603544 original size:43 final size:43
Alignment explanation
Indices: 60603296--60603552 Score: 250
Period size: 43 Copynumber: 6.0 Consensus size: 43
60603286 GCCGCAATAG
* *
60603296 ACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCACGAAAGA
1 ACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAAA-A
* * ** * * *
60603340 A-CCTAATCTTTAGTGGCGCTTTCCCCTCAAACGCCGC-AATAG
1 ACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAA-AA
* * *
60603382 ACCCTGATCTATAGTGGCGCTTCGACCACAAACGCCACTAAAGA
1 ACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAAA-A
* ** * *
60603426 A-CCTAATCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAG
1 ACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAAAA
* * ** *
60603468 ACCATGATCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAA
1 ACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAAAA
* *
60603511 ACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAA
1 ACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAAA
60603553 TTTGGCAGAT
Statistics
Matches: 171, Mismatches: 37, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
42 4 0.02
43 163 0.95
44 4 0.02
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (43 bp):
ACCCTGATCTTTAGCGGCGCTTTGACCACAAACGCCACTAAAA
Found at i:60603887 original size:21 final size:21
Alignment explanation
Indices: 60603861--60603973 Score: 127
Period size: 21 Copynumber: 5.4 Consensus size: 21
60603851 TTTGACGCTG
60603861 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
**
60603882 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
60603903 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
60603924 CTGTACTTCTCTCGTTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
60603945 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
60603966 ATCTGCTT
1 CTCTGCTT
60603974 TAAGCTGCTG
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 78 1.00
ACGTcount: A:0.04, C:0.42, G:0.18, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:60608840 original size:9 final size:9
Alignment explanation
Indices: 60608804--60609208 Score: 206
Period size: 9 Copynumber: 48.0 Consensus size: 9
60608794 AATTGCACGG
60608804 GTAAGTTAT
1 GTAAGTTAT
*
60608813 GT-A-TTGT
1 GTAAGTTAT
*
60608820 GTAAGCTAT
1 GTAAGTTAT
*
60608829 GTAAGTTGT
1 GTAAGTTAT
60608838 GT-A-TTAT
1 GTAAGTTAT
60608845 GTAAGTTAT
1 GTAAGTTAT
60608854 -T-A-TTAT
1 GTAAGTTAT
60608860 GCTTTAAGTTAT
1 G---TAAGTTAT
*
60608872 GTAAGTAAT
1 GTAAGTTAT
60608881 GT-A-TTAT
1 GTAAGTTAT
*
60608888 GTAAGTTGT
1 GTAAGTTAT
*
60608897 GT-A-TAAT
1 GTAAGTTAT
*
60608904 GTTAGTTAT
1 GTAAGTTAT
**
60608913 CAAAGTTAT
1 GTAAGTTAT
60608922 GT-A-TTAT
1 GTAAGTTAT
60608929 GTAAGTTAT
1 GTAAGTTAT
*
60608938 TTAAGTTAT
1 GTAAGTTAT
*
60608947 GTAA--CAT
1 GTAAGTTAT
*
60608954 GTAAATTAT
1 GTAAGTTAT
60608963 GTAAGTTAT
1 GTAAGTTAT
* *
60608972 GTAGGCTAT
1 GTAAGTTAT
* *
60608981 GTATGTTAA
1 GTAAGTTAT
*
60608990 GTAAGTAAT
1 GTAAGTTAT
60608999 GT-A-TTAT
1 GTAAGTTAT
*
60609006 GTAAGTTGT
1 GTAAGTTAT
*
60609015 GT-A-TAAT
1 GTAAGTTAT
*
60609022 GTTAGTTAT
1 GTAAGTTAT
**
60609031 CAAAGTTAT
1 GTAAGTTAT
60609040 GT-A-TTAT
1 GTAAGTTAT
60609047 GTAAGTTAT
1 GTAAGTTAT
*
60609056 TTAAGTTAT
1 GTAAGTTAT
*
60609065 GTAA--CAT
1 GTAAGTTAT
*
60609072 GTAAATTAT
1 GTAAGTTAT
60609081 GTAAGTTAT
1 GTAAGTTAT
*
60609090 GTAGGTTAT
1 GTAAGTTAT
* *
60609099 GTATGTTAA
1 GTAAGTTAT
*
60609108 GTAAGTAAT
1 GTAAGTTAT
60609117 GT-A-TTAT
1 GTAAGTTAT
*
60609124 GTAAGTTGT
1 GTAAGTTAT
*
60609133 GT-A-TAAT
1 GTAAGTTAT
*
60609140 GTTAGTTAT
1 GTAAGTTAT
**
60609149 CAAAGTTAT
1 GTAAGTTAT
60609158 GT-A-TTAT
1 GTAAGTTAT
***
60609165 GTGTTTCTAT
1 GTAAGT-TAT
*
60609175 TTAAGTTAT
1 GTAAGTTAT
*
60609184 GTAAGTTGT
1 GTAAGTTAT
60609193 GT-A-TTAT
1 GTAAGTTAT
60609200 GTAAGTTAT
1 GTAAGTTAT
60609209 TAAAAATTGA
Statistics
Matches: 292, Mismatches: 69, Indels: 70
0.68 0.16 0.16
Matches are distributed among these distances:
6 4 0.01
7 73 0.25
8 24 0.08
9 179 0.61
10 6 0.02
11 1 0.00
12 5 0.02
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:60608845 original size:16 final size:16
Alignment explanation
Indices: 60608826--60609148 Score: 144
Period size: 16 Copynumber: 19.8 Consensus size: 16
60608816 TTGTGTAAGC
*
60608826 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
60608842 TATGTAAGTTAT-TAT
1 TATGTAAGTTATGTAT
*
60608857 TATGCT---TTAAG--T
1 TATG-TAAGTTATGTAT
*
60608869 TATGTAAGTAATGTAT
1 TATGTAAGTTATGTAT
*
60608885 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * **
60608901 AATGTTAGTTATCAAAGT
1 TATGTAAGTTAT-GTA-T
60608919 TATGT-A-TTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
60608935 TATTTAAGTTATGTAA
1 TATGTAAGTTATGTAT
* *
60608951 CATGTAAATTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
60608969 TATGTAGGCTATGTATGT
1 TATGTAAGTTATGTA--T
* *
60608987 TAAGTAAGTAATGTAT
1 TATGTAAGTTATGTAT
*
60609003 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * **
60609019 AATGTTAGTTATCAAAGT
1 TATGTAAGTTAT-GTA-T
60609037 TATGT-A-TTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
60609053 TATTTAAGTTATGTAA
1 TATGTAAGTTATGTAT
* *
60609069 CATGTAAATTATGTAAGT
1 TATGTAAGTTATGT-A-T
*
60609087 TATGTAGGTTATGTATGT
1 TATGTAAGTTATGTA--T
* *
60609105 TAAGTAAGTAATGTAT
1 TATGTAAGTTATGTAT
*
60609121 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* *
60609137 AATGTTAGTTAT
1 TATGTAAGTTAT
60609149 CAAAGTTATG
Statistics
Matches: 227, Mismatches: 57, Indels: 46
0.69 0.17 0.14
Matches are distributed among these distances:
11 1 0.00
12 5 0.02
13 3 0.01
14 3 0.01
15 7 0.03
16 126 0.56
17 12 0.05
18 70 0.31
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:60608897 original size:59 final size:58
Alignment explanation
Indices: 60608826--60609208 Score: 269
Period size: 59 Copynumber: 6.5 Consensus size: 58
60608816 TTGTGTAAGC
*
60608826 TATGTAAGTTGTGTATTATGTAAGTTAT-TA-TTATGCTTTAAGTTATGTAAGTAATGTAT
1 TATGTAAGTTGTGTATAATGTAAGTTATATAGTTATG---TAAGTTATGTAAGTAATGTAT
* * * *
60608885 TATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGT-A-TTATGTAAGTTATTTAAGT
1 TATGTAAGTTGTGTATAATGTAAGTTAT-ATAGTTATGTAAGTTATGTAAGTAATGT-A-T
** ** * * * * *
60608944 TATGTAACATGTAAATTATGTAAGTTATGTAGGCTATGTATGTTAAGTAAGTAATGTAT
1 TATGTAAGTTGTGTATAATGTAAGTTATATA-GTTATGTAAGTTATGTAAGTAATGTAT
* * * *
60609003 TATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGT-A-TTATGTAAGTTATTTAAGT
1 TATGTAAGTTGTGTATAATGTAAGTTAT-ATAGTTATGTAAGTTATGTAAGTAATGT-A-T
** ** * * * *
60609062 TATGTAACATGTAAATTATGTAAGTTATGTAGGTTATGTATGTTAAGTAAGTAATGTAT
1 TATGTAAGTTGTGTATAATGTAAGTTATATA-GTTATGTAAGTTATGTAAGTAATGTAT
* * *** * *
60609121 TATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGT-A-TTATGTGTTTCTATTTAAGT
1 TATGTAAGTTGTGTATAATGTAAGTTAT-ATAGTTATGTAAGTTATGTAAGT-AATGT-A-T
*
60609181 TATGTAAGTTGTGTATTATGTAAGTTAT
1 TATGTAAGTTGTGTATAATGTAAGTTAT
60609209 TAAAAATTGA
Statistics
Matches: 246, Mismatches: 60, Indels: 35
0.72 0.18 0.10
Matches are distributed among these distances:
57 31 0.13
58 8 0.03
59 146 0.59
60 31 0.13
61 25 0.10
62 5 0.02
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.46
Consensus pattern (58 bp):
TATGTAAGTTGTGTATAATGTAAGTTATATAGTTATGTAAGTTATGTAAGTAATGTAT
Found at i:60608912 original size:25 final size:25
Alignment explanation
Indices: 60608864--60609017 Score: 118
Period size: 25 Copynumber: 6.1 Consensus size: 25
60608854 TATTATGCTT
60608864 TAAGTTATGTAAGTAATGT-A-TTATG
1 TAAGTTATGT-A-TAATGTAAGTTATG
* * *
60608889 TAAGTTGTGTATAATGTTAGTTATC
1 TAAGTTATGTATAATGTAAGTTATG
* * *
60608914 AAAGTTATGTATTATGTAAGTTATT
1 TAAGTTATGTATAATGTAAGTTATG
*
60608939 TAAGTTATGTA-ACATGTAAATTATG
1 TAAGTTATGTATA-ATGTAAGTTATG
* *
60608964 TAAGTTATGTAGGCT-ATGTATGTTAAG
1 TAAGTTATGTA---TAATGTAAGTTATG
* * *
60608991 TAAGTAATGTATTATGTAAGTTGTG
1 TAAGTTATGTATAATGTAAGTTATG
60609016 TA
1 TA
60609018 TAATGTTAGT
Statistics
Matches: 103, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
23 6 0.06
24 3 0.03
25 75 0.73
27 19 0.18
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (25 bp):
TAAGTTATGTATAATGTAAGTTATG
Found at i:60609019 original size:118 final size:118
Alignment explanation
Indices: 60608867--60609208 Score: 594
Period size: 118 Copynumber: 2.9 Consensus size: 118
60608857 TATGCTTTAA
*
60608867 GTTATGTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTA
1 GTTAAGTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTA
60608932 AGTTATTTAAGTTATGTAACATGTAAATTATGTAAGTTATGTAGGCTATGTAT
66 AGTTATTTAAGTTATGTAACATGTAAATTATGTAAGTTATGTAGGCTATGTAT
60608985 GTTAAGTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTA
1 GTTAAGTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTA
*
60609050 AGTTATTTAAGTTATGTAACATGTAAATTATGTAAGTTATGTAGGTTATGTAT
66 AGTTATTTAAGTTATGTAACATGTAAATTATGTAAGTTATGTAGGCTATGTAT
*
60609103 GTTAAGTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTG
1 GTTAAGTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTA
** ** **
60609168 TTTCTATTTAAGTTATGTAAGTTGTGTATTATGTAAGTTAT
66 AGT-TATTTAAGTTATGTAACATGTAAATTATGTAAGTTAT
60609209 TAAAAATTGA
Statistics
Matches: 214, Mismatches: 9, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
118 181 0.85
119 33 0.15
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (118 bp):
GTTAAGTAAGTAATGTATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTA
AGTTATTTAAGTTATGTAACATGTAAATTATGTAAGTTATGTAGGCTATGTAT
Found at i:60609036 original size:25 final size:25
Alignment explanation
Indices: 60609008--60609092 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
60608998 TGTATTATGT
* *
60609008 AAGTTGTGTATAATGTTAGTTATCA
1 AAGTTATGTATAATGTAAGTTATCA
* **
60609033 AAGTTATGTATTATGTAAGTTATTT
1 AAGTTATGTATAATGTAAGTTATCA
* **
60609058 AAGTTATGTA-ACATGTAAATTATGT
1 AAGTTATGTATA-ATGTAAGTTATCA
60609083 AAGTTATGTA
1 AAGTTATGTA
60609093 GGTTATGTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.45
Consensus pattern (25 bp):
AAGTTATGTATAATGTAAGTTATCA
Found at i:60609193 original size:26 final size:25
Alignment explanation
Indices: 60609039--60609208 Score: 82
Period size: 25 Copynumber: 6.7 Consensus size: 25
60609029 ATCAAAGTTA
* *
60609039 TGTATTATGTAAGTTATTTAAGT-TA
1 TGTATTATGTAAGTTATGT-AGTATG
** *
60609064 TGTAACATGTAAATTATGTAAGTTATG
1 TGTATTATGTAAGTTATGT-AG-TATG
* * * *
60609091 TAG-GTTATGTATGTTAAGTAAGTA-A
1 T-GTATTATGTAAGTTATGT-AGTATG
*
60609116 TGTATTATGTAAGTTGTGTA-TAATG
1 TGTATTATGTAAGTTATGTAGT-ATG
** *
60609141 T-TAGTTATCAAAGTTATGTATTATG
1 TGTA-TTATGTAAGTTATGTAGTATG
* *
60609166 TGTTTCTATTTAAGTTATGTAAGT-TG
1 TGTAT-TATGTAAGTTATGT-AGTATG
60609192 TGTATTATGTAAGTTAT
1 TGTATTATGTAAGTTAT
60609209 TAAAAATTGA
Statistics
Matches: 108, Mismatches: 26, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
23 1 0.01
24 5 0.05
25 61 0.56
26 23 0.21
27 17 0.16
28 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (25 bp):
TGTATTATGTAAGTTATGTAGTATG
Found at i:60609425 original size:121 final size:121
Alignment explanation
Indices: 60609211--60609488 Score: 504
Period size: 121 Copynumber: 2.3 Consensus size: 121
60609201 TAAGTTATTA
* *
60609211 AAAATTGAAATGTAGGATATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
1 AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
*
60609276 AATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTCATT-TCTAAT
66 AATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTCATTGAC-AAT
60609332 AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
1 AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
*
60609397 AATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTTATTGACAAT
66 AATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTCATTGACAAT
60609453 AAAATTGAAATATAGGTTATATATCCATACCATATA
1 AAAATTGAAATATAGGTTATATATCCATACCATATA
60609489 GCTAAATTTT
Statistics
Matches: 152, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
121 151 0.99
122 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (121 bp):
AAAATTGAAATATAGGTTATATATCCATACCATATATGGGGTGATATATTAAAAATATAGGTTTT
AATATTTAAAAATAACATTTACAATTATTTTTAAAATTATAAAATTCATTGACAAT
Found at i:60609508 original size:2 final size:2
Alignment explanation
Indices: 60609501--60609531 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
60609491 TAAATTTTTA
60609501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60609532 AAGTTTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60609558 original size:18 final size:18
Alignment explanation
Indices: 60609535--60609623 Score: 101
Period size: 18 Copynumber: 4.8 Consensus size: 18
60609525 ATATATAAAG
60609535 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
60609553 TTTAAGTAATGTAAGTTATAAA
1 TTTAAGTAATGTAA--TAT--A
**
60609575 TTTTTGTAA-GTAATATA
1 TTTAAGTAATGTAATATA
60609592 TTTAAGTAATGTAATATA
1 TTTAAGTAATGTAATATA
*
60609610 TTTTAGTAA-GTAAT
1 TTTAAGTAATGTAAT
60609624 GTAAGTAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
17 13 0.21
18 30 0.49
19 3 0.05
20 3 0.05
21 4 0.07
22 8 0.13
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (18 bp):
TTTAAGTAATGTAATATA
Found at i:60609613 original size:35 final size:37
Alignment explanation
Indices: 60609539--60609623 Score: 120
Period size: 39 Copynumber: 2.3 Consensus size: 37
60609529 ATAAAGTTTA
60609539 AGTAATGTAATATATTTAAGTAATGTAAGTTATAAATTTT
1 AGTAA-GTAATATATTTAAGTAATGTAAG-TAT-AATTTT
*
60609579 TGTAAGTAATATATTTAAGTAATGTAA-TAT-ATTTT
1 AGTAAGTAATATATTTAAGTAATGTAAGTATAATTTT
60609614 AGTAAGTAAT
1 AGTAAGTAAT
60609624 GTAAGTAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
35 14 0.33
37 3 0.07
39 22 0.51
40 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (37 bp):
AGTAAGTAATATATTTAAGTAATGTAAGTATAATTTT
Found at i:60609618 original size:31 final size:31
Alignment explanation
Indices: 60609537--60609641 Score: 91
Period size: 31 Copynumber: 3.5 Consensus size: 31
60609527 ATATAAAGTT
60609537 TAAGTAATGTAATATA--TT--TAAGTAATG
1 TAAGTAATGTAATATATTTTAGTAAGTAATG
* * *
60609564 TAAGT--TATAA-ATTTTTGTAAGTAA-TATATT
1 TAAGTAATGTAATATATTT-T-AGTAAGTA-ATG
60609594 TAAGTAATGTAATATATTTTAGTAAGTAATG
1 TAAGTAATGTAATATATTTTAGTAAGTAATG
*
60609625 TAAGTAATTTAATATAT
1 TAAGTAATGTAATATAT
60609642 ACTTTNNNNN
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
24 2 0.03
25 4 0.07
26 1 0.02
27 6 0.10
29 2 0.03
30 10 0.17
31 23 0.38
32 7 0.12
33 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (31 bp):
TAAGTAATGTAATATATTTTAGTAAGTAATG
Found at i:60615075 original size:41 final size:41
Alignment explanation
Indices: 60615006--60615203 Score: 238
Period size: 41 Copynumber: 4.8 Consensus size: 41
60614996 TTATTATTAC
* * * *
60615006 TAGCGGCACTTTTTTAAAAACGCCGCTAAAGGCCACAGCAA
1 TAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCAGAGCAT
* * ** *
60615047 TACCGGCGCTTCTTTAAAAATGCCGCTAAAGATCTGAGCAT
1 TAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCAGAGCAT
60615088 TAGCGGCGCTT-TTTCAAAAACGCCGCTAAAGGCCAGAGCAT
1 TAGCGGCGCTTCTTT-AAAAACGCCGCTAAAGGCCAGAGCAT
*
60615129 TAGCGGCGCTTAC-TCAAAAACGCCGCTAAAGGCCAGAGCAT
1 TAGCGGCGCTT-CTTTAAAAACGCCGCTAAAGGCCAGAGCAT
* * * *
60615170 TAGCGTCGTTTATTCAAAAACGCCGCTAAAGGCC
1 TAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCC
60615204 CCAAAAACTC
Statistics
Matches: 135, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.02
41 131 0.97
42 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.21
Consensus pattern (41 bp):
TAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCAGAGCAT
Found at i:60615148 original size:82 final size:82
Alignment explanation
Indices: 60615006--60615203 Score: 265
Period size: 82 Copynumber: 2.4 Consensus size: 82
60614996 TTATTATTAC
* * * *
60615006 TAGCGGCACTTTTTTAAAAACGCCGCTAAAGGCCACAGCAATACCGGCGCTTCTTTAAAAATGCC
1 TAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCACAGCAATACCGGCGCTTCTTCAAAAACGCC
* *
60615071 GCTAAAGATCTGAGCAT
66 GCTAAAGACCAGAGCAT
* * *
60615088 TAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTAC-TCAAAAACGC
1 TAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCACAGCAATACCGGCGCTT-CTTCAAAAACGC
*
60615152 CGCTAAAGGCCAGAGCAT
65 CGCTAAAGACCAGAGCAT
*
60615170 TAGCGTCG-TTTATTCAAAAACGCCGCTAAAGGCC
1 TAGCGGCGCTTT-TTCAAAAACGCCGCTAAAGGCC
60615204 CCAAAAACTC
Statistics
Matches: 103, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
81 3 0.03
82 99 0.96
83 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.21
Consensus pattern (82 bp):
TAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCACAGCAATACCGGCGCTTCTTCAAAAACGCC
GCTAAAGACCAGAGCAT
Found at i:60615332 original size:40 final size:41
Alignment explanation
Indices: 60615258--60615391 Score: 152
Period size: 40 Copynumber: 3.4 Consensus size: 41
60615248 GCACTTTTCA
60615258 GAAAA-CGCCGCTAATGCT-TATTTTTAGCGGCGTTTTTG-
1 GAAAAGCGCCGCTAATGCTCTATTTTTAGCGGCGTTTTTGT
* **
60615296 GATAAGCGCCGCTAATGCTCTACCTTTAGCGGCG-TTTTGT
1 GAAAAGCGCCGCTAATGCTCTATTTTTAGCGGCGTTTTTGT
* * *
60615336 TAAAAGCGCCGCTAATGCTCGATTTTTAGTGGCGTTTTTTGT
1 GAAAAGCGCCGCTAATGCTCTATTTTTAGCGGCG-TTTTTGT
**
60615378 CCAAA-CGCCGCTAA
1 GAAAAGCGCCGCTAA
60615392 AAGCCTGTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
38 4 0.05
39 18 0.22
40 40 0.50
41 9 0.11
42 9 0.11
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (41 bp):
GAAAAGCGCCGCTAATGCTCTATTTTTAGCGGCGTTTTTGT
Found at i:60620149 original size:3 final size:3
Alignment explanation
Indices: 60620141--60620179 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
60620131 AATATTAAAG
60620141 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
60620180 CAATTGAGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:60620656 original size:30 final size:31
Alignment explanation
Indices: 60620588--60620671 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
60620578 AAGATTTTAA
* *
60620588 TTTAATAAAAAATAAAATTATACTTTAACCCT
1 TTTAA-AAATAATAAAATTATAATTTAACCCT
* * *
60620620 TTTAAAAATAATAAGATTTTAATTTAATCC-
1 TTTAAAAATAATAAAATTATAATTTAACCCT
* *
60620650 TTTAAAAATTATAAAAATATAA
1 TTTAAAAATAATAAAATTATAA
60620672 ACTACTAGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
30 18 0.42
31 20 0.47
32 5 0.12
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (31 bp):
TTTAAAAATAATAAAATTATAATTTAACCCT
Found at i:60624215 original size:18 final size:18
Alignment explanation
Indices: 60624181--60624219 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
60624171 TGAAAGGGTC
60624181 ACAAAGAAAAGCAAAATT
1 ACAAAGAAAAGCAAAATT
*
60624199 ACAAA-AAAAGACTAAATT
1 ACAAAGAAAAG-CAAAATT
60624217 ACA
1 ACA
60624220 CAATGTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.67, C:0.13, G:0.08, T:0.13
Consensus pattern (18 bp):
ACAAAGAAAAGCAAAATT
Found at i:60624433 original size:60 final size:59
Alignment explanation
Indices: 60624364--60624498 Score: 171
Period size: 59 Copynumber: 2.3 Consensus size: 59
60624354 GACAAAATTG
**
60624364 AATAATTGAGTGACTATTTTATAACTTTTCATAGTTGGATGACCAAAAAAGAAATTTACT
1 AATAATTGAGTGACTATTTTATAA-TTTTCATAAATGGATGACCAAAAAAGAAATTTACT
* * * * * * *
60624424 AGTAGTTGAGTGGCCATTTTGTAATTTTCATAAATGGGTGACCGAAAAAGAAATTTACT
1 AATAATTGAGTGACTATTTTATAATTTTCATAAATGGATGACCAAAAAAGAAATTTACT
*
60624483 AATAATTGATTGACTA
1 AATAATTGAGTGACTA
60624499 CTAATGTAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
59 42 0.69
60 19 0.31
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (59 bp):
AATAATTGAGTGACTATTTTATAATTTTCATAAATGGATGACCAAAAAAGAAATTTACT
Found at i:60625557 original size:2 final size:2
Alignment explanation
Indices: 60625550--60625579 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60625540 TTCTCAATAA
60625550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60625580 TTGTCCCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60629891 original size:16 final size:17
Alignment explanation
Indices: 60629851--60629894 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
60629841 TTCTCGACAT
* *
60629851 AGTTGTTCTCAATTTAG
1 AGTTGTTCTGAATTAAG
60629868 AGGTTGTTCTGAA-TAAG
1 A-GTTGTTCTGAATTAAG
60629885 AGTTGTTCTG
1 AGTTGTTCTG
60629895 CGGTAATGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.38
17 5 0.21
18 10 0.42
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.43
Consensus pattern (17 bp):
AGTTGTTCTGAATTAAG
Found at i:60629975 original size:16 final size:15
Alignment explanation
Indices: 60629950--60629979 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
60629940 CCGGAAAAAC
60629950 ACAATTGTTCTAAAT
1 ACAATTGTTCTAAAT
60629965 ACAAGTTGTTCTAAA
1 ACAA-TTGTTCTAAA
60629980 CAACGGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (15 bp):
ACAATTGTTCTAAAT
Found at i:60634718 original size:12 final size:12
Alignment explanation
Indices: 60634701--60634731 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
60634691 GAAATGGAGA
60634701 ATCATCATCACC
1 ATCATCATCACC
*
60634713 ATCATCATCAGC
1 ATCATCATCACC
60634725 ATCATCA
1 ATCATCA
60634732 ATATGGTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.26
Consensus pattern (12 bp):
ATCATCATCACC
Found at i:60638712 original size:6 final size:6
Alignment explanation
Indices: 60638701--60638768 Score: 136
Period size: 6 Copynumber: 11.3 Consensus size: 6
60638691 TTTGCATTCA
60638701 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
60638749 ATATGT ATATGT ATATGT AT
1 ATATGT ATATGT ATATGT AT
60638769 GACTACGTGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATATGT
Found at i:60642402 original size:26 final size:26
Alignment explanation
Indices: 60642339--60642403 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 26
60642329 AACACTATCA
60642339 TAAATATAATAAATATTTTATTATAT
1 TAAATATAATAAATATTTTATTATAT
* *
60642365 TAAAAAACATAATAAATATTTTATTGTAT
1 T---AAATATAATAAATATTTTATTATAT
60642394 TAAATATAAT
1 TAAATATAAT
60642404 TTTTAAAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 9 0.27
29 24 0.73
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
TAAATATAATAAATATTTTATTATAT
Found at i:60646036 original size:171 final size:170
Alignment explanation
Indices: 60645744--60646132 Score: 584
Period size: 171 Copynumber: 2.3 Consensus size: 170
60645734 TCAATTGATT
* * * *
60645744 TAAATTCTAAATTCTTTCCTAAATTAAGTTAATTAAACAGTAATTAAAGAAGGTTTCTCGTTAGT
1 TAAATTATAAATTCATTACTAAATTAA-TTAATTAAACAGTAATTAAAGAAGGTTTCCCGTTAGT
* *
60645809 AAAAACCTTCAACTCAGATTGATCTAGTTTCAGTGATGTGATCATTGCATAGATTAACGAAACTA
65 AAAAACCTCCAACTCAGATTGATCTAGTTTCAATGATGTGATCATTGCATAGATTAACGAAACTA
* *
60645874 AATCAGATCTAAAAATCAGTGATGTGAATAG-GCCATGAAGC
130 AATCAAATCTAAAAATCAGTGATGTGAATAGTG-CATAAAGC
60645915 TAAATTATAAATTCATTACTAAATTAATCTAATTAAACAGTAATTAAAGAAGGTTTCCCGTCT-G
1 TAAATTATAAATTCATTACTAAATTAAT-TAATTAAACAGTAATTAAAGAAGGTTTCCCGT-TAG
* *
60645979 TAAAAACCTCCAACTCAGATTGATCTAGTTTCAATGATGTGATTATTTCATAGATTAACGAAACT
64 TAAAAACCTCCAACTCAGATTGATCTAGTTTCAATGATGTGATCATTGCATAGATTAACGAAACT
*
60646044 AAATCAAATCTAAAAATCAGTGATGTGATTAGTGCATAAAGC
129 AAATCAAATCTAAAAATCAGTGATGTGAATAGTGCATAAAGC
* * * *
60646086 TAAATTATAAATTCATTGCTCAATTAATTTAATCAAACAGTTATTAA
1 TAAATTATAAATTCATTACTAAATTAA-TTAATTAAACAGTAATTAA
60646133 CAAGCTTTGT
Statistics
Matches: 199, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
170 1 0.01
171 195 0.98
172 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (170 bp):
TAAATTATAAATTCATTACTAAATTAATTAATTAAACAGTAATTAAAGAAGGTTTCCCGTTAGTA
AAAACCTCCAACTCAGATTGATCTAGTTTCAATGATGTGATCATTGCATAGATTAACGAAACTAA
ATCAAATCTAAAAATCAGTGATGTGAATAGTGCATAAAGC
Found at i:60646675 original size:31 final size:30
Alignment explanation
Indices: 60646619--60646676 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
60646609 CAATCTACAT
60646619 TATTTTTTAAATTAAAAAATATTTATATTA
1 TATTTTTTAAATTAAAAAATATTTATATTA
* *
60646649 TATTATTTTAATATTTAATAAT-TTTATA
1 TATT-TTTTAA-ATTAAAAAATATTTATA
60646677 CAATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 4 0.17
31 12 0.50
32 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TATTTTTTAAATTAAAAAATATTTATATTA
Found at i:60651220 original size:87 final size:87
Alignment explanation
Indices: 60651071--60651241 Score: 279
Period size: 87 Copynumber: 2.0 Consensus size: 87
60651061 CGTAGCTAAA
* * *
60651071 GTCGTACCGGAATCCTTGACTAAAAAGGGAAAAGATAAAGTCGACATCGAATAGCTTTGAATTCC
1 GTCGTACCGAAATCCTCGACTAAAAAGGGAAAAGATAAAGTCGACATCGAATAGCTTGGAATTCC
60651136 TAGTTTGTATTTCTATAATAAC
66 TAGTTTGTATTTCTATAATAAC
* * *
60651158 GTCGTACCGAAATCCTCGACTAAAAGGGGAAAAGATAAAGTCGACTTCGAATAGCTTGGAATTTC
1 GTCGTACCGAAATCCTCGACTAAAAAGGGAAAAGATAAAGTCGACATCGAATAGCTTGGAATTCC
*
60651223 TGGTTTGTATTTCTATAAT
66 TAGTTTGTATTTCTATAAT
60651242 CTGAACCTAG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (87 bp):
GTCGTACCGAAATCCTCGACTAAAAAGGGAAAAGATAAAGTCGACATCGAATAGCTTGGAATTCC
TAGTTTGTATTTCTATAATAAC
Found at i:60651462 original size:16 final size:16
Alignment explanation
Indices: 60651437--60651470 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
60651427 ATGAATATAT
* *
60651437 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
60651453 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
60651469 AT
1 AT
60651471 TGGATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:60659124 original size:19 final size:18
Alignment explanation
Indices: 60659091--60659127 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
60659081 GTTGAAGCGG
*
60659091 TTTAATATTTTTTTAATT
1 TTTAATATTTATTTAATT
60659109 TTTAATTATTTATTTAATT
1 TTTAA-TATTTATTTAATT
60659128 ATTATTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTAATATTTATTTAATT
Found at i:60659415 original size:31 final size:31
Alignment explanation
Indices: 60659380--60659438 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
60659370 AAGTTTAATG
* *
60659380 ACCAAAATAAATCTAGTTGCTAAGTTCATGT
1 ACCAAAATAAACCTAGTTGCCAAGTTCATGT
* *
60659411 ACCAAAGTGAACCTAGTTGCCAAGTTCA
1 ACCAAAATAAACCTAGTTGCCAAGTTCA
60659439 AAGGCCGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (31 bp):
ACCAAAATAAACCTAGTTGCCAAGTTCATGT
Found at i:60662319 original size:2 final size:2
Alignment explanation
Indices: 60662267--60662306 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
60662257 TACGTATTCG
* * *
60662267 TA TA TT TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60662307 AATTTTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:60676015 original size:2 final size:2
Alignment explanation
Indices: 60676008--60676032 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60675998 CAAAGGGCTA
60676008 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
60676033 GAAAAAAGAA
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:60693683 original size:15 final size:15
Alignment explanation
Indices: 60693663--60693712 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
60693653 TGAGAATGAT
60693663 AGTGATGATGCTGAC
1 AGTGATGATGCTGAC
* * *
60693678 AGTGATGAGGATGAT
1 AGTGATGATGCTGAC
60693693 AGTGATGATGCTGAC
1 AGTGATGATGCTGAC
*
60693708 TGTGA
1 AGTGA
60693713 CTATCATCCT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.36, T:0.28
Consensus pattern (15 bp):
AGTGATGATGCTGAC
Found at i:60693692 original size:30 final size:30
Alignment explanation
Indices: 60693653--60693712 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
60693643 TGGTTAATGG
60693653 TGAGAATGATAGTGATGATGCTGACAGTGA
1 TGAGAATGATAGTGATGATGCTGACAGTGA
* *
60693683 TGAGGATGATAGTGATGATGCTGACTGTGA
1 TGAGAATGATAGTGATGATGCTGACAGTGA
60693713 CTATCATCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.35, T:0.28
Consensus pattern (30 bp):
TGAGAATGATAGTGATGATGCTGACAGTGA
Found at i:60696840 original size:55 final size:55
Alignment explanation
Indices: 60696780--60696896 Score: 216
Period size: 55 Copynumber: 2.1 Consensus size: 55
60696770 TTATGGTTTT
*
60696780 TTTCCAATCACTGTATCCTTCCATTTTTGGGTCTGTAATGTAATGAATTATGACC
1 TTTCCAATCACTGTATCCTTCCATTTCTGGGTCTGTAATGTAATGAATTATGACC
*
60696835 TTTCCAATCGCTGTATCCTTCCATTTCTGGGTCTGTAATGTAATGAATTATGACC
1 TTTCCAATCACTGTATCCTTCCATTTCTGGGTCTGTAATGTAATGAATTATGACC
60696890 TTTCCAA
1 TTTCCAA
60696897 ATTTGGCTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (55 bp):
TTTCCAATCACTGTATCCTTCCATTTCTGGGTCTGTAATGTAATGAATTATGACC
Found at i:60697985 original size:15 final size:15
Alignment explanation
Indices: 60697965--60698014 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
60697955 TGAGAATGAT
60697965 AGTGATGATGCTGAC
1 AGTGATGATGCTGAC
* * *
60697980 AGTGATGAGGATGAT
1 AGTGATGATGCTGAC
60697995 AGTGATGATGCTGAC
1 AGTGATGATGCTGAC
*
60698010 TGTGA
1 AGTGA
60698015 CTATCATCCT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.36, T:0.28
Consensus pattern (15 bp):
AGTGATGATGCTGAC
Found at i:60697995 original size:30 final size:30
Alignment explanation
Indices: 60697955--60698014 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
60697945 TGGTTAATGG
60697955 TGAGAATGATAGTGATGATGCTGACAGTGA
1 TGAGAATGATAGTGATGATGCTGACAGTGA
* *
60697985 TGAGGATGATAGTGATGATGCTGACTGTGA
1 TGAGAATGATAGTGATGATGCTGACAGTGA
60698015 CTATCATCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.35, T:0.28
Consensus pattern (30 bp):
TGAGAATGATAGTGATGATGCTGACAGTGA
Found at i:60707794 original size:2 final size:2
Alignment explanation
Indices: 60707787--60707811 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60707777 AAATGAATTT
60707787 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
60707812 GAATTGAATA
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:60708393 original size:38 final size:39
Alignment explanation
Indices: 60708341--60708423 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
60708331 ATTTGCCGGC
*
60708341 TTACTGATCAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATCAGGCACTTTATGTGCCGAATACTGTTACTG
* *
60708379 TTACTGATTC-GGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGA-TCAGGCACTTTATGTGCCGAATACTGTTACTG
60708418 TTACTG
1 TTACTG
60708424 TTACCGATTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 12 0.30
39 28 0.70
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (39 bp):
TTACTGATCAGGCACTTTATGTGCCGAATACTGTTACTG
Found at i:60708433 original size:45 final size:45
Alignment explanation
Indices: 60708368--60708517 Score: 237
Period size: 45 Copynumber: 3.3 Consensus size: 45
60708358 ATGTGCCGAC
* *
60708368 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTGT
*
60708413 TACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTGT
* * *
60708458 TACAGTTACTGTTACAGATTCAACACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTGT
*
60708503 TATTGTTACTGTTAC
1 TACTGTTACTGTTAC
60708518 TGCTACCGTT
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 97 1.00
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGACACTTTGTGTGTCGAATACTGT
Found at i:60708515 original size:6 final size:6
Alignment explanation
Indices: 60708497--60708540 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
60708487 GTGTGTTGAA
* * *
60708497 TACTGT TATTGT TACTGT TACTGC TACCGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
60708541 TATTGGTGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:60709210 original size:2 final size:2
Alignment explanation
Indices: 60709203--60709232 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60709193 GTAAGATTTA
60709203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60709233 GTTGTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60719376 original size:38 final size:38
Alignment explanation
Indices: 60719325--60719402 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
60719315 TCCATTGCTA
* * *
60719325 AGGGTGGGTTTGGATAGGCGAG-GCGTTTACTTGCGTTT
1 AGGGTGAGTTTGGATAGGCG-GTGCGTTTACCTGCGGTT
*
60719363 AGGGTGAGTTTGGATGGGCGGTGCGTTTACCTGCGGTT
1 AGGGTGAGTTTGGATAGGCGGTGCGTTTACCTGCGGTT
60719401 AG
1 AG
60719403 TGTAAAAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 1 0.03
38 34 0.97
ACGTcount: A:0.13, C:0.12, G:0.44, T:0.32
Consensus pattern (38 bp):
AGGGTGAGTTTGGATAGGCGGTGCGTTTACCTGCGGTT
Found at i:60721170 original size:3 final size:3
Alignment explanation
Indices: 60721164--60721191 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
60721154 TAAAAAAAAC
60721164 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
60721192 GATGATGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:60722420 original size:55 final size:55
Alignment explanation
Indices: 60722359--60722475 Score: 225
Period size: 55 Copynumber: 2.1 Consensus size: 55
60722349 TTATGGTTTT
*
60722359 TTTCCAATCACTGTATCCTTCCATTTTTGGGTCTGTAATGTAATGAATTATGACC
1 TTTCCAATCACTGTATCCTTCCATTTCTGGGTCTGTAATGTAATGAATTATGACC
60722414 TTTCCAATCACTGTATCCTTCCATTTCTGGGTCTGTAATGTAATGAATTATGACC
1 TTTCCAATCACTGTATCCTTCCATTTCTGGGTCTGTAATGTAATGAATTATGACC
60722469 TTTCCAA
1 TTTCCAA
60722476 ATTTGGCTAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (55 bp):
TTTCCAATCACTGTATCCTTCCATTTCTGGGTCTGTAATGTAATGAATTATGACC
Found at i:60731377 original size:16 final size:17
Alignment explanation
Indices: 60731356--60731390 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
60731346 GGTAAAGTAC
*
60731356 AATTTTATTAA-TATAA
1 AATTTTATAAATTATAA
60731372 AATTTTATAAATTATAA
1 AATTTTATAAATTATAA
60731389 AA
1 AA
60731391 GAGCCTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTTATAAATTATAA
Found at i:60732098 original size:15 final size:15
Alignment explanation
Indices: 60732053--60732099 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
60732043 ATAACTTAAA
*
60732053 TTCAACACTTAAATT
1 TTCAACACTTAATTT
* *
60732068 TTCAATACTTATTTT
1 TTCAACACTTAATTT
*
60732083 TTCAACACTTACTTT
1 TTCAACACTTAATTT
60732098 TT
1 TT
60732100 TTAACTTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (15 bp):
TTCAACACTTAATTT
Found at i:60732619 original size:2 final size:2
Alignment explanation
Indices: 60732612--60732658 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
60732602 CAATACATTT
* *
60732612 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60732654 TA TA T
1 TA TA T
60732659 TTTTAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60733101 original size:22 final size:22
Alignment explanation
Indices: 60733059--60733101 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
60733049 AATTATGAAT
* *
60733059 TTTATATTTATATTATTTTTAA
1 TTTATATTTATATGATATTTAA
60733081 TTTATATTTATTATGA-ATTTA
1 TTTATATTTA-TATGATATTTA
60733102 GGGTTGTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTATATTTATATGATATTTAA
Found at i:60750452 original size:18 final size:18
Alignment explanation
Indices: 60750388--60750462 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 18
60750378 CTTTTAAAAT
*
60750388 AATTATAATTTAATTTAA
1 AATTATAATTTAATTTAC
* * *
60750406 AATTATTAGTTAAAAATTGTGC
1 AATTA-TAATT--TAATT-TAC
60750428 TAATTATAATTTAATTTAC
1 -AATTATAATTTAATTTAC
* *
60750447 AATTATTAGTTAATTT
1 AATTATAATTTAATTT
60750463 TATTAATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
18 19 0.44
19 6 0.14
20 4 0.09
21 4 0.09
22 5 0.12
23 5 0.12
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (18 bp):
AATTATAATTTAATTTAC
Found at i:60753417 original size:101 final size:101
Alignment explanation
Indices: 60753239--60753490 Score: 351
Period size: 101 Copynumber: 2.5 Consensus size: 101
60753229 ATCCATAGTC
* * *
60753239 ATATGCTTCAACGCACTCGAACCCATGTCCTCCTGCATCGGCAACAATGTTCATGCCCAGAACTA
1 ATATGCTTCAACGCACTCGAACCCATGTCCTCCTGCATTGACAACAATGCTCATGCCCAGAACTA
** *
60753304 CCCATAGTCCCTCTTCAACTCTTAAATAGGAGGATA
66 CCCATAGTCCCTCCCCAACCCTTAAATAGGAGGATA
* * * * *
60753340 ATGTGCTTCAACGCACTCGAACTCATGTCTTCTTGCATTGACAACAATGCTCATGCCTAGAACTA
1 ATATGCTTCAACGCACTCGAACCCATGTCCTCCTGCATTGACAACAATGCTCATGCCCAGAACTA
60753405 CCCATAGTCCCTCCCCAACCCTTAAATAGGAGGATA
66 CCCATAGTCCCTCCCCAACCCTTAAATAGGAGGATA
* * * * * *
60753441 ATACGCTTCATCGCATTCGAACCCACGTCCTCCTACACTGACAACAATGC
1 ATATGCTTCAACGCACTCGAACCCATGTCCTCCTGCATTGACAACAATGC
60753491 CAATACTGAT
Statistics
Matches: 130, Mismatches: 21, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 130 1.00
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.25
Consensus pattern (101 bp):
ATATGCTTCAACGCACTCGAACCCATGTCCTCCTGCATTGACAACAATGCTCATGCCCAGAACTA
CCCATAGTCCCTCCCCAACCCTTAAATAGGAGGATA
Found at i:60767491 original size:2 final size:2
Alignment explanation
Indices: 60767484--60767509 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60767474 TGGATTGATG
60767484 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
60767510 TAAAATTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60769577 original size:2 final size:2
Alignment explanation
Indices: 60769570--60769596 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60769560 AGAGTTAATT
60769570 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
60769597 TTTAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60773248 original size:22 final size:23
Alignment explanation
Indices: 60773208--60773250 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
60773198 AAAGGATAAA
**
60773208 TTTTAATTTTTATTTCAAATATT
1 TTTTAATTTTTATACCAAATATT
60773231 TTTTAA-TTTTATACCAAATA
1 TTTTAATTTTTATACCAAATA
60773251 AAATCATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTAATTTTTATACCAAATATT
Found at i:60773870 original size:97 final size:97
Alignment explanation
Indices: 60773703--60773883 Score: 272
Period size: 97 Copynumber: 1.9 Consensus size: 97
60773693 TACGTGGACG
* * * *
60773703 TATTATGTTTAAAGGGAATTGTCCAAATGAACATCATTTGGTCATCAGACCAATTACGAGGGTTC
1 TATTATGTTTAAAGAGAATTGTCCAAATGAACATCATTCGGCCATCAGACCAATTACAAGGGTTC
*
60773768 TTTTTATTCTCGAATGTTGATATACATGCATA
66 ATTTTATTCTCGAATGTTGATATACATGCATA
* * * * *
60773800 TATTATGTTTAAAGAGAGTTGTCCAAATGAACATTATTCGGCCGTTAGACTAATTACAAGGGTTC
1 TATTATGTTTAAAGAGAATTGTCCAAATGAACATCATTCGGCCATCAGACCAATTACAAGGGTTC
60773865 ATTTTATTCTCGAATGTTG
66 ATTTTATTCTCGAATGTTG
60773884 TTATTAAGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 74 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (97 bp):
TATTATGTTTAAAGAGAATTGTCCAAATGAACATCATTCGGCCATCAGACCAATTACAAGGGTTC
ATTTTATTCTCGAATGTTGATATACATGCATA
Found at i:60779980 original size:18 final size:17
Alignment explanation
Indices: 60779939--60779981 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
60779929 TGAATGGACT
60779939 TATTTTTTTACCTAAAC
1 TATTTTTTTACCTAAAC
60779956 TCATTTTTTTAGCCTAATAC
1 T-ATTTTTTTA-CCTAA-AC
60779976 T-TTTTT
1 TATTTTT
60779982 CCAAACCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 1 0.04
18 14 0.61
19 5 0.22
20 3 0.13
ACGTcount: A:0.23, C:0.16, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTTTTTACCTAAAC
Found at i:60790673 original size:162 final size:162
Alignment explanation
Indices: 60790380--60790696 Score: 541
Period size: 162 Copynumber: 2.0 Consensus size: 162
60790370 TTCTTCTCTA
60790380 TAACCTCTACAACCATCTACACCACTATAGTCCGATGACTCTCTATCCCACAAGAATAAACCGGT
1 TAACCTCTACAACCATCTACACCACTATAGTCCGATGACTCTCTATCCCACAAGAATAAACCGGT
* * *
60790445 ACCTTCTTGTCATCTTTCTCCCTTTGTTGGTTCCTACTATCCACATGAAGTAATAGTAGGCTAAA
66 ACCTTCTTGTCATCTTTCTCCCTTTGTTGATTCCTACAATCCACATGAAGTAATAGTAGACTAAA
60790510 GGGTT-AAAGATTGAAAATGTTGTTCCTCAAC
131 GGGTTAAAAGATTGAAAATGTTGTTCCTCAAC
*
60790541 TAACCTCTACAACCATCTACACCATTATAGTCCGATGACTCTCTATCGCC-CAAGAATAAA-CGG
1 TAACCTCTACAACCATCTACACCACTATAGTCCGATGACTCTCTATC-CCACAAGAATAAACCGG
*
60790604 ATACCTTTCTTGTCATCTTTCTCCCTTTGTTGATTCCTACAATCTACATGAAGTAATAGTAGACT
65 -TACC-TTCTTGTCATCTTTCTCCCTTTGTTGATTCCTACAATCCACATGAAGTAATAGTAGACT
60790669 AAAGGGTTAAAAGATTGAAAATGTTGTT
128 AAAGGGTTAAAAGATTGAAAATGTTGTT
60790697 GAGGAAATTA
Statistics
Matches: 147, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
160 3 0.02
161 60 0.41
162 65 0.44
163 19 0.13
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (162 bp):
TAACCTCTACAACCATCTACACCACTATAGTCCGATGACTCTCTATCCCACAAGAATAAACCGGT
ACCTTCTTGTCATCTTTCTCCCTTTGTTGATTCCTACAATCCACATGAAGTAATAGTAGACTAAA
GGGTTAAAAGATTGAAAATGTTGTTCCTCAAC
Found at i:60793208 original size:47 final size:47
Alignment explanation
Indices: 60793153--60793243 Score: 141
Period size: 47 Copynumber: 1.9 Consensus size: 47
60793143 ATAGAAAATT
*
60793153 ATAAAAATTAAAT-AGAAATTTTAATAATCTATAAAA-TATATAAATAC
1 ATAAAAATTAAATGA-AAATTTTAA-AATCTAAAAAATTATATAAATAC
60793200 ATAAAAATTAAATGAAAATTTTAAAATCTAAAAAATTATATAAA
1 ATAAAAATTAAATGAAAATTTTAAAATCTAAAAAATTATATAAA
60793244 ATATTTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
46 10 0.24
47 30 0.73
48 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (47 bp):
ATAAAAATTAAATGAAAATTTTAAAATCTAAAAAATTATATAAATAC
Found at i:60793442 original size:1 final size:1
Alignment explanation
Indices: 60793436--60793460 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
60793426 TATTTTCTGC
60793436 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
60793461 TCACTCGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:60793529 original size:6 final size:6
Alignment explanation
Indices: 60793518--60793542 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
60793508 TACGGAAGCC
60793518 AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
60793543 TCCCTTCGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Done.