Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 12 of 18
Found at i:1984852 original size:2 final size:2
Alignment explanation
Indices: 1984845--1984876 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1984835 TTCAATATGG
1984845 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1984877 TTAATTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1987595 original size:27 final size:27
Alignment explanation
Indices: 1987535--1987587 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1987525 TTTAAATAAT
* * *
1987535 CACAACACTTGATAAATAATCAAGTGA
1 CACAACTCTTAATAAATAATCAAGAGA
*
1987562 CACAACTCTTAATAAATAATTAAGAG
1 CACAACTCTTAATAAATAATCAAGAG
1987588 TTACAACTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.25
Consensus pattern (27 bp):
CACAACTCTTAATAAATAATCAAGAGA
Found at i:1995503 original size:3 final size:3
Alignment explanation
Indices: 1995495--1995528 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1995485 TAATGTCGTA
1995495 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1995529 CAATTTGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1998860 original size:20 final size:20
Alignment explanation
Indices: 1998837--1998888 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1998827 ATTTTTCTGG
* * *
1998837 ATTGGTAAAAATTTAATTGA
1 ATTGATAAAAATTAAATTAA
*
1998857 ATTGATAAGAATTAAATTAA
1 ATTGATAAAAATTAAATTAA
1998877 ATTTGATAAAAA
1 A-TTGATAAAAA
1998889 AATTATTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.37
Consensus pattern (20 bp):
ATTGATAAAAATTAAATTAA
Found at i:2002032 original size:3 final size:3
Alignment explanation
Indices: 2002026--2002055 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2002016 AACAAAACAA
2002026 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2002056 GATGATGATG
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:2004353 original size:3 final size:3
Alignment explanation
Indices: 2004345--2004381 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2004335 TTTCAATGTC
2004345 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2004382 CTACAATTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2007965 original size:25 final size:25
Alignment explanation
Indices: 2007937--2007995 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
2007927 AAAAAATTAT
**
2007937 ATATTTTTATCATAT-TTTTATATTG
1 ATATTTTTAT-ATATGTTGAATATTG
**
2007962 ATATTTGAATATATGTTGAATATTG
1 ATATTTTTATATATGTTGAATATTG
2007987 ATATTTTTA
1 ATATTTTTA
2007996 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (25 bp):
ATATTTTTATATATGTTGAATATTG
Found at i:2010325 original size:3 final size:3
Alignment explanation
Indices: 2010319--2010345 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2010309 AACAAAACAA
2010319 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
2010346 GATGATGATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2010350 original size:3 final size:3
Alignment explanation
Indices: 2010344--2010372 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2010334 AATAATAATA
2010344 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
2010373 CTACAATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:2011625 original size:27 final size:27
Alignment explanation
Indices: 2011595--2011666 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
2011585 ATCTTTTGTG
2011595 TTTGTCAAAAATAGT-AGTTACTTTATA
1 TTTGTCAAAAATAGTGA-TTACTTTATA
* *
2011622 TTTGTCAAAAAATAGTGATTCCTTTTTA
1 TTTGTC-AAAAATAGTGATTACTTTATA
* *
2011650 TTTATCAAAAATTGTGA
1 TTTGTCAAAAATAGTGA
2011667 CTTATTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 16 0.41
28 22 0.56
29 1 0.03
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (27 bp):
TTTGTCAAAAATAGTGATTACTTTATA
Found at i:2011675 original size:24 final size:24
Alignment explanation
Indices: 2011647--2011701 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2011637 TGATTCCTTT
*
2011647 TTATTTATCAAAAATTGTGACTTA
1 TTATTTATCAAAAATTGTGACTAA
* *
2011671 TTATTTGTCAAAATTTGTGACTAA
1 TTATTTATCAAAAATTGTGACTAA
2011695 TT-TTTAT
1 TTATTTAT
2011702 TGCAAAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (24 bp):
TTATTTATCAAAAATTGTGACTAA
Found at i:2016155 original size:27 final size:27
Alignment explanation
Indices: 2016111--2016170 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
2016101 CGTGTTTGTA
*
2016111 AAAAATGGTGATTACTTTATATTTATC
1 AAAAATAGTGATTACTTTATATTTATC
* * * * *
2016138 AAAAATAGTGGTTCCTTTTTGTTTATT
1 AAAAATAGTGATTACTTTATATTTATC
2016165 AAAAAT
1 AAAAAT
2016171 TGTAACTTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.45
Consensus pattern (27 bp):
AAAAATAGTGATTACTTTATATTTATC
Found at i:2018571 original size:18 final size:19
Alignment explanation
Indices: 2018550--2018587 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2018540 TATATAAATT
2018550 TTAAAACATATAT-TTTTA
1 TTAAAACATATATATTTTA
**
2018568 TTAAGTCATATATATTTTA
1 TTAAAACATATATATTTTA
2018587 T
1 T
2018588 AATCATATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (19 bp):
TTAAAACATATATATTTTA
Found at i:2024700 original size:20 final size:21
Alignment explanation
Indices: 2024652--2024701 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2024642 AAAGTTCAAC
2024652 TTTTA-ATTATTTCAAAAAAT
1 TTTTATATTATTTCAAAAAAT
*
2024672 TATTT-TATTATTT-AAAATAT
1 T-TTTATATTATTTCAAAAAAT
2024692 TTTTATATTA
1 TTTTATATTA
2024702 AAATGAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 10 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTATATTATTTCAAAAAAT
Found at i:2026133 original size:2 final size:2
Alignment explanation
Indices: 2026126--2026182 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2026116 AAATTAGCCC
2026126 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2026168 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
2026183 AAGAATTTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2026815 original size:2 final size:2
Alignment explanation
Indices: 2026808--2026838 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2026798 ATAAAGCCTC
2026808 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2026839 ACGCATAGTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2031503 original size:25 final size:24
Alignment explanation
Indices: 2031457--2031504 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2031447 AAAAATAGCC
* * *
2031457 AAGTAATTTTCTTATTTTTTTAAA
1 AAGTAAATTACTTATTTATTTAAA
2031481 AAGTAAATTACTTATTTAATTTAA
1 AAGTAAATTACTTATTT-ATTTAA
2031505 TTGATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (24 bp):
AAGTAAATTACTTATTTATTTAAA
Found at i:2035224 original size:26 final size:27
Alignment explanation
Indices: 2035194--2035321 Score: 84
Period size: 26 Copynumber: 4.6 Consensus size: 27
2035184 AGATAAGATT
2035194 ATATAAATATATATAAAATA-ATTAAA
1 ATATAAATATATATAAAATATATTAAA
*
2035220 ATAT-AATATAATATAAAATATTTTAAA
1 ATATAAATAT-ATATAAAATATATTAAA
* * *
2035247 ATTTATATAATATAAATTATTAATATATCAAA
1 A--TATA-AATATATA-TA-AAATATATTAAA
* * *
2035279 AT-TAGTATAAATATAAAATAT-TTTAA
1 ATATA-AATATATATAAAATATATTAAA
*
2035305 ATATAATTATAATATAA
1 ATATAAATAT-ATATAA
2035322 TTATATATAT
Statistics
Matches: 77, Mismatches: 15, Indels: 19
0.69 0.14 0.17
Matches are distributed among these distances:
25 5 0.06
26 21 0.27
27 19 0.25
28 2 0.03
29 10 0.13
30 3 0.04
31 7 0.09
32 10 0.13
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (27 bp):
ATATAAATATATATAAAATATATTAAA
Found at i:2035225 original size:16 final size:16
Alignment explanation
Indices: 2035204--2035310 Score: 58
Period size: 17 Copynumber: 6.4 Consensus size: 16
2035194 ATATAAATAT
2035204 ATATAAAATAATTAAA
1 ATATAAAATAATTAAA
*
2035220 ATATAATATAATATAAA
1 ATATAAAATAAT-TAAA
2035237 ATATTTTAAAAT--TTATATA
1 ATA---TAAAATAATTA-A-A
* *
2035256 ATAT-AAATTATTAAT
1 ATATAAAATAATTAAA
* *
2035271 ATATCAAAATTAGTATAA
1 ATAT-AAAATAATTA-AA
* *
2035289 ATATAAAATATTTTAA
1 ATATAAAATAATTAAA
2035305 ATATAA
1 ATATAA
2035311 TTATAATATA
Statistics
Matches: 71, Mismatches: 9, Indels: 22
0.70 0.09 0.22
Matches are distributed among these distances:
15 8 0.11
16 21 0.30
17 26 0.37
18 7 0.10
19 4 0.06
20 5 0.07
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (16 bp):
ATATAAAATAATTAAA
Found at i:2035320 original size:11 final size:11
Alignment explanation
Indices: 2035304--2035344 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
2035294 AAATATTTTA
2035304 AATATAATTAT
1 AATATAATTAT
2035315 AATATAATTAT
1 AATATAATTAT
2035326 ATATATTAA-TAT
1 A-ATA-TAATTAT
2035338 AATATAA
1 AATATAA
2035345 ATTACTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.11
11 15 0.54
12 7 0.25
13 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATATAATTAT
Found at i:2035620 original size:3 final size:3
Alignment explanation
Indices: 2035606--2035641 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2035596 ACTTGGATAT
*
2035606 TTA TTC TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2035642 GTTAATCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2040693 original size:12 final size:10
Alignment explanation
Indices: 2040654--2040687 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2040644 CAATATTAAA
*
2040654 AAAATA-ATT
1 AAAATATATC
2040663 AAAATATATC
1 AAAATATATC
2040673 AAAATATATC
1 AAAATATATC
2040683 AAAAT
1 AAAAT
2040688 CTATATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.26
10 17 0.74
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAATATATC
Found at i:2041175 original size:134 final size:133
Alignment explanation
Indices: 2040936--2041203 Score: 491
Period size: 134 Copynumber: 2.0 Consensus size: 133
2040926 TCCCTCAATA
*
2040936 GTAAACATGAACTTTAGCCTCTAACAGATACAGGTCCATTTTAACTACAAGTCTGGAAATTTACT
1 GTAAACATGAACTTTAACCTCTAACAGATACAGGTCCATTTTAACTACAAGTCTGGAAATTTACT
* * *
2041001 AGGGACTACCCTACATGTAATGATCCAAAATACAACTAAGAAGAATTTTGTTCTCTCGGTTAATT
66 AGGGACTACCCTACATGTAATGATCCAAAATACAACTAAGAAGAATTGTGATATCTCGGTTAATT
2041066 TGG
131 TGG
2041069 GTAAACATGAACTTTAACCTCTAACAGATACAGGTCCATTTTAACTACCAAGTCTGGAAATTTAC
1 GTAAACATGAACTTTAACCTCTAACAGATACAGGTCCATTTTAACTA-CAAGTCTGGAAATTTAC
2041134 TAGGGACTACCCTACATGTAATGATCCAAAATACAACTAAGAAGAATTGTGATATCTCGGTTAAT
65 TAGGGACTACCCTACATGTAATGATCCAAAATACAACTAAGAAGAATTGTGATATCTCGGTTAAT
2041199 TTGG
130 TTGG
2041203 G
1 G
2041204 CTTAGATAAA
Statistics
Matches: 130, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
133 46 0.35
134 84 0.65
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (133 bp):
GTAAACATGAACTTTAACCTCTAACAGATACAGGTCCATTTTAACTACAAGTCTGGAAATTTACT
AGGGACTACCCTACATGTAATGATCCAAAATACAACTAAGAAGAATTGTGATATCTCGGTTAATT
TGG
Found at i:2043974 original size:30 final size:30
Alignment explanation
Indices: 2043933--2044014 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 30
2043923 GTTTTGGGCT
*
2043933 CTTCCTCTTCTTCTTCTTCCTCGGAAGATC
1 CTTCCTCTTCTTCTTCTTCCTCCGAAGATC
* *
2043963 CTTCTTCTTCTTCTTCTTCTTCCGAAGATGTC
1 CTTCCTCTTCTTCTTCTTCCTCCGAAGA--TC
* *
2043995 GCCTCCTCGTCTTCTTCTTC
1 -CTTCCTCTTCTTCTTCTTC
2044015 GGATGAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
30 25 0.58
32 2 0.05
33 16 0.37
ACGTcount: A:0.07, C:0.37, G:0.10, T:0.46
Consensus pattern (30 bp):
CTTCCTCTTCTTCTTCTTCCTCCGAAGATC
Found at i:2044381 original size:17 final size:18
Alignment explanation
Indices: 2044354--2044395 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
2044344 TATTTAAAAA
*
2044354 AATTAAAATATTTTTTAT
1 AATTAAAATATATTTTAT
*
2044372 -ATTAATATATATTTTAT
1 AATTAAAATATATTTTAT
2044389 AATTAAA
1 AATTAAA
2044396 TTTAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTAAAATATATTTTAT
Found at i:2045514 original size:15 final size:16
Alignment explanation
Indices: 2045493--2045544 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 16
2045483 TAAGAGAAAA
2045493 TATTTTAAAAATTATT
1 TATTTTAAAAATTATT
**
2045509 TA-TTTAATTATTATT
1 TATTTTAAAAATTATT
2045524 TAATTTTAAATAATATATT
1 T-ATTTTAAA-AAT-TATT
2045543 TA
1 TA
2045545 AAAGATTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 12 0.43
16 3 0.11
17 5 0.18
18 3 0.11
19 5 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTAAAAATTATT
Found at i:2045896 original size:30 final size:31
Alignment explanation
Indices: 2045826--2045904 Score: 74
Period size: 32 Copynumber: 2.6 Consensus size: 31
2045816 AATAATTACA
* *
2045826 TTAATATTATTATAATTTAAAAAAATTTAAAT
1 TTAAAATTATAAT-ATTTAAAAAAATTTAAAT
** *
2045858 AAACAAATTATAATATTTAACAAAATTT-AAT
1 TTA-AAATTATAATATTTAAAAAAATTTAAAT
2045889 TTAAAATTA-AA-ATTTA
1 TTAAAATTATAATATTTA
2045905 TTATTAACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
28 5 0.13
29 2 0.05
30 6 0.15
31 4 0.10
32 14 0.36
33 8 0.21
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (31 bp):
TTAAAATTATAATATTTAAAAAAATTTAAAT
Found at i:2046087 original size:30 final size:30
Alignment explanation
Indices: 2046051--2046124 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
2046041 AACTTGTAAA
2046051 TTAAAAGATTATTCTATCCTTAGTTAGAAC
1 TTAAAAGATTATTCTATCCTTAGTTAGAAC
*
2046081 TTAAAAGATTATTCTATCCTTAGTTCGAAC
1 TTAAAAGATTATTCTATCCTTAGTTAGAAC
2046111 TTAAAAGATTATTC
1 TTAAAAGATTATTC
2046125 CTTAATGGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (30 bp):
TTAAAAGATTATTCTATCCTTAGTTAGAAC
Found at i:2046340 original size:2 final size:2
Alignment explanation
Indices: 2046335--2046379 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2046325 ATAAGCATAC
*
2046335 AT AT AT AT AT AT AT AT GT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2046376 AT AT
1 AT AT
2046380 CACCATGGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2046602 original size:21 final size:20
Alignment explanation
Indices: 2046578--2046635 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
2046568 AATATAAATA
2046578 AATATTTGATATAAATAATTT
1 AATATTTGATATAAAT-ATTT
2046599 AATATTT--TATAAAT-TTT
1 AATATTTGATATAAATATTT
*
2046616 CATATATTGAATATAAATAT
1 AATAT-TTG-ATATAAATAT
2046636 AAGATATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
17 7 0.23
18 2 0.06
19 7 0.23
21 14 0.45
22 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (20 bp):
AATATTTGATATAAATATTT
Found at i:2047115 original size:17 final size:18
Alignment explanation
Indices: 2047093--2047133 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
2047083 ATTTTTTATG
*
2047093 ATATAAATTATATATA-T
1 ATATAAATAATATATATT
2047110 ATATAAATAATATATATT
1 ATATAAATAATATATATT
2047128 ATATAA
1 ATATAA
2047134 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAAATAATATATATT
Found at i:2053116 original size:39 final size:39
Alignment explanation
Indices: 2053047--2053270 Score: 129
Period size: 39 Copynumber: 5.7 Consensus size: 39
2053037 GGACCTGAGT
* * * *
2053047 TATCACAAGATTCCTCTGATTTTCTGTTTGGCCCCAAAA
1 TATCACAAGAATCTTCAGATTTTCTCTTTGGCCCCAAAA
* * **
2053086 TATCACAAGAAGCTTCAGATTGTCTCTTTGGCCTTGAGAAA
1 TATCACAAGAATCTTCAGATTTTCTCTTTGGCC-CCA-AAA
* * *
2053127 T-T-ACAGGAATCTTCGGATTTTCTCTTTGGCCCTAAGAA
1 TATCACAAGAATCTTCAGATTTTCTCTTTGGCCCCAA-AA
** ** *
2053165 -ATCACAAGAATCTTCTA-A-TTTCTGCTTTATCCCTGAGA
1 TATCACAAGAATCTTC-AGATTTTCT-CTTTGGCCCCAAAA
** * * *
2053203 TATCGGAAGAATCTACTGATTTTCTCTTTGG-CCCATAAT
1 TATCACAAGAATCTTCAGATTTTCTCTTTGGCCCCA-AAA
* *
2053242 TATCACAAGAATTTTCTGAATTTT-TCTTT
1 TATCACAAGAATCTTCAG-ATTTTCTCTTT
2053271 TGCTCTGAGA
Statistics
Matches: 139, Mismatches: 34, Indels: 24
0.71 0.17 0.12
Matches are distributed among these distances:
37 1 0.01
38 12 0.09
39 110 0.79
40 12 0.09
41 4 0.03
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (39 bp):
TATCACAAGAATCTTCAGATTTTCTCTTTGGCCCCAAAA
Found at i:2053202 original size:78 final size:76
Alignment explanation
Indices: 2053064--2053287 Score: 198
Period size: 78 Copynumber: 2.9 Consensus size: 76
2053054 AGATTCCTCT
* * * * *
2053064 GATTTTCTGTTTGGCCCCAAAATATCACAAGAAGCTTC-AGATTGTCTCTTTGGCCTTGAGAAAT
1 GATTTTCTCTTTGGCCCTAAAA-ATCACAAGAATCTTCTA-ATT-TCTCTTTAGCCCTGAGAAAT
* * *
2053128 TACAGGAATCTTCG
63 CACAAGAATCTACG
* *
2053142 GATTTTCTCTTTGGCCCTAAGAAATCACAAGAATCTTCTAATTTCTGCTTTATCCCTGAGATATC
1 GATTTTCTCTTTGGCCCTAA-AAATCACAAGAATCTTCTAATTTCT-CTTTAGCCCTGAGAAATC
** *
2053207 GGAAGAATCTACT
64 ACAAGAATCTACG
** * * * * *
2053220 GATTTTCTCTTTGGCCCATAATTATCACAAGAATTTTCTGAATTTTTCTTTTGCTCTGAGATATC
1 GATTTTCTCTTTGGCCC-TAAAAATCACAAGAATCTTCT-AATTTCTCTTTAGCCCTGAGAAATC
2053285 ACA
64 ACA
2053288 GGCATCAACA
Statistics
Matches: 119, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
77 3 0.03
78 104 0.87
79 12 0.10
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (76 bp):
GATTTTCTCTTTGGCCCTAAAAATCACAAGAATCTTCTAATTTCTCTTTAGCCCTGAGAAATCAC
AAGAATCTACG
Found at i:2057806 original size:19 final size:18
Alignment explanation
Indices: 2057780--2057816 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2057770 ATTTTAGCTA
*
2057780 ATTTTAATTTTAAAATAT
1 ATTTTAATATTAAAATAT
2057798 ATTTATAATATTAAAATAT
1 ATTT-TAATATTAAAATAT
2057817 TAATATACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTAATATTAAAATAT
Found at i:2059407 original size:29 final size:29
Alignment explanation
Indices: 2059374--2059458 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
2059364 ATTAATTACC
*
2059374 TCGAAAAGATATACGAATTATTGATTGAT
1 TCGAAAAGATATATGAATTATTGATTGAT
* * *
2059403 TCGAAAAAATATATGAATTATT-A-AGGT
1 TCGAAAAGATATATGAATTATTGATTGAT
*
2059430 TTGAAAAAGAATATATGAATTATTGATTG
1 TCG-AAAAG-ATATATGAATTATTGATTG
2059459 GCTCAAAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 4 0.09
28 5 0.11
29 34 0.76
30 1 0.02
31 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.35
Consensus pattern (29 bp):
TCGAAAAGATATATGAATTATTGATTGAT
Found at i:2060606 original size:34 final size:34
Alignment explanation
Indices: 2060560--2060692 Score: 187
Period size: 34 Copynumber: 3.9 Consensus size: 34
2060550 GTAAAAACCA
*
2060560 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2060594 TCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
2060628 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
2060662 CCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGTAACCTACCAAAT
2060693 TTCCTGTGGT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
33 3 0.03
34 80 0.92
35 4 0.05
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2060780 original size:19 final size:19
Alignment explanation
Indices: 2060724--2060786 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
2060714 TGGTTGTCGA
**
2060724 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
*
2060743 TGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
2060762 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
2060781 GTTACT
1 GGTACT
2060787 GTACACGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:2064918 original size:34 final size:34
Alignment explanation
Indices: 2064852--2065036 Score: 255
Period size: 34 Copynumber: 5.5 Consensus size: 34
2064842 AAGTGGGAGA
* *
2064852 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2064885 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2064919 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
2064953 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
2064987 ATTGTTGACTAAATGAGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2065021 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2065037 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 13 0.10
34 119 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2065892 original size:4 final size:4
Alignment explanation
Indices: 2065883--2065926 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
2065873 TTCCTTATCC
* * *
2065883 ATTT ATTT ATTA ATTT ATTT ATTA ATTT ATTT ATTT ATGT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2065927 TTTTTTTTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:2065926 original size:12 final size:12
Alignment explanation
Indices: 2065883--2065917 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
2065873 TTCCTTATCC
2065883 ATTTATTTATTA
1 ATTTATTTATTA
2065895 ATTTATTTATTA
1 ATTTATTTATTA
2065907 ATTTATTTATT
1 ATTTATTTATT
2065918 TATGTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
ATTTATTTATTA
Found at i:2066247 original size:6 final size:6
Alignment explanation
Indices: 2066236--2066269 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2066226 TAAAATATCA
* *
2066236 TATATT TATATT TATATT TAAATA TATATT TATA
1 TATATT TATATT TATATT TATATT TATATT TATA
2066270 AATATTATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TATATT
Found at i:2066253 original size:12 final size:12
Alignment explanation
Indices: 2066230--2066274 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
2066220 TATATTTAAA
2066230 ATATCATATATTT
1 ATAT-ATATATTT
*
2066243 ATATTTATATTT
1 ATATATATATTT
*
2066255 AAATATATATTT
1 ATATATATATTT
*
2066267 ATAAATAT
1 ATATATAT
2066275 TATACATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATATATATTT
Found at i:2066308 original size:23 final size:25
Alignment explanation
Indices: 2066259--2066308 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
2066249 ATATTTAAAT
* *
2066259 ATATATTTATAAATATTATACATAA
1 ATATATTTAAAAATATTATACAAAA
2066284 ATAT-TTTAAAAATATTAT-CAAAA
1 ATATATTTAAAAATATTATACAAAA
2066307 AT
1 AT
2066309 TCGAGTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.26
24 13 0.57
25 4 0.17
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATATTTAAAAATATTATACAAAA
Found at i:2074065 original size:25 final size:25
Alignment explanation
Indices: 2074031--2074084 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
2074021 TCTTTCCCCT
* ** *
2074031 TTTTTATAATTATTTTTTAATATAA
1 TTTTAATAATTATTCATAAATATAA
2074056 TTTTAATAATTATTCATAAATATAA
1 TTTTAATAATTATTCATAAATATAA
2074081 TTTT
1 TTTT
2074085 TTATTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTAATAATTATTCATAAATATAA
Found at i:2074973 original size:16 final size:16
Alignment explanation
Indices: 2074947--2075005 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
2074937 AAATGGATTG
*
2074947 ATTATTTTTAAATTCGA
1 ATTA-TTTTAAATTCAA
* *
2074964 ATTATTTTAATTTTAA
1 ATTATTTTAAATTCAA
* *
2074980 ATTATTTTGAGTTCAA
1 ATTATTTTAAATTCAA
2074996 ATTATTTTAA
1 ATTATTTTAA
2075006 TTTTATATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
16 31 0.89
17 4 0.11
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (16 bp):
ATTATTTTAAATTCAA
Found at i:2075015 original size:16 final size:16
Alignment explanation
Indices: 2074963--2075018 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
2074953 TTTAAATTCG
2074963 AATTATTTTAATTTTA
1 AATTATTTTAATTTTA
* * *
2074979 AATTATTTTGAGTTCA
1 AATTATTTTAATTTTA
2074995 AATTATTTTAATTTTA
1 AATTATTTTAATTTTA
*
2075011 TATTATTT
1 AATTATTT
2075019 CGAATTTGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (16 bp):
AATTATTTTAATTTTA
Found at i:2075024 original size:26 final size:30
Alignment explanation
Indices: 2074959--2075018 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
2074949 TATTTTTAAA
2074959 TTCGAATTATTTTAATTTTAAATTATTTTGAG
1 TTCGAATTATTTTAATTTT-AATTA-TTTGAG
*
2074991 TTCAAATTATTTTAATTTTATATTATTT
1 TTCGAATTATTTTAATTTTA-ATTATTT
2075019 CGAATTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (30 bp):
TTCGAATTATTTTAATTTTAATTATTTGAG
Found at i:2078201 original size:28 final size:29
Alignment explanation
Indices: 2078147--2078206 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
2078137 CATGTCTTTA
2078147 TTTAAATGTTATGTCTTTACATAACAA-T
1 TTTAAATGTTATGTCTTTACATAACAACT
*
2078175 TTTAAATGTTGTGTTCTTT-CA-ACACAACT
1 TTTAAATGTTATG-TCTTTACATA-ACAACT
2078204 TTT
1 TTT
2078207 TGATGCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.04
28 18 0.64
29 9 0.32
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.48
Consensus pattern (29 bp):
TTTAAATGTTATGTCTTTACATAACAACT
Found at i:2078278 original size:17 final size:17
Alignment explanation
Indices: 2078241--2078292 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2078231 TAATATTTCG
*
2078241 AATTAAAT-ATTAATA-
1 AATTAAATAAATAATAT
2078256 AA-TAAATAAATAATAT
1 AATTAAATAAATAATAT
2078272 AATTAAAATAAA-AATAT
1 AATT-AAATAAATAATAT
2078289 AATT
1 AATT
2078293 GCATATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 2 0.06
17 10 0.31
18 7 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTAAATAAATAATAT
Found at i:2080499 original size:28 final size:31
Alignment explanation
Indices: 2080467--2080544 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 31
2080457 ATCGTTTAAA
*
2080467 AATTAATATATAAAGATTTAAT-TAT-A-TT
1 AATTAATATATAAAGATTAAATCTATCACTT
* *
2080495 AATTAAAAATATAAAGATTAAATCTGTCACTT
1 AATT-AATATATAAAGATTAAATCTATCACTT
2080527 AATT-ATATTATAAAGATT
1 AATTAATA-TATAAAGATT
2080545 GATTGTTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.10
29 16 0.39
30 4 0.10
31 11 0.27
32 6 0.15
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (31 bp):
AATTAATATATAAAGATTAAATCTATCACTT
Found at i:2086447 original size:16 final size:18
Alignment explanation
Indices: 2086428--2086464 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
2086418 ATAAATAAAA
2086428 TTTAAAATTTA-AA-TAT
1 TTTAAAATTTATAATTAT
*
2086444 TTTAATATTTATAATTAT
1 TTTAAAATTTATAATTAT
2086462 TTT
1 TTT
2086465 TTAAATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTAAAATTTATAATTAT
Found at i:2086626 original size:17 final size:18
Alignment explanation
Indices: 2086604--2086638 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2086594 TTAATTTTTC
2086604 TATAA-TTAAAAAAATTA
1 TATAAGTTAAAAAAATTA
2086621 TATAATGTTAAAAAAATT
1 TATAA-GTTAAAAAAATT
2086639 TAAAATACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
19 11 0.69
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TATAAGTTAAAAAAATTA
Found at i:2086950 original size:21 final size:20
Alignment explanation
Indices: 2086905--2086942 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2086895 GATAATATAA
* *
2086905 AATATTTTTAAAAATAAAAT
1 AATAATTTTAAAAAGAAAAT
2086925 AATAATTTTAAAAAGAAA
1 AATAATTTTAAAAAGAAA
2086943 GATGATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AATAATTTTAAAAAGAAAAT
Found at i:2087052 original size:125 final size:126
Alignment explanation
Indices: 2086910--2087160 Score: 345
Period size: 125 Copynumber: 2.0 Consensus size: 126
2086900 TATAAAATAT
2086910 TTTTAAAAATAAAATAATAATTTTAAAAAGAAAG-ATGATAAATATTTATTAAAATCAT-TT-CG
1 TTTTAAAAATAAAATAATAATTTT-AAAAGAAAGCATGATAAATATTTATTAAAA--ATGTTACG
2086972 CTTT-TTTTACTTTTAAC-TTTTAAAT-AAAAAATTATTTAAAAT-GAATCGATGTAGAATTTAT
63 CTTTATTTTA-TTTTAACTTTTTAAATAAAAAAATTATTTAAAATAG-ATCGATGTAGAATTTAT
2087033 A
126 A
* * * *
2087034 TTTTAAAAAGTAAAATAATACTTTTAAAAGGAAGCATGATAAATATTTATTAAAAATGTTATGTT
1 TTTTAAAAA-TAAAATAATAATTTTAAAAGAAAGCATGATAAATATTTATTAAAAATGTTACGCT
* *
2087099 TTATTTTATTTTCACTTTTTAAGTAAAAAAATTATTTAAAATAGATCGATGTAGAATTTATA
65 TTATTTTATTTTAACTTTTTAAATAAAAAAATTATTTAAAATAGATCGATGTAGAATTTATA
2087161 GAATGAATCG
Statistics
Matches: 113, Mismatches: 6, Indels: 13
0.86 0.05 0.10
Matches are distributed among these distances:
123 2 0.02
124 19 0.17
125 44 0.39
126 12 0.11
127 35 0.31
128 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (126 bp):
TTTTAAAAATAAAATAATAATTTTAAAAGAAAGCATGATAAATATTTATTAAAAATGTTACGCTT
TATTTTATTTTAACTTTTTAAATAAAAAAATTATTTAAAATAGATCGATGTAGAATTTATA
Found at i:2087691 original size:2 final size:2
Alignment explanation
Indices: 2087684--2087712 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2087674 ACATCTGCAT
2087684 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
2087713 ATTATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2088161 original size:12 final size:12
Alignment explanation
Indices: 2088141--2088176 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2088131 CCCTATTTAC
*
2088141 ATATATATATAT
1 ATATTTATATAT
*
2088153 ATATTTATATTT
1 ATATTTATATAT
2088165 ATATTTATATAT
1 ATATTTATATAT
2088177 TGTGTTTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATTTATATAT
Found at i:2088939 original size:2 final size:2
Alignment explanation
Indices: 2088932--2088968 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
2088922 CGTTCTTAAA
*
2088932 AT AT AT AT AT AT AT AT AA ACT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
2088969 GTATTGAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 31 0.97
3 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2088955 original size:19 final size:19
Alignment explanation
Indices: 2088928--2088967 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2088918 TTCACGTTCT
2088928 TAAAATATATATATATATA
1 TAAAATATATATATATATA
*
2088947 TAAACTATATATATATATA
1 TAAAATATATATATATATA
2088966 TA
1 TA
2088968 TGTATTGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAATATATATATATATA
Found at i:2089612 original size:23 final size:26
Alignment explanation
Indices: 2089586--2089639 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 26
2089576 CTTTTTTAGC
2089586 AAAATAAATTAT-AATTTAAA-A-AT
1 AAAATAAATTATAAATTTAAATATAT
* *
2089609 AAAA-AATTTTTAAATTTAAATATAT
1 AAAATAAATTATAAATTTAAATATAT
2089634 AAAATA
1 AAAATA
2089640 TTATTCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 5 0.20
23 12 0.48
24 1 0.04
25 6 0.24
26 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAATAAATTATAAATTTAAATATAT
Found at i:2092542 original size:4 final size:4
Alignment explanation
Indices: 2092533--2092567 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
2092523 AAAAAGGTTA
*
2092533 AAAT AAAT AAAT ATAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2092568 ATCTTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:2093955 original size:17 final size:17
Alignment explanation
Indices: 2093920--2093988 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 17
2093910 AAAATTATAT
* * *
2093920 TTTAAATTAAATATATA
1 TTTATATTAATTATTTA
*
2093937 TTTTTATTAATTATTTA
1 TTTATATTAATTATTTA
2093954 -TTATATATAATT-TTTA
1 TTTATAT-TAATTATTTA
2093970 TTTAATATTAA--ATTTA
1 TTT-ATATTAATTATTTA
2093986 TTT
1 TTT
2093989 TTAAAATATT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
16 16 0.37
17 23 0.53
18 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATATTAATTATTTA
Found at i:2094929 original size:14 final size:13
Alignment explanation
Indices: 2094905--2094939 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
2094895 AATATATAAA
2094905 TAAATTTAAAATT
1 TAAATTTAAAATT
2094918 TAAATCTTAAAATT
1 TAAAT-TTAAAATT
2094932 TATAATTT
1 TA-AATTT
2094940 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 12 0.60
15 3 0.15
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:2095650 original size:16 final size:16
Alignment explanation
Indices: 2095621--2095667 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2095611 TATATTCTAA
* *
2095621 ATTAAATATATATTTT
1 ATTAATTATTTATTTT
*
2095637 ATTAATTATTTATTAT
1 ATTAATTATTTATTTT
2095653 ATATAATT-TTTATTT
1 AT-TAATTATTTATTT
2095668 AATATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTAATTATTTATTTT
Found at i:2096442 original size:19 final size:19
Alignment explanation
Indices: 2096406--2096466 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
2096396 GATTTTATTT
*
2096406 AAATTATTA-TTTAATAATA
1 AAATTAATATTTTAAT-ATA
*
2096425 AAATATATAAATTTTAATATA
1 AAAT-TA-ATATTTTAATATA
*
2096446 AAATTAATATTTTAATTTA
1 AAATTAATATTTTAATATA
2096465 AA
1 AA
2096467 TAATAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 17 0.49
20 4 0.11
21 8 0.23
22 6 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTAATATTTTAATATA
Found at i:2096446 original size:21 final size:21
Alignment explanation
Indices: 2096415--2096473 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 21
2096405 TAAATTATTA
2096415 TTTAATAATAAAATATATAAAT
1 TTTAAT-ATAAAATATATAAAT
*
2096437 TTTAATATAAAAT-TA-ATAT
1 TTTAATATAAAATATATAAAT
*
2096456 TTTAAT-TTAAATA-ATAAA
1 TTTAATATAAAATATATAAA
2096474 AAAATTTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
20 2 0.06
21 7 0.22
22 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAATATAAAATATATAAAT
Found at i:2100193 original size:2 final size:2
Alignment explanation
Indices: 2100181--2100232 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
2100171 CAATCACCAT
*
2100181 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2100223 TA TA TA TA TA
1 TA TA TA TA TA
2100233 AAGACTTCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2100999 original size:12 final size:12
Alignment explanation
Indices: 2100982--2101015 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
2100972 AGTTTGAAAA
2100982 ATTATTAAATAT
1 ATTATTAAATAT
2100994 ATTATTAATATAT
1 ATTATTAA-ATAT
2101007 ATT-TTAAAT
1 ATTATTAAAT
2101016 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 12 0.57
13 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTATTAAATAT
Found at i:2103834 original size:26 final size:27
Alignment explanation
Indices: 2103805--2103875 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
2103795 ATAAAATTTT
*
2103805 ATTAAAAATATATTTAATTATT-AAAA
1 ATTAAAAATATATATAATTATTAAAAA
* * *
2103831 ATT-AAAATAAAATATATTTTTTAAAAA
1 ATTAAAAAT-ATATATAATTATTAAAAA
2103858 ATTAAAAATATAATATAA
1 ATTAAAAATAT-ATATAA
2103876 ACAAACCTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
25 5 0.14
26 12 0.34
27 8 0.23
28 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATTAAAAATATATATAATTATTAAAAA
Found at i:2103865 original size:28 final size:29
Alignment explanation
Indices: 2103809--2103874 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
2103799 AATTTTATTA
*
2103809 AAAATATATTTAATTATTAAAAATTAAAAT
1 AAAATATATTT-ATTATAAAAAATTAAAAT
2103839 AAAATATATTT-TT-TAAAAAATTAAAAAT
1 AAAATATATTTATTATAAAAAATT-AAAAT
*
2103867 ATAATATA
1 AAAATATA
2103875 AACAAACCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 8 0.24
28 14 0.42
30 11 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
AAAATATATTTATTATAAAAAATTAAAAT
Found at i:2104288 original size:2 final size:2
Alignment explanation
Indices: 2104281--2104322 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2104271 GTTCATTTTC
2104281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2104323 TCTTTCTAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2104475 original size:7 final size:7
Alignment explanation
Indices: 2104465--2104490 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2104455 TTTTTTCCTT
2104465 TTCATTC
1 TTCATTC
2104472 TTCATTC
1 TTCATTC
2104479 TTCATTC
1 TTCATTC
2104486 TTCAT
1 TTCAT
2104491 CAATGCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (7 bp):
TTCATTC
Found at i:2105547 original size:2 final size:2
Alignment explanation
Indices: 2105542--2105569 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2105532 TTATTTAATG
2105542 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
2105570 CTTTAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2128481 original size:29 final size:29
Alignment explanation
Indices: 2128420--2128482 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
2128410 ATTTTTAATT
* * * *
2128420 TATATTTAAATAAATTTTAAATATTTTAC
1 TATATTTAAATAAATCTTAAAAAATATAC
2128449 TATATTTAAATAAAATCTTAAAAAATATA-
1 TATATTTAAAT-AAATCTTAAAAAATATAC
2128478 TATAT
1 TATAT
2128483 CAATGTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (29 bp):
TATATTTAAATAAATCTTAAAAAATATAC
Found at i:2130517 original size:29 final size:29
Alignment explanation
Indices: 2130491--2130555 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
2130481 ATTACAATTA
2130491 AAGATATGCTAATAAAGCATTGACAATGC
1 AAGATATGCTAATAAAGCATTGACAATGC
* *
2130520 AACATATGCTGATAAAGCATTGACAATGC
1 AAGATATGCTAATAAAGCATTGACAATGC
2130549 AAGATAT
1 AAGATAT
2130556 TTTAAAAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.25
Consensus pattern (29 bp):
AAGATATGCTAATAAAGCATTGACAATGC
Found at i:2131015 original size:11 final size:11
Alignment explanation
Indices: 2130996--2131074 Score: 54
Period size: 11 Copynumber: 7.1 Consensus size: 11
2130986 GGGAAGAACA
2130996 GGTGATGACAT
1 GGTGATGACAT
*
2131007 GGTGCTGACAT
1 GGTGATGACAT
*
2131018 -GTCGATGATAT
1 GGT-GATGACAT
*
2131029 GGTGTTGACAT
1 GGTGATGACAT
*
2131040 -GTCGATGATAT
1 GGT-GATGACAT
* *
2131051 GGTGTTGACGT
1 GGTGATGACAT
*
2131062 GGCTAATGACAT
1 GG-TGATGACAT
2131074 G
1 G
2131075 TCACTGCGTG
Statistics
Matches: 50, Mismatches: 13, Indels: 9
0.69 0.18 0.12
Matches are distributed among these distances:
10 4 0.08
11 35 0.70
12 11 0.22
ACGTcount: A:0.23, C:0.11, G:0.34, T:0.32
Consensus pattern (11 bp):
GGTGATGACAT
Found at i:2131030 original size:22 final size:22
Alignment explanation
Indices: 2130999--2131059 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
2130989 AAGAACAGGT
* *
2130999 GATGACATGGTGCTGACATGTC
1 GATGATATGGTGTTGACATGTC
2131021 GATGATATGGTGTTGACATGTC
1 GATGATATGGTGTTGACATGTC
2131043 GATGATATGGTGTTGAC
1 GATGATATGGTGTTGAC
2131060 GTGGCTAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.23, C:0.11, G:0.33, T:0.33
Consensus pattern (22 bp):
GATGATATGGTGTTGACATGTC
Found at i:2131831 original size:76 final size:76
Alignment explanation
Indices: 2131705--2131859 Score: 310
Period size: 76 Copynumber: 2.0 Consensus size: 76
2131695 ATTGATTATA
2131705 TGATAGCACGTTTAAGAGTGAACTATTTATTCAATGAAAAAAAAAAGCATTTGTGTTATAGAAAA
1 TGATAGCACGTTTAAGAGTGAACTATTTATTCAATGAAAAAAAAAAGCATTTGTGTTATAGAAAA
2131770 AAATTAAAAAG
66 AAATTAAAAAG
2131781 TGATAGCACGTTTAAGAGTGAACTATTTATTCAATGAAAAAAAAAAGCATTTGTGTTATAGAAAA
1 TGATAGCACGTTTAAGAGTGAACTATTTATTCAATGAAAAAAAAAAGCATTTGTGTTATAGAAAA
2131846 AAATTAAAAAG
66 AAATTAAAAAG
2131857 TGA
1 TGA
2131860 AATTCTTAAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.29
Consensus pattern (76 bp):
TGATAGCACGTTTAAGAGTGAACTATTTATTCAATGAAAAAAAAAAGCATTTGTGTTATAGAAAA
AAATTAAAAAG
Found at i:2137648 original size:17 final size:18
Alignment explanation
Indices: 2137626--2137662 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2137616 ATTATATGAA
2137626 ATATGAGAT-AAATTAAT
1 ATATGAGATAAAATTAAT
*
2137643 ATATGATATAAAATTAAT
1 ATATGAGATAAAATTAAT
2137661 AT
1 AT
2137663 GGAAGATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (18 bp):
ATATGAGATAAAATTAAT
Found at i:2137856 original size:18 final size:18
Alignment explanation
Indices: 2137825--2137862 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2137815 ACATACAACA
*
2137825 TTTTCTTTCTTTTTC-CT
1 TTTTCTTTCCTTTTCTCT
2137842 TTTTCCTTTCCTTTTCTCT
1 TTTT-CTTTCCTTTTCTCT
2137861 TT
1 TT
2137863 CTCTATATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 10 0.56
19 4 0.22
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTCTTTCCTTTTCTCT
Found at i:2138773 original size:16 final size:16
Alignment explanation
Indices: 2138754--2138805 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2138744 CAAAATTTTG
2138754 AATTTAAAAAAATTTA
1 AATTTAAAAAAATTTA
* * *
2138770 AATTGAATAAAATTCA
1 AATTTAAAAAAATTTA
* *
2138786 AACTTCAAAAAATTTGA
1 AATTTAAAAAAATTT-A
2138803 AAT
1 AAT
2138806 GTTCAAAATC
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
16 23 0.88
17 3 0.12
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.33
Consensus pattern (16 bp):
AATTTAAAAAAATTTA
Found at i:2139189 original size:16 final size:15
Alignment explanation
Indices: 2139143--2139190 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
2139133 CTCAAATTAT
*
2139143 AATTAATTTAAAATT
1 AATTAATTTAAAATA
2139158 AATTAAATTTAAAATA
1 AATT-AATTTAAAATA
2139174 AATTAGATTTAAAATA
1 AATTA-ATTTAAAATA
2139190 A
1 A
2139191 TAAAATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 5 0.17
16 25 0.83
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AATTAATTTAAAATA
Found at i:2139195 original size:24 final size:24
Alignment explanation
Indices: 2139167--2139213 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2139157 TAATTAAATT
*
2139167 TAAAATAAATTAGATTTAAAATAA
1 TAAAATAAATTAAATTTAAAATAA
*
2139191 TAAAATAATTTAAATTTAAAATA
1 TAAAATAAATTAAATTTAAAATA
2139214 GATCAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
TAAAATAAATTAAATTTAAAATAA
Found at i:2139230 original size:40 final size:39
Alignment explanation
Indices: 2139124--2139232 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 39
2139114 CATAAAGACC
2139124 TTAAAA-AAACTCAAATTATAATTAATTTAAAATTAATTAAAT
1 TTAAAATAAA-TCAAATTATAA-TAA--TAAAATTAATTAAAT
* * *
2139166 TTAAAATAAATTAGATTTAAAATAATAAAA-TAATTTAAAT
1 TTAAAATAAATCA-AATTATAATAATAAAATTAA-TTAAAT
*
2139206 TTAAAATAGATCAAATTCATAATAATA
1 TTAAAATAAATCAAATT-ATAATAATA
2139233 TTAAATTTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
39 6 0.11
40 30 0.54
42 11 0.20
43 9 0.16
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (39 bp):
TTAAAATAAATCAAATTATAATAATAAAATTAATTAAAT
Found at i:2139418 original size:2 final size:2
Alignment explanation
Indices: 2139413--2139442 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2139403 GTGTGTAGTG
2139413 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
2139443 GAATAAGAAT
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):
TA
Found at i:2139725 original size:20 final size:22
Alignment explanation
Indices: 2139677--2139738 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 22
2139667 TATTGAATCG
*
2139677 AATTTGAA-TAATTTTATTTTAT
1 AATTTAAATTAATTTTA-TTTAT
2139699 AATTTAAATTAATTTTATTT-T
1 AATTTAAATTAATTTTATTTAT
2139720 -ATTTAAATTAATATTTATT
1 AATTTAAATTAAT-TTTATT
2139739 AATTAAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 12 0.32
21 7 0.19
22 10 0.27
23 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
AATTTAAATTAATTTTATTTAT
Found at i:2139747 original size:20 final size:19
Alignment explanation
Indices: 2139692--2139748 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
2139682 GAATAATTTT
2139692 ATTTTA-TAATTTAAATTA
1 ATTTTATTAATTTAAATTA
*
2139710 ATTTTATTTTATTTAAATTA
1 ATTTTA-TTAATTTAAATTA
*
2139730 ATATTTATTAATTAAAATT
1 AT-TTTATTAATTTAAATT
2139749 TTTTTAATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 6 0.18
20 23 0.70
21 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTATTAATTTAAATTA
Found at i:2141014 original size:2 final size:2
Alignment explanation
Indices: 2141007--2141043 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2140997 ATTGTTGGTT
2141007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2141044 TGAAATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2141794 original size:16 final size:18
Alignment explanation
Indices: 2141759--2141801 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
2141749 TTTTTATATA
2141759 AAATAATTTAATTAATTTT
1 AAAT-ATTTAATTAATTTT
2141778 AAATATTT-ATT-ATTTT
1 AAATATTTAATTAATTTT
*
2141794 AAAGATTT
1 AAATATTT
2141802 TTTTTTTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 12 0.52
17 3 0.13
18 4 0.17
19 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
AAATATTTAATTAATTTT
Found at i:2142107 original size:21 final size:19
Alignment explanation
Indices: 2142080--2142133 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
2142070 ATAATTAATA
2142080 TTTTAATAAATTATT-TAT
1 TTTTAATAAATTATTATAT
*
2142098 TAAATTTAATAATATAATTATAT
1 T---TTTAATAA-ATTATTATAT
2142121 TTTTAATAAATTA
1 TTTTAATAAATTA
2142134 AACATCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 1 0.03
19 3 0.10
20 8 0.28
21 8 0.28
22 5 0.17
23 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAATAAATTATTATAT
Found at i:2150403 original size:21 final size:21
Alignment explanation
Indices: 2150378--2150424 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2150368 CAAGTGAAAT
2150378 ATAAAGATTTATTTAGATACA
1 ATAAAGATTTATTTAGATACA
*
2150399 ATAAAGATTTATTTATATACA
1 ATAAAGATTTATTTAGATACA
2150420 ATAAA
1 ATAAA
2150425 AATGTAAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.38
Consensus pattern (21 bp):
ATAAAGATTTATTTAGATACA
Found at i:2150722 original size:28 final size:30
Alignment explanation
Indices: 2150665--2150723 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
2150655 TCGTATTTTG
* *
2150665 TTAATATATTTTGTTATGTTATAATCATTT
1 TTAATATATTTTGATATGTTATAATAATTT
*
2150695 TTAATATATTTT-ATAT-TTAT-ATAAATT
1 TTAATATATTTTGATATGTTATAATAATTT
2150722 TT
1 TT
2150724 GATACGTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 3 0.12
30 12 0.46
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (30 bp):
TTAATATATTTTGATATGTTATAATAATTT
Found at i:2153517 original size:17 final size:17
Alignment explanation
Indices: 2153486--2153518 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2153476 CTTAATTCCC
2153486 TTTTTTAGATCAATTTA
1 TTTTTTAGATCAATTTA
2153503 TTTTTGTAGAT-AATTT
1 TTTTT-TAGATCAATTT
2153519 TTAATTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (17 bp):
TTTTTTAGATCAATTTA
Found at i:2154777 original size:14 final size:13
Alignment explanation
Indices: 2154758--2154787 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
2154748 AATTTGACCC
2154758 TTTTTTTCTCTTTT
1 TTTTTTTC-CTTTT
2154772 TTTTTTTCCTTTT
1 TTTTTTTCCTTTT
2154785 TTT
1 TTT
2154788 GGATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTCCTTTT
Found at i:2156405 original size:25 final size:28
Alignment explanation
Indices: 2156377--2156428 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 28
2156367 TCTAAACTTG
2156377 TATTATAACTT-AA-TTAA-TAAAAATA
1 TATTATAACTTAAATTTAATTAAAAATA
* *
2156402 TATTTTTACTTAAATTTAATTAAAAAT
1 TATTATAACTTAAATTTAATTAAAAAT
2156429 TATAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 9 0.41
26 2 0.09
27 4 0.18
28 7 0.32
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (28 bp):
TATTATAACTTAAATTTAATTAAAAATA
Found at i:2157387 original size:17 final size:19
Alignment explanation
Indices: 2157365--2157407 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
2157355 AATAATTCAC
*
2157365 AATTTTAGGTA-TTT-TAA
1 AATTTTAGATATTTTATAA
*
2157382 AATTTTATATATTTTATAA
1 AATTTTAGATATTTTATAA
2157401 AATTTTA
1 AATTTTA
2157408 AGATTTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 3 0.14
19 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
AATTTTAGATATTTTATAA
Found at i:2158576 original size:16 final size:16
Alignment explanation
Indices: 2158543--2158598 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
2158533 ATATCATTTA
* *
2158543 ATTAAATA-TATTTTT
1 ATTAAATATTAATTAT
2158558 ATTAAATATTAATTAT
1 ATTAAATATTAATTAT
* *
2158574 ATTTAATATTTATTAAAT
1 ATTAAATATTAATT--AT
2158592 ATTAAAT
1 ATTAAAT
2158599 TTATTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
15 8 0.24
16 17 0.52
18 8 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTAAATATTAATTAT
Found at i:2158600 original size:16 final size:16
Alignment explanation
Indices: 2158557--2158603 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
2158547 AATATATTTT
*
2158557 TATTAAATATTAATTATA
1 TATTAAAT-TT-ATTAAA
2158575 T-TTAATATTTATTAAA
1 TATTAA-ATTTATTAAA
2158591 TATTAAATTTATT
1 TATTAAATTTATT
2158604 TTTTAATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 13 0.50
17 10 0.38
18 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAAATTTATTAAA
Found at i:2158850 original size:3 final size:3
Alignment explanation
Indices: 2158844--2158870 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2158834 TTCTCTTTCT
2158844 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2158871 AATATTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2162577 original size:2 final size:2
Alignment explanation
Indices: 2162570--2162601 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2162560 ATTACAAATG
2162570 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
2162602 AAAGAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2165048 original size:2 final size:2
Alignment explanation
Indices: 2165043--2165086 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2165033 CGTGTGTGTG
2165043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2165085 TA
1 TA
2165087 ATACTAACTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2165833 original size:11 final size:12
Alignment explanation
Indices: 2165805--2165845 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2165795 TTTTTTTGTC
*
2165805 AAAATAAAATAT
1 AAAATTAAATAT
2165817 AAAATTAAATA-
1 AAAATTAAATAT
*
2165828 AAAATTAAATTT
1 AAAATTAAATAT
2165840 AAAATT
1 AAAATT
2165846 TAAGTGCACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:2166355 original size:3 final size:3
Alignment explanation
Indices: 2166347--2166371 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2166337 TACTAACTAC
2166347 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2166372 GGTCTGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2167155 original size:6 final size:6
Alignment explanation
Indices: 2167146--2167179 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
2167136 TTAAAAAAGT
* *
2167146 AAAAAA AAAAAC AAAAAC AAAAAT AAAAAC AAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAA
2167180 GATGAAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.88, C:0.09, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAAAC
Found at i:2167413 original size:20 final size:22
Alignment explanation
Indices: 2167377--2167432 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
2167367 GTAAAATTTA
* *
2167377 AATTATTATTTAAAAATATAAAT
1 AATTTTTATTTAAATATA-AAAT
2167400 -ATTTTTATTTAAATATAAAAT
1 AATTTTTATTTAAATATAAAAT
2167421 AAATTTTTATTT
1 -AATTTTTATTT
2167433 TTTATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 4 0.14
22 15 0.52
23 10 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTTTTATTTAAATATAAAAT
Found at i:2168159 original size:13 final size:14
Alignment explanation
Indices: 2168131--2168161 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
2168121 TACAAATTTT
2168131 AATAATATTTATTA
1 AATAATATTTATTA
2168145 AATAA-ATTTATTA
1 AATAATATTTATTA
2168158 AATA
1 AATA
2168162 TAAATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATAATATTTATTA
Found at i:2176335 original size:14 final size:13
Alignment explanation
Indices: 2176288--2176337 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
2176278 AATACGAATG
2176288 TAATATAAAAAAA
1 TAATATAAAAAAA
2176301 TAAT-TAAAATAAGA
1 TAATATAAAA-AA-A
*
2176315 GAATATAAAGAAAA
1 TAATATAAA-AAAA
2176329 TAATATAAA
1 TAATATAAA
2176338 TATGACATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 5 0.16
13 6 0.19
14 13 0.42
15 6 0.19
16 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (13 bp):
TAATATAAAAAAA
Found at i:2177446 original size:20 final size:20
Alignment explanation
Indices: 2177409--2177456 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2177399 GTGTTAAAAT
*
2177409 ATATATAAAATAAAATATTA
1 ATATATAAAATAAAATATAA
*
2177429 ATATATAAAA-AATTATATAA
1 ATATATAAAATAA-AATATAA
*
2177449 ATTTATAA
1 ATATATAA
2177457 TATTTTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATATAAAATAAAATATAA
Found at i:2184371 original size:28 final size:28
Alignment explanation
Indices: 2184340--2184397 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
2184330 AAAAATAATG
*
2184340 TTATATTATTAATATAATAACTTATAAC
1 TTATATTATTAATATAATAACTGATAAC
*
2184368 TTATATTATTAATATGATAACTGATAAC
1 TTATATTATTAATATAATAACTGATAAC
2184396 TT
1 TT
2184398 TTTTATCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (28 bp):
TTATATTATTAATATAATAACTGATAAC
Found at i:2184920 original size:28 final size:26
Alignment explanation
Indices: 2184888--2185016 Score: 86
Period size: 26 Copynumber: 4.7 Consensus size: 26
2184878 CAATACAAAT
2184888 TTTATAATATATTTTGAATATTTATATA
1 TTTATAATATATTTT-AAT-TTTATATA
* *
2184916 TTTATCTTATATTTTTTTAATTTTATATA
1 TTTA--TAATA-TATTTTAATTTTATATA
*
2184945 TTTTTAAT-TATATTTATATTATTATATA
1 TTTATAATATAT-TTTA-ATT-TTATATA
* * *
2184973 TTTA-AGTAAATTTTAATTATATAT-
1 TTTATAATATATTTTAATTTTATATA
2184997 TATTAT-ATAATATTTTAATT
1 T-TTATAAT-ATATTTTAATT
2185017 ATTTTTTGTA
Statistics
Matches: 80, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
24 1 0.01
25 11 0.14
26 17 0.21
27 12 0.15
28 16 0.20
29 11 0.14
30 7 0.09
31 5 0.06
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (26 bp):
TTTATAATATATTTTAATTTTATATA
Found at i:2184943 original size:16 final size:16
Alignment explanation
Indices: 2184894--2184953 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
2184884 AAATTTTATA
*
2184894 ATATATTTTGAATATTT
1 ATATATTTTTAAT-TTT
*
2184911 ATATA--TTT-ATCTT
1 ATATATTTTTAATTTT
*
2184924 ATATTTTTTTAATTTT
1 ATATATTTTTAATTTT
2184940 ATATATTTTTAATT
1 ATATATTTTTAATT
2184954 ATATTTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 6 0.17
14 2 0.06
15 5 0.14
16 17 0.49
17 5 0.14
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
ATATATTTTTAATTTT
Found at i:2184958 original size:30 final size:30
Alignment explanation
Indices: 2184886--2184959 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
2184876 ACCAATACAA
* *
2184886 ATTT-TATAATATATTTTGAATATTTATAT
1 ATTTATATTATATTTTTTGAATATTTATAT
* *
2184915 ATTTATCTTATATTTTTTTAAT-TTTATAT
1 ATTTATATTATATTTTTTGAATATTTATAT
*
2184944 ATTTTTAATTATATTT
1 ATTTAT-ATTATATTT
2184960 ATATTATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 16 0.43
30 21 0.57
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (30 bp):
ATTTATATTATATTTTTTGAATATTTATAT
Found at i:2184972 original size:16 final size:16
Alignment explanation
Indices: 2184909--2184976 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 16
2184899 TTTTGAATAT
*
2184909 TTATATATTTATCTTA
1 TTATATATTTATATTA
* *
2184925 -TATTTTTTTA-ATT-
1 TTATATATTTATATTA
2184938 TTATATA-TT-T-TTA
1 TTATATATTTATATTA
*
2184951 AT-TATATTTATATTA
1 TTATATATTTATATTA
2184966 TTATATATTTA
1 TTATATATTTA
2184977 AGTAAATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 14
0.64 0.12 0.24
Matches are distributed among these distances:
12 6 0.16
13 5 0.13
14 7 0.18
15 12 0.32
16 8 0.21
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATATATTTATATTA
Found at i:2189859 original size:17 final size:17
Alignment explanation
Indices: 2189815--2189856 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2189805 AATATTGGTT
2189815 TTATTAATTACAATTGA
1 TTATTAATTACAATTGA
*
2189832 TTCATTTAATTA-ATTTGA
1 TT-A-TTAATTACAATTGA
2189850 TTATTAA
1 TTATTAA
2189857 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 4 0.18
17 3 0.14
18 8 0.36
19 7 0.32
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (17 bp):
TTATTAATTACAATTGA
Found at i:2190295 original size:19 final size:19
Alignment explanation
Indices: 2190271--2190317 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
2190261 ATCATAATCT
2190271 TTAATACTAAAATA-TTATA
1 TTAATACTAAAATACTTA-A
*
2190290 TTAATA-TTAAATACTTAA
1 TTAATACTAAAATACTTAA
2190308 TATAATACTA
1 T-TAATACTA
2190318 TTTATTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 8 0.35
19 14 0.61
20 1 0.04
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAATACTAAAATACTTAA
Found at i:2190493 original size:21 final size:21
Alignment explanation
Indices: 2190451--2190525 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 21
2190441 CATTAAAAAC
* * *
2190451 TATTTATCATTAAATTATTAA
1 TATTTAACATTAAAATAATAA
*
2190472 TTTTTAACATTAAAATAATAA
1 TATTTAACATTAAAATAATAA
* * *
2190493 TATTTAATACTAAAAT-ATTA
1 TATTTAACATTAAAATAATAA
*
2190513 TA-TTAATATTAAA
1 TATTTAACATTAAA
2190526 TACTTAAAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 10 0.22
20 5 0.11
21 30 0.67
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTTAACATTAAAATAATAA
Found at i:2190519 original size:47 final size:47
Alignment explanation
Indices: 2190466--2190563 Score: 119
Period size: 47 Copynumber: 2.1 Consensus size: 47
2190456 ATCATTAAAT
* *
2190466 TATTAATTTTTAACA-TTAAAATAATAATATTTAATACTAAAATATTA
1 TATTAATATTAAACACTTAAAATAATAATA-TTAATACTAAAATATTA
* * * *
2190513 TATTAATATTAAATACTTAAAATAATACTATTATTATTAAAATATTA
1 TATTAATATTAAACACTTAAAATAATAATATTAATACTAAAATATTA
2190560 -ATTA
1 TATTA
2190564 TAAAAATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
46 4 0.09
47 27 0.61
48 13 0.30
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (47 bp):
TATTAATATTAAACACTTAAAATAATAATATTAATACTAAAATATTA
Found at i:2190550 original size:28 final size:26
Alignment explanation
Indices: 2190490--2190553 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
2190480 ATTAAAATAA
* *
2190490 TAATATTTAATACTAAAATATTATAT
1 TAATATTAAATACTAAAATAATATAT
2190516 TAATATTAAATACTTAAAATAATACTAT
1 TAATATTAAATAC-TAAAATAATA-TAT
*
2190544 TATTATTAAA
1 TAATATTAAA
2190554 ATATTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 12 0.36
27 9 0.27
28 12 0.36
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (26 bp):
TAATATTAAATACTAAAATAATATAT
Found at i:2190560 original size:28 final size:26
Alignment explanation
Indices: 2190490--2190560 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 26
2190480 ATTAAAATAA
* * *
2190490 TAATATTTAATACTAAAATATTATAT
1 TAATATTAAATATTAAAATAATATAT
2190516 TAATATTAAATACTTAAAATAATACTAT
1 TAATATTAAATA-TTAAAATAATA-TAT
*
2190544 TATTATTAAAATATTAA
1 TAATATT-AAATATTAA
2190561 TTATAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 11 0.29
27 9 0.24
28 13 0.34
29 5 0.13
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (26 bp):
TAATATTAAATATTAAAATAATATAT
Found at i:2190578 original size:44 final size:47
Alignment explanation
Indices: 2190481--2190604 Score: 139
Period size: 44 Copynumber: 2.7 Consensus size: 47
2190471 ATTTTTAACA
* * *
2190481 TTAAAATAATAATATTTAATACTAAAATATTATATTAATATTAAATAC
1 TTAAAATAATAATA-TTATTATTAAAATATTATATTAATATAAAATAC
* *
2190529 TTAAAATAATACTATTATTATTAAAATATTA-ATT-ATA-AAAATAT
1 TTAAAATAATAATATTATTATTAAAATATTATATTAATATAAAATAC
* *
2190573 TTAAAAT-ATAATGATAATTATTAAAATGTTAT
1 TTAAAATAATAAT-ATTATTATTAAAATATTAT
2190605 TTCTATTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
43 4 0.06
44 28 0.42
45 3 0.05
46 3 0.05
47 15 0.23
48 13 0.20
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (47 bp):
TTAAAATAATAATATTATTATTAAAATATTATATTAATATAAAATAC
Found at i:2194409 original size:15 final size:16
Alignment explanation
Indices: 2194383--2194412 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2194373 TTTTATTAAA
2194383 ATATTAAATAAATTTT
1 ATATTAAATAAATTTT
2194399 ATATT-AATAAATTT
1 ATATTAAATAAATTT
2194413 AAAGATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTAAATAAATTTT
Done.