Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 18 of 373
Found at i:5130998 original size:24 final size:23
Alignment explanation
Indices: 5130945--5131017 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 23
5130935 CATGGAATAG
*
5130945 TATAAGAAATATATAACTAAT-TGCA
1 TATAAAAAATATATAA-TAATAT--A
5130970 T-TAAAAAATATATACATAATATA
1 TATAAAAAATATATA-ATAATATA
* *
5130993 TATAAAATACATATAAT-ATATA
1 TATAAAAAATATATAATAATATA
5131015 TAT
1 TAT
5131018 GTATTAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
22 8 0.19
23 4 0.10
24 27 0.64
25 3 0.07
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (23 bp):
TATAAAAAATATATAATAATATA
Found at i:5131001 original size:11 final size:11
Alignment explanation
Indices: 5130974--5131017 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
5130964 ATTGCATTAA
*
5130974 AAAATATATAC
1 AAAATATATAT
*
5130985 ATAATATATAT
1 AAAATATATAT
*
5130996 AAAATACATAT
1 AAAATATATAT
*
5131007 AATATATATAT
1 AAAATATATAT
5131018 GTATTAGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAATATATAT
Found at i:5132499 original size:29 final size:28
Alignment explanation
Indices: 5132466--5132535 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 28
5132456 ATAAATAGAT
5132466 TTAAATTTTAAAATATAAA-ACTAAAAAAA
1 TTAAATTTTAAAA-ATAAATA-TAAAAAAA
*
5132495 TTAAATTCTTAAAAATAAATATATAAAAA
1 TTAAATT-TTAAAAATAAATATAAAAAAA
5132524 TTAAATTTTAAA
1 TTAAATTTTAAA
5132536 TTTATGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
28 5 0.13
29 26 0.68
30 7 0.18
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
TTAAATTTTAAAAATAAATATAAAAAAA
Found at i:5132508 original size:15 final size:14
Alignment explanation
Indices: 5132466--5132535 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
5132456 ATAAATAGAT
5132466 TTAAATTTTAAAATA
1 TTAAATTTTAAAA-A
* * **
5132481 TAAAACTAAAAAAA
1 TTAAATTTTAAAAA
5132495 TTAAATTCTTAAAAA
1 TTAAATT-TTAAAAA
*
5132510 -TAAATATATAAAAA
1 TTAAAT-TTTAAAAA
5132524 TTAAATTTTAAA
1 TTAAATTTTAAA
5132536 TTTATGAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
14 22 0.52
15 20 0.48
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAAATTTTAAAAA
Found at i:5132820 original size:110 final size:110
Alignment explanation
Indices: 5132627--5132846 Score: 379
Period size: 110 Copynumber: 2.0 Consensus size: 110
5132617 AAAGCAAGGG
* *
5132627 TTTCATTGACTCGTGAGTCTCATTAGCCGACACCAAGTCCCAATAATCAAACTTAGACATCATTA
1 TTTCATTGACTCGTGAGTCACATTAGCCGACACCAAGACCCAATAATCAAACTTAGACATCATTA
5132692 CTATTTTATGTTTCACGTTATAATCCAATCCACATATA-TATATAT
66 CTATTTTATGTTTCACGTTATAATCCAATCCA-ATATATTATATAT
* *
5132737 TTTCATTGACTCGTGAGTCACATTAGTCGACACCAAGACCCAATAATCAAGCTTAGACATCATTA
1 TTTCATTGACTCGTGAGTCACATTAGCCGACACCAAGACCCAATAATCAAACTTAGACATCATTA
*
5132802 CTATTTTATGTTTCACGTTATAATCCAATCCAATTTATTATATAT
66 CTATTTTATGTTTCACGTTATAATCCAATCCAATATATTATATAT
5132847 ATATATATAT
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
109 4 0.04
110 100 0.96
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.36
Consensus pattern (110 bp):
TTTCATTGACTCGTGAGTCACATTAGCCGACACCAAGACCCAATAATCAAACTTAGACATCATTA
CTATTTTATGTTTCACGTTATAATCCAATCCAATATATTATATAT
Found at i:5136572 original size:18 final size:19
Alignment explanation
Indices: 5136549--5136587 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5136539 TCAAATTTTT
5136549 TAGTA-TTAAATTAAAAAA
1 TAGTATTTAAATTAAAAAA
* *
5136567 TAGTATTTTAATTAATAAA
1 TAGTATTTAAATTAAAAAA
5136586 TA
1 TA
5136588 CAATTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TAGTATTTAAATTAAAAAA
Found at i:5141227 original size:20 final size:20
Alignment explanation
Indices: 5141190--5141227 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5141180 AGTCTTTAAA
*
5141190 TTTTTAAATGATATAAATAT
1 TTTTTAAATAATATAAATAT
5141210 TTTTTAAATTAATA-AAAT
1 TTTTTAAA-TAATATAAAT
5141228 TATCATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTTAAATAATATAAATAT
Found at i:5143594 original size:3 final size:3
Alignment explanation
Indices: 5143560--5143622 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
5143550 AATATCCTTG
* * * *
5143560 TTA TTT TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* *
5143606 GTA TATA TTT TTA TTA T
1 TTA T-TA TTA TTA TTA T
5143623 GTACGTGTAT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5143632 original size:23 final size:23
Alignment explanation
Indices: 5143567--5143633 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
5143557 TTGTTATTTT
*
5143567 TATTAGTATTAT-TAGTA-T-TA
1 TATTATTATTATGTAGTAGTATA
*
5143587 CTATTATTATTATGTATTAGTATA
1 -TATTATTATTATGTAGTAGTATA
*
5143611 TATTTTTATTATGTACGT-GTATA
1 TATTATTATTATGTA-GTAGTATA
5143634 CATATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 11 0.29
22 4 0.11
23 20 0.53
24 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.55
Consensus pattern (23 bp):
TATTATTATTATGTAGTAGTATA
Found at i:5143735 original size:3 final size:3
Alignment explanation
Indices: 5143722--5143757 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
5143712 TATTCCAATG
* *
5143722 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5143758 GTTTATGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5169641 original size:20 final size:20
Alignment explanation
Indices: 5169609--5169655 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5169599 CGGCAATGTT
*
5169609 TAAGTTGTGAAAGA-CTATGG
1 TAAGTTGTAAAAGATC-ATGG
*
5169629 TATGTTGTAAAAGATCATGG
1 TAAGTTGTAAAAGATCATGG
5169649 TAAGTTG
1 TAAGTTG
5169656 CAAGTGGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (20 bp):
TAAGTTGTAAAAGATCATGG
Found at i:5172893 original size:27 final size:26
Alignment explanation
Indices: 5172863--5172962 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 26
5172853 GGTGGCTACG
*
5172863 CCACAATTATTTGATCTGGTGGCTCTA
1 CCAC-ATTATCTGATCTGGTGGCTCTA
* *
5172890 CCACATATATCTGTTCTGGTGGCTCTG
1 CCACAT-TATCTGATCTGGTGGCTCTA
* *
5172917 CCACGATTATCTGTATCTGGTGACTCTG
1 CCAC-ATTATCTG-ATCTGGTGGCTCTA
* *
5172945 TCACATTATCTGTTCTGG
1 CCACATTATCTGATCTGG
5172963 CAGCCATGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.11
27 39 0.62
28 17 0.27
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (26 bp):
CCACATTATCTGATCTGGTGGCTCTA
Found at i:5172955 original size:54 final size:54
Alignment explanation
Indices: 5172852--5172962 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
5172842 GGAAGCGTCT
* *
5172852 TGGTGGCTACGCCACAATTATTTGATCTGGTGGCTCTACCACATATATCTGTTC
1 TGGTGGCTACGCCACAATTATCTGATCTGGTGACTCTACCACATATATCTGTTC
* **
5172906 TGGTGGCT-CTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTC
1 TGGTGGCTAC-GCCACAATTATCTG-ATCTGGTGACTCTACCACATATATCTGTTC
5172960 TGG
1 TGG
5172963 CAGCCATGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
53 1 0.02
54 32 0.64
55 17 0.34
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
TGGTGGCTACGCCACAATTATCTGATCTGGTGACTCTACCACATATATCTGTTC
Found at i:5179986 original size:20 final size:19
Alignment explanation
Indices: 5179948--5179986 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5179938 TTTGGATAAC
*
5179948 TTTTTGAAAAACATATTAA
1 TTTTCGAAAAACATATTAA
*
5179967 TTTTCGAAAACACATCTTAA
1 TTTTCGAAAA-ACATATTAA
5179987 ACAGTTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTCGAAAAACATATTAA
Found at i:5183977 original size:26 final size:26
Alignment explanation
Indices: 5183947--5183998 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5183937 TGAAATGCCC
5183947 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
5183973 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5183999 GTCAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:5188584 original size:27 final size:26
Alignment explanation
Indices: 5188538--5188647 Score: 114
Period size: 27 Copynumber: 4.1 Consensus size: 26
5188528 AGGAAGCGTT
* *
5188538 TGGTGGCTATG-CACAAATATCTGATC
1 TGGTGGCTCTGCCAC-ATTATCTGATC
*
5188564 TGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTCTGCCACAT-TATCTGATC
5188591 TGGTGGCTCTGCCACGATTATCTGTATC
1 TGGTGGCTCTGCCAC-ATTATCTG-ATC
* ** *
5188619 TGGTGACTCTATCACATTATCTGTTC
1 TGGTGGCTCTGCCACATTATCTGATC
5188645 TGG
1 TGG
5188648 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
26 16 0.22
27 40 0.56
28 16 0.22
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTGATC
Found at i:5188642 original size:54 final size:53
Alignment explanation
Indices: 5188538--5188647 Score: 141
Period size: 54 Copynumber: 2.1 Consensus size: 53
5188528 AGGAAGCGTT
* *
5188538 TGGTGGCTATGCACAAATATCTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATGCACAAATATCTGATCTGGTGACTCTACCACATATATCTGTTC
* * * *
5188591 TGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTATCACAT-TATCTGTTC
1 TGGTGGCTATG-CACAAATATCTG-ATCTGGTGACTCTACCACATATATCTGTTC
5188645 TGG
1 TGG
5188648 CAGCCATGCT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
53 10 0.20
54 22 0.45
55 17 0.35
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (53 bp):
TGGTGGCTATGCACAAATATCTGATCTGGTGACTCTACCACATATATCTGTTC
Found at i:5190890 original size:21 final size:20
Alignment explanation
Indices: 5190850--5190900 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
5190840 CTCTCACATT
* *
5190850 TTTTATTATTTTATTTATTTA
1 TTTTATT-TATTATTAATTTA
5190871 CTTTTATTTATTATTAATTTA
1 -TTTTATTTATTATTAATTTA
5190892 TTATTATTT
1 TT-TTATTT
5190901 CTTCATCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.65
22 7 0.27
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTATTTATTATTAATTTA
Found at i:5193114 original size:17 final size:19
Alignment explanation
Indices: 5193085--5193130 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
5193075 ACAATAATAT
5193085 AAAATA-ATGATATGTACAA
1 AAAATATAT-ATATGTACAA
*
5193104 AAAATATATATATGTACAT
1 AAAATATATATATGTACAA
5193123 AAAATATA
1 AAAATATA
5193131 CACTAATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (19 bp):
AAAATATATATATGTACAA
Found at i:5193266 original size:34 final size:33
Alignment explanation
Indices: 5193205--5193271 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
5193195 CAATATGGTG
* *
5193205 TTTAAAAATATATATATATGTATATATAATAATA
1 TTTAAAAATATATACATAAGTATATATAA-AATA
*
5193239 TTTAAGAATATATACATAAG-ATGATATAAAATA
1 TTTAAAAATATATACATAAGTAT-ATATAAAATA
5193272 CATACATGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 6 0.21
34 23 0.79
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (33 bp):
TTTAAAAATATATACATAAGTATATATAAAATA
Found at i:5193339 original size:24 final size:24
Alignment explanation
Indices: 5193226--5193340 Score: 61
Period size: 24 Copynumber: 5.0 Consensus size: 24
5193216 ATATATATGT
*
5193226 ATATATA-ATAATAT-T-T-AAGA
1 ATATATACATAATATATATAAAAA
*
5193246 ATATATACATAAGATGATAT--AAA
1 ATATATACATAATAT-ATATAAAAA
* * *
5193269 ATACATACATGGAATA-GTATAAGAA
1 ATATATACAT--AATATATATAAAAA
5193294 ATATATA-ACTAAT-TGCAT-TAAAAA
1 ATATATACA-TAATAT--ATATAAAAA
5193318 ATATATACATAATATATATAAAA
1 ATATATACATAATATATATAAAA
5193341 TACATAAATA
Statistics
Matches: 71, Mismatches: 9, Indels: 26
0.67 0.08 0.25
Matches are distributed among these distances:
20 7 0.10
21 6 0.08
23 20 0.28
24 23 0.32
25 15 0.21
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (24 bp):
ATATATACATAATATATATAAAAA
Found at i:5194852 original size:28 final size:29
Alignment explanation
Indices: 5194797--5194865 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
5194787 ATAAATAGAT
5194797 TTAAATTTTAAAATATAAAACTAAAAAAA
1 TTAAATTTTAAAATATAAAACTAAAAAAA
* *
5194826 TTAAATTCTTAAAATA-AATA-TATAAAAA
1 TTAAATT-TTAAAATATAAAACTAAAAAAA
5194854 TTAAATTTTAAA
1 TTAAATTTTAAA
5194866 TTTATGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 5 0.14
28 14 0.38
29 10 0.27
30 8 0.22
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (29 bp):
TTAAATTTTAAAATATAAAACTAAAAAAA
Found at i:5195150 original size:110 final size:110
Alignment explanation
Indices: 5194957--5195176 Score: 379
Period size: 110 Copynumber: 2.0 Consensus size: 110
5194947 AAAGCAAGGG
* *
5194957 TTTCATTGACTCGTGAGTCTCATTAGCCGACACCAAGTCCCAATAATCAAACTTAGACATCATTA
1 TTTCATTGACTCGTGAGTCACATTAGCCGACACCAAGACCCAATAATCAAACTTAGACATCATTA
5195022 CTATTTTATGTTTCACGTTATAATCCAATCCACATATA-TATATAT
66 CTATTTTATGTTTCACGTTATAATCCAATCCA-ATATATTATATAT
* *
5195067 TTTCATTGACTCGTGAGTCACATTAGTCGACACCAAGACCCAATAATCAAGCTTAGACATCATTA
1 TTTCATTGACTCGTGAGTCACATTAGCCGACACCAAGACCCAATAATCAAACTTAGACATCATTA
*
5195132 CTATTTTATGTTTCACGTTATAATCCAATCCAATTTATTATATAT
66 CTATTTTATGTTTCACGTTATAATCCAATCCAATATATTATATAT
5195177 ATATATATAT
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
109 4 0.04
110 100 0.96
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.36
Consensus pattern (110 bp):
TTTCATTGACTCGTGAGTCACATTAGCCGACACCAAGACCCAATAATCAAACTTAGACATCATTA
CTATTTTATGTTTCACGTTATAATCCAATCCAATATATTATATAT
Found at i:5198902 original size:18 final size:19
Alignment explanation
Indices: 5198879--5198917 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5198869 TCAAATTTTT
5198879 TAGTA-TTAAATTAAAAAA
1 TAGTATTTAAATTAAAAAA
* *
5198897 TAGTATTTTAATTAATAAA
1 TAGTATTTAAATTAAAAAA
5198916 TA
1 TA
5198918 CAATTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TAGTATTTAAATTAAAAAA
Found at i:5203565 original size:20 final size:20
Alignment explanation
Indices: 5203528--5203565 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5203518 AGTCTTTAAA
*
5203528 TTTTTAAATGATATAAATAT
1 TTTTTAAATAATATAAATAT
5203548 TTTTTAAATTAATA-AAAT
1 TTTTTAAA-TAATATAAAT
5203566 TATCATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTTAAATAATATAAATAT
Found at i:5205934 original size:3 final size:3
Alignment explanation
Indices: 5205900--5205962 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
5205890 AATATCCTTG
* * * *
5205900 TTA TTT TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* *
5205946 GTA TATA TTT TTA TTA T
1 TTA T-TA TTA TTA TTA T
5205963 GTACGTGTAT
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5205972 original size:23 final size:23
Alignment explanation
Indices: 5205907--5205973 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 23
5205897 TTGTTATTTT
*
5205907 TATTAGTATTAT-TAGTA-T-TA
1 TATTATTATTATGTAGTAGTATA
*
5205927 CTATTATTATTATGTATTAGTATA
1 -TATTATTATTATGTAGTAGTATA
*
5205951 TATTTTTATTATGTACGT-GTATA
1 TATTATTATTATGTA-GTAGTATA
5205974 CATATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 11 0.29
22 4 0.11
23 20 0.53
24 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.55
Consensus pattern (23 bp):
TATTATTATTATGTAGTAGTATA
Found at i:5206074 original size:3 final size:3
Alignment explanation
Indices: 5206061--5206096 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
5206051 TATTCCAATG
* *
5206061 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5206097 GTTTATGCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5224264 original size:20 final size:21
Alignment explanation
Indices: 5224235--5224279 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
5224225 ATTGAAAAAG
5224235 AAGAAAAAAAACTAAATCCAC
1 AAGAAAAAAAACTAAATCCAC
5224256 AAGAAAAAAAACTAAATCCAC
1 AAGAAAAAAAACTAAATCCAC
5224277 AAG
1 AAG
5224280 TTACGCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.09
Consensus pattern (21 bp):
AAGAAAAAAAACTAAATCCAC
Found at i:5230334 original size:29 final size:29
Alignment explanation
Indices: 5230302--5230364 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
5230292 TTTTTTTTTT
* **
5230302 AAATACGGGATTAAGTTAATTTTATAGAA
1 AAATACGGAATTAAGCCAATTTTATAGAA
* *
5230331 AAATTATGGAATTAGGCCAATTTTATAGAA
1 AAA-TACGGAATTAAGCCAATTTTATAGAA
5230361 AAAT
1 AAAT
5230365 TATTGGAACT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.33
Consensus pattern (29 bp):
AAATACGGAATTAAGCCAATTTTATAGAA
Found at i:5230807 original size:18 final size:19
Alignment explanation
Indices: 5230767--5230807 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
5230757 AAACTTACAA
5230767 ATATAAAAATTCATTATAT
1 ATATAAAAATTCATTATAT
*
5230786 -TATAAAAATT-ATTTTAT
1 ATATAAAAATTCATTATAT
5230803 ATATA
1 ATATA
5230808 TTTTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAAAAATTCATTATAT
Found at i:5234370 original size:18 final size:18
Alignment explanation
Indices: 5234332--5234374 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
5234322 GATTAAACGA
5234332 ATTTATAATTTTATTAATT
1 ATTTATAATTTTA-TAATT
5234351 ATTTATAAATTTTA-AATT
1 ATTTAT-AATTTTATAATT
5234369 ATTTAT
1 ATTTAT
5234375 TTGATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.43
19 6 0.26
20 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTATAATTTTATAATT
Found at i:5234801 original size:11 final size:11
Alignment explanation
Indices: 5234785--5234818 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
5234775 TCATACAATT
5234785 ATATAAAATAA
1 ATATAAAATAA
5234796 ATATAAAATAA
1 ATATAAAATAA
*
5234807 ATACAAAATAA
1 ATATAAAATAA
5234818 A
1 A
5234819 AAGAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (11 bp):
ATATAAAATAA
Found at i:5236671 original size:29 final size:27
Alignment explanation
Indices: 5236624--5236678 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
5236614 AAATATAATA
* *
5236624 AAAATTAATTATATTAAAATTAAAAAT
1 AAAATTAAATATATTAAAAATAAAAAT
5236651 AAAATATAAATATGATTAAAAATAAAAA
1 AAAAT-TAAATAT-ATTAAAAATAAAAA
5236679 AACAACATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 6 0.25
29 13 0.54
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAATTAAATATATTAAAAATAAAAAT
Found at i:5248889 original size:19 final size:17
Alignment explanation
Indices: 5248865--5248909 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
5248855 AAAAATTACA
5248865 AAAAAATTAAAATAACTTT
1 AAAAAATTAAAAT-A-TTT
*
5248884 AAAAAATCAAAATATTT
1 AAAAAATTAAAATATTT
5248901 ATAAAAATT
1 A-AAAAATT
5248910 TCTAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 7 0.30
19 12 0.52
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAAATTAAAATATTT
Found at i:5249570 original size:22 final size:21
Alignment explanation
Indices: 5249503--5249568 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
5249493 TTAATGGACA
5249503 ATTTTTTAATAAAAAAATAATTT
1 ATTTTTT--TAAAAAAATAATTT
* * *
5249526 ACTTTTCTAAAAATTATAATTT
1 ATTTTTTTAAAAA-AATAATTT
5249548 ATTTTTTTAAAAAAATAATTT
1 ATTTTTTTAAAAAAATAATTT
5249569 TACTCTTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 13 0.36
22 18 0.50
23 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTTTTTTAAAAAAATAATTT
Found at i:5255192 original size:805 final size:771
Alignment explanation
Indices: 5253752--5255195 Score: 1867
Period size: 803 Copynumber: 1.8 Consensus size: 771
5253742 GAACACTAGT
* ** *
5253752 TTCAACAAACGTTTTAAAAAAATAGATTTTTAACAATCAAGGTAACAAACCATAAAATAGTACGA
1 TTCAACAAACATTTTAAAAAAATAGATCCTTAACAATCAAGGTAACAAACCATAAAATAGTACAA
* *
5253817 AGACAGAGTAATTGTAACATACCTTGTTCGGGTTAAACCGATAACTCGAGAAACGAATATCACAT
66 AGACAGAGTAATTGTAACATACCTTGCTCGGGTTAAACCGATAACCCGAGAAACGAATATCACAT
* * * *
5253882 TAGGTACTAAATCACTTAAATATCAAATATATCTTCTTTATACTTATTCAATTCAGGCTACTCAA
131 TAGGCACTAAATCACTTAAATATCAAATATATCTTATTTATACTTATTCAATTCAGACTACCCAA
* *
5253947 ATCATTTCTAAACATTTACTAACATATTTAATCATCAAAATGTATTAAATTAACATTCAATATAT
196 ATCATTTCCAAACATTTACTAACATATTTAATCATCAAAATGTATTAAATTAACATCCAATATAT
* *
5254012 TATATTTTCATTCTTATTACCAAATACCATGTAATTTCTCAACATTGTCATTTAAACATAGCATA
261 CATATTTTCATTCTTATTACCAAATACCATGTAATTTCCCAACATTGTCATTTAAACATAGCATA
* * * * * *
5254077 AACGCCTTTCGTACATTGTCATTCTGTCTAAAATCATATACTAAAAGAGCTTTGAAACTTTAAGG
326 AACACCTATCGAACATTGTCATTCTGTCCAAAATCATATACCAAAAGAGCTTTGAAACTTCAAGG
* * * * * * * *
5254142 GTTGATCTGATCCTTGTGAAGAAGTACTTCACATATTTTTAATCTACTTTCTTTCACCTACATGT
391 ATTAATATGATCCTCGTGAAGAAGTACTTCACATATCTTCAATCAACTTTCTTTCACCTACATAT
* * * *
5254207 TTAGATAAACGCATTAAGTTATATAAATAGCCTAGTAAATAGTCAACTAAACTCAATCTTACCAT
456 TTAAACAAACGCATTAAGCTATATAAATAGCCTAGTAAATACTCAACTAAACTCAATCTTACCAT
* *
5254272 ATATATATAATTTAATTAATTTTTAATAATATTTATTCAAATAGTTTCTTCCACTAATATACTTA
521 ATATATATAATTTAATTAATTTTTAATAACATTTATTCAAACAGTTTCTTCCACTAATATACTTA
* *
5254337 AACTTTTAATTAATTTCCAAAACATAAAATCATTTAAATAAGCTTTATAACTTAAATAAATTTTA
586 AACTTTTAATTAATTTCCAAAACATAAAATCATCTAAATAAACTTTATAACTTAAATAAATTTTA
5254402 ACTTTCTACAATCATGTCCAAAAATGATATTTTAACCTTCAACCACGATATTTATAATAATGGGG
651 ACTTTCTACAATCATGTCCAAAAATGATATTTTAACCTTCAACCACGATATTTATAATAATGGGG
5254467 AACACTAAAATTTACAAACCACATTTTTCCATAACAATAGTAATTTTTCTAAAGCA
716 AACACTAAAATTTACAAACCACATTTTTCCATAACAATAGTAATTTTTCTAAAGCA
* * *
5254523 TTCAACAAACATTTTAAAAAAATAGATCCTTAACAATCAAGGTAGCAAACC-TCGAAGTAGTACA
1 TTCAACAAACATTTTAAAAAAATAGATCCTTAACAATCAAGGTAACAAACCAT-AAAATAGTACA
* * *
5254587 AAGACAAAGAGTAATTGTAACA-ACTCTCT-CTCGGGTTAAACCGATAACCCGAGGAATGAATGT
65 AAGAC--AGAGTAATTGTAACATAC-CT-TGCTCGGGTTAAACCGATAACCCGAGAAACGAATAT
* *
5254650 CACATTAGGCACTAAGTCACTTAAATATCAAATATATATTTTTTATATTTAATTTTATTCTTATA
126 CACATTAGGCACTAAATCACTTAAATATC-AA-ATATA---TCT-TATTT-A---TA--C-T-T-
* * *
5254715 AAATTCAATTTAGACTTCCCAAATCATTTCCAAACTTTTACTATA-ATATTTAATCATCAAAATG
176 --ATTCAATTCAGACTACCCAAATCATTTCCAAACATTTACTA-ACATATTTAATCATCAAAATG
*
5254779 TATTAGATTAACATCCAA-ATTATCATATTTTCATTCTTATTACCAAATACCATGTAATTTCCCA
238 TATTAAATTAACATCCAATA-TATCATATTTTCATTCTTATTACCAAATACCATGTAATTTCCCA
5254843 GCATTGTCATTTAAGTACTATTTAAACATAGCATAAACACCTAAT-GAACA-TGTCATTTCTATG
302 --A----CA-TT--GT-C-ATTTAAACATAGCATAAACACCT-ATCGAACATTGTCA-TTC--TG
* *
5254906 TCCAAAATCATATACCAAAAGAGTTTTGAAACTTCGAGGATTAATATGATCCTCGTGAAGAAGTA
352 TCCAAAATCATATACCAAAAGAGCTTTGAAACTTCAAGGATTAATATGATCCTCGTGAAGAAGTA
* * * ** * *
5254971 CTTCTCGTATCTTCAATCAATTTTCTTTCACCTATGTATTTAAACAAATGCATTAAGCTATATGA
417 CTTCACATATCTTCAATCAACTTTCTTTCACCTACATATTTAAACAAACGCATTAAGCTATATAA
** * * * *
5255036 ATAGTTTAGTAAGTACTCAATTGAATTCAATCTTACCATATATATATATAATTTAATTAATTTTT
482 ATAGCCTAGTAAATACTCAACTAAACTCAATCTTACC--ATATATATATAATTTAATTAATTTTT
* ** *
5255101 AATAACATTTATTCACACAGTTTCTTTTAGTAATATACTTAAACTTTTAATTAATTTCCAAAACA
545 AATAACATTTATTCAAACAGTTTCTTCCACTAATATACTTAAACTTTTAATTAATTTCCAAAACA
5255166 TAAAATCATCTAAATAAACTTTATAACTTA
610 TAAAATCATCTAAATAAACTTTATAACTTA
5255196 TAGTTTTCAA
Statistics
Matches: 565, Mismatches: 67, Indels: 48
0.83 0.10 0.07
Matches are distributed among these distances:
770 1 0.00
771 60 0.11
772 2 0.00
773 73 0.13
774 3 0.01
775 5 0.01
778 2 0.00
779 4 0.01
780 1 0.00
783 2 0.00
785 1 0.00
786 1 0.00
787 1 0.00
789 1 0.00
790 112 0.20
791 1 0.00
792 1 0.00
796 2 0.00
797 2 0.00
799 2 0.00
800 6 0.01
801 29 0.05
802 1 0.00
803 139 0.25
805 113 0.20
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.36
Consensus pattern (771 bp):
TTCAACAAACATTTTAAAAAAATAGATCCTTAACAATCAAGGTAACAAACCATAAAATAGTACAA
AGACAGAGTAATTGTAACATACCTTGCTCGGGTTAAACCGATAACCCGAGAAACGAATATCACAT
TAGGCACTAAATCACTTAAATATCAAATATATCTTATTTATACTTATTCAATTCAGACTACCCAA
ATCATTTCCAAACATTTACTAACATATTTAATCATCAAAATGTATTAAATTAACATCCAATATAT
CATATTTTCATTCTTATTACCAAATACCATGTAATTTCCCAACATTGTCATTTAAACATAGCATA
AACACCTATCGAACATTGTCATTCTGTCCAAAATCATATACCAAAAGAGCTTTGAAACTTCAAGG
ATTAATATGATCCTCGTGAAGAAGTACTTCACATATCTTCAATCAACTTTCTTTCACCTACATAT
TTAAACAAACGCATTAAGCTATATAAATAGCCTAGTAAATACTCAACTAAACTCAATCTTACCAT
ATATATATAATTTAATTAATTTTTAATAACATTTATTCAAACAGTTTCTTCCACTAATATACTTA
AACTTTTAATTAATTTCCAAAACATAAAATCATCTAAATAAACTTTATAACTTAAATAAATTTTA
ACTTTCTACAATCATGTCCAAAAATGATATTTTAACCTTCAACCACGATATTTATAATAATGGGG
AACACTAAAATTTACAAACCACATTTTTCCATAACAATAGTAATTTTTCTAAAGCA
Found at i:5258525 original size:13 final size:13
Alignment explanation
Indices: 5258488--5258530 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 13
5258478 ATAATTTTTT
5258488 TTTTAATTTTTAAAA
1 TTTT-ATTTTT-AAA
5258503 TGTCTTATTTTTAAA
1 T-T-TTATTTTTAAA
5258518 TTTTATTTTTAAA
1 TTTTATTTTTAAA
5258531 AATTAAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.42
14 1 0.04
15 5 0.19
16 7 0.27
17 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (13 bp):
TTTTATTTTTAAA
Found at i:5263983 original size:16 final size:18
Alignment explanation
Indices: 5263961--5263999 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
5263951 TGGCAGTTGA
5263961 ATTTATTTTT-ATAATTT
1 ATTTATTTTTAATAATTT
5263978 -TTTATTTTTAATAATTT
1 ATTTATTTTTAATAATTT
5263995 ATTTA
1 ATTTA
5264000 CTTTGAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 7 0.35
18 4 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTATTTTTAATAATTT
Found at i:5264355 original size:21 final size:22
Alignment explanation
Indices: 5264330--5264388 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
5264320 AATTTGTGTA
*
5264330 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
5264351 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
5264373 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
5264389 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:5264403 original size:26 final size:24
Alignment explanation
Indices: 5264359--5264408 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
5264349 ATTTGTTTTA
*
5264359 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
5264383 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
5264409 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:5264573 original size:6 final size:5
Alignment explanation
Indices: 5264556--5264591 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
5264546 AATTTGTATG
*
5264556 GACCC GACCC GAACCC GACCC GGCCC GACCC GACCC
1 GACCC GACCC G-ACCC GACCC GACCC GACCC GACCC
5264592 ATGATCACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.19, C:0.58, G:0.22, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:5264775 original size:19 final size:19
Alignment explanation
Indices: 5264751--5264801 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
5264741 TGAATTTTGA
5264751 CATTTTTATATTTTAAATT
1 CATTTTTATATTTTAAATT
5264770 CATTTTTAT-TTTT---TT
1 CATTTTTATATTTTAAATT
5264785 CATATTTT-TATTTTAAA
1 CAT-TTTTATATTTTAAA
5264802 AAAATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
15 6 0.22
16 8 0.30
18 4 0.15
19 9 0.33
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (19 bp):
CATTTTTATATTTTAAATT
Found at i:5265585 original size:18 final size:18
Alignment explanation
Indices: 5265531--5265621 Score: 57
Period size: 19 Copynumber: 5.1 Consensus size: 18
5265521 TTTTTTCTTT
* *
5265531 ATAATTTTCTAGTATTTT-
1 ATAATTTTTTAAT-TTTTA
*
5265549 ATATATTTTTCTAAATTTTA
1 ATA-ATTTTT-TAATTTTTA
5265569 ATAATTTTTTAATTTTTA
1 ATAATTTTTTAATTTTTA
*
5265587 TGTTAA-TTTTTAA-TTTTA
1 --ATAATTTTTTAATTTTTA
*
5265605 AT--TTTCTTAATTTTTA
1 ATAATTTTTTAATTTTTA
5265621 A
1 A
5265622 AATCATGACC
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
15 6 0.10
16 7 0.12
18 16 0.27
19 22 0.37
20 8 0.14
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (18 bp):
ATAATTTTTTAATTTTTA
Found at i:5265594 original size:12 final size:13
Alignment explanation
Indices: 5265577--5265609 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5265567 TAATAATTTT
5265577 TTAATTTTT-ATG
1 TTAATTTTTAATG
*
5265589 TTAATTTTTAATT
1 TTAATTTTTAATG
5265602 TTAATTTT
1 TTAATTTT
5265610 CTTAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
TTAATTTTTAATG
Found at i:5269221 original size:3 final size:3
Alignment explanation
Indices: 5269213--5269247 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5269203 CACCAAATTT
5269213 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5269248 GAAACTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5272583 original size:14 final size:15
Alignment explanation
Indices: 5272564--5272599 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
5272554 CAATAAAGTT
5272564 GAAATATTTT-ATAA
1 GAAATATTTTAATAA
5272578 GAAATATTTTAATAA
1 GAAATATTTTAATAA
*
5272593 TAAATAT
1 GAAATAT
5272600 GGAAAATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
GAAATATTTTAATAA
Found at i:5272935 original size:19 final size:18
Alignment explanation
Indices: 5272908--5272943 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5272898 CCAATATTTA
*
5272908 AATTTTTTTCTAGAAAATC
1 AATTATTTTCTA-AAAATC
5272927 AATTATTTTCTAAAAAT
1 AATTATTTTCTAAAAAT
5272944 TCCTTTTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (18 bp):
AATTATTTTCTAAAAATC
Found at i:5281238 original size:27 final size:27
Alignment explanation
Indices: 5281208--5281272 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
5281198 TATATATAAC
*
5281208 TAACAGATT-AAATCTTGCTTAACACAA
1 TAACA-ATTCAAATATTGCTTAACACAA
* *
5281235 TAACATTTCAAATATTGTTTAACACAA
1 TAACAATTCAAATATTGCTTAACACAA
5281262 TTAA-AATTCAA
1 -TAACAATTCAA
5281273 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 2 0.06
27 27 0.84
28 3 0.09
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (27 bp):
TAACAATTCAAATATTGCTTAACACAA
Found at i:5290350 original size:33 final size:33
Alignment explanation
Indices: 5290311--5290380 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
5290301 ACAAACATAC
* *
5290311 AAAGTAATAATTAAATAATGTATGATATACAAA
1 AAAGTAATAATTAAATAATGCATGACATACAAA
5290344 AAAGTAATAATTAAATAATGCATGACATACAAA
1 AAAGTAATAATTAAATAATGCATGACATACAAA
5290377 AAAG
1 AAAG
5290381 AGTAATACGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.59, C:0.06, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAGTAATAATTAAATAATGCATGACATACAAA
Found at i:5290954 original size:18 final size:19
Alignment explanation
Indices: 5290901--5290955 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 19
5290891 AATAAATGTT
*
5290901 ATATAATAAGATATAATTTAA
1 ATATAAT-AGATATAA-TGAA
*
5290922 ATAT-ATAGGAAATAA-GAA
1 ATATAATA-GATATAATGAA
5290940 ATATAATAGATATAAT
1 ATATAATAGATATAAT
5290956 ATAAAACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
18 12 0.43
19 4 0.14
20 8 0.29
21 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (19 bp):
ATATAATAGATATAATGAA
Found at i:5291036 original size:3 final size:3
Alignment explanation
Indices: 5291028--5291111 Score: 52
Period size: 3 Copynumber: 27.7 Consensus size: 3
5291018 CAAGTAAATT
* * *
5291028 ATA ATA ATA AT- ATA A-A GATA ATA ATA ATA ATTT GTGA A-A AAA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA A-TA AT-A ATA ATA ATA
5291073 ATA TATA ATAA ATA ATA ATA AT- ATA TATA ATA A-A ATA AT
1 ATA -ATA AT-A ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT
5291112 CTTATAATGT
Statistics
Matches: 65, Mismatches: 5, Indels: 22
0.71 0.05 0.24
Matches are distributed among these distances:
2 9 0.14
3 45 0.69
4 11 0.17
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5291109 original size:17 final size:18
Alignment explanation
Indices: 5290940--5291111 Score: 84
Period size: 17 Copynumber: 9.9 Consensus size: 18
5290930 GAAATAAGAA
5290940 ATATAATAGAT-ATAATAT
1 ATATAATA-ATAATAATAT
*
5290958 A-A-AACAATGAA-AATAT
1 ATATAATAAT-AATAATAT
* * *
5290974 ATAT-GTAAGAACAATAT
1 ATATAATAATAATAATAT
5290991 ATATAAATAATTAATAA-AT
1 ATAT-AATAA-TAATAATAT
* *
5291010 ATATAATGCA-AGTAA-AT
1 ATATAAT-AATAATAATAT
*
5291027 -TATAATAATAAT-ATAA
1 ATATAATAATAATAATAT
*
5291043 AGATAATAATAATAAT-T
1 ATATAATAATAATAATAT
* *
5291060 -TGTGAA-AAAAATAATAT
1 ATAT-AATAATAATAATAT
5291077 ATAATAAATAATAATAATAT
1 AT-AT-AATAATAATAATAT
5291097 ATATAATAA-AATAAT
1 ATATAATAATAATAAT
5291112 CTTATAATGT
Statistics
Matches: 116, Mismatches: 20, Indels: 37
0.67 0.12 0.21
Matches are distributed among these distances:
15 4 0.03
16 29 0.25
17 40 0.34
18 12 0.10
19 15 0.13
20 16 0.14
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (18 bp):
ATATAATAATAATAATAT
Found at i:5291117 original size:20 final size:22
Alignment explanation
Indices: 5290987--5291111 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 22
5290977 TGTAAGAACA
5290987 ATATAT-ATAAATAATTAATAAAT
1 ATATATAATAAATAA-TAAT-AAT
*
5291010 ATATAATGCAAGTAAATTATAATAAT
1 ATAT-AT--AA-TAAATAATAATAAT
*
5291036 A-ATATAA-AGATAATAATAAT
1 ATATATAATAAATAATAATAAT
**
5291056 A-AT-TTGTGAAA-AA-AAT-A-
1 ATATATAAT-AAATAATAATAAT
5291073 ATATATAATAAATAATAATAAT
1 ATATATAATAAATAATAATAAT
5291095 ATATATAATAAAATAAT
1 ATATATAAT-AAATAAT
5291112 CTTATAATGT
Statistics
Matches: 80, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
17 1 0.01
18 6 0.08
19 8 0.10
20 19 0.24
21 3 0.04
22 11 0.14
23 11 0.14
24 4 0.05
25 2 0.03
26 4 0.05
27 5 0.06
28 6 0.08
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (22 bp):
ATATATAATAAATAATAATAAT
Found at i:5293377 original size:5 final size:5
Alignment explanation
Indices: 5293367--5293398 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5293357 TTGTGTGTTC
5293367 TTTAT TTTAT TTTAT TTTA- TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
5293399 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:5293391 original size:9 final size:9
Alignment explanation
Indices: 5293367--5293397 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
5293357 TTGTGTGTTC
5293367 TTTATTTTA
1 TTTATTTTA
5293376 TTTTATTTTA
1 -TTTATTTTA
5293386 TTTATTTTA
1 TTTATTTTA
5293395 TTT
1 TTT
5293398 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:5293391 original size:14 final size:15
Alignment explanation
Indices: 5293367--5293398 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
5293357 TTGTGTGTTC
5293367 TTTATTTTATTTTAT
1 TTTATTTTATTTTAT
5293382 TTTA-TTTATTTTAT
1 TTTATTTTATTTTAT
5293396 TTT
1 TTT
5293399 TCACAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTATTTTATTTTAT
Found at i:5298053 original size:51 final size:51
Alignment explanation
Indices: 5297977--5298076 Score: 200
Period size: 51 Copynumber: 2.0 Consensus size: 51
5297967 TTTTGTTACC
5297977 TCCATTCAAGTATGGGCGAGGTAACTTTTAGTTGGAAAGTTAAAAAGTTCT
1 TCCATTCAAGTATGGGCGAGGTAACTTTTAGTTGGAAAGTTAAAAAGTTCT
5298028 TCCATTCAAGTATGGGCGAGGTAACTTTTAGTTGGAAAGTTAAAAAGTT
1 TCCATTCAAGTATGGGCGAGGTAACTTTTAGTTGGAAAGTTAAAAAGTT
5298077 TACTTTCTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (51 bp):
TCCATTCAAGTATGGGCGAGGTAACTTTTAGTTGGAAAGTTAAAAAGTTCT
Found at i:5322907 original size:44 final size:45
Alignment explanation
Indices: 5322821--5323443 Score: 527
Period size: 44 Copynumber: 14.1 Consensus size: 45
5322811 GTCATTGAAC
*
5322821 CAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
*
5322866 CAGATCTTGTCTTCCCATA-TGGTGGCGGAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
*** *** *
5322910 CAGATCTTGTCTTCATGTATTGG-CATGAAGTAGATCGAAGATAG
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
* * * * * * * * *
5322954 CAGGTCCTATCTTCCTATATTGATAG-GAAGTGGATCCAAG-ATG
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
* *
5322997 TAAATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
*** * * **
5323042 CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAG
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
* * * * * *
5323086 CAGAT-TCTATCTTCCTATATTGGTAG-GAAGTGGACCGAAG-ATG
1 CAGATCT-TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
*
5323129 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAG
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
*** * * **
5323174 CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAG
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
* ** * * * *
5323218 CAGATCCTACCTTCCTATATTGGTAG-GAAGTGGATCGAAGATA-
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
* * *
5323261 CAGATCTTGTCTTCCCATATTGGTGGCGAATTAGATAGCAGAAAG
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
*** * * **
5323306 CAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAG
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
* * * * * * * *
5323350 CAGATCCTATCTTCCTATATTGATAG-GAAGTGGATCCAAGATA-
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
* *
5323393 CAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAG
1 CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
5323438 CAGATC
1 CAGATC
5323444 GACGATGGCG
Statistics
Matches: 452, Mismatches: 111, Indels: 30
0.76 0.19 0.05
Matches are distributed among these distances:
43 83 0.18
44 276 0.61
45 93 0.21
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (45 bp):
CAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAG
Found at i:5323030 original size:132 final size:132
Alignment explanation
Indices: 5322821--5323443 Score: 971
Period size: 132 Copynumber: 4.7 Consensus size: 132
5322811 GTCATTGAAC
* * * * * * *
5322821 CAGATCTTGTCTTCCCATATTGATGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCCCATA-
1 CAGATCCTATCTTCCTATATTGATAG-GAAGTGGATCCAAGATA-CAGATCTTGTCTTCCCATAT
* *
5322885 TGGTGGCGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAG
64 TGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG
*
5322950 ATAG
129 GTAG
* ** *
5322954 CAGGTCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATGTAAATCTTGTCTTCCCATATTG
1 CAGATCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATATTG
5323019 GTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGT
66 GTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGT
5323084 AG
131 AG
* * *
5323086 CAGATTCTATCTTCCTATATTGGTAGGAAGTGGA-CCGAAGATGCAGATCTTGTCTTCCCATATT
1 CAGATCCTATCTTCCTATATTGATAGGAAGTGGATCC-AAGATACAGATCTTGTCTTCCCATATT
*
5323150 GGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGG
65 GGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGG
5323215 TAG
130 TAG
* * *
5323218 CAGATCCTACCTTCCTATATTGGTAGGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATATTG
1 CAGATCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATATTG
* * *
5323283 GTGGCGAATTAGATAGCAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGT
66 GTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGT
5323348 AG
131 AG
*
5323350 CAGATCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATACTG
1 CAGATCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATATTG
*
5323415 GTGGTGAAGTAGATCGAAGAAAGCAGATC
66 GTGGCGAAGTAGATCGAAGAAAGCAGATC
5323444 GACGATGGCG
Statistics
Matches: 453, Mismatches: 34, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
131 19 0.04
132 412 0.91
133 22 0.05
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (132 bp):
CAGATCCTATCTTCCTATATTGATAGGAAGTGGATCCAAGATACAGATCTTGTCTTCCCATATTG
GTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGT
AG
Found at i:5325057 original size:3 final size:3
Alignment explanation
Indices: 5325039--5325089 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
5325029 TTAAATATCC
* * * *
5325039 TTA TTA TTT TTA -TA TTA TTA TTA TTA TTA GTA TTA CTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5325086 TTA T
1 TTA T
5325090 GTACTAGTGT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5325220 original size:3 final size:3
Alignment explanation
Indices: 5325212--5325256 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
5325202 TATTCCAATG
5325212 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5325257 GTTTATGCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5325394 original size:38 final size:39
Alignment explanation
Indices: 5325309--5325406 Score: 96
Period size: 38 Copynumber: 2.6 Consensus size: 39
5325299 TATACGTACT
* *
5325309 TATACATACTTAAATATATTTTTTCACATTTCACAATTC
1 TATACATACTTAAATATATTTATGCACATTTCACAATTC
* * * *
5325348 T-TATATACTTACATATATTTATGCATATTTTAC-A-TC
1 TATACATACTTAAATATATTTATGCACATTTCACAATTC
*
5325384 ATATACATACTTATATAT-TTTAT
1 -TATACATACTTAAATATATTTAT
5325407 ACTCTTAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
36 2 0.04
37 7 0.14
38 39 0.80
39 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.01, T:0.49
Consensus pattern (39 bp):
TATACATACTTAAATATATTTATGCACATTTCACAATTC
Found at i:5327743 original size:16 final size:15
Alignment explanation
Indices: 5327700--5327745 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
5327690 AGGCCCATCC
5327700 ATATTATTTTATTTTA
1 ATATT-TTTTATTTTA
*
5327716 ATATTTAATTATTTTA
1 ATATTT-TTTATTTTA
5327732 TATATTTTTTATTT
1 -ATATTTTTTATTT
5327746 ATTGAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 19 0.73
17 6 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATATTTTTTATTTTA
Found at i:5332376 original size:14 final size:14
Alignment explanation
Indices: 5332359--5332385 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5332349 TATACAATAA
5332359 CAACATAATAGTAG
1 CAACATAATAGTAG
5332373 CAACATAATAGTA
1 CAACATAATAGTA
5332386 AAATTGTAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (14 bp):
CAACATAATAGTAG
Found at i:5334230 original size:22 final size:22
Alignment explanation
Indices: 5334186--5334237 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
5334176 AATAATAAAA
5334186 ATAAAT-TTAATTATAAAATAT
1 ATAAATATTAATTATAAAATAT
5334207 ATAAATATTAA-TATAAAATAAT
1 ATAAATATTAATTATAAAAT-AT
*
5334229 ATTAATATT
1 ATAAATATT
5334238 TTGTTATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATAAATATTAATTATAAAATAT
Found at i:5354850 original size:18 final size:19
Alignment explanation
Indices: 5354810--5354861 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
5354800 ATTTCAGTTA
*
5354810 AAATTAAATTAA-TTAATT
1 AAATTAACTTAATTTAATT
*
5354828 AAATTGACTTAATTTAATT
1 AAATTAACTTAATTTAATT
*
5354847 -AATTAATTTAATTTA
1 AAATTAACTTAATTTA
5354862 GTCGGAGGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 23 0.79
19 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
AAATTAACTTAATTTAATT
Found at i:5358042 original size:43 final size:43
Alignment explanation
Indices: 5357992--5358143 Score: 223
Period size: 43 Copynumber: 3.5 Consensus size: 43
5357982 TTTATTTGAA
*
5357992 AAAAACGCCGCTAAAAGCCATGACCTTTAGCGGCGCTTTTCCC
1 AAAAACGCCGCTAAAAGCCATGACCTTTAGCGGCACTTTTCCC
* * * * *
5358035 ACAAACGCCGCTAAAGGCCATGACCTTTAGAGGCACTTTTTCT
1 AAAAACGCCGCTAAAAGCCATGACCTTTAGCGGCACTTTTCCC
* *
5358078 AAAAACGCCGCTAAAGGCCATGACCTTTAGCGGCACTTTTCTC
1 AAAAACGCCGCTAAAAGCCATGACCTTTAGCGGCACTTTTCCC
*
5358121 AAAAACGCCGCTAAAAGTCATGA
1 AAAAACGCCGCTAAAAGCCATGA
5358144 AATTCAAAAA
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 96 1.00
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (43 bp):
AAAAACGCCGCTAAAAGCCATGACCTTTAGCGGCACTTTTCCC
Found at i:5358184 original size:28 final size:27
Alignment explanation
Indices: 5358152--5358206 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
5358142 GAAATTCAAA
*
5358152 AAAAATTATAAAATATTATAAAAGTCATG
1 AAAAA-TATAAAAAATT-TAAAAGTCATG
*
5358181 AAAAATATAAAAAATTTAAAATTCAT
1 AAAAATATAAAAAATTTAAAAGTCAT
5358207 TATCAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.38
28 10 0.42
29 5 0.21
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (27 bp):
AAAAATATAAAAAATTTAAAAGTCATG
Found at i:5361909 original size:18 final size:18
Alignment explanation
Indices: 5361886--5361929 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5361876 AGGGATTTTG
* *
5361886 GGGGAAATTTAG-GGATT
1 GGGGAAATGTAGAGAATT
5361903 AGGGGAAATGTAGAGAATT
1 -GGGGAAATGTAGAGAATT
5361922 GGGGAAAT
1 GGGGAAAT
5361930 CTTTTTTGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.41, T:0.23
Consensus pattern (18 bp):
GGGGAAATGTAGAGAATT
Found at i:5362131 original size:62 final size:66
Alignment explanation
Indices: 5362059--5362270 Score: 209
Period size: 75 Copynumber: 3.0 Consensus size: 66
5362049 CGTCGTTTTC
5362059 ATAGTATTTTTTGTGGCGTTTTTTTAAT-C-TC-TT-AATTTTCATATTTATTTTTATTTGTTAT
1 ATAGTATTTTTTGTGGCGTTTTTTTAATCCATCTTTAAATTTTCATATTTATTTTTATTTGTTAT
5362120 A
66 A
* * *
5362121 ATAGTGTTTTTTGTGGCGTTTTTTAAAAAAATGCCACTAATCTTTTAATTTTCATATTTATTTTT
1 ATAGTATTTTTTGTGGCGTTTTTT----TAAT--C-C--ATCTTTAAATTTTCATATTTATTTTT
5362186 ATTTGTTATA
57 ATTTGTTATA
5362196 ATAGTATTTTTTGTGGCGTTTTTTTAAAAATGCACTAATCTCTT-AATTTTCATATTTATTTTTA
1 ATAGTATTTTTTGTGGCGTTTTTTT---AAT-C-C--ATCT-TTAAATTTTCATATTTATTTTTA
5362260 TTTGTTATA
58 TTTGTTATA
5362269 AT
1 AT
5362271 TTGGAAGCCA
Statistics
Matches: 128, Mismatches: 5, Indels: 23
0.82 0.03 0.15
Matches are distributed among these distances:
62 23 0.18
66 3 0.02
70 1 0.01
73 42 0.33
74 7 0.05
75 52 0.41
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.58
Consensus pattern (66 bp):
ATAGTATTTTTTGTGGCGTTTTTTTAATCCATCTTTAAATTTTCATATTTATTTTTATTTGTTAT
A
Found at i:5362162 original size:75 final size:73
Alignment explanation
Indices: 5362083--5362270 Score: 331
Period size: 75 Copynumber: 2.5 Consensus size: 73
5362073 GGCGTTTTTT
*
5362083 TAATCTCTTAATTTTCATATTTATTTTTATTTGTTATAATAGTGTTTTTTGTGGCGTTTTTTAAA
1 TAATCTCTTAATTTTCATATTTATTTTTATTTGTTATAATAGTATTTTTTGTGGCGTTTTTT-AA
5362148 AAAATGCCAC
65 AAAATG-CAC
* *
5362158 TAATCTTTTAATTTTCATATTTATTTTTATTTGTTATAATAGTATTTTTTGTGGCGTTTTTTTAA
1 TAATCTCTTAATTTTCATATTTATTTTTATTTGTTATAATAGTATTTTTTGTGGCGTTTTTTAAA
5362223 AAATGCAC
66 AAATGCAC
5362231 TAATCTCTTAATTTTCATATTTATTTTTATTTGTTATAAT
1 TAATCTCTTAATTTTCATATTTATTTTTATTTGTTATAAT
5362271 TTGGAAGCCA
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
73 42 0.39
74 7 0.06
75 60 0.55
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.57
Consensus pattern (73 bp):
TAATCTCTTAATTTTCATATTTATTTTTATTTGTTATAATAGTATTTTTTGTGGCGTTTTTTAAA
AAATGCAC
Found at i:5362585 original size:28 final size:28
Alignment explanation
Indices: 5362541--5362629 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
5362531 TTAACACTTA
*
5362541 AAACTTAAACCCTTAACACATAACCCCT
1 AAACTTAAACCCTTAACACATAACCCAT
*
5362569 AAACTTTAAACCC-TAACACATAATCCAT
1 AAAC-TTAAACCCTTAACACATAACCCAT
*** * *
5362597 AAACCTTAAAATATTAACTCATAAACCAT
1 AAA-CTTAAACCCTTAACACATAACCCAT
5362626 AAAC
1 AAAC
5362630 CCCTAACCCC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
28 26 0.51
29 25 0.49
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (28 bp):
AAACTTAAACCCTTAACACATAACCCAT
Found at i:5362658 original size:22 final size:21
Alignment explanation
Indices: 5362633--5362701 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
5362623 CATAAACCCC
*
5362633 TAACCCCTAACCCCAATCCCAT
1 TAACGCCTAACCCCAATCCC-T
* *
5362655 TAACGCCTAACCCTTATTCCCT
1 TAACGCCTAACCC-CAATCCCT
*
5362677 TAACGCCTAACCCCTATCCCCT
1 TAACGCCTAACCCCAAT-CCCT
5362699 TAA
1 TAA
5362702 AACCTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 1 0.03
22 33 0.85
23 5 0.13
ACGTcount: A:0.28, C:0.45, G:0.03, T:0.25
Consensus pattern (21 bp):
TAACGCCTAACCCCAATCCCT
Found at i:5362860 original size:36 final size:36
Alignment explanation
Indices: 5362782--5362873 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
5362772 ACTAATTAAT
* * *
5362782 CTAAACCCTAAACCTCTTAACCCCTATCCCATAAACA
1 CTAAACTCTAAACC-CTTAACCCCAAGCCCATAAACA
* *
5362819 CTAAACTCTAAACCCTTAACCCCAAGCCCTTACAC-
1 CTAAACTCTAAACCCTTAACCCCAAGCCCATAAACA
5362854 CTTAAACTCT-AACCC-TAACC
1 C-TAAACTCTAAACCCTTAACC
5362874 ATTAAGCCCT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
34 5 0.10
35 6 0.12
36 25 0.51
37 13 0.27
ACGTcount: A:0.36, C:0.41, G:0.01, T:0.22
Consensus pattern (36 bp):
CTAAACTCTAAACCCTTAACCCCAAGCCCATAAACA
Found at i:5362985 original size:46 final size:46
Alignment explanation
Indices: 5362933--5363026 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
5362923 CTTCAAATAC
* *
5362933 TAGTTAACTCTTAAACCTTAAACCCTAAACCATATATCTTAAATCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
5362979 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
5363025 TA
1 TA
5363027 AACTATAAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
Found at i:5363353 original size:40 final size:42
Alignment explanation
Indices: 5363198--5363364 Score: 184
Period size: 41 Copynumber: 4.1 Consensus size: 42
5363188 GTTATATGAC
* * *
5363198 TTTTAGCGGCATTTTT-CCAAAAGCGCCGATAATGCTCTGGT
1 TTTTAGCGGCGTTTTTGCTAAAAGCGCCGCTAATGCTCTGGT
*
5363239 TTTTAGCGGCG-TTTTGCCAAAAGCGCCGCTAATGCTCT-GT
1 TTTTAGCGGCGTTTTTGCTAAAAGCGCCGCTAATGCTCTGGT
* *
5363279 TTTTCGCGGCGTTTTTGACTAAAA-CGCCGCTATTGCTCTGGT
1 TTTTAGCGGCGTTTTTG-CTAAAAGCGCCGCTAATGCTCTGGT
* * * *
5363321 TTTT-GTGGCGTTTTTGGTAAAA-CGCCGCTATTGCTATGTGT
1 TTTTAGCGGCGTTTTTGCTAAAAGCGCCGCTAATGCTCTG-GT
5363362 TTT
1 TTT
5363365 ACAATTTTTG
Statistics
Matches: 113, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
40 36 0.32
41 66 0.58
42 11 0.10
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (42 bp):
TTTTAGCGGCGTTTTTGCTAAAAGCGCCGCTAATGCTCTGGT
Found at i:5363752 original size:14 final size:15
Alignment explanation
Indices: 5363725--5363753 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5363715 AATTTTATGA
5363725 ATTTCATGATGTGTT
1 ATTTCATGATGTGTT
5363740 ATTTCAT-ATGTGTT
1 ATTTCATGATGTGTT
5363754 GATGATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (15 bp):
ATTTCATGATGTGTT
Found at i:5363946 original size:50 final size:51
Alignment explanation
Indices: 5363869--5363997 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
5363859 GACCATGGCA
**
5363869 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCAAATCAAGGACAAA-TG
*
5363920 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCAAATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCAAATCAAGGACAAATG
* * *
5363970 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
5363998 CTGATCAGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 43 0.61
51 27 0.39
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCAAATCAAGGACAAATG
Found at i:5364011 original size:31 final size:31
Alignment explanation
Indices: 5363973--5364181 Score: 307
Period size: 31 Copynumber: 6.8 Consensus size: 31
5363963 ACAAATGACA
*
5363973 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
5364004 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
5364035 AGTGAAAAGTGGTAG-TTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTT-CGGCTACCTGATC
5364066 AGTGAAAAGTGGTAG-TTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTT-CGGCTACCTGATC
* *
5364097 AGTGAAAAGTGGTAGCTCCGGCAACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
5364128 TGTGAAAA-TGGTAGCTCCGGCTACCTGATT
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
5364158 AGTGAATAGTGGTAGCTTCGGCTA
1 AGTGAAAAGTGGTAGCTTCGGCTA
5364182 TAAGTGACAA
Statistics
Matches: 165, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
30 28 0.17
31 136 0.82
32 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:5368184 original size:46 final size:46
Alignment explanation
Indices: 5368132--5368359 Score: 260
Period size: 46 Copynumber: 4.9 Consensus size: 46
5368122 CTCTGAAATG
* * * *
5368132 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
* *
5368178 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATG-
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GA
* **
5368224 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGATGGGA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-CAGA
* * *
5368271 AAATGAATAAAACCATGGTTGAAAGATGCCATGGCAACATGACAGA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
* * * * ** *
5368317 AAACGAGCAAAACCATAGTTGAAAGATATTATGGCATCATGAC
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
5368360 GAAGATAAAT
Statistics
Matches: 159, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
46 119 0.75
47 40 0.25
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (46 bp):
AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACAGA
Found at i:5368332 original size:93 final size:92
Alignment explanation
Indices: 5368143--5368358 Score: 263
Period size: 93 Copynumber: 2.3 Consensus size: 92
5368133 AATGTGTAAG
* * ** *
5368143 ACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACC
1 ACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATGAATAAAACCATGGTTGAAAGATACC
* * * *
5368208 ATGGCAACGTGACATGAAATGAATAAG
66 ATGGCAACATGACATGAAACGAACAAA
* *
5368235 ACCATGGTTGAAAGATACCATGGCAACATGATGGGAAAATGAATAAAACCATGGTTGAAAGATGC
1 ACCATGGTTGAAAGATACCATGGCAACATGAT-AGAAAATGAATAAAACCATGGTTGAAAGATAC
*
5368300 CATGGCAACATGACA-GAAAACGAGCAAA
65 CATGGCAACATGACATG-AAACGAACAAA
* ** *
5368328 ACCATAGTTGAAAGATATTATGGCATCATGA
1 ACCATGGTTGAAAGATACCATGGCAACATGA
5368359 CGAAGATAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
92 32 0.30
93 74 0.70
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (92 bp):
ACCATGGTTGAAAGATACCATGGCAACATGATAGAAAATGAATAAAACCATGGTTGAAAGATACC
ATGGCAACATGACATGAAACGAACAAA
Found at i:5370827 original size:53 final size:52
Alignment explanation
Indices: 5370748--5370850 Score: 145
Period size: 53 Copynumber: 2.0 Consensus size: 52
5370738 GAAGGAAAAG
*
5370748 ATGTGATATGTACTTCCGTATAAGACCATAGCTAGGCTATGGCATCGGTACA
1 ATGTGATATGTACTTCCGTATAAGACCATAGCTAGGATATGGCATCGGTACA
* * *
5370800 ATGTGATAATGTGA-TTTCGTATAAGACCATATCTGGGATATGGCATCGGTA
1 ATGTGAT-ATGT-ACTTCCGTATAAGACCATAGCTAGGATATGGCATCGGTA
5370851 TGATATGTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
52 7 0.16
53 37 0.82
54 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (52 bp):
ATGTGATATGTACTTCCGTATAAGACCATAGCTAGGATATGGCATCGGTACA
Found at i:5370872 original size:46 final size:50
Alignment explanation
Indices: 5370761--5370875 Score: 139
Period size: 53 Copynumber: 2.3 Consensus size: 50
5370751 TGATATGTAC
*
5370761 TTCCGTATAAGACCATAGCTAGGCTATGGCATCGGTACAATGTGATAATGTGA
1 TTCCGTATAAGACCATAGCTAGGATATGGCATCGGT--AA-GTGATAATGTGA
* * *
5370814 TTTCGTATAAGACCATATCTGGGATATGGCATCGGT-A-TGAT-ATGTGA
1 TTCCGTATAAGACCATAGCTAGGATATGGCATCGGTAAGTGATAATGTGA
5370861 -TCCGTATAAGACCAT
1 TTCCGTATAAGACCAT
5370876 GACAGGGCTA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
46 14 0.25
47 6 0.11
48 4 0.07
50 1 0.02
53 32 0.56
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (50 bp):
TTCCGTATAAGACCATAGCTAGGATATGGCATCGGTAAGTGATAATGTGA
Found at i:5370888 original size:46 final size:50
Alignment explanation
Indices: 5370761--5370895 Score: 138
Period size: 53 Copynumber: 2.7 Consensus size: 50
5370751 TGATATGTAC
5370761 TTCCGTATAAGACCATAGCTA-GGCTATGGCATCGGTACAATGTGATAATGTGA
1 TTCCGTATAAGACCATAGC-AGGGCTATGGCATCGGT--AA-GTGATAATGTGA
* * * *
5370814 TTTCGTATAAGACCATATCTGGGATATGGCATCGGT-A-TGAT-ATGTGA
1 TTCCGTATAAGACCATAGCAGGGCTATGGCATCGGTAAGTGATAATGTGA
*
5370861 -TCCGTATAAGACCAT-GACAGGGCTATGGCTTCGGT
1 TTCCGTATAAGACCATAG-CAGGGCTATGGCATCGGT
5370896 GTGTGATGTG
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
46 29 0.41
47 6 0.08
48 4 0.06
50 1 0.01
53 31 0.44
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (50 bp):
TTCCGTATAAGACCATAGCAGGGCTATGGCATCGGTAAGTGATAATGTGA
Found at i:5371968 original size:22 final size:22
Alignment explanation
Indices: 5371870--5371961 Score: 71
Period size: 22 Copynumber: 4.1 Consensus size: 22
5371860 TATATATTAG
* *
5371870 AAATAC-TAATAACATAAAAAT
1 AAATACATAATAATATTAAAAT
* * * *
5371891 ATATATATTAATAATACT-ACAT
1 AAATACA-TAATAATATTAAAAT
**
5371913 AAATATGTACATATATATTAAAAT
1 AAATACATA-ATA-ATATTAAAAT
5371937 AAATACATAATAATATTAAAAT
1 AAATACATAATAATATTAAAAT
5371959 AAA
1 AAA
5371962 ATAATAAGTG
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
21 6 0.11
22 24 0.44
23 14 0.26
24 10 0.19
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.33
Consensus pattern (22 bp):
AAATACATAATAATATTAAAAT
Found at i:5372155 original size:27 final size:26
Alignment explanation
Indices: 5372113--5372203 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 26
5372103 AAATAGATAT
* *
5372113 AATAATATATACATAATATGGTATTA
1 AATAATATATACATAACATAGTATTA
* *
5372139 AATATATATATATATAACATAGTATTC
1 AATA-ATATATACATAACATAGTATTA
* * * *
5372166 AAGAATATGTACATGAGAT-G-ATATA
1 AATAATATATACATAACATAGTAT-TA
5372191 AA-AATATATACAT
1 AATAATATATACAT
5372204 GGAATAGTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
24 12 0.23
25 4 0.08
26 15 0.29
27 21 0.40
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (26 bp):
AATAATATATACATAACATAGTATTA
Found at i:5372421 original size:46 final size:43
Alignment explanation
Indices: 5372360--5372479 Score: 136
Period size: 46 Copynumber: 2.6 Consensus size: 43
5372350 ATGGTGTTAG
5372360 AAATATATAAT-ATAATATTAGAAATATACAT-ACAATAGTATAA
1 AAATATATAATAATAATATTA-AAATATACATAACAATA-TATAA
*
5372403 AAGATATATAACTAATAATATTAAAATATATACATAATAATATATAA
1 AA-ATATATAA-TAATAATATT-AAA-ATATACATAACAATATATAA
5372450 AAATATATATATAATATAATATTAAAATAT
1 AAATATATA-AT-A-ATAATATTAAAATAT
5372480 TTACATAATA
Statistics
Matches: 67, Mismatches: 1, Indels: 15
0.81 0.01 0.18
Matches are distributed among these distances:
43 2 0.03
44 8 0.12
45 1 0.01
46 22 0.33
47 21 0.31
48 13 0.19
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (43 bp):
AAATATATAATAATAATATTAAAATATACATAACAATATATAA
Found at i:5372439 original size:26 final size:25
Alignment explanation
Indices: 5372366--5372503 Score: 130
Period size: 24 Copynumber: 5.7 Consensus size: 25
5372356 TTAGAAATAT
*
5372366 ATAAT-ATAATATTAGAA-ATATAC
1 ATAATAATAATATTAAAATATATAC
* * *
5372389 AT-ACAATAGTA-TAAAAGATAT--
1 ATAATAATAATATTAAAATATATAC
5372410 ATAACTAATAATATTAAAATATATAC
1 ATAA-TAATAATATTAAAATATATAC
* *
5372436 ATAATAAT-ATATAAAAATATATAT
1 ATAATAATAATATTAAAATATATAC
*
5372460 ATAAT-ATAATATTAAAATATTTAC
1 ATAATAATAATATTAAAATATATAC
5372484 ATAATATATACATATTAAAA
1 ATAATA-ATA-ATATTAAAA
5372504 ATAAAAAACG
Statistics
Matches: 93, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
21 2 0.02
22 6 0.06
23 19 0.20
24 46 0.49
25 4 0.04
26 7 0.08
27 9 0.10
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (25 bp):
ATAATAATAATATTAAAATATATAC
Found at i:5372446 original size:14 final size:13
Alignment explanation
Indices: 5372406--5372471 Score: 61
Period size: 14 Copynumber: 5.3 Consensus size: 13
5372396 AGTATAAAAG
5372406 ATATATAACTAATA
1 ATATATAA-TAATA
5372420 ATAT-TAA-AAT-
1 ATATATAATAATA
*
5372430 ATATA-CATAATA
1 ATATATAATAATA
*
5372442 ATATATAAAAATA
1 ATATATAATAATA
5372455 TATATATAAT-ATA
1 -ATATATAATAATA
5372468 ATAT
1 ATAT
5372472 TAAAATATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 5 0.12
11 6 0.14
12 9 0.21
13 11 0.26
14 12 0.28
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATATAATAATA
Found at i:5372473 original size:48 final size:49
Alignment explanation
Indices: 5372362--5372493 Score: 170
Period size: 48 Copynumber: 2.8 Consensus size: 49
5372352 GGTGTTAGAA
* *
5372362 ATATATAATATAATATTAGAA-ATATACAT-ACAATAGTATAAAAGATAT
1 ATATATAATATAATATTAAAATATATACATAATAATA-TATAAAAGATAT
5372410 ATA-ACT-A-ATAATATTAAAATATATACATAATAATATATAAAA-ATAT
1 ATATA-TAATATAATATTAAAATATATACATAATAATATATAAAAGATAT
*
5372456 ATATATAATATAATATTAAAATATTTACATAAT-ATATA
1 ATATATAATATAATATTAAAATATATACATAATAATATA
5372494 CATATTAAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
46 19 0.25
47 24 0.32
48 32 0.43
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (49 bp):
ATATATAATATAATATTAAAATATATACATAATAATATATAAAAGATAT
Found at i:5374066 original size:23 final size:25
Alignment explanation
Indices: 5374040--5374086 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
5374030 TATCATTCAT
*
5374040 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
5374063 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
5374087 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:5374407 original size:46 final size:46
Alignment explanation
Indices: 5374347--5374696 Score: 446
Period size: 46 Copynumber: 8.0 Consensus size: 46
5374337 TTTGACGTAA
* * * * * *
5374347 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* ** * * *
5374393 TGCCATGGTATCTTTCAACCAAGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
5374439 TGCCATGGTATCTCTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5374485 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5374531 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5374569 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5374615 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
5374653 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
5374697 AGAGCACACT
Statistics
Matches: 270, Mismatches: 17, Indels: 34
0.84 0.05 0.11
Matches are distributed among these distances:
38 66 0.24
39 2 0.01
40 6 0.02
41 2 0.01
43 2 0.01
44 6 0.02
45 6 0.02
46 180 0.67
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.37
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:5374463 original size:92 final size:88
Alignment explanation
Indices: 5374347--5374696 Score: 455
Period size: 84 Copynumber: 4.0 Consensus size: 88
5374337 TTTGACGTAA
* * * *
5374347 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CA--TTCT-TCAGGTTGCCATGGTATCTTTCAAC
* ** * * *
5374412 CAAGGTCTTATTCTTTTCATGTCACGT
62 CATGGTCTTACACATTTCATATCAGGT
*
5374439 TGCCATGGTATCTCTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CAT-TC-T-TCAGGTTGCCATGGTATCTTTCAAC
5374504 CATGGTCTTACACATTTCATATCAGGT
62 CATGGTCTTACACATTTCATATCAGGT
*
5374531 TGCCATGGTATCTTTCAACCATGGTCTTA-CA--C-ACAGGTTGCCATGGTATCTTTCAACCATG
1 TGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAACCATG
5374592 GTCTTACACATTTCATATCAGGT
66 GTCTTACACATTTCATATCAGGT
*
5374615 TGCCATGGTATCTTTCAACCATGGTCTTA-CA--C-ACAGGTTGCCATGGTATCTTTCAACCATG
1 TGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAACCATG
5374676 GTCTTACACATTTCATATCAG
66 GTCTTACACATTTCATATCAG
5374697 AGAGCACACT
Statistics
Matches: 241, Mismatches: 15, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
84 133 0.55
87 1 0.00
90 3 0.01
91 2 0.01
92 102 0.42
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.37
Consensus pattern (88 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAACCATG
GTCTTACACATTTCATATCAGGT
Found at i:5374577 original size:38 final size:38
Alignment explanation
Indices: 5374526--5374685 Score: 248
Period size: 38 Copynumber: 4.0 Consensus size: 38
5374516 CATTTCATAT
5374526 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
5374564 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A
5374609 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 -CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
5374648 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
5374686 TTTCATATCA
Statistics
Matches: 114, Mismatches: 0, Indels: 16
0.88 0.00 0.12
Matches are distributed among these distances:
38 71 0.62
39 1 0.01
40 3 0.03
41 1 0.01
43 1 0.01
44 3 0.03
45 1 0.01
46 33 0.29
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:5376910 original size:31 final size:32
Alignment explanation
Indices: 5376834--5376910 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 32
5376824 CTAATAAAAT
*
5376834 AATAATAAAATATCTTATTAAAGTATTAATAA
1 AATAATAAAATATCTAATTAAAGTATTAATAA
**
5376866 AATAAT-ATTTATCTAATTAAA-TAATT-ATAA
1 AATAATAAAATATCTAATTAAAGT-ATTAATAA
*
5376896 AATATTAAAATATCT
1 AATAATAAAATATCT
5376911 CTAGCATCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
30 10 0.27
31 21 0.57
32 6 0.16
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (32 bp):
AATAATAAAATATCTAATTAAAGTATTAATAA
Found at i:5380244 original size:54 final size:54
Alignment explanation
Indices: 5380158--5380316 Score: 297
Period size: 54 Copynumber: 3.0 Consensus size: 54
5380148 AACCTAAATA
5380158 TTGTATAATTTGA---TTTTTTTCAGTTTTATTTTATTTGGGACATTAAATTTT
1 TTGTATAATTTGATTTTTTTTTTCAGTTTTATTTTATTTGGGACATTAAATTTT
5380209 TTGTATAATTTGATTTTTTTTTTCAGTTTTATTTTATTTGGGACATTAAATTTT
1 TTGTATAATTTGATTTTTTTTTTCAGTTTTATTTTATTTGGGACATTAAATTTT
5380263 TTGTATAATTTGATTTTTTTTTTCAGTTTTATTTTATTTGGGACATTAAATTTT
1 TTGTATAATTTGATTTTTTTTTTCAGTTTTATTTTATTTGGGACATTAAATTTT
5380317 AGTTTTAAAA
Statistics
Matches: 105, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
51 13 0.12
54 92 0.88
ACGTcount: A:0.23, C:0.04, G:0.11, T:0.62
Consensus pattern (54 bp):
TTGTATAATTTGATTTTTTTTTTCAGTTTTATTTTATTTGGGACATTAAATTTT
Found at i:5387556 original size:38 final size:39
Alignment explanation
Indices: 5387437--5387603 Score: 210
Period size: 39 Copynumber: 4.3 Consensus size: 39
5387427 CTTTAACCCA
* ** * * *
5387437 GATATTTTTCCAGTACGTAGCCTGCAGACCTCAAGTTCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
* * * *
5387476 GATATATTTCTAGCATATAGCCTGCAGATCTCATGTCCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
*
5387515 GATATTTTTCCAGCATATGGCCT-CGGACCTCATGTCCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
*
5387553 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGGCCG
1 GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
*
5387592 AATATTTTTCCA
1 GATATTTTTCCA
5387604 ATCTCATATA
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 35 0.32
39 76 0.68
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (39 bp):
GATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCG
Found at i:5398389 original size:135 final size:135
Alignment explanation
Indices: 5398037--5398375 Score: 502
Period size: 135 Copynumber: 2.5 Consensus size: 135
5398027 GATTGTAGAT
* * * *
5398037 ATCATAAGCCTTATCTTCACTGAGCAGGAGTGGAGCATGCT-AA-ATACCAGATCTTATCTTCAC
1 ATCATCAGCTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
* * * * *
5398100 TGAGCAGGGGTGAAGCAGATCAAATTTTAGATAATTTTATCTCCACGTACCGGCGATGGAGCAGG
66 TGAGCAGGAGTGAAGCAGATCAAATTTTAGAGAATCTTATCTCCACGTACCGGCGATGGAACAGA
5398165 TTCCA
131 TTCCA
* *
5398170 ATCATCAACTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTTAT
1 ATCATCAGCTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
* *
5398235 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAACAGA
66 TGAGCAGGAGTGAAGCAGATCAAATTTTAGAGAATCTTATCTCCACGTACCGGCGATGGAACAGA
*
5398300 TTTCA
131 TTCCA
* * * *
5398305 ATCATCAGCTTTATCTTTACTGAGCAGGAGTGGAGTAGGCTAAATATACTAGATCTTATCTTCGT
1 ATCATCAGCTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
5398370 TGAGCA
66 TGAGCA
5398376 AGAGCGGATC
Statistics
Matches: 184, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
133 37 0.20
134 2 0.01
135 145 0.79
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (135 bp):
ATCATCAGCTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
TGAGCAGGAGTGAAGCAGATCAAATTTTAGAGAATCTTATCTCCACGTACCGGCGATGGAACAGA
TTCCA
Found at i:5400407 original size:14 final size:15
Alignment explanation
Indices: 5400380--5400408 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5400370 AATTTTATGA
5400380 ATTTCATAATGTGTT
1 ATTTCATAATGTGTT
5400395 ATTTCAT-ATGTGTT
1 ATTTCATAATGTGTT
5400409 GATGATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (15 bp):
ATTTCATAATGTGTT
Found at i:5400601 original size:50 final size:51
Alignment explanation
Indices: 5400524--5400652 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
5400514 GACCATGGCA
5400524 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
5400575 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
5400625 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
5400653 CTGATCAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:5400666 original size:31 final size:31
Alignment explanation
Indices: 5400628--5400690 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
5400618 ACAAATGACA
*
5400628 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAACTTCAGCTACCTGATC
*
5400659 AGTGAAAAGTGGTAACTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAACTTCAGCTACCTGATC
5400690 A
1 A
5400691 CCGGCTACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAACTTCAGCTACCTGATC
Found at i:5400700 original size:46 final size:46
Alignment explanation
Indices: 5400648--5400736 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
5400638 GGTAGCTTCA
* *
5400648 GCTACCTGATCAGTGAAAAGTGGTAACTTCTGCTACCTGATCACCG
1 GCTACCTGATCAGTGAAAAGTGGTAACTCCGGCTACCTGATCACCG
*
5400694 GCTACCTGATCAGTGAAAAGTGGTAGCTCCGGCTACCTGATCA
1 GCTACCTGATCAGTGAAAAGTGGTAACTCCGGCTACCTGATCA
5400737 GTGAAAAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.25
Consensus pattern (46 bp):
GCTACCTGATCAGTGAAAAGTGGTAACTCCGGCTACCTGATCACCG
Found at i:5400729 original size:31 final size:31
Alignment explanation
Indices: 5400691--5400791 Score: 166
Period size: 31 Copynumber: 3.3 Consensus size: 31
5400681 TACCTGATCA
5400691 CCGGCTACCTGATCAGTGAAAAGTGGTAGCT
1 CCGGCTACCTGATCAGTGAAAAGTGGTAGCT
*
5400722 CCGGCTACCTGATCAGTGAAAAATGGTAGCT
1 CCGGCTACCTGATCAGTGAAAAGTGGTAGCT
* *
5400753 CCGGCTACCTGATCAGTGAATAGTGGTAGTT
1 CCGGCTACCTGATCAGTGAAAAGTGGTAGCT
*
5400784 TCGGCTAC
1 CCGGCTAC
5400792 AAGTGACAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (31 bp):
CCGGCTACCTGATCAGTGAAAAGTGGTAGCT
Found at i:5400835 original size:17 final size:17
Alignment explanation
Indices: 5400813--5400847 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5400803 GACAAGTGAT
5400813 TTCCGTATAAGACCATA
1 TTCCGTATAAGACCATA
*
5400830 TTCCGTATAAGACTATA
1 TTCCGTATAAGACCATA
5400847 T
1 T
5400848 CTAGGATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (17 bp):
TTCCGTATAAGACCATA
Found at i:5400903 original size:47 final size:46
Alignment explanation
Indices: 5400833--5400956 Score: 149
Period size: 47 Copynumber: 2.7 Consensus size: 46
5400823 GACCATATTC
* * * *
5400833 CGTATAAGACTATATCTAGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * *
5400879 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * *
5400926 CGTGTAAGACCATAGCTGGGCTATGGCATCG
1 CGTATAAGACCATATCTGGGATATGGCATCG
5400957 ATATATGAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 27 0.41
47 39 0.59
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
Found at i:5400951 original size:46 final size:43
Alignment explanation
Indices: 5400884--5401039 Score: 147
Period size: 42 Copynumber: 3.6 Consensus size: 43
5400874 TGCTACTGTA
* * *
5400884 TAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGAT-TCGTG
1 TAAGACCATAGCTGGGCTATGGCATCA--GAGATATG-AATAT-GTG
*
5400930 TAAGACCATAGCTGGGCTATGGCATC-GATATATGAATATGTG
1 TAAGACCATAGCTGGGCTATGGCATCAGAGATATGAATATGTG
* ** * *
5400972 TAAGACCATAGCTGGACTATGGCATCA-TTATGTGAAAATGTG
1 TAAGACCATAGCTGGGCTATGGCATCAGAGATATGAATATGTG
* **
5401014 TAAGACCATAGTTGAACTATGGCATC
1 TAAGACCATAGCTGGGCTATGGCATC
5401040 GAAAAAATGA
Statistics
Matches: 98, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
42 66 0.67
43 8 0.08
46 24 0.24
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (43 bp):
TAAGACCATAGCTGGGCTATGGCATCAGAGATATGAATATGTG
Found at i:5400985 original size:42 final size:43
Alignment explanation
Indices: 5400927--5401041 Score: 171
Period size: 42 Copynumber: 2.7 Consensus size: 43
5400917 TATGTGATTC
* *
5400927 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGACTATGGCATCGATTATATGAAAAT
*
5400969 GTGTAAGACCATAGCTGGACTATGGCATC-ATTATGTGAAAAT
1 GTGTAAGACCATAGCTGGACTATGGCATCGATTATATGAAAAT
* *
5401011 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGACTATGGCATCGA
5401042 AAAAATGAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 64 0.97
43 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGACTATGGCATCGATTATATGAAAAT
Found at i:5402584 original size:21 final size:22
Alignment explanation
Indices: 5402542--5402584 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5402532 TAAACGAATT
* *
5402542 ACAATATTATTTAACTACATAA
1 ACAATATAATTTAACTAAATAA
5402564 ACAATATAATTT-ACTAAATAA
1 ACAATATAATTTAACTAAATAA
5402585 TTACATGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
ACAATATAATTTAACTAAATAA
Found at i:5402612 original size:21 final size:21
Alignment explanation
Indices: 5402588--5402629 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5402578 TAAATAATTA
5402588 CATGTAAAGAACTATTTTAGG
1 CATGTAAAGAACTATTTTAGG
5402609 CATGTAAAGAACTATTTTAGG
1 CATGTAAAGAACTATTTTAGG
5402630 TATGCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (21 bp):
CATGTAAAGAACTATTTTAGG
Found at i:5405539 original size:36 final size:36
Alignment explanation
Indices: 5405499--5405572 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
5405489 AATTAAAGCG
5405499 TTCAAAATTAACTCAAAACAAAAACAATGGAGTAAC
1 TTCAAAATTAACTCAAAACAAAAACAATGGAGTAAC
*
5405535 TTCAAAATTAACTCAAAATAAAAACAATGGAGTAAC
1 TTCAAAATTAACTCAAAACAAAAACAATGGAGTAAC
5405571 TT
1 TT
5405573 ACTTATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (36 bp):
TTCAAAATTAACTCAAAACAAAAACAATGGAGTAAC
Found at i:5406197 original size:36 final size:36
Alignment explanation
Indices: 5406157--5406229 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
5406147 TGCGCATGAC
* *
5406157 TTAAATGAAGCAAAACATTATATATATGCATTAATA
1 TTAAATGAAGCAAAACAGTATACATATGCATTAATA
*
5406193 TTAAATGAAGCTAAACAGTATACATATGCATTAATA
1 TTAAATGAAGCAAAACAGTATACATATGCATTAATA
5406229 T
1 T
5406230 ATATATGCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (36 bp):
TTAAATGAAGCAAAACAGTATACATATGCATTAATA
Found at i:5406362 original size:43 final size:42
Alignment explanation
Indices: 5406272--5406404 Score: 118
Period size: 43 Copynumber: 3.3 Consensus size: 42
5406262 CTAATTATGA
** **
5406272 TATATATATGCAATTATGCATGACTTAAATGAAGTTAAATGG
1 TATATATATGCAATTATGCATGACTTAAATGAAGCAAAACAG
* *
5406314 AATATATATGC-ATTATGCGCATGACTTAAATGAAGCAAAACAT
1 TATATATATGCAATTAT--GCATGACTTAAATGAAGCAAAACAG
* *
5406357 TATATATATGC-CTTA---AT-A-TTAAATGAAGCTAAACAG
1 TATATATATGCAATTATGCATGACTTAAATGAAGCAAAACAG
*
5406393 TATACATATGCA
1 TATATATATGCA
5406405 TTAATATATA
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
36 26 0.34
37 1 0.01
38 2 0.03
41 5 0.06
42 10 0.13
43 33 0.43
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (42 bp):
TATATATATGCAATTATGCATGACTTAAATGAAGCAAAACAG
Found at i:5406379 original size:36 final size:36
Alignment explanation
Indices: 5406339--5406411 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
5406329 TGCGCATGAC
* * *
5406339 TTAAATGAAGCAAAACATTATATATATGCCTTAATA
1 TTAAATGAAGCAAAACAGTATACATATGCATTAATA
*
5406375 TTAAATGAAGCTAAACAGTATACATATGCATTAATA
1 TTAAATGAAGCAAAACAGTATACATATGCATTAATA
5406411 T
1 T
5406412 ATATATGCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.33
Consensus pattern (36 bp):
TTAAATGAAGCAAAACAGTATACATATGCATTAATA
Found at i:5406544 original size:43 final size:42
Alignment explanation
Indices: 5406450--5406549 Score: 121
Period size: 43 Copynumber: 2.4 Consensus size: 42
5406440 TCTGCTAATT
* **
5406450 ATGGTATATATATGCAATTATGCATGACTTAAATGAAGTTAA
1 ATGGTATATATATGCAATTATGCATGACTTAAATAAAGCAAA
*
5406492 ATGGAATATATATGC-ATTATGCGCATGACTTAAATAAAGCAAA
1 ATGGTATATATATGCAATTAT--GCATGACTTAAATAAAGCAAA
**
5406535 ATTTTATATATATGC
1 ATGGTATATATATGC
5406550 CTTAATATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 5 0.10
42 14 0.29
43 30 0.61
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (42 bp):
ATGGTATATATATGCAATTATGCATGACTTAAATAAAGCAAA
Found at i:5406673 original size:141 final size:141
Alignment explanation
Indices: 5406497--5406785 Score: 463
Period size: 141 Copynumber: 2.0 Consensus size: 141
5406487 GTTAAATGGA
** *
5406497 ATATATATGCATTATGCGCATGACTTAAATAAAGCAAAATTTTATATATATGCCTTAATATTAAA
1 ATATATATGCATTAT-CGCATGACTTAAATAAAGCAAAACATTATATATATGCATTAATATTAAA
* * *
5406562 TGAAGCTAAACAGTATACATATGCATTAATATATATATGCTTGGCTTAACTCAAGCTAAACCTGC
65 TGAAGCTAAACAGTATACATATGCATTAAGATATATATGCTTGACTTAAATCAAGCTAAACCTGC
*
5406627 TAATTATGGTAT
130 TAATAATGGTAT
*
5406639 ATATATATGCAATTAT-GCATGACTTAAATGAAGCAAAACATTATATATATGCATTAATATTAAA
1 ATATATATGC-ATTATCGCATGACTTAAATAAAGCAAAACATTATATATATGCATTAATATTAAA
* *
5406703 TGAAGCTAAACAGTATACATATGCATTAAGATATATATGCTTGACTTAAATGAAGTTAAACCTGC
65 TGAAGCTAAACAGTATACATATGCATTAAGATATATATGCTTGACTTAAATCAAGCTAAACCTGC
5406768 TAATAATGGTAT
130 TAATAATGGTAT
5406780 ATATAT
1 ATATAT
5406786 GCATGACTTA
Statistics
Matches: 136, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
141 121 0.89
142 10 0.07
143 5 0.04
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (141 bp):
ATATATATGCATTATCGCATGACTTAAATAAAGCAAAACATTATATATATGCATTAATATTAAAT
GAAGCTAAACAGTATACATATGCATTAAGATATATATGCTTGACTTAAATCAAGCTAAACCTGCT
AATAATGGTAT
Found at i:5406686 original size:182 final size:183
Alignment explanation
Indices: 5406145--5406671 Score: 986
Period size: 182 Copynumber: 2.9 Consensus size: 183
5406135 AATATATATA
*
5406145 TATGCGCATGACTTAAATGAAGCAAAACATTATATATATGCATTAATATTAAATGAAGCTAAACA
1 TATGCGCATGACTTAAATGAAGCAAAACATTATATATATGCCTTAATATTAAATGAAGCTAAACA
5406210 GTATACATATGCATTAATATATATATGCTTGGCTTAACTCAAGCTAAACCTGCTAATTAT-GATA
66 GTATACATATGCATTAATATATATATGCTTGGCTTAACTCAAGCTAAACCTGCTAATTATGGATA
5406274 TATATATGCAATTATGCATGACTTAAATGAAGTTAAATGGAATATATATGCAT
131 TATATATGCAATTATGCATGACTTAAATGAAGTTAAATGGAATATATATGCAT
5406327 TATGCGCATGACTTAAATGAAGCAAAACATTATATATATGCCTTAATATTAAATGAAGCTAAACA
1 TATGCGCATGACTTAAATGAAGCAAAACATTATATATATGCCTTAATATTAAATGAAGCTAAACA
*
5406392 GTATACATATGCATTAATATATATATGCTTGGCTTAACTCAAGCTAAATCTGCTAATTATGG-TA
66 GTATACATATGCATTAATATATATATGCTTGGCTTAACTCAAGCTAAACCTGCTAATTATGGATA
5406456 TATATATGCAATTATGCATGACTTAAATGAAGTTAAATGGAATATATATGCAT
131 TATATATGCAATTATGCATGACTTAAATGAAGTTAAATGGAATATATATGCAT
* **
5406509 TATGCGCATGACTTAAATAAAGCAAAATTTTATATATATGCCTTAATATTAAATGAAGCTAAACA
1 TATGCGCATGACTTAAATGAAGCAAAACATTATATATATGCCTTAATATTAAATGAAGCTAAACA
5406574 GTATACATATGCATTAATATATATATGCTTGGCTTAACTCAAGCTAAACCTGCTAATTATGGTAT
66 GTATACATATGCATTAATATATATATGCTTGGCTTAACTCAAGCTAAACCTGCTAATTATGG-AT
5406639 ATATATATGCAATTATGCATGACTTAAATGAAG
130 ATATATATGCAATTATGCATGACTTAAATGAAG
5406672 CAAAACATTA
Statistics
Matches: 336, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
182 301 0.90
183 1 0.00
184 34 0.10
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (183 bp):
TATGCGCATGACTTAAATGAAGCAAAACATTATATATATGCCTTAATATTAAATGAAGCTAAACA
GTATACATATGCATTAATATATATATGCTTGGCTTAACTCAAGCTAAACCTGCTAATTATGGATA
TATATATGCAATTATGCATGACTTAAATGAAGTTAAATGGAATATATATGCAT
Found at i:5406688 original size:42 final size:37
Alignment explanation
Indices: 5406638--5406731 Score: 102
Period size: 36 Copynumber: 2.5 Consensus size: 37
5406628 AATTATGGTA
*
5406638 TATATATATGCAATTATGCATGACTTAAATGAAGCAAAACAT
1 TATATATATGCAATTA---AT-A-TTAAATGAAGCAAAACAG
*
5406680 TATATATATGC-ATTAATATTAAATGAAGCTAAACAG
1 TATATATATGCAATTAATATTAAATGAAGCAAAACAG
*
5406716 TATACATATGC-ATTAA
1 TATATATATGCAATTAA
5406732 GATATATATG
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
36 31 0.63
37 1 0.02
38 2 0.04
41 4 0.08
42 11 0.22
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (37 bp):
TATATATATGCAATTAATATTAAATGAAGCAAAACAG
Found at i:5406704 original size:36 final size:36
Alignment explanation
Indices: 5406662--5406731 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
5406652 TATGCATGAC
* *
5406662 TTAAATGAAGCAAAACATTATATATATGCATTAATA
1 TTAAATGAAGCAAAACAGTATACATATGCATTAATA
*
5406698 TTAAATGAAGCTAAACAGTATACATATGCATTAA
1 TTAAATGAAGCAAAACAGTATACATATGCATTAA
5406732 GATATATATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (36 bp):
TTAAATGAAGCAAAACAGTATACATATGCATTAATA
Found at i:5406796 original size:45 final size:45
Alignment explanation
Indices: 5406733--5406822 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
5406723 ATGCATTAAG
* **
5406733 ATATATATGCTTGACTTAAATGAAGTTAAACCTGCTAATAATGGT
1 ATATATATGCATGACTTAAATGAAACTAAACCTGCTAATAATGGT
*
5406778 ATATATATGCATGACTTAAATGAAACTAAACCTGTTAATAATGGT
1 ATATATATGCATGACTTAAATGAAACTAAACCTGCTAATAATGGT
5406823 TAATTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (45 bp):
ATATATATGCATGACTTAAATGAAACTAAACCTGCTAATAATGGT
Done.