Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 24
Found at i:784277 original size:23 final size:23
Alignment explanation
Indices: 784234--784277 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
784224 AATATTTTTT
*
784234 TAAAATAATTTAGAATGTTAATG
1 TAAAATAATTTAGAATATTAATG
784257 TAAAATAATTTAAGAA-ATTAA
1 TAAAATAATTT-AGAATATTAA
784278 GAATTTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (23 bp):
TAAAATAATTTAGAATATTAATG
Found at i:784979 original size:15 final size:14
Alignment explanation
Indices: 784937--784983 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
784927 AATTTATTTT
784937 TTAAATTTAATTAC
1 TTAAATTTAATTAC
784951 TTAAATTTTAAATTAC
1 TTAAA-TTT-AATTAC
784967 TCCT-AATTTAATTAC
1 T--TAAATTTAATTAC
784982 TT
1 TT
784984 TAACTTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 10 0.34
16 10 0.34
17 2 0.07
18 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAAATTTAATTAC
Found at i:791912 original size:28 final size:28
Alignment explanation
Indices: 791875--791983 Score: 209
Period size: 28 Copynumber: 3.9 Consensus size: 28
791865 GATATAGTAG
*
791875 AATAGTTATACATCATTAAACTTCAAAT
1 AATAATTATACATCATTAAACTTCAAAT
791903 AATAATTATACATCATTAAACTTCAAAT
1 AATAATTATACATCATTAAACTTCAAAT
791931 AATAATTATACATCATTAAACTTCAAAT
1 AATAATTATACATCATTAAACTTCAAAT
791959 AATAATTATACATCATTAAACTTCA
1 AATAATTATACATCATTAAACTTCA
791984 TAAAGCTCTA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 80 1.00
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.36
Consensus pattern (28 bp):
AATAATTATACATCATTAAACTTCAAAT
Found at i:801952 original size:16 final size:17
Alignment explanation
Indices: 801925--801971 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
801915 TAATAAATTT
*
801925 ATAATTTTTAATAATCA
1 ATAATATTTAATAATCA
801942 A-AATATTTAATAA--A
1 ATAATATTTAATAATCA
*
801956 ATAATATTTTATAATC
1 ATAATATTTAATAATC
801972 GAAACTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 11 0.44
17 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAATATTTAATAATCA
Found at i:809656 original size:37 final size:38
Alignment explanation
Indices: 809622--809700 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 38
809612 TTTTTATATT
809622 TTTAATTTTGTAAA-ACAAAT-TATATAAATATTATAAA
1 TTTAATTTTGTAAAGA-AAATATATATAAATATTATAAA
* *
809659 TTTAATTTTTTAAAGAAAATATATATAAATATTTTATAA
1 TTTAATTTTGTAAAGAAAATATATATAAATATTATA-AA
809698 TTT
1 TTT
809701 GTAATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 17 0.46
38 15 0.41
39 5 0.14
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (38 bp):
TTTAATTTTGTAAAGAAAATATATATAAATATTATAAA
Found at i:812357 original size:2 final size:2
Alignment explanation
Indices: 812350--812386 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
812340 TAAGCCATTA
812350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
812387 GATTTACAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:817938 original size:21 final size:21
Alignment explanation
Indices: 817912--817951 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
817902 TATAAACCAC
*
817912 TGTGGACTTCCATATCAACAA
1 TGTGGACCTCCATATCAACAA
*
817933 TGTGGACCTCCATGTCAAC
1 TGTGGACCTCCATATCAAC
817952 TCCGTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTGGACCTCCATATCAACAA
Found at i:826866 original size:23 final size:23
Alignment explanation
Indices: 826840--826889 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
826830 GTATGATTTT
826840 TAAAA-AAATGAAAATTTAGGTAC
1 TAAAACAAAT-AAAATTTAGGTAC
* * *
826863 TAAAACGAATCAAGTTTAGGTAC
1 TAAAACAAATAAAATTTAGGTAC
826886 TAAA
1 TAAA
826890 CACGTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (23 bp):
TAAAACAAATAAAATTTAGGTAC
Found at i:828366 original size:20 final size:19
Alignment explanation
Indices: 828316--828370 Score: 87
Period size: 18 Copynumber: 2.9 Consensus size: 19
828306 TCAGTAATTC
828316 TATTCCCA-GGTAATCTTT
1 TATTCCCATGGTAATCTTT
828334 TATT-CCATGGTAATCTTT
1 TATTCCCATGGTAATCTTT
828352 TATTCCCACTGGTAATCTT
1 TATTCCCA-TGGTAATCTT
828371 ACATCCCGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.09
18 18 0.53
19 3 0.09
20 10 0.29
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (19 bp):
TATTCCCATGGTAATCTTT
Found at i:832436 original size:14 final size:14
Alignment explanation
Indices: 832412--832443 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
832402 ATATCATTTT
832412 ATATT-AAAATAAA
1 ATATTAAAAATAAA
832425 ATATTAAAAATAAA
1 ATATTAAAAATAAA
832439 A-ATTA
1 ATATTA
832444 CTATTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATATTAAAAATAAA
Found at i:836740 original size:17 final size:15
Alignment explanation
Indices: 836702--836740 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 15
836692 CTAATTCTTA
836702 TTAATTAAAATATTT
1 TTAATTAAAATATTT
836717 TTCAATTAATAATATTAT
1 TT-AATTAA-AATATT-T
836735 TTAATT
1 TTAATT
836741 CACTAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 6 0.29
17 10 0.48
18 3 0.14
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TTAATTAAAATATTT
Found at i:837512 original size:35 final size:34
Alignment explanation
Indices: 837466--837578 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
837456 AAAACAATCC
*
837466 TCAATTTCATTCTAAACCACAAATTCTAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCTAAAATAAT
*
837501 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCTAAAATAAT
* * *
837536 TCAATTACATTCTAAAATCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCTAAAATAAT
837571 TCAATTTC
1 TCAATTTC
837579 TGTTTTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.91
36 5 0.07
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCTAAAATAAT
Found at i:838684 original size:35 final size:34
Alignment explanation
Indices: 838636--838747 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 34
838626 ATTCCTCCTT
* *
838636 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
* *
838671 TAATTGAATTATTTTGGAATTTAGGGTTTATAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
838706 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
838741 AAATTGA
1 AAATTGA
838748 GGAATGTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 65 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:839007 original size:18 final size:18
Alignment explanation
Indices: 838986--839020 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
838976 TTTGAATTTG
838986 TTTAAGATTTTTAAAAAT
1 TTTAAGATTTTTAAAAAT
**
839004 TTTAATTTTTTTAAAAA
1 TTTAAGATTTTTAAAAA
839021 GAAATTATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTAAGATTTTTAAAAAT
Found at i:840522 original size:27 final size:24
Alignment explanation
Indices: 840459--840522 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 24
840449 ATGATATTGA
* *
840459 TGATGACTTAGATGATAATGCTAT
1 TGATGACTTTGATGATAATGCTAC
*
840483 TGATGA-TTCTGATGATGAACTTCTAAC
1 TGATGACTT-TGATGAT-AA-TGCT-AC
840510 TGATGACTTTGAT
1 TGATGACTTTGAT
840523 TCAGATTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 2 0.06
24 12 0.38
25 2 0.06
26 3 0.09
27 11 0.34
28 2 0.06
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (24 bp):
TGATGACTTTGATGATAATGCTAC
Found at i:845677 original size:74 final size:74
Alignment explanation
Indices: 845580--845758 Score: 247
Period size: 74 Copynumber: 2.4 Consensus size: 74
845570 AAATGACTAA
* * *
845580 GGGTATCAATACCTCTA-G-GGGGTATCGGTATCCATTGGGCATTCTGTTTTTCTCGGTA-CCAA
1 GGGTATCAGTACC-CTATGAGGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTC-GAAGCCAA
845642 AATTGACATAG
64 AATTGACATAG
*
845653 GGGTATCAGTACCCTATGAGGGGTATCGGTACCCATTTGGCATTCTGTTTTTCTCGAAGCCAAAA
1 GGGTATCAGTACCCTATGAGGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGAAGCCAAAA
845718 TTGACATAG
66 TTGACATAG
* *
845727 GAGTATCGGTACACCCTATGAGGGGTATCGGT
1 GGGTATCAGT--ACCCTATGAGGGGTATCGGT
845759 GCCTCCCTAT
Statistics
Matches: 95, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
72 3 0.03
73 15 0.16
74 57 0.60
76 20 0.21
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (74 bp):
GGGTATCAGTACCCTATGAGGGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGAAGCCAAAA
TTGACATAG
Found at i:849451 original size:3 final size:3
Alignment explanation
Indices: 849443--849477 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
849433 TCATATTTCA
849443 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
849478 CAAATATTAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:852783 original size:35 final size:34
Alignment explanation
Indices: 852737--852850 Score: 147
Period size: 35 Copynumber: 3.3 Consensus size: 34
852727 AAAACAATCC
*
852737 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
852772 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * * * *
852807 TAAATTACATTCTAAAATCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
852842 TCAATTTCA
1 TCAATTTCA
852851 GTTTTTTTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.91
36 5 0.07
ACGTcount: A:0.44, C:0.21, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:853956 original size:35 final size:34
Alignment explanation
Indices: 853908--854019 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 34
853898 ATTCCTCCTT
* *
853908 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
* *
853943 TAATTGAATTATTTTGGAATTTAGGGTTTATAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
853978 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
854013 AAATTGA
1 AAATTGA
854020 GGAATTTTTG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 65 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:858056 original size:2 final size:2
Alignment explanation
Indices: 858049--858076 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
858039 ATCAAACATA
858049 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
858077 TAAATTAAAT
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:859035 original size:28 final size:26
Alignment explanation
Indices: 858997--859053 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
858987 ATCTTGAAAA
858997 ATATTCTAAAATAATC-TAAAAATAAT
1 ATATTCTAAAATAATCAT-AAAATAAT
*
859023 ATATATCTAAAAATATTCATAAAATAAT
1 ATAT-TCT-AAAATAATCATAAAATAAT
859051 ATA
1 ATA
859054 AATATTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 4 0.15
27 3 0.11
28 19 0.70
29 1 0.04
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (26 bp):
ATATTCTAAAATAATCATAAAATAAT
Found at i:859283 original size:2 final size:2
Alignment explanation
Indices: 859276--859337 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
859266 AATTTTAATA
859276 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
859318 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
859338 GCGCTCACCC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:874855 original size:24 final size:23
Alignment explanation
Indices: 874819--874885 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
874809 GTAATAATTC
874819 TAAAATATTAAAAATATATTTTT
1 TAAAATATTAAAAATATATTTTT
* *
874842 T-AAATATATGAAAATAAATTATTT
1 TAAAATAT-TAAAAATATATT-TTT
874866 TAAAA-ATTAAAAA-ATATTTT
1 TAAAATATTAAAAATATATTTT
874886 AAAGAATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 2 0.05
22 10 0.27
23 16 0.43
24 6 0.16
25 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (23 bp):
TAAAATATTAAAAATATATTTTT
Found at i:875622 original size:90 final size:86
Alignment explanation
Indices: 875487--875656 Score: 286
Period size: 90 Copynumber: 1.9 Consensus size: 86
875477 TTTTTTTCCT
875487 TTAAATATTATTTAATTAAAAAAAAGGCTCATTGATTGAATTTAAATTGAAATGTAATATTTATT
1 TTAAATATTATTTAATTAAAAAAAAGGCTCATTGATTGAATTTAAATTGAAATGTAATATTTATT
875552 TAAACTACAATTAAACTATAG
66 TAAACTACAATTAAACTATAG
*
875573 TTAAATATTATTTAATTCAAATAAGAAAAGGTTCATTGATTGAATTTAAATTGAAATGTAATATT
1 TTAAATATTATTTAATT--AA-AA-AAAAGGCTCATTGATTGAATTTAAATTGAAATGTAATATT
*
875638 TATTTAAACTACAGTTAAA
62 TATTTAAACTACAATTAAA
875657 ACTAATGCAT
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
86 17 0.22
88 2 0.03
89 2 0.03
90 57 0.73
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (86 bp):
TTAAATATTATTTAATTAAAAAAAAGGCTCATTGATTGAATTTAAATTGAAATGTAATATTTATT
TAAACTACAATTAAACTATAG
Found at i:876774 original size:48 final size:46
Alignment explanation
Indices: 876720--876813 Score: 161
Period size: 48 Copynumber: 2.0 Consensus size: 46
876710 TCAACATAAT
*
876720 ATATTTAGGGATTAATATAAAATAATATTTAAATTATATATTTTTTAC
1 ATATTTAAGGATTAATATAAAATAATATTTAAA-TA-ATATTTTTTAC
876768 ATATTTAAGGATTAATATAAAATAATATTTAAATAATATTTTTTAC
1 ATATTTAAGGATTAATATAAAATAATATTTAAATAATATTTTTTAC
876814 GTTTAGATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 11 0.24
47 2 0.04
48 32 0.71
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (46 bp):
ATATTTAAGGATTAATATAAAATAATATTTAAATAATATTTTTTAC
Found at i:876799 original size:24 final size:24
Alignment explanation
Indices: 876720--876799 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
876710 TCAACATAAT
*
876720 ATATTTAGGGATTAATATAAAATA
1 ATATTTAAGGATTAATATAAAATA
****
876744 ATATTTAA--ATTATATATTTTTTA
1 ATATTTAAGGATTA-ATATAAAATA
876767 CATATTTAAGGATTAATATAAAATA
1 -ATATTTAAGGATTAATATAAAATA
876792 ATATTTAA
1 ATATTTAA
876800 ATAATATTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
22 4 0.09
23 6 0.14
24 23 0.53
25 6 0.14
26 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.45
Consensus pattern (24 bp):
ATATTTAAGGATTAATATAAAATA
Found at i:880774 original size:21 final size:21
Alignment explanation
Indices: 880748--880830 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 21
880738 CAGATCCCCA
*
880748 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
880769 GGGGGGAATCGGTTCCCCT-T
1 GGGGGGAATCGATTCCCCTGT
* * *
880789 CAAAGGGGGAATCGGTTCCCTCAG-
1 ---GGGGGGAATCGATTCCC-CTGT
880813 GGGGAGGAATCGATTCCC
1 GGGG-GGAATCGATTCCC
880831 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
20 1 0.02
21 20 0.40
22 12 0.24
23 16 0.32
24 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:880809 original size:22 final size:22
Alignment explanation
Indices: 880770--880831 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
880760 TTCCCCTGTG
880770 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCCTTCAAA
**
880793 GGGGGAATCGGTTCCC-TCAGG
1 GGGGGAATCGGTTCCCTTCAAA
*
880814 GGGAGGAATCGATTCCCT
1 GGG-GGAATCGGTTCCCT
880832 CTGCACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.18
22 15 0.44
23 13 0.38
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.21
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTTCAAA
Found at i:891434 original size:14 final size:14
Alignment explanation
Indices: 891417--891451 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
891407 ACTTAGTTAA
891417 TATTAATTTAAATG
1 TATTAATTTAAATG
891431 TATTAATTTAAATG
1 TATTAATTTAAATG
891445 TATTAAT
1 TATTAAT
891452 ATTTTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (14 bp):
TATTAATTTAAATG
Found at i:893785 original size:2 final size:2
Alignment explanation
Indices: 893780--893815 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
893770 ATTTGATTTA
893780 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
893816 TATTTTGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:893831 original size:19 final size:20
Alignment explanation
Indices: 893802--893851 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
893792 ATATATATAT
*
893802 ATATATATATATATTATTTTG
1 ATATATATAAAT-TTATTTTG
*
893823 ATATTTATAAATTTATTTTTG
1 ATATATATAAATTTA-TTTTG
*
893844 GTATATAT
1 ATATATAT
893852 TATTTAATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
ATATATATAAATTTATTTTG
Found at i:898972 original size:21 final size:21
Alignment explanation
Indices: 898946--898992 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
898936 CCAATATTGT
898946 AATGTCAAAATTAGGTGCAAC
1 AATGTCAAAATTAGGTGCAAC
*
898967 AATGTCAAAATTAGGTGCAAT
1 AATGTCAAAATTAGGTGCAAC
898988 AATGT
1 AATGT
898993 TTAAAAATTA
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:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (21 bp):
AATGTCAAAATTAGGTGCAAC
Found at i:903642 original size:21 final size:21
Alignment explanation
Indices: 903595--903635 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
903585 CCCAATATTG
903595 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
903616 CAATGTCAAAATTAGGTGCA
1 CAATGTCAAAATTAGGTGCA
903636 CTAATGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:904655 original size:24 final size:25
Alignment explanation
Indices: 904608--904655 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
904598 TAAAATGTTA
*
904608 AATTTTTCTTAATATTTTTCAGTTG
1 AATTTTTCTTAATATTTTTAAGTTG
904633 AATTTTT-TATAATA-TTTTAAGTT
1 AATTTTTCT-TAATATTTTTAAGTT
904656 TAACCGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.60
Consensus pattern (25 bp):
AATTTTTCTTAATATTTTTAAGTTG
Found at i:906501 original size:26 final size:27
Alignment explanation
Indices: 906440--906495 Score: 67
Period size: 31 Copynumber: 1.9 Consensus size: 27
906430 CGAGTATTGC
906440 TGAGCTCGACTCGACTCGAAAACTCTAAAA
1 TGAGCTCGACTCGACTCGAAAACTC---AA
*
906470 TAGAGCTCGACTCGACTTGAAAACTC
1 T-GAGCTCGACTCGACTCGAAAACTC
906496 GTGAGCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
30 1 0.04
31 23 0.96
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (27 bp):
TGAGCTCGACTCGACTCGAAAACTCAA
Found at i:933407 original size:21 final size:23
Alignment explanation
Indices: 933368--933413 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
933358 AAGTTGAACT
*
933368 TTAATTTAGATAATTTAAAT-TA
1 TTAATTTAGATAATATAAATATA
*
933390 TTAA-TTATATAATATAAATATA
1 TTAATTTAGATAATATAAATATA
933412 TT
1 TT
933414 TAAAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAATTTAGATAATATAAATATA
Found at i:935483 original size:71 final size:73
Alignment explanation
Indices: 935347--935494 Score: 264
Period size: 71 Copynumber: 2.1 Consensus size: 73
935337 GTAAAAAGAA
*
935347 AAAAAAGATGGACAAGGACGGGATTTGGTGGGTTTTTCTAATTGGTAGTTGAAAAAACTGACTGA
1 AAAAAAGATGGACAAGGACGGGATCTGGTGGGTTTTTCTAATTGGTAGTTGAAAAAACTGACTGA
935412 AATCAAAG
66 AATCAAAG
*
935420 AAAAAA-ATGGGCAAGGACGGGATCTGGTGGG-TTTTCTAATTGGTAGTTGAAAAAACTGACTGA
1 AAAAAAGATGGACAAGGACGGGATCTGGTGGGTTTTTCTAATTGGTAGTTGAAAAAACTGACTGA
935483 AATCAAAG
66 AATCAAAG
935491 AAAA
1 AAAA
935495 TAGTTACGCT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
71 44 0.60
72 23 0.32
73 6 0.08
ACGTcount: A:0.40, C:0.09, G:0.27, T:0.24
Consensus pattern (73 bp):
AAAAAAGATGGACAAGGACGGGATCTGGTGGGTTTTTCTAATTGGTAGTTGAAAAAACTGACTGA
AATCAAAG
Found at i:937424 original size:21 final size:21
Alignment explanation
Indices: 937400--937443 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
937390 TAATAAAAAA
*
937400 TTATTTAAAAAATTATTATTT
1 TTATTTAAAAAATTAATATTT
*
937421 TTATTTAAAATATTAATATTT
1 TTATTTAAAAAATTAATATTT
937442 TT
1 TT
937444 TAATATTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTAAAAAATTAATATTT
Found at i:937546 original size:3 final size:3
Alignment explanation
Indices: 937529--937570 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
937519 AATAAAATCG
* *
937529 ATA A-A ATA TATA ATA ATA ATA AAA ATA ATA AAA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
937571 TTTATGATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:937562 original size:9 final size:9
Alignment explanation
Indices: 937531--937568 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
937521 TAAAATCGAT
937531 AAAATATATA
1 AAAATA-ATA
*
937541 ATAATAATA
1 AAAATAATA
937550 AAAATAATA
1 AAAATAATA
937559 AAAATAATA
1 AAAATAATA
937568 A
1 A
937569 TATTTATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 21 0.81
10 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AAAATAATA
Found at i:960444 original size:22 final size:22
Alignment explanation
Indices: 960385--960441 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
960375 TATCGGTGGC
960385 GGATCCAGAAATTTAAGAATGG
1 GGATCCAGAAATTTAAGAATGG
*
960407 GGATCCATAAATTTAAGAAT-G
1 GGATCCAGAAATTTAAGAATGG
960428 GGAGTCCA-AAATTT
1 GGA-TCCAGAAATTT
960442 TAATTTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 10 0.30
22 23 0.70
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (22 bp):
GGATCCAGAAATTTAAGAATGG
Found at i:960976 original size:2 final size:2
Alignment explanation
Indices: 960969--960996 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
960959 CAATAATGCA
960969 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
960997 TCAAATAAAC
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:961117 original size:236 final size:228
Alignment explanation
Indices: 960657--961122 Score: 769
Period size: 236 Copynumber: 2.0 Consensus size: 228
960647 AATTTATACT
*
960657 ACTAAAATTAAAAGGGTTCATTAATAATATTTTTTAAAATATATTATGATAAATTTTACAATAAC
1 ACTAAAATTAAAAGGG-TCATTAATAATATTTTTAAAAATATATTATGATAAATTTTACAATAAC
960722 ATCAACGCAATAATGCAATATATATATATATATATATATATTCAAATTAAACAACAATGATAAAT
65 ATCAACGCAATAATGCAATATATATATATATATATATATATTCAAATTAAACAACAATGA-AAAT
960787 TACTATGTAATATAAACTAGGTCAATTACATAAATTTCCCCGACTATAAGATATTTGTTGATCTT
129 TACTATGTAATATAAACTAGGTCAATTACATAAATTTCCCCGACTATAAGATATTTGTTGATCTT
960852 TTGACTATAAAAAATTATCAATGGTCCATCGACTA
194 TTGACTATAAAAAATTATCAATGGTCCATCGACTA
960887 ACTAAAATTAAAA-GG-CATTAATAATATTTTTAAAATATATTATTATGATAAATTTTACAATAA
1 ACTAAAATTAAAAGGGTCATTAATAATATTTTTAAAA-ATA-TATTATGATAAATTTTACAATAA
960950 CATCAAACGCAATAATGCAATATATATATATATATATATATATATATTCAAA-TAAACAACAATG
64 CATC-AACGCAATAATGC---A-ATATATATATATATATATATATATTCAAATTAAACAACAATG
961014 -AAATTATCTATGTAATATAAACTAGGTCAATTACATAAATTTCCCCCGACTATAAGATATTACT
124 AAAATTA-CTATGTAATATAAACTAGGTCAATTACATAAATTT-CCCCGACTATAAGATA-T--T
961078 TGTTGATCTTTTGACTATAAAAAATTATCAATGGTCCATCGACTA
184 TGTTGATCTTTTGACTATAAAAAATTATCAATGGTCCATCGACTA
961123 TATTGTATTC
Statistics
Matches: 223, Mismatches: 1, Indels: 18
0.92 0.00 0.07
Matches are distributed among these distances:
227 19 0.09
228 3 0.01
229 29 0.13
230 26 0.12
231 6 0.03
232 35 0.16
233 29 0.13
234 30 0.13
236 46 0.21
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.36
Consensus pattern (228 bp):
ACTAAAATTAAAAGGGTCATTAATAATATTTTTAAAAATATATTATGATAAATTTTACAATAACA
TCAACGCAATAATGCAATATATATATATATATATATATATTCAAATTAAACAACAATGAAAATTA
CTATGTAATATAAACTAGGTCAATTACATAAATTTCCCCGACTATAAGATATTTGTTGATCTTTT
GACTATAAAAAATTATCAATGGTCCATCGACTA
Found at i:961420 original size:158 final size:156
Alignment explanation
Indices: 961123--961436 Score: 594
Period size: 158 Copynumber: 2.0 Consensus size: 156
961113 CCATCGACTA
961123 TATTGTATTCCTTTTGAGCCCCAACTATTAAATTTATAAATGACCACCCGACTATTCATTATATT
1 TATTGTATTCCTTTTGAGCCCCAACTATTAAATTTATAAATGACCACCCGACTATTCATTATATT
961188 CTAAATTCGTCATTTCCATTAAAATTAACGACAATCTAAGATGAATGTTAACATGTTGATTGAGA
66 CTAAATTCGTCATTTCCATTAAAATTAACGACAATCTAAGATGAATGTTAACATGTTGATTGAGA
961253 TATAATAAAA-TTGATCACAGAGTCT
131 TATAATAAAATTTGATCACAGAGTCT
961278 TATTGTATTCCTTTTTGAGCCCCAACTATTAAATTTATAAAATGACCACCCGACTATTCATTATA
1 TATTGTATTCC-TTTTGAGCCCCAACTATTAAATTTAT-AAATGACCACCCGACTATTCATTATA
961343 TTCTAAATTCGTCATTTCCATTAAAAATTAACGACAATCTAAGATGAATGTTAACATGTTGATTG
64 TTCTAAATTCGTCATTTCCATT-AAAATTAACGACAATCTAAGATGAATGTTAACATGTTGATTG
961408 AGATATAATAAAATTTGATCACAGAGTCT
128 AGATATAATAAAATTTGATCACAGAGTCT
961437 CAAACACTAT
Statistics
Matches: 155, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
155 11 0.07
156 26 0.17
157 48 0.31
158 55 0.35
159 15 0.10
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (156 bp):
TATTGTATTCCTTTTGAGCCCCAACTATTAAATTTATAAATGACCACCCGACTATTCATTATATT
CTAAATTCGTCATTTCCATTAAAATTAACGACAATCTAAGATGAATGTTAACATGTTGATTGAGA
TATAATAAAATTTGATCACAGAGTCT
Found at i:962493 original size:20 final size:19
Alignment explanation
Indices: 962449--962494 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
962439 TAAAATAATT
962449 ATAAATTAATATATATTTA
1 ATAAATTAATATATATTTA
* * *
962468 AAAAATTAATCATTTATTTC
1 ATAAATTAAT-ATATATTTA
962488 ATAAATT
1 ATAAATT
962495 CCGAAATACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAAATTAATATATATTTA
Found at i:963892 original size:2 final size:2
Alignment explanation
Indices: 963887--963913 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
963877 TATATGATTA
963887 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
963914 CTTTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:969595 original size:2 final size:2
Alignment explanation
Indices: 969588--969620 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
969578 ATAATATTTA
969588 AT AT AT AT AT -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
969621 TAAATGATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:971275 original size:17 final size:17
Alignment explanation
Indices: 971243--971276 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
971233 TCTATTTGAA
* *
971243 AATTTTGACTTTTAATT
1 AATTTTGAATTGTAATT
971260 AATTTTGAATTGTAATT
1 AATTTTGAATTGTAATT
971277 TTATAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (17 bp):
AATTTTGAATTGTAATT
Found at i:972658 original size:35 final size:35
Alignment explanation
Indices: 972612--972684 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
972602 ACAAATTGGG
972612 AGTTGGGCAAAGCAAATGAATGCATTGATGGAGGT
1 AGTTGGGCAAAGCAAATGAATGCATTGATGGAGGT
972647 AGTTGGGCAAAGCAAATGAATGCATTGATGGAGGT
1 AGTTGGGCAAAGCAAATGAATGCATTGATGGAGGT
972682 AGT
1 AGT
972685 GACCCTATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.34, T:0.23
Consensus pattern (35 bp):
AGTTGGGCAAAGCAAATGAATGCATTGATGGAGGT
Found at i:975640 original size:31 final size:31
Alignment explanation
Indices: 975604--975683 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
975594 AGTCAAAAAA
*
975604 TAGTTTAGGCACTTATTTAGAGAAAACAATG
1 TAGTTTAGACACTTATTTAGAGAAAACAATG
*
975635 TAGTTTAGACACTTATTTGGAGAAAACAATG
1 TAGTTTAGACACTTATTTAGAGAAAACAATG
975666 TAGTTTAGACACTTATTT
1 TAGTTTAGACACTTATTT
975684 TGGTATTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (31 bp):
TAGTTTAGACACTTATTTAGAGAAAACAATG
Found at i:983905 original size:19 final size:19
Alignment explanation
Indices: 983863--983948 Score: 72
Period size: 19 Copynumber: 4.6 Consensus size: 19
983853 ATTACTATAT
*
983863 TTATATATT-ATAATTATTTA
1 TTATAT-TTAATAATTA-ATA
983883 TTATATTTAATAATTAATA
1 TTATATTTAATAATTAATA
* *
983902 TTAT-TATTAATTATTATTA
1 TTATAT-TTAATAATTAATA
* *
983921 TTATATTTATTTATT-ATA
1 TTATATTTAATAATTAATA
983939 TT-TATTTAAT
1 TTATATTTAAT
983949 TTACACGTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
17 7 0.12
18 5 0.09
19 31 0.54
20 14 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATTTAATAATTAATA
Found at i:983914 original size:16 final size:16
Alignment explanation
Indices: 983893--983924 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
983883 TTATATTTAA
983893 TAATTAATATTATTAT
1 TAATTAATATTATTAT
*
983909 TAATTATTATTATTAT
1 TAATTAATATTATTAT
983925 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTAATATTATTAT
Found at i:983944 original size:13 final size:13
Alignment explanation
Indices: 983845--983946 Score: 88
Period size: 13 Copynumber: 8.0 Consensus size: 13
983835 TATAAAATAT
*
983845 TTAT-TTTAATTA
1 TTATATTTATTTA
* *
983857 CTATATTTATATA
1 TTATATTTATTTA
*
983870 TTATAATTATTTA
1 TTATATTTATTTA
* *
983883 TTATATTTAATAA
1 TTATATTTATTTA
983896 TTA-ATATTA-TTA
1 TTATAT-TTATTTA
983908 TTA-A-TTATTATTA
1 TTATATTTA-T-TTA
983921 TTATATTTATTTA
1 TTATATTTATTTA
983934 TTATATTTATTTA
1 TTATATTTATTTA
983947 ATTTACACGT
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
10 3 0.04
12 11 0.15
13 54 0.74
14 2 0.03
15 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATATTTATTTA
Found at i:983944 original size:22 final size:22
Alignment explanation
Indices: 983842--983944 Score: 97
Period size: 22 Copynumber: 4.8 Consensus size: 22
983832 TTTTATAAAA
* *
983842 TATTTATTTTAATTACTATATT
1 TATTTATTATAATTATTATATT
*
983864 TATATATTATAATTATT-TATT
1 TATTTATTATAATTATTATATT
*
983885 ATATTTA--ATAATTAATAT-TAT
1 -TATTTATTATAATTATTATAT-T
* *
983906 TATTAATTATTATTATTATATT
1 TATTTATTATAATTATTATATT
*
983928 TATTTATTATATTTATT
1 TATTTATTATAATTATT
983945 TAATTTACAC
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
20 14 0.22
21 6 0.09
22 43 0.67
23 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTATTATAATTATTATATT
Found at i:986025 original size:51 final size:51
Alignment explanation
Indices: 985949--986099 Score: 223
Period size: 51 Copynumber: 3.0 Consensus size: 51
985939 CCAACCAGCT
* * *
985949 GGTGACTGTGTAGCTCCACCGAATCAG-CTGGTTTCGGTGTCGCCGACTGCG
1 GGTGACTGCGTAGCTCCACCGAATCAGCCT-GTTTCGGTATCGCCGACTGCC
* *
986000 GGTGACCGCGTAGCTCCATCGAATCAGCCTGTTTCGGTATCGCCGACTGCC
1 GGTGACTGCGTAGCTCCACCGAATCAGCCTGTTTCGGTATCGCCGACTGCC
* *
986051 GGTGACTGCGCAGCTCCACCGGATCAGCCTGTTTCGGTATCGCCGACTG
1 GGTGACTGCGTAGCTCCACCGAATCAGCCTGTTTCGGTATCGCCGACTG
986100 TCGGCGATGC
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 88 0.98
52 2 0.02
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.24
Consensus pattern (51 bp):
GGTGACTGCGTAGCTCCACCGAATCAGCCTGTTTCGGTATCGCCGACTGCC
Found at i:993350 original size:29 final size:29
Alignment explanation
Indices: 993315--993414 Score: 200
Period size: 29 Copynumber: 3.4 Consensus size: 29
993305 TCCCCAAGCA
993315 TAGGTCGCCATGCCCTCTGGGCGACCTTG
1 TAGGTCGCCATGCCCTCTGGGCGACCTTG
993344 TAGGTCGCCATGCCCTCTGGGCGACCTTG
1 TAGGTCGCCATGCCCTCTGGGCGACCTTG
993373 TAGGTCGCCATGCCCTCTGGGCGACCTTG
1 TAGGTCGCCATGCCCTCTGGGCGACCTTG
993402 TAGGTCGCCATGC
1 TAGGTCGCCATGC
993415 ACTCCCTCCT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.11, C:0.34, G:0.31, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCTGGGCGACCTTG
Found at i:993480 original size:14 final size:14
Alignment explanation
Indices: 993458--993504 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
993448 CCTCGCATAG
*
993458 CTCGCTCGGATGGC
1 CTCGGTCGGATGGC
993472 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
* *
993486 CTAGATCGGATGGC
1 CTCGGTCGGATGGC
993500 CTCGG
1 CTCGG
993505 ATGCTCTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.11, C:0.30, G:0.38, T:0.21
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:995083 original size:16 final size:16
Alignment explanation
Indices: 995064--995113 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
995054 AAGTATCTAA
995064 TTTAACTAAAGAATAG
1 TTTAACTAAAGAATAG
* * *
995080 TTTAA--ATA-CATAA
1 TTTAACTAAAGAATAG
995093 TTTAACTAAAGAATAG
1 TTTAACTAAAGAATAG
995109 TTTAA
1 TTTAA
995114 GCACCTAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 8 0.32
14 2 0.08
15 2 0.08
16 13 0.52
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (16 bp):
TTTAACTAAAGAATAG
Found at i:995084 original size:29 final size:29
Alignment explanation
Indices: 995051--995114 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
995041 CATATAATGA
995051 TTTAAGTATC-TAATTTAACTAAAGAATAG
1 TTTAAGTA-CATAATTTAACTAAAGAATAG
*
995080 TTTAAATACATAATTTAACTAAAGAATAG
1 TTTAAGTACATAATTTAACTAAAGAATAG
995109 TTTAAG
1 TTTAAG
995115 CACCTAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 31 0.97
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTAAGTACATAATTTAACTAAAGAATAG
Found at i:997459 original size:6 final size:6
Alignment explanation
Indices: 997448--997480 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
997438 GAATGAGTTC
997448 GGGTCT GGGTCT GGGTCT GGGTCT GGGTCT GGG
1 GGGTCT GGGTCT GGGTCT GGGTCT GGGTCT GGG
997481 GCGGATATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.55, T:0.30
Consensus pattern (6 bp):
GGGTCT
Found at i:1002753 original size:19 final size:19
Alignment explanation
Indices: 1002731--1002767 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1002721 CTGTTCTGAC
1002731 TGTAACGTTTGTTACTGCA
1 TGTAACGTTTGTTACTGCA
*
1002750 TGTAATGTTTGTTACTGC
1 TGTAACGTTTGTTACTGC
1002768 TTTTTTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.46
Consensus pattern (19 bp):
TGTAACGTTTGTTACTGCA
Found at i:1012893 original size:63 final size:61
Alignment explanation
Indices: 1012777--1012905 Score: 154
Period size: 63 Copynumber: 2.1 Consensus size: 61
1012767 TTAAACAAAC
* * * *
1012777 AATAATATATTTTAATTTGACATATTCAAAAGATATAATCACCTTTTACTATTCAAACTTA
1 AATAATATATTTTAATTTGAAATATTCAAAAGATACAATCACCTTTTAATATTCAAAATTA
* *
1012838 AATAGATACTATTTTGATTTGAAATATTCAAAAAGATACAA-CA-ATCTTTAATATTCAAAATTA
1 AATA-ATA-TATTTTAATTTGAAATATTC-AAAAGATACAATCACCT-TTTAATATTCAAAATTA
1012901 AATAA
1 AATAA
1012906 GTAACAAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
61 4 0.07
62 5 0.09
63 39 0.67
64 10 0.17
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.38
Consensus pattern (61 bp):
AATAATATATTTTAATTTGAAATATTCAAAAGATACAATCACCTTTTAATATTCAAAATTA
Found at i:1016553 original size:29 final size:29
Alignment explanation
Indices: 1016500--1016584 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
1016490 AACCCAACCC
**
1016500 ATAGGTCGCCATGCACTCCCAGCGACCTC
1 ATAGGTCGCCATGCACTCCCAGCGACCAA
* ***
1016529 CTAGGTCGCCATGCACTCTGGGCGACCAA
1 ATAGGTCGCCATGCACTCCCAGCGACCAA
* * *
1016558 AGAGGTCGCCATGCACGCCCGGCGACC
1 ATAGGTCGCCATGCACTCCCAGCGACC
1016585 TTGTCTCCTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.20, C:0.39, G:0.27, T:0.14
Consensus pattern (29 bp):
ATAGGTCGCCATGCACTCCCAGCGACCAA
Found at i:1016766 original size:29 final size:29
Alignment explanation
Indices: 1016729--1016785 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1016719 GGGTTAAAAG
* *
1016729 CTTGGTCACCGGGCGTGCATGGCGACCTC
1 CTTGGTCACCCGGAGTGCATGGCGACCTC
1016758 CTTGGTCACCCGGAGTGCATGGCGACCT
1 CTTGGTCACCCGGAGTGCATGGCGACCT
1016786 AGGAGGTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.33, G:0.33, T:0.21
Consensus pattern (29 bp):
CTTGGTCACCCGGAGTGCATGGCGACCTC
Found at i:1016828 original size:26 final size:27
Alignment explanation
Indices: 1016769--1016831 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
1016759 TTGGTCACCC
1016769 GGAGTGCATGGCGACCTAGGAGGTTGG
1 GGAGTGCATGGCGACCTAGGAGGTTGG
*
1016796 GGAGTGCATGGCGACCTATG-GGTTGG
1 GGAGTGCATGGCGACCTAGGAGGTTGG
**
1016822 GTTGTGCATG
1 GGAGTGCATG
1016832 TCCCATGCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.16, C:0.14, G:0.46, T:0.24
Consensus pattern (27 bp):
GGAGTGCATGGCGACCTAGGAGGTTGG
Found at i:1018089 original size:20 final size:20
Alignment explanation
Indices: 1018066--1018110 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1018056 TAGTTCCATT
1018066 ACCTTCTATGA-AGTTTTAAA
1 ACCTTCT-TGAGAGTTTTAAA
* *
1018086 ACCTTCTTTAGTGTTTTAAA
1 ACCTTCTTGAGAGTTTTAAA
1018106 ACCTT
1 ACCTT
1018111 TCACAATGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (20 bp):
ACCTTCTTGAGAGTTTTAAA
Found at i:1018171 original size:20 final size:20
Alignment explanation
Indices: 1018148--1018189 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1018138 ATCTAGGACG
1018148 TTCCAAAATATTCTAAAACT
1 TTCCAAAATATTCTAAAACT
* * *
1018168 TTCCATAATGTTCTAAACCT
1 TTCCAAAATATTCTAAAACT
1018188 TT
1 TT
1018190 TTATTGTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.40
Consensus pattern (20 bp):
TTCCAAAATATTCTAAAACT
Found at i:1018471 original size:60 final size:60
Alignment explanation
Indices: 1018350--1018472 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
1018340 GTCTATCAAT
* * * *
1018350 TATATAGTATTGTTTTATTAAGTCTATCGACTATTAAAAGTTATAAAATGATTATTGGAC
1 TATAGAGTATTGTTTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATCACTGGAC
* * *
1018410 TATAGAGTATTGTTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATGGTCACCT-GAC
1 TATAGAGTATTGTTTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATCA-CTGGAC
1018470 TAT
1 TAT
1018473 TCATTGTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 54 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (60 bp):
TATAGAGTATTGTTTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATCACTGGAC
Found at i:1024304 original size:18 final size:18
Alignment explanation
Indices: 1024281--1024333 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1024271 AGGACAAATC
*
1024281 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
1024299 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
* *
1024317 AGTGGCCATTCGAGACA
1 AGTGGTCATTCGGGACA
1024334 AATATAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:1025849 original size:19 final size:19
Alignment explanation
Indices: 1025827--1025872 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1025817 CGTAAAATCT
1025827 TTCAATATATATAAACA-AA
1 TTCAATATATA-AAACATAA
*
1025846 TTCAGATATCTAAAACATAA
1 TTCA-ATATATAAAACATAA
1025866 TTCAATA
1 TTCAATA
1025873 ATACACTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (19 bp):
TTCAATATATAAAACATAA
Found at i:1025859 original size:18 final size:20
Alignment explanation
Indices: 1025827--1025869 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1025817 CGTAAAATCT
1025827 TTCA-ATATATATAAACA-AA
1 TTCAGATATATA-AAACATAA
*
1025846 TTCAGATATCTAAAACATAA
1 TTCAGATATATAAAACATAA
1025866 TTCA
1 TTCA
1025870 ATAATACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (20 bp):
TTCAGATATATAAAACATAA
Found at i:1030059 original size:16 final size:17
Alignment explanation
Indices: 1030029--1030062 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1030019 TTTTTGAATT
*
1030029 ATATAGATAAGATTTAG
1 ATATAGATAAAATTTAG
1030046 ATATA-ATAAAATTTAG
1 ATATAGATAAAATTTAG
1030062 A
1 A
1030063 ATTCATCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (17 bp):
ATATAGATAAAATTTAG
Found at i:1031361 original size:20 final size:20
Alignment explanation
Indices: 1031324--1031362 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1031314 ACAAAAACTG
* **
1031324 ATAATTTATGCATTAATTAT
1 ATAATTTATCCAAAAATTAT
1031344 ATAATTTATCCAAAAATTA
1 ATAATTTATCCAAAAATTA
1031363 ATGATTTCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (20 bp):
ATAATTTATCCAAAAATTAT
Found at i:1036708 original size:16 final size:16
Alignment explanation
Indices: 1036687--1036730 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
1036677 TTTAAAGATC
1036687 TAAAAAGGTGAATGCG
1 TAAAAAGGTGAATGCG
1036703 TAAAAAGGTGAATGCG
1 TAAAAAGGTGAATGCG
1036719 TAAAAAGGTGAA
1 TAAAAAGGTGAA
1036731 GAGAGTGCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.48, C:0.05, G:0.30, T:0.18
Consensus pattern (16 bp):
TAAAAAGGTGAATGCG
Found at i:1037638 original size:2 final size:2
Alignment explanation
Indices: 1037624--1037692 Score: 124
Period size: 2 Copynumber: 35.5 Consensus size: 2
1037614 ATTATATCTC
1037624 AT AT AT A- AT -T 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
1037664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1037693 ATTATATCTA
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 63 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1037639 original size:10 final size:10
Alignment explanation
Indices: 1037624--1037704 Score: 71
Period size: 12 Copynumber: 7.9 Consensus size: 10
1037614 ATTATATCTC
1037624 ATATATAATT
1 ATATATAATT
1037634 ATATAT-A-T
1 ATATATAATT
1037642 ATATAT-A-T
1 ATATATAATT
1037650 ATATATATATAT
1 ATATATA-AT-T
1037662 ATATATATATAT
1 ATATATA-AT-T
1037674 ATATATATATAT
1 ATATATA-AT-T
1037686 ATATATAATT
1 ATATATAATT
*
1037696 ATATCTAAT
1 ATATATAAT
1037705 AAACTCAATT
Statistics
Matches: 66, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
8 15 0.23
9 1 0.02
10 16 0.24
11 2 0.03
12 32 0.48
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (10 bp):
ATATATAATT
Found at i:1041545 original size:60 final size:59
Alignment explanation
Indices: 1041438--1041611 Score: 163
Period size: 60 Copynumber: 2.9 Consensus size: 59
1041428 GTTTGAAAAC
* * ** **
1041438 ATGACTTATATTTTAGATT-GATCCTTAAACTTTTAAATGTTTCAATTTCATCCTTAAATT
1 ATGA-TTATATTTTAAATTAG-TCCTCAAACTTTTAAACATTTCAATTTCATCCCCAAATT
* *
1041498 ATGATTATCATTTTAAATTAGTCCTCAAACTTTTAAACATTTTAATTTCACCCCCAAATT
1 ATGATTAT-ATTTTAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCCCCAAATT
** * * * *
1041558 ATTCCTT-TATTTTCAATTAGTCCCCAAAATTTTTAAACATTCCAATTTCATCCC
1 A-TGATTATATTTTAAATTAGTCCTC-AAACTTTTAAACATTTCAATTTCATCCC
1041612 AAACTATACA
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
59 19 0.20
60 71 0.76
61 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.44
Consensus pattern (59 bp):
ATGATTATATTTTAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCCCCAAATT
Found at i:1053370 original size:8 final size:8
Alignment explanation
Indices: 1053354--1053401 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
1053344 TTCTATTTGA
*
1053354 ATATGTTT
1 ATATATTT
1053362 ATATATTT
1 ATATATTT
1053370 ATATATATAT
1 ATATAT-T-T
*
1053380 ATATATAT
1 ATATATTT
1053388 ATATATATT
1 ATATAT-TT
1053397 ATATA
1 ATATA
1053402 GTTCACAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 20 0.59
9 7 0.21
10 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (8 bp):
ATATATTT
Found at i:1053374 original size:2 final size:2
Alignment explanation
Indices: 1053361--1053401 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1053351 TGAATATGTT
*
1053361 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
1053402 GTTCACAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1053505 original size:36 final size:37
Alignment explanation
Indices: 1053426--1053691 Score: 285
Period size: 37 Copynumber: 7.2 Consensus size: 37
1053416 TGAAAATACG
* *
1053426 TATATAATATATATTTTTTAAAA-ACCTTTTGAAAA-T
1 TATATAATATATAATTTTTAAAACA-TTTTTGAAAACT
* ** *
1053462 GAATATAATATATGGTTTTTAAAACACTTTTGAAAAC-
1 -TATATAATATATAATTTTTAAAACATTTTTGAAAACT
* * * *
1053499 TGTATAATATATAGTTTTTAAAATATTTTAGGAAAA--
1 TATATAATATATAATTTTTAAAACATTTT-TGAAAACT
*
1053535 TATATAATATATGATTTTTAAAATCA-TTTTGAAAACT
1 TATATAATATATAATTTTTAAAA-CATTTTTGAAAACT
*
1053572 TATATAATATATAATTTTTGAAAACATTTTTTTAAAACT
1 TATATAATATATAATTTTT-AAAACA-TTTTTGAAAACT
*
1053611 TATATAATATATAGTTTTTGAAAACATTTTTGAAAACT
1 TATATAATATATAATTTTT-AAAACATTTTTGAAAACT
*
1053649 TATATAATATATGATTTTTGAAAACATTTTTGAAAA-T
1 TATATAATATATAATTTTT-AAAACATTTTTGAAAACT
1053686 TATATA
1 TATATA
1053692 GTTTTTAAAA
Statistics
Matches: 200, Mismatches: 20, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
35 5 0.03
36 47 0.23
37 63 0.31
38 50 0.25
39 35 0.17
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
TATATAATATATAATTTTTAAAACATTTTTGAAAACT
Found at i:1053511 original size:38 final size:35
Alignment explanation
Indices: 1053432--1053691 Score: 221
Period size: 38 Copynumber: 7.1 Consensus size: 35
1053422 TACGTATATA
* *
1053432 ATATATAT-TTTTTAAAA-ACCTTTTGAAAA-TGAAT
1 ATATATATGTTTTTAAAACA-TTTTTGAAAACT-TAT
*
1053466 ATAATATATGGTTTTTAAAACACTTTTGAAAACTGTAT
1 AT-ATATAT-GTTTTTAAAACATTTTTGAAAACT-TAT
* *
1053504 A-ATATATAGTTTTTAAAATATTTTAGGAAAA--TAT
1 ATATATAT-GTTTTTAAAACATTTT-TGAAAACTTAT
1053538 ATAATATATGATTTTTAAAATCA-TTTTGAAAACTTAT
1 AT-ATATATG-TTTTTAAAA-CATTTTTGAAAACTTAT
* *
1053575 ATAATATATAATTTTTGAAAACATTTTTTTAAAACTTAT
1 AT-ATATAT-GTTTTT-AAAACA-TTTTTGAAAACTTAT
1053614 ATAATATATAGTTTTTGAAAACATTTTTGAAAACTTAT
1 AT-ATATAT-GTTTTT-AAAACATTTTTGAAAACTTAT
1053652 ATAATATATGATTTTTGAAAACATTTTTGAAAA-TTAT
1 AT-ATATATG-TTTTT-AAAACATTTTTGAAAACTTAT
1053689 ATA
1 ATA
1053692 GTTTTTAAAA
Statistics
Matches: 198, Mismatches: 11, Indels: 32
0.82 0.05 0.13
Matches are distributed among these distances:
34 6 0.03
35 12 0.06
36 39 0.20
37 51 0.26
38 55 0.28
39 35 0.18
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (35 bp):
ATATATATGTTTTTAAAACATTTTTGAAAACTTAT
Found at i:1053642 original size:12 final size:12
Alignment explanation
Indices: 1053625--1053684 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
1053615 TAATATATAG
1053625 TTTTTGAAAACA
1 TTTTTGAAAACA
1053637 TTTTTGAAAAC-
1 TTTTTGAAAACA
* *
1053648 TTATAT-AATATATGA
1 TT-TTTGAA-A-A-CA
1053663 TTTTTGAAAACA
1 TTTTTGAAAACA
1053675 TTTTTGAAAA
1 TTTTTGAAAA
1053685 TTATATAGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
11 4 0.11
12 25 0.66
13 2 0.05
14 3 0.08
15 4 0.11
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:1053710 original size:31 final size:32
Alignment explanation
Indices: 1053669--1053755 Score: 122
Period size: 31 Copynumber: 2.7 Consensus size: 32
1053659 ATGATTTTTG
1053669 AAAACATTTTTGAAAATTATATAGTTTTT-AA
1 AAAACATTTTTGAAAATTATATAGTTTTTAAA
* * *
1053700 AAAACTTTTTTTAAGATTATATAGTTTTTAAA
1 AAAACATTTTTGAAAATTATATAGTTTTTAAA
*
1053732 AAAACATTTTTGAAATTTTATATA
1 AAAACATTTTTGAAA-ATTATATA
1053756 TAATATATAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 26 0.55
32 14 0.30
33 7 0.15
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (32 bp):
AAAACATTTTTGAAAATTATATAGTTTTTAAA
Found at i:1053764 original size:42 final size:42
Alignment explanation
Indices: 1053717--1053799 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
1053707 TTTTTAAGAT
* *
1053717 TATATAGTTTTTAAAAAAACATTTTTGAAATTTTATATATAA
1 TATATAGTTTTTAAAAAAACATTTTTAAAAATTTATATATAA
* *
1053759 TATATAGTTTTTTAAAAAACCTTTTTAAAAATTTATATATA
1 TATATAGTTTTTAAAAAAACATTTTTAAAAATTTATATATA
1053800 TAGTTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (42 bp):
TATATAGTTTTTAAAAAAACATTTTTAAAAATTTATATATAA
Found at i:1053828 original size:35 final size:38
Alignment explanation
Indices: 1053717--1053829 Score: 101
Period size: 36 Copynumber: 2.9 Consensus size: 38
1053707 TTTTTAAGAT
*
1053717 TATATAG-TTTTTAAAAAAACATTTTTGAAATTTTATATATAA
1 TATATAGTTTTTTAAAAAAAC-TTTTT--AA--TTATTTATAA
* **
1053759 TATATAGTTTTTTAAAAAACCTTTTTAAAAATTTAT-A
1 TATATAGTTTTTTAAAAAAACTTTTTAATTATTTATAA
1053796 TATATAG-TTTTTAAAAAATAC-TTTT-ATTATTTAT
1 TATATAGTTTTTTAAAAAA-ACTTTTTAATTATTTAT
1053830 TTATTATTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
35 7 0.11
36 15 0.24
37 9 0.15
38 5 0.08
40 2 0.03
42 12 0.19
43 12 0.19
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (38 bp):
TATATAGTTTTTTAAAAAAACTTTTTAATTATTTATAA
Found at i:1053830 original size:7 final size:7
Alignment explanation
Indices: 1053818--1053896 Score: 60
Period size: 7 Copynumber: 11.4 Consensus size: 7
1053808 AAAAAATACT
1053818 TTTATTA
1 TTTATTA
1053825 TTTATT-
1 TTTATTA
1053831 TATTATTA
1 T-TTATTA
*
1053839 TTTTATTC
1 -TTTATTA
*
1053847 TTTATCA
1 TTTATTA
1053854 TTT-TTA
1 TTTATTA
1053860 -TTACTTA
1 TTTA-TTA
1053867 TTT-TTA
1 TTTATTA
*
1053873 -TTCTTA
1 TTTATTA
1053879 TTTATTTA
1 TTTA-TTA
1053887 TTTATTA
1 TTTATTA
1053894 TTT
1 TTT
1053897 CTTTTCCAGG
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
5 4 0.07
6 9 0.16
7 30 0.52
8 14 0.24
9 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:1053885 original size:29 final size:27
Alignment explanation
Indices: 1053822--1053896 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 27
1053812 AATACTTTTA
1053822 TTATTTA--TTTATTATTATTTTATTC
1 TTATTTATTTTTATTATTATTTTATTC
*
1053847 TT-TATCATTTTTATTACTTATTTTTATTC
1 TTAT-TTATTTTTATTA-TTA-TTTTATTC
*
1053876 TTATTTATTTAT-TTATTATTT
1 TTATTTATTTTTATTATTATTT
1053897 CTTTTCCAGG
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
24 1 0.02
25 4 0.10
26 3 0.07
27 10 0.24
28 6 0.15
29 16 0.39
30 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (27 bp):
TTATTTATTTTTATTATTATTTTATTC
Found at i:1054491 original size:31 final size:30
Alignment explanation
Indices: 1054456--1054521 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
1054446 AAACAAAAAC
*
1054456 AGAAAAAACAAGAAAGCAAATATTCTACACA
1 AGAAAAAACAA-AAAGCAAATATTATACACA
* * *
1054487 AG-AAAACCCACAAGCAAATATTATACACA
1 AGAAAAAACAAAAAGCAAATATTATACACA
1054516 AGAAAA
1 AGAAAA
1054522 CCCACGAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 19 0.63
30 9 0.30
31 2 0.07
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.12
Consensus pattern (30 bp):
AGAAAAAACAAAAAGCAAATATTATACACA
Found at i:1054501 original size:29 final size:29
Alignment explanation
Indices: 1054469--1054531 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
1054459 AAAAACAAGA
*
1054469 AAGCAAATATTCTACACAAGAAAACCCAC
1 AAGCAAATATTATACACAAGAAAACCCAC
1054498 AAGCAAATATTATACACAAGAAAACCCAC
1 AAGCAAATATTATACACAAGAAAACCCAC
*
1054527 GAGCA
1 AAGCA
1054532 CAAGACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.52, C:0.25, G:0.10, T:0.13
Consensus pattern (29 bp):
AAGCAAATATTATACACAAGAAAACCCAC
Found at i:1055196 original size:15 final size:15
Alignment explanation
Indices: 1055177--1055218 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1055167 CTACTTTATT
1055177 TTTTTTTATTTT-AC
1 TTTTTTTATTTTGAC
*
1055191 TATTTTTCATTTTGAC
1 T-TTTTTTATTTTGAC
1055207 TTTTTATTATTT
1 TTTTT-TTATTT
1055219 GTTTTCTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.04
15 14 0.61
16 8 0.35
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTTTATTTTGAC
Found at i:1055296 original size:2 final size:2
Alignment explanation
Indices: 1055291--1055320 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1055281 CTTTTTTTAA
1055291 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
1055321 TATCTTTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1055410 original size:10 final size:11
Alignment explanation
Indices: 1055385--1055410 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1055375 ACTCCATTAC
1055385 TTTTTCCTTTA
1 TTTTTCCTTTA
1055396 TTTTTCCTTTA
1 TTTTTCCTTTA
1055407 TTTT
1 TTTT
1055411 GTTTTGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTCCTTTA
Found at i:1055446 original size:26 final size:24
Alignment explanation
Indices: 1055392--1055460 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 24
1055382 TACTTTTTCC
* *
1055392 TTTATTTTTCCTTTATTTTGTTTTG
1 TTTATTTTT-GTTTATTTTGTTGTG
*
1055417 TTTATTGCTTTTTTTATTTTGTATGT-
1 TTTATT--TTTGTTTATTTTGT-TGTG
1055443 TTTATTTTTGTTTATTTT
1 TTTATTTTTGTTTATTTT
1055461 ATCAGTCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 11 0.29
25 6 0.16
26 16 0.42
27 5 0.13
ACGTcount: A:0.10, C:0.04, G:0.09, T:0.77
Consensus pattern (24 bp):
TTTATTTTTGTTTATTTTGTTGTG
Found at i:1055490 original size:19 final size:18
Alignment explanation
Indices: 1055453--1055513 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
1055443 TTTATTTTTG
*
1055453 TTTATTTTATCA-GTCTA
1 TTTATTTTATCATTTCTA
*
1055470 TTTATTTTGTTCATTTCTA
1 TTTATTTT-ATCATTTCTA
1055489 TTTTATTTTATCATTT-T-
1 -TTTATTTTATCATTTCTA
1055506 TTTATTTT
1 TTTATTTT
1055514 TTTATGTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.21
17 8 0.21
18 4 0.11
19 10 0.26
20 8 0.21
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTATTTTATCATTTCTA
Found at i:1062933 original size:84 final size:85
Alignment explanation
Indices: 1062773--1062936 Score: 222
Period size: 84 Copynumber: 1.9 Consensus size: 85
1062763 CTCGTTGAGT
* * * * * * *
1062773 TCATTGATTAAAATAAGTATTCTTCTTCTTTAAAGTTCCAATTTCGAACAATTGTATCTGCAAAG
1 TCATTAATTAAAAGAAATATTCTTCTTCTTTAAAGTTCAAAGTTCGAACAATTGTATCAGCAAAA
* *
1062838 TGTGGATGTATCAATTAAAC
66 AGTGGACGTATCAATTAAAC
*
1062858 TCATTAATTAAAAGAAATATTCTTCTTCTTT-AAGTTCAAAGTTCGAACAATTGTGTCAGCAAAA
1 TCATTAATTAAAAGAAATATTCTTCTTCTTTAAAGTTCAAAGTTCGAACAATTGTATCAGCAAAA
*
1062922 AGTGTACGTATCAAT
66 AGTGGACGTATCAAT
1062937 GATAAGAAGA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
84 40 0.59
85 28 0.41
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (85 bp):
TCATTAATTAAAAGAAATATTCTTCTTCTTTAAAGTTCAAAGTTCGAACAATTGTATCAGCAAAA
AGTGGACGTATCAATTAAAC
Found at i:1069646 original size:69 final size:69
Alignment explanation
Indices: 1069564--1069694 Score: 183
Period size: 69 Copynumber: 1.9 Consensus size: 69
1069554 AATTTCACGT
* * *
1069564 TCCCTGTCTCGTTC-ACGATCACTCTCGTGCCTTCTTGACCTGCTACTGCTTCTCTCTCTCCTCT
1 TCCCTCTCCCGTTCTAC-ATCACTCTCGTGCCTTCTCGACCTGCTACTGCTTCTCTCTCTCCTCT
1069628 CCCTC
65 CCCTC
* * * *
1069633 TCCCTCTCCCGTTCTTCCTCCCTTTCGTGCCTTCTCGACCTGCTACTGCTTCTCTCTCTCCT
1 TCCCTCTCCCGTTCTACATCACTCTCGTGCCTTCTCGACCTGCTACTGCTTCTCTCTCTCCT
1069695 TTCTTCCTCC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 53 0.98
70 1 0.02
ACGTcount: A:0.05, C:0.45, G:0.11, T:0.39
Consensus pattern (69 bp):
TCCCTCTCCCGTTCTACATCACTCTCGTGCCTTCTCGACCTGCTACTGCTTCTCTCTCTCCTCTC
CCTC
Found at i:1069796 original size:33 final size:33
Alignment explanation
Indices: 1069684--1069796 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 33
1069674 GCTACTGCTT
*
1069684 CTCTCTCTCCTTTCTTCCTCCCTTTCCCTTTCC
1 CTCTCTCTCCTCTCTTCCTCCCTTTCCCTTTCC
* * *
1069717 CTTTCCCTCCTCTCCCTATCCTTCTCTTTCTCCTTATCC
1 CTCTCTCTCCTCT--CT-TCC-TCCCTTTC-CCTT-TCC
* *
1069756 CTATCTCTCCTCTCTCTCC-CCCTTTCCATTTCC
1 CTCTCTCTCCTCTCT-TCCTCCCTTTCCCTTTCC
1069789 CTCTCTCT
1 CTCTCTCT
1069797 ACTGCTCCTC
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
33 20 0.31
34 3 0.05
35 8 0.12
36 3 0.05
37 12 0.19
38 4 0.06
39 14 0.22
ACGTcount: A:0.04, C:0.50, G:0.00, T:0.46
Consensus pattern (33 bp):
CTCTCTCTCCTCTCTTCCTCCCTTTCCCTTTCC
Found at i:1069907 original size:57 final size:57
Alignment explanation
Indices: 1069836--1069958 Score: 201
Period size: 57 Copynumber: 2.2 Consensus size: 57
1069826 CTCTCTCCCT
* *
1069836 ATCGCGGCTGCTTCTATGGCGTTCCTTATCACGGTCTCGCCTCTCCTCACCGTCCTC
1 ATCGCGGCTCCTTCTATGGCGTTCCTTATCACGATCTCGCCTCTCCTCACCGTCCTC
**
1069893 ATCGCGGCTCCTTCTATGGCGTTCCTTATCACGATCTCGCCTCTCCTCGTCGTCCTC
1 ATCGCGGCTCCTTCTATGGCGTTCCTTATCACGATCTCGCCTCTCCTCACCGTCCTC
*
1069950 GTCGCGGCT
1 ATCGCGGCT
1069959 GCCTCTCGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.08, C:0.40, G:0.20, T:0.32
Consensus pattern (57 bp):
ATCGCGGCTCCTTCTATGGCGTTCCTTATCACGATCTCGCCTCTCCTCACCGTCCTC
Found at i:1070811 original size:33 final size:33
Alignment explanation
Indices: 1070769--1070857 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
1070759 AACACGTTGG
*
1070769 GCATCCGAGGCCATCCGACCGAGCTATGCGAGA
1 GCATCCGAGGACATCCGACCGAGCTATGCGAGA
* *
1070802 GCATCCGAGGTCATCCGACCGAGCTATGCTAGA
1 GCATCCGAGGACATCCGACCGAGCTATGCGAGA
*
1070835 GCATCCGAGGATATCCGACCGAG
1 GCATCCGAGGACATCCGACCGAG
1070858 GCCATCCGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.25, C:0.31, G:0.29, T:0.15
Consensus pattern (33 bp):
GCATCCGAGGACATCCGACCGAGCTATGCGAGA
Found at i:1070923 original size:80 final size:80
Alignment explanation
Indices: 1070773--1070923 Score: 214
Period size: 80 Copynumber: 1.9 Consensus size: 80
1070763 CGTTGGGCAT
* * *
1070773 CCGAGGCCATCCGACCGAGCTATGCGAGAGCATCCGAGGTCATCCGACCGAGCTATGCTAGAGCA
1 CCGAGGCCATCCGAACGAGCTATGCGAGAGCATCCGAGGTCAGCCGACCGAGCTATGCGAGAGCA
*
1070838 TCCGAGGATATCCGA
66 GCCGAGGATATCCGA
* * * *
1070853 CCGAGGCCATCCGAACGAGCTATGCGGGGGCATCCGATGGT-AGCCGAGCGAGCTATGCGAGGGC
1 CCGAGGCCATCCGAACGAGCTATGCGAGAGCATCCGA-GGTCAGCCGACCGAGCTATGCGAGAGC
1070917 AGCCGAG
65 AGCCGAG
1070924 CGAGGGTAGG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
80 59 0.95
81 3 0.05
ACGTcount: A:0.23, C:0.30, G:0.34, T:0.13
Consensus pattern (80 bp):
CCGAGGCCATCCGAACGAGCTATGCGAGAGCATCCGAGGTCAGCCGACCGAGCTATGCGAGAGCA
GCCGAGGATATCCGA
Found at i:1070964 original size:29 final size:29
Alignment explanation
Indices: 1070931--1070991 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
1070921 GAGCGAGGGT
*
1070931 AGGTCGCTCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
1070960 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
1070989 AGG
1 AGG
1070992 GCGACCTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.21, C:0.28, G:0.36, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:1071008 original size:42 final size:42
Alignment explanation
Indices: 1070949--1071029 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 42
1070939 CGGAGTGCAT
1070949 GGCGACCTACAAGGTCGCCCGG-AGTGCATGGCGACCTACAAG
1 GGCGACCTACAAGGTCGCCCGGAAG-GCATGGCGACCTACAAG
* *
1070991 GGCGACCTATAAGGTCGCCTGGAAGGCATGGCGACCTAC
1 GGCGACCTACAAGGTCGCCCGGAAGGCATGGCGACCTAC
1071030 GGCCAACACT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 34 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.30, G:0.33, T:0.14
Consensus pattern (42 bp):
GGCGACCTACAAGGTCGCCCGGAAGGCATGGCGACCTACAAG
Found at i:1073289 original size:29 final size:29
Alignment explanation
Indices: 1073234--1073289 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
1073224 AAAATATGCG
*
1073234 ATGACATAGATTATTTTATTATTTTTATT
1 ATGACATAGATTATTTTATTATATTTATT
1073263 ATGACATA-ATGT-TTTTATTAATATTTA
1 ATGACATAGAT-TATTTTATT-ATATTTA
1073290 ATGTCAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (29 bp):
ATGACATAGATTATTTTATTATATTTATT
Found at i:1075513 original size:14 final size:14
Alignment explanation
Indices: 1075494--1075541 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1075484 CCAAAAATAT
1075494 TTTTAATTCCTCCA
1 TTTTAATTCCTCCA
* **
1075508 TTTTAATTCTTATA
1 TTTTAATTCCTCCA
1075522 TTTTTAATTCCTCCA
1 -TTTTAATTCCTCCA
1075537 TTTTA
1 TTTTA
1075542 GGGTAAATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTAATTCCTCCA
Found at i:1075539 original size:15 final size:15
Alignment explanation
Indices: 1075492--1075540 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1075482 CACCAAAAAT
1075492 ATTTTTAATTCCTCC
1 ATTTTTAATTCCTCC
* **
1075507 A-TTTTAATTCTTAT
1 ATTTTTAATTCCTCC
1075521 ATTTTTAATTCCTCC
1 ATTTTTAATTCCTCC
1075536 ATTTT
1 ATTTT
1075541 AGGGTAAATC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.22, C:0.18, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTAATTCCTCC
Found at i:1086691 original size:31 final size:31
Alignment explanation
Indices: 1086656--1086729 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
1086646 GGTTCGTCCG
1086656 ATTTAAGTCCCTAACGTTACCGGTCCGTTCA
1 ATTTAAGTCCCTAACGTTACCGGTCCGTTCA
** * *
1086687 ATTTAAGTCTTTAACGTTATCGGTCCGTTCG
1 ATTTAAGTCCCTAACGTTACCGGTCCGTTCA
*
1086718 ATTTTAGTCCCT
1 ATTTAAGTCCCT
1086730 CAATCATGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.39
Consensus pattern (31 bp):
ATTTAAGTCCCTAACGTTACCGGTCCGTTCA
Found at i:1088248 original size:21 final size:22
Alignment explanation
Indices: 1088222--1088269 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1088212 TTTGTGGCAT
1088222 TTTTCTT-T-TCTCTATGACATG
1 TTTTCTTCTGTCT-TATGACATG
*
1088243 TTTTCTTCTGTCTTGTGACATG
1 TTTTCTTCTGTCTTATGACATG
1088265 TTTTC
1 TTTTC
1088270 AGTCGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 14 0.58
23 3 0.12
ACGTcount: A:0.10, C:0.19, G:0.12, T:0.58
Consensus pattern (22 bp):
TTTTCTTCTGTCTTATGACATG
Found at i:1088851 original size:43 final size:43
Alignment explanation
Indices: 1088768--1088980 Score: 195
Period size: 43 Copynumber: 5.0 Consensus size: 43
1088758 ACTTTCCACC
* *
1088768 TTTATAATTGAGGCTCCTAATTTTTT-AATATCA-TATTTTACA
1 TTTATAATTGAAGCTCCTAATTTTTTCAATCTCACT-TTTTACA
* *
1088810 TTTATAATTGAAGCTCCTAACTTTTTCAATCTCATTTTTTAC-
1 TTTATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTTTACA
* * * * * *
1088852 TTATATAATTTAGGCCCCTAATTTTTTCAAGCTAACCTTTTACA
1 TT-TATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTTTACA
* * * * *
1088896 TTTAAAATTG-AGTCCCCTAATTTTTTTAATCTTACTTTTTACC
1 TTTATAATTGAAG-CTCCTAATTTTTTCAATCTCACTTTTTACA
*
1088939 TTTATAATT-AAGGTCCTTAATTTTTTCAATCAT-ACTTTTTAC
1 TTTATAATTGAAGCTCC-TAATTTTTTCAATC-TCACTTTTTAC
1088981 TTTTTTATAG
Statistics
Matches: 140, Mismatches: 23, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
42 29 0.21
43 107 0.76
44 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (43 bp):
TTTATAATTGAAGCTCCTAATTTTTTCAATCTCACTTTTTACA
Found at i:1088980 original size:86 final size:84
Alignment explanation
Indices: 1088751--1088977 Score: 237
Period size: 86 Copynumber: 2.7 Consensus size: 84
1088741 CATATGTCAA
** * * *
1088751 CAATCTTACTTTCCACCTTTATAATTGAGGCTCCTAATTTTTTAATATCATA-TTTTACATTTAT
1 CAATCTTACTTTTTACCTTTATAATTAAGG-TCCTAATTTTTTCA-ATCATACTTTTACATTTAA
*
1088815 AATTGAAGCTCCTAACTTTTT
64 AATTGAAGCCCCTAACTTTTT
* * * * *
1088836 CAATCTCATTTTTTA-CTTATATAATTTAGGCCCCTAATTTTTTCAAGC-TAACCTTTTACATTT
1 CAATCTTACTTTTTACCTT-TATAATTAAGG-TCCTAATTTTTTCAATCAT-A-CTTTTACATTT
*
1088899 AAAATTG-AGTCCCCTAATTTTTT
62 AAAATTGAAG-CCCCTAACTTTTT
*
1088922 TAATCTTACTTTTTACCTTTATAATTAAGGTCCTTAATTTTTTCAATCATACTTTT
1 CAATCTTACTTTTTACCTTTATAATTAAGGTCC-TAATTTTTTCAATCATACTTTT
1088978 TACTTTTTTA
Statistics
Matches: 117, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
83 1 0.01
84 6 0.05
85 43 0.37
86 63 0.54
87 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.48
Consensus pattern (84 bp):
CAATCTTACTTTTTACCTTTATAATTAAGGTCCTAATTTTTTCAATCATACTTTTACATTTAAAA
TTGAAGCCCCTAACTTTTT
Found at i:1091317 original size:14 final size:14
Alignment explanation
Indices: 1091295--1091326 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1091285 CGTTGGGCAT
1091295 CCGAAGGCATCCGA
1 CCGAAGGCATCCGA
*
1091309 CCGAGGGCATCCGA
1 CCGAAGGCATCCGA
1091323 CCGA
1 CCGA
1091327 TGCCATTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.38, G:0.31, T:0.06
Consensus pattern (14 bp):
CCGAAGGCATCCGA
Found at i:1091431 original size:29 final size:29
Alignment explanation
Indices: 1091388--1091493 Score: 194
Period size: 29 Copynumber: 3.7 Consensus size: 29
1091378 GAGAAGCAGG
*
1091388 AGGAGTGCATGGCGACCTACAAGGTCGCT
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
1091417 AGGAGTGCATTGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
1091446 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
1091475 AGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
1091494 TGCTGGGAAG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 74 1.00
ACGTcount: A:0.25, C:0.25, G:0.34, T:0.16
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:1092028 original size:2 final size:2
Alignment explanation
Indices: 1092021--1092055 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1092011 AAATAAAACA
1092021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1092056 GTTAAAACTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1092575 original size:21 final size:21
Alignment explanation
Indices: 1092542--1092584 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1092532 CATTTGAATT
*
1092542 AATTAATATATATCAAACATA
1 AATTAATAAATATCAAACATA
*
1092563 AATTTATAAATATCAAACATA
1 AATTAATAAATATCAAACATA
1092584 A
1 A
1092585 TATCAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTAATAAATATCAAACATA
Found at i:1092602 original size:2 final size:2
Alignment explanation
Indices: 1092595--1092621 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1092585 TATCAAAATA
1092595 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1092622 AAATCAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1092706 original size:24 final size:22
Alignment explanation
Indices: 1092669--1092712 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1092659 TTAAAATTTA
1092669 CAAATACTAAATCAACATATAAT
1 CAAATACTAAATCAA-ATATAAT
*
1092692 CAAATCACTATATCAAATATA
1 CAAAT-ACTAAATCAAATATA
1092713 TATTTCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
CAAATACTAAATCAAATATAAT
Found at i:1093440 original size:21 final size:22
Alignment explanation
Indices: 1093392--1093437 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1093382 AAATTTTAAA
1093392 TTTT-ATTTAAAATAATTATTT
1 TTTTAATTTAAAATAATTATTT
1093413 TTTTAATTTAAAATAATTATTT
1 TTTTAATTTAAAATAATTATTT
1093435 TTT
1 TTT
1093438 AATGGACTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTAATTTAAAATAATTATTT
Found at i:1102391 original size:36 final size:35
Alignment explanation
Indices: 1102314--1102393 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 35
1102304 AAATAATATC
*
1102314 TAAAA-TTTAGTTTTTTTTATTTTAGTACCCGTCAT
1 TAAAATTTTAGTTTTTTTTATTTTAATACCCGT-AT
1102349 TGAAAATTTTAGTTTTTTTTCATTTTAATACTCCGT-T
1 T-AAAATTTTAGTTTTTTTT-ATTTTAATAC-CCGTAT
1102386 TAAAATTT
1 TAAAATTT
1102394 AACATTAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
35 1 0.03
36 11 0.28
37 15 0.38
38 9 0.22
39 4 0.10
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (35 bp):
TAAAATTTTAGTTTTTTTTATTTTAATACCCGTAT
Found at i:1106073 original size:48 final size:48
Alignment explanation
Indices: 1106002--1106100 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
1105992 TCTCTTTAAT
1106002 ATTATTTTCGAATATTTATAATTATTTTATTATATATAAAAAAGTAAA
1 ATTATTTTCGAATATTTATAATTATTTTATTATATATAAAAAAGTAAA
1106050 ATTATTTTCGAATATTTATAATTATTTTATTATATATAAAAAAGTAAA
1 ATTATTTTCGAATATTTATAATTATTTTATTATATATAAAAAAGTAAA
1106098 ATT
1 ATT
1106101 GTATAAAATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.48
Consensus pattern (48 bp):
ATTATTTTCGAATATTTATAATTATTTTATTATATATAAAAAAGTAAA
Found at i:1120244 original size:31 final size:31
Alignment explanation
Indices: 1120208--1120289 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
1120198 TAAAACATTT
* *
1120208 ATTAAACTTTATCAAACTATTA-AAAATGACC
1 ATTAAAC-TTATCAAAATATTATAAAATAACC
* * *
1120239 ATTAAACTAATTAAAATGTTATAAAATAACC
1 ATTAAACTTATCAAAATATTATAAAATAACC
*
1120270 CTTAAACTTATCAAAATATT
1 ATTAAACTTATCAAAATATT
1120290 TATTACTATT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 10 0.24
31 31 0.76
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.34
Consensus pattern (31 bp):
ATTAAACTTATCAAAATATTATAAAATAACC
Found at i:1120580 original size:11 final size:12
Alignment explanation
Indices: 1120564--1120592 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1120554 GTATATTTTC
1120564 AATATTCTAAA-
1 AATATTCTAAAT
1120575 AATATTCTAAAT
1 AATATTCTAAAT
1120587 AATATT
1 AATATT
1120593 ACCTTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
AATATTCTAAAT
Done.