Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 30
Found at i:777706 original size:54 final size:54
Alignment explanation
Indices: 777574--777735 Score: 190
Period size: 54 Copynumber: 3.1 Consensus size: 54
777564 ATAATCACTG
** *
777574 GTTCGTAAAATTTTTGACAATACATTCAT-CTTTTCCTGTGGTTTCTG-TC-GA-
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTT-CTGTGGTTTCTGCTCAGAT
* * * *
777625 GAT-GTAAAACACTTGACAACACCTTCATCCTTTTCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAGAT
* * *
777678 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCCTGTGATTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAGAT
777732 GTTC
1 GTTC
777736 TCAATCATTG
Statistics
Matches: 92, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
50 31 0.34
51 9 0.10
52 2 0.02
53 2 0.02
54 48 0.52
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAGAT
Found at i:785870 original size:14 final size:14
Alignment explanation
Indices: 785832--785885 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
785822 CATAAAAATA
* *
785832 CAAATGCAAAGATG
1 CAAATGTAAATATG
785846 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
785861 CAATTGTAAAAATG
1 CAAATGTAAATATG
*
785875 TAAATGTAAAT
1 CAAATGTAAAT
785886 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:787561 original size:16 final size:16
Alignment explanation
Indices: 787530--787579 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 16
787520 TTAATACATG
787530 AATAAAATAA-AT--A
1 AATAAAATAATATAAA
787543 AATAAAATAATATAAA
1 AATAAAATAATATAAA
*
787559 AATAATAAGTAATAAAAA
1 AATAA-AA-TAATATAAA
787577 AAT
1 AAT
787580 TTGAAAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 10 0.32
14 2 0.06
16 6 0.19
17 2 0.06
18 11 0.35
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
AATAAAATAATATAAA
Found at i:787571 original size:18 final size:16
Alignment explanation
Indices: 787535--787579 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
787525 ACATGAATAA
*
787535 AATAAATAAATAAAAT
1 AATAAAAAAATAAAAT
*
787551 AATATAAAAATAATAAGT
1 AATAAAAAAATAA-AA-T
787569 AATAAAAAAAT
1 AATAAAAAAAT
787580 TTGAAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
17 2 0.08
18 11 0.46
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
AATAAAAAAATAAAAT
Found at i:789248 original size:15 final size:15
Alignment explanation
Indices: 789224--789255 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
789214 CCTCGGTAAG
789224 TTTCTCTTCTTTCTT
1 TTTCTCTTCTTTCTT
*
789239 TTTCTTTTCTTTCTT
1 TTTCTCTTCTTTCTT
789254 TT
1 TT
789256 CTGCTGCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTCTTCTTTCTT
Found at i:789334 original size:19 final size:19
Alignment explanation
Indices: 789310--789346 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
789300 TTTGTTTCTC
789310 TGTATTTCTCT-TCTCTCTG
1 TGTATTT-TCTGTCTCTCTG
789329 TGTATTTTCTGTCTCTCT
1 TGTATTTTCTGTCTCTCT
789347 TTGTCTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.05, C:0.24, G:0.11, T:0.59
Consensus pattern (19 bp):
TGTATTTTCTGTCTCTCTG
Found at i:789751 original size:3 final size:3
Alignment explanation
Indices: 789743--789847 Score: 147
Period size: 3 Copynumber: 35.0 Consensus size: 3
789733 TATATATATT
*
789743 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
789791 TAA TAA TAT TTA TAG TAA TTA TAA TAA TAA TAA TAA TAA TTA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
789839 TAA TAA TAA
1 TAA TAA TAA
789848 AAAATAAATC
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:792592 original size:7 final size:7
Alignment explanation
Indices: 792559--792676 Score: 58
Period size: 7 Copynumber: 17.4 Consensus size: 7
792549 ATTTAAATGT
792559 ATATATA
1 ATATATA
792566 ATAT-TA
1 ATATATA
*
792572 TTA-ATA
1 ATATATA
792578 AT-TA-A
1 ATATATA
792583 ATATAT-
1 ATATATA
792589 A-ATATA
1 ATATATA
792595 ATAT-TA
1 ATATATA
* *
792601 AAAAATAA
1 ATATAT-A
792609 ATATATA
1 ATATATA
792616 ATATA-A
1 ATATATA
792622 ATATATTA
1 ATATA-TA
792630 ATA-ATTA
1 ATATA-TA
*
792637 ATAAATA
1 ATATATA
792644 ATAT-TA
1 ATATATA
*
792650 TATATATG
1 -ATATATA
*
792658 TTATTATA
1 ATA-TATA
792666 ATAATATA
1 AT-ATATA
792674 ATA
1 ATA
792677 ATATTTTATA
Statistics
Matches: 85, Mismatches: 11, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
5 7 0.08
6 24 0.28
7 32 0.38
8 21 0.25
9 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (7 bp):
ATATATA
Found at i:792599 original size:26 final size:26
Alignment explanation
Indices: 792559--792652 Score: 104
Period size: 26 Copynumber: 3.6 Consensus size: 26
792549 ATTTAAATGT
792559 ATATATAATAT--TATTAATAATTAA
1 ATATATAATATAATATTAATAATTAA
* *
792583 ATATATAATATAATATTAAAAAATAA
1 ATATATAATATAATATTAATAATTAA
792609 ATATATAATATAAATATATTAATAATT-A
1 ATATATAATAT--A-ATATTAATAATTAA
* *
792637 ATAAATAATATTATAT
1 ATATATAATATAATAT
792653 ATATGTTATT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
24 11 0.19
25 4 0.07
26 22 0.37
28 12 0.20
29 10 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATATAATATAATATTAATAATTAA
Found at i:792600 original size:19 final size:19
Alignment explanation
Indices: 792573--792676 Score: 61
Period size: 19 Copynumber: 5.3 Consensus size: 19
792563 ATAATATTAT
792573 TAATAATTAAATATATAATA
1 TAAT-ATTAAATATATAATA
* *
792593 TAATATTAAAAAATAAATATA
1 TAATATT-AAATATATA-ATA
792614 TAATA-TAAATATATTAATA
1 TAATATTAAATATA-TAATA
* * *
792633 -ATTAATAAATA-ATATTA
1 TAATATTAAATATATAATA
* *
792650 TATATATGTTATTATAATAATA
1 TA-ATAT-TAAATAT-ATAATA
792672 TAATA
1 TAATA
792677 ATATTTTATA
Statistics
Matches: 64, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
17 4 0.06
18 5 0.08
19 20 0.31
20 17 0.27
21 11 0.17
22 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (19 bp):
TAATATTAAATATATAATA
Found at i:792667 original size:33 final size:32
Alignment explanation
Indices: 792558--792688 Score: 118
Period size: 33 Copynumber: 4.2 Consensus size: 32
792548 AATTTAAATG
*
792558 TATATATA-ATATTATTAATAATTAAAT-ATA-
1 TATATATATATATTAATAATAA-TAAATAATAT
792588 TA-ATATA-ATATTAA-AA-AATAAAT-ATAT
1 TATATATATATATTAATAATAATAAATAATAT
* *
792615 AATATAAATATATTAATAATTAATAAATAATAT
1 TATATATATATATTAATAA-TAATAAATAATAT
*
792648 TATATATATGTTATT-ATAATAATATAATAATAT
1 TATATATAT-ATATTAATAATAATA-AATAATAT
*
792681 TTTATATA
1 TATATATA
792689 AAAAAATTCC
Statistics
Matches: 85, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
26 8 0.09
27 3 0.04
28 6 0.07
29 18 0.21
30 4 0.05
32 12 0.14
33 30 0.35
34 4 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
TATATATATATATTAATAATAATAAATAATAT
Found at i:795616 original size:60 final size:60
Alignment explanation
Indices: 795489--795616 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
795479 ATTTGTCCCT
* * * * *
795489 AAACTTTTAGATATTTCAATTTCATCCCTAAACTACAACTATCATTCTAAACTAGTTCTT
1 AAACTTTTAGATATTTCAATTTCACCCCCAAACTACAACAATCATTCTAAACTAGTCCTC
* * * *
795549 AAGCTTTT-GAATATTTCAATTTCACCCCCAAACTATGAA-AATCATTCTAAATTGGTCCTC
1 AAACTTTTAG-ATATTTCAATTTCACCCCCAAACTA-CAACAATCATTCTAAACTAGTCCTC
795609 AAACTTTT
1 AAACTTTT
795617 TTGAACATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
59 1 0.02
60 53 0.95
61 2 0.04
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.38
Consensus pattern (60 bp):
AAACTTTTAGATATTTCAATTTCACCCCCAAACTACAACAATCATTCTAAACTAGTCCTC
Found at i:795878 original size:61 final size:61
Alignment explanation
Indices: 795813--795932 Score: 143
Period size: 61 Copynumber: 2.0 Consensus size: 61
795803 TTAGAAAGAG
* * * * *
795813 GTCATAGTTTTAAGGATGAAATTAGAATGTTCAAAAGA-TTAAAGACTAATATAAAATGAAA
1 GTCATAATTTGAA-GATGAAATTAGAATATTAAAAAAATTTAAAGACTAATATAAAATGAAA
* * * *
795874 GTCATAATTTGGAGATGAAATTAGAATATTAAAAAAATTTAAGGATTAATTTAAAATGA
1 GTCATAATTTGAAGATGAAATTAGAATATTAAAAAAATTTAAAGACTAATATAAAATGA
795933 GAATTACAGT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 21 0.43
61 28 0.57
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.32
Consensus pattern (61 bp):
GTCATAATTTGAAGATGAAATTAGAATATTAAAAAAATTTAAAGACTAATATAAAATGAAA
Found at i:796428 original size:13 final size:13
Alignment explanation
Indices: 796410--796434 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
796400 TTGTTGGTTA
796410 ATTTTTATAAATT
1 ATTTTTATAAATT
796423 ATTTTTATAAAT
1 ATTTTTATAAAT
796435 ATAGTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATTTTTATAAATT
Found at i:796468 original size:35 final size:33
Alignment explanation
Indices: 796416--796481 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 33
796406 GTTAATTTTT
*
796416 ATAAATTATTTTTATAAATATAGT-ATATAATGA
1 ATAAATTATTTTTATAAAAATA-TAATATAATGA
796449 ATAATATTATTTATTATAAAAATATAATATAAT
1 ATAA-ATTATTT-TTATAAAAATATAATATAAT
796482 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 4 0.14
34 8 0.28
35 17 0.59
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (33 bp):
ATAAATTATTTTTATAAAAATATAATATAATGA
Found at i:796476 original size:23 final size:22
Alignment explanation
Indices: 796449--796511 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
796439 TATATAATGA
796449 ATAATATTATTTATTATAAAAAT
1 ATAATATTATTTATT-TAAAAAT
* *
796472 ATAATA-TAATTATTTTAAAAT
1 ATAATATTATTTATTTAAAAAT
* *
796493 ATTAAAATAATTTATTTAA
1 A-TAATATTATTTATTTAA
796512 TATATTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 7 0.22
22 11 0.34
23 14 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAATATTATTTATTTAAAAAT
Found at i:796484 original size:22 final size:21
Alignment explanation
Indices: 796449--796511 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 21
796439 TATATAATGA
*
796449 ATAATATTATTTATTATAAAAAT
1 ATAATA-TAATTATT-TAAAAAT
*
796472 ATAATATAATTATTTTAAAAT
1 ATAATATAATTATTTAAAAAT
*
796493 ATTAAAATAATTTATTTAA
1 A-TAATATAA-TTATTTAA
796512 TATATTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 7 0.21
22 14 0.41
23 13 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAATATAATTATTTAAAAAT
Found at i:797265 original size:21 final size:21
Alignment explanation
Indices: 797228--797267 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
797218 ACTTTACCCT
797228 AAAAATTATAATATTAAAATA
1 AAAAATTATAATATTAAAATA
*
797249 AAAACATTAT-ATTTTAAAA
1 AAAA-ATTATAATATTAAAA
797268 ATTATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAATTATAATATTAAAATA
Found at i:797282 original size:22 final size:23
Alignment explanation
Indices: 797257--797299 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
797247 TAAAAACATT
797257 ATATTTTAAA-AATTATTAATAA
1 ATATTTTAAATAATTATTAATAA
*
797279 ATATTTTAAATATTTATTAAT
1 ATATTTTAAATAATTATTAAT
797300 TCAATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATAATTATTAATAA
Found at i:797325 original size:17 final size:17
Alignment explanation
Indices: 797305--797338 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
797295 TTAATTCAAT
*
797305 AATATTATTTTCTAATA
1 AATAATATTTTCTAATA
*
797322 AATAATATTTTTTAATA
1 AATAATATTTTCTAATA
797339 TTTTACTATA
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:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
AATAATATTTTCTAATA
Found at i:797490 original size:30 final size:29
Alignment explanation
Indices: 797439--797497 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
797429 TATATTAAAA
* *
797439 TTATTAAAAATATATTTAAAAATTAATATT
1 TTATTAAAAATATACTAAAAAATT-ATATT
797469 TTATT-AAAATGATACTAAAAAATTATATT
1 TTATTAAAAAT-ATACTAAAAAATTATATT
797498 ATTACATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
TTATTAAAAATATACTAAAAAATTATATT
Found at i:809718 original size:19 final size:19
Alignment explanation
Indices: 809677--809721 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
809667 AACGTGTGCT
* * *
809677 TCCCCTCCCCTGCTCTTCC
1 TCCCCTCCCCTGCCCTACA
*
809696 TCCCCTTCCCTGCCCTACA
1 TCCCCTCCCCTGCCCTACA
809715 TCCCCTC
1 TCCCCTC
809722 TCCTTTCGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.04, C:0.62, G:0.04, T:0.29
Consensus pattern (19 bp):
TCCCCTCCCCTGCCCTACA
Found at i:810106 original size:13 final size:12
Alignment explanation
Indices: 810067--810104 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
810057 GGTTTTTTGC
810067 AAATAAAATATTT
1 AAATAAAA-ATTT
810080 -AA-AAAAATTT
1 AAATAAAAATTT
810090 AAATAAAAATTT
1 AAATAAAAATTT
810102 AAA
1 AAA
810105 ATTACCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.17
11 6 0.26
12 13 0.57
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATAAAAATTT
Found at i:810661 original size:37 final size:37
Alignment explanation
Indices: 810620--810725 Score: 100
Period size: 37 Copynumber: 3.0 Consensus size: 37
810610 ATTATATTAG
810620 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
1 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
* * *** *
810657 ATAATA-ATCGAGTGACCAAA-A--CA---TAAATTAG
1 ATAATATAT-AAGTGACCAAATAGGTAGTTTACCCTAA
810688 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
1 ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
810725 A
1 A
810726 AAACCATAAT
Statistics
Matches: 49, Mismatches: 12, Indels: 16
0.64 0.16 0.21
Matches are distributed among these distances:
31 20 0.41
32 3 0.06
34 2 0.04
36 3 0.06
37 21 0.43
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.27
Consensus pattern (37 bp):
ATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
Found at i:810716 original size:68 final size:66
Alignment explanation
Indices: 810527--810725 Score: 262
Period size: 63 Copynumber: 3.0 Consensus size: 66
810517 TTGAAAAAAA
*
810527 AATAATCAAGTGACCAAAATATAAAATTAGATAATACATAAGTGACCAAATAGGTAGTTTACCCT
1 AATAATC-AGTGACCAAAA-AT-AAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCT
810592 AAAT
63 AAAT
* ** * *
810596 AAAAATACA-T-A--TGAATTATATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
1 AATAAT-CAGTGACCAAAAATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAA
810657 AT
65 AT
810659 AATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
1 AATAATC-AGTGACCAAAA-ATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTA
810724 AA
64 AA
810726 AAACCATAAT
Statistics
Matches: 112, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
62 1 0.01
63 50 0.45
64 2 0.02
65 3 0.03
67 3 0.03
68 46 0.41
69 6 0.05
70 1 0.01
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (66 bp):
AATAATCAGTGACCAAAAATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAA
T
Found at i:812231 original size:18 final size:17
Alignment explanation
Indices: 812210--812243 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
812200 TTTTATTTAC
*
812210 TTTTTATATTTTCTAATA
1 TTTTTAAATTTT-TAATA
812228 TTTTTAAATTTTTAAT
1 TTTTTAAATTTTTAAT
812244 TAAAATCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTAAATTTTTAATA
Found at i:812351 original size:21 final size:21
Alignment explanation
Indices: 812326--812375 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
812316 ATTATTCACA
* *
812326 CATGAATTATCATATTAATAT
1 CATGAACTATCATAGTAATAT
812347 CATGAACTATCATAGTAATAT
1 CATGAACTATCATAGTAATAT
812368 -AGTGAACT
1 CA-TGAACT
812376 GTCAGTGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (21 bp):
CATGAACTATCATAGTAATAT
Found at i:823445 original size:20 final size:21
Alignment explanation
Indices: 823400--823445 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
823390 GAGATTTGGG
* * *
823400 ATTTTGCGAGTTTTAAATTGA
1 ATTTTACGAATTTTAAAATGA
823421 ATTTTACGAATTTTAAAAT-A
1 ATTTTACGAATTTTAAAATGA
823441 ATTTT
1 ATTTT
823446 TAAAAAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.50
Consensus pattern (21 bp):
ATTTTACGAATTTTAAAATGA
Found at i:824563 original size:210 final size:208
Alignment explanation
Indices: 823978--824617 Score: 721
Period size: 210 Copynumber: 3.1 Consensus size: 208
823968 AAACCCAGAA
* * * * * * * *
823978 AACTATTTTAAACACAGAATTGTCCATGTGATAAAACCCATTTCTAAGTAATTTAGAGCAAATAC
1 AACTATTTTTAACAC--AACTGTTCATGTGATAAAACCTATTTATGAGTAATCTAGAGCGAATAC
* * * ** * ** *
824043 TGTAGAGTTCTATTACATGAGTGAACCTC-TCAATCGAGTTTTCTCAA-TTTATAATTGTTAGAA
64 TGCAGAGTTCCATTACACGAACGAACCTCTTC-ATCCAGTTTTCT-AAGTTTA-AAACGCTAGAA
*
824106 T-TCGAACATTTTCTCCATAAGATTC-GA-----AACC---CTTAAGACACCTAACGACTCATTC
126 TCTCG-ATA-TTTCTCCATAAGATTCGGAGCTCTAACCTTACTTAAGACACCTAACGACTCATTC
** *
824161 CGCTACACCGATTACAAGAG
189 CGCTACACTAATTATAAGAG
* * * * * * *
824181 AGCTAACTTTTACAAAAAACTGTTCATGTTATAAAGCCTATTTATGAGTAATCTAGAGCGAATTC
1 AACT-ATTTTTA-ACACAACTGTTCATGTGATAAAACCTATTTATGAGTAATCTAGAGCGAATAC
824246 TGCAGAGTTCCATTACACGAACGAACCTCTTCATCCAGTTTTCTAAGTTTAAAACGCTAGAATCT
64 TGCAGAGTTCCATTACACGAACGAACCTCTTCATCCAGTTTTCTAAGTTTAAAACGCTAGAATCT
* *
824311 CGATATTTCTCCATAAGATTCGGAGCTCTAACCTTGCTTAAGACACCTAACGACTCATTCCACTA
129 CGATATTTCTCCATAAGATTCGGAGCTCTAACCTTACTTAAGACACCTAACGACTCATTCCGCTA
824376 CACTAATTATAAGAG
194 CACTAATTATAAGAG
* *
824391 AACTATTTTTTAACACAACTGTTCATGTGATAAAACCTATTTCTGTGTAATCTAGAGCGAATACT
1 AACTA-TTTTTAACACAACTGTTCATGTGATAAAACCTATTTATGAGTAATCTAGAGCGAATACT
* * * * *
824456 GCAGAGTTCCGTTACATGAACGAACCTCTTCGTCCAGTTTTCTATGTTTAAAACGCTAGAATTTC
65 GCAGAGTTCCATTACACGAACGAACCTCTTCATCCAGTTTTCTAAGTTTAAAACGCTAGAATCTC
* *
824521 -ATTGTTTTCTCCATAAGATTCGGAGCTCTAACCTTACTTAAGACACCTAAGGACTCATTCCGCT
130 GA-T-ATTTCTCCATAAGATTCGGAGCTCTAACCTTACTTAAGACACCTAACGACTCATTCCGCT
*
824585 ACACTAAATATAAGAG
193 ACACTAATTATAAGAG
824601 AACTATTTTTAACACAA
1 AACTATTTTTAACACAA
824618 AATTGTTTAT
Statistics
Matches: 372, Mismatches: 48, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
201 16 0.04
202 15 0.04
203 83 0.22
204 7 0.02
205 2 0.01
207 4 0.01
208 1 0.00
209 120 0.32
210 124 0.33
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (208 bp):
AACTATTTTTAACACAACTGTTCATGTGATAAAACCTATTTATGAGTAATCTAGAGCGAATACTG
CAGAGTTCCATTACACGAACGAACCTCTTCATCCAGTTTTCTAAGTTTAAAACGCTAGAATCTCG
ATATTTCTCCATAAGATTCGGAGCTCTAACCTTACTTAAGACACCTAACGACTCATTCCGCTACA
CTAATTATAAGAG
Found at i:834965 original size:2 final size:2
Alignment explanation
Indices: 834960--834994 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
834950 TATATTGTTA
834960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
834995 TCATTCTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:836173 original size:22 final size:22
Alignment explanation
Indices: 836148--836229 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 22
836138 TATATCACGG
*
836148 AAGTGCCTTAGCACTAATACTA
1 AAGTGCCTTAGCACTGATACTA
836170 AAGTGCCTTAGCACTGATAC-A
1 AAGTGCCTTAGCACTGATACTA
*
836191 GAAGTG-CATACGCACTGATACTA
1 -AAGTGCCTTA-GCACTGATACTA
* *
836214 AAGTGGCTTAGTACTG
1 AAGTGCCTTAGCACTG
836230 GGAGAGAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.08
22 44 0.85
23 4 0.08
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
AAGTGCCTTAGCACTGATACTA
Found at i:836552 original size:18 final size:20
Alignment explanation
Indices: 836505--836553 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
836495 TGGGTATGAC
* *
836505 AGTATCGGTACTGGCCTCAT
1 AGTATCGATACTGGCCCCAT
*
836525 AGTATTGATACT-GCCCCA-
1 AGTATCGATACTGGCCCCAT
836543 AGTATCGATAC
1 AGTATCGATAC
836554 CAAAATTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 5 0.20
20 10 0.40
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTGGCCCCAT
Found at i:839212 original size:2 final size:2
Alignment explanation
Indices: 839205--839236 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
839195 ACTATTTAAC
*
839205 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
839237 TAGTTTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:839650 original size:16 final size:16
Alignment explanation
Indices: 839598--839652 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
839588 TTTATCCTAA
839598 TTTTAATTATTTCATT-
1 TTTTAA-TATTTCATTC
* *
839614 TTTTAGTTATTTCA-AC
1 TTTTA-ATATTTCATTC
*
839630 CTTTAATATTTCATTC
1 TTTTAATATTTCATTC
839646 TTTTAAT
1 TTTTAAT
839653 TATCAAAGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 7 0.23
16 23 0.77
ACGTcount: A:0.25, C:0.11, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTTAATATTTCATTC
Found at i:839871 original size:18 final size:18
Alignment explanation
Indices: 839840--839874 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
839830 TAGTTTTCAA
*
839840 ATAAAAATTTATTTGATT
1 ATAAAAATTCATTTGATT
*
839858 ATAAATATTCATTTGAT
1 ATAAAAATTCATTTGAT
839875 CATGATTGAA
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:0.03, G:0.06, T:0.49
Consensus pattern (18 bp):
ATAAAAATTCATTTGATT
Found at i:844281 original size:16 final size:16
Alignment explanation
Indices: 844260--844293 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
844250 TGGCACGGTG
844260 GGGGTGTCGCCAGAGC
1 GGGGTGTCGCCAGAGC
844276 GGGGTGTCGCCAGAGC
1 GGGGTGTCGCCAGAGC
844292 GG
1 GG
844294 TGGCTGGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.53, T:0.12
Consensus pattern (16 bp):
GGGGTGTCGCCAGAGC
Found at i:861912 original size:110 final size:110
Alignment explanation
Indices: 861718--861934 Score: 355
Period size: 110 Copynumber: 2.0 Consensus size: 110
861708 GATCAAAAAG
* * *
861718 GTCAACGATCTCGTATAATTAAATCTCTTTTGTGACAGTTTATTTGATGCATTCAAAACCGCTCA
1 GTCAACGATCTCATATAATTAAATCTCTTTTGTGACAATTTATTTGATCCATTCAAAACCGCTCA
861783 TAAAACAATATGTCAAATTGATTTTATCAATCGTCAAGCCTTCTA
66 TAAAACAATATGTCAAATTGATTTTATCAATCGTCAAGCCTTCTA
861828 GTCAACGATCTCATATAATTAAATCTCTTTTGTGACAATTTATTTGATCCATTCAAAACCGCTC-
1 GTCAACGATCTCATATAATTAAATCTCTTTTGTGACAATTTATTTGATCCATTCAAAACCGCTCA
* * * *
861892 TCAAAACAATATGTCGAATTGATTTTATCTATCTTCAGGCCTT
66 T-AAAACAATATGTCAAATTGATTTTATCAATCGTCAAGCCTT
861935 TTTATTTATT
Statistics
Matches: 99, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
109 1 0.01
110 98 0.99
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (110 bp):
GTCAACGATCTCATATAATTAAATCTCTTTTGTGACAATTTATTTGATCCATTCAAAACCGCTCA
TAAAACAATATGTCAAATTGATTTTATCAATCGTCAAGCCTTCTA
Found at i:864483 original size:4 final size:4
Alignment explanation
Indices: 864474--864511 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
864464 AAACAGCAGT
864474 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
864512 TTCAGTGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:865184 original size:9 final size:9
Alignment explanation
Indices: 865170--865217 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
865160 AAAAATGAAG
865170 AAATAAATA
1 AAATAAATA
*
865179 AAATAAAAA
1 AAATAAATA
865188 AAATAAATA
1 AAATAAATA
865197 AAATAAA-A
1 AAATAAATA
865205 AAATAAATA
1 AAATAAATA
865214 AAAT
1 AAAT
865218 TTAAAGAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 8 0.22
9 28 0.78
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAATA
Found at i:865206 original size:17 final size:17
Alignment explanation
Indices: 865157--865217 Score: 88
Period size: 17 Copynumber: 3.6 Consensus size: 17
865147 AATTGAGTTT
* *
865157 TAAA-AAAATGAAGAAA
1 TAAATAAAATAAAAAAA
865173 TAAATAAAATAAAAAAAA
1 TAAATAAAAT-AAAAAAA
865191 TAAATAAAATAAAAAAA
1 TAAATAAAATAAAAAAA
865208 TAAATAAAAT
1 TAAATAAAAT
865218 TTAAAGAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
16 4 0.10
17 22 0.54
18 15 0.37
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAATAAAATAAAAAAA
Found at i:866415 original size:12 final size:12
Alignment explanation
Indices: 866400--866446 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
866390 AAATGAGAAA
866400 AAAATAATAAAT
1 AAAATAATAAAT
866412 AAAATAA-ATAAT
1 AAAATAATA-AAT
*
866424 AATAATGATAAAT
1 AA-AATAATAAAT
*
866437 AAAAAAATAA
1 AAAATAATAA
866447 CAAGAGGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 1 0.03
12 18 0.62
13 9 0.31
14 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:866422 original size:16 final size:15
Alignment explanation
Indices: 866397--866438 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
866387 AAAAAATGAG
866397 AAAA-AAATAATAAAT
1 AAAATAAATAAT-AAT
866412 AAAATAAATAATAAT
1 AAAATAAATAATAAT
*
866427 AATGATAAATAA
1 AA-AATAAATAA
866439 AAAAATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (15 bp):
AAAATAAATAATAAT
Found at i:866570 original size:37 final size:37
Alignment explanation
Indices: 866472--866571 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 37
866462 TTAAAATAAA
*
866472 AAAAATATTTTTCAAAAATCTATATAATATATATTTTAT
1 AAAAATA-TTTTC-AAAATATATATAATATATATTTTAT
* *
866511 AAAAATATTTT-AAAATTATATATTATATATACTTTTTT
1 AAAAATATTTTCAAAA-TATATATAATATATA-TTTTAT
*
866549 AAAAATGTTTTCAAAAT-TATATA
1 AAAAATATTTTCAAAATATATATA
866572 GTTTTCAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
36 4 0.08
37 18 0.34
38 20 0.38
39 11 0.21
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
AAAAATATTTTCAAAATATATATAATATATATTTTAT
Found at i:866620 original size:29 final size:30
Alignment explanation
Indices: 866556--866634 Score: 106
Period size: 29 Copynumber: 2.6 Consensus size: 30
866546 TTTAAAAATG
*
866556 TTTTCAAAATTATATAGTTTTCAAAAAATATT
1 TTTTAAAAATTATATA-TTTTC-AAAAATATT
*
866588 TTTTAAAAATTATATATTTTC-AAAATGTT
1 TTTTAAAAATTATATATTTTCAAAAATATT
*
866617 TTTTAAAAACTATATATT
1 TTTTAAAAATTATATATT
866635 ATATTTACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 24 0.55
31 5 0.11
32 15 0.34
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTTAAAAATTATATATTTTCAAAAATATT
Found at i:867297 original size:20 final size:21
Alignment explanation
Indices: 867277--867316 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
867267 CAAAATATTT
*
867277 GAAAAATGATCAATCCCTTTG
1 GAAAAAGGATCAATCCCTTTG
* *
867298 GTAAAAGGATCGATCCCTT
1 GAAAAAGGATCAATCCCTT
867317 GTGCCTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
GAAAAAGGATCAATCCCTTTG
Found at i:870031 original size:21 final size:21
Alignment explanation
Indices: 870006--870057 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
869996 CTGTCATGTT
* *
870006 AATATTATAGATTATTATATC
1 AATATTATAAATTATCATATC
* *
870027 AATATCATAAATTATCATGTC
1 AATATTATAAATTATCATATC
*
870048 AACATTATAA
1 AATATTATAA
870058 TAATCAATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (21 bp):
AATATTATAAATTATCATATC
Found at i:875734 original size:2 final size:2
Alignment explanation
Indices: 875727--875785 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
875717 TAGTTTACCC
875727 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
875769 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
875786 GTAAATGTCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:876536 original size:14 final size:14
Alignment explanation
Indices: 876514--876578 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
876504 CGATAATATA
876514 TTCATTTATGTTCG
1 TTCATTTATGTTCG
*
876528 TTTATTTATG-TCTG
1 TTCATTTATGTTC-G
** * *
876542 TTTGTTCATGTTTG
1 TTCATTTATGTTCG
*
876556 TTCGTTTATGTTCG
1 TTCATTTATGTTCG
876570 TTCATTTAT
1 TTCATTTAT
876579 ATTTAGGTCA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 2 0.05
14 38 0.93
15 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.15, T:0.62
Consensus pattern (14 bp):
TTCATTTATGTTCG
Found at i:876966 original size:23 final size:23
Alignment explanation
Indices: 876940--877005 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
876930 TTGTGATTTA
* * *
876940 TGTTCATTTATATTCTTTTGTTT
1 TGTTCATTTATATTCGTTTATTG
* *
876963 TGTTCATCTATGTTCGTTTATTG
1 TGTTCATTTATATTCGTTTATTG
* *
876986 TGTTCTTTTATGTTCGTTTA
1 TGTTCATTTATATTCGTTTA
877006 CATCCGTGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.12, C:0.11, G:0.14, T:0.64
Consensus pattern (23 bp):
TGTTCATTTATATTCGTTTATTG
Found at i:880669 original size:19 final size:19
Alignment explanation
Indices: 880630--880669 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
880620 AACCCAGTTT
* *
880630 TGTTGCAAACTAGTAACAA
1 TGTTACAAACTAGGAACAA
*
880649 TGTTACAAACTAGGAATAA
1 TGTTACAAACTAGGAACAA
880668 TG
1 TG
880670 AGCAGGCCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (19 bp):
TGTTACAAACTAGGAACAA
Found at i:885317 original size:20 final size:19
Alignment explanation
Indices: 885292--885338 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
885282 ATGCGGTTTT
885292 GAAACTTTGAAGAAAATTTC
1 GAAACTTTG-AGAAAATTTC
* *
885312 GAAACTTTTGAGAAAGTTTT
1 GAAAC-TTTGAGAAAATTTC
885332 GAAACTT
1 GAAACTT
885339 AGTGAAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 18 0.75
21 4 0.17
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (19 bp):
GAAACTTTGAGAAAATTTC
Found at i:885592 original size:11 final size:11
Alignment explanation
Indices: 885576--885611 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
885566 TTTAAAAATC
885576 TTTAAACATAT
1 TTTAAACATAT
885587 TTTAAAC--AT
1 TTTAAACATAT
885596 TTTAAACATAT
1 TTTAAACATAT
885607 TTTAA
1 TTTAA
885612 TTAACTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (11 bp):
TTTAAACATAT
Found at i:885609 original size:20 final size:21
Alignment explanation
Indices: 885562--885611 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
885552 ATAGTGTTTT
885562 CATA-TTTAAAAATCTTTAAA
1 CATATTTTAAAAATCTTTAAA
*
885582 CATATTTTAAACAT-TTTAAA
1 CATATTTTAAAAATCTTTAAA
885602 CATATTTTAA
1 CATATTTTAA
885612 TTAACTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (21 bp):
CATATTTTAAAAATCTTTAAA
Found at i:886356 original size:32 final size:31
Alignment explanation
Indices: 886320--886380 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
886310 TTTAAAACAC
886320 ATGAAAAACAAATTTGACCAAAAATCATTATG
1 ATGAAAAACAAATTT-ACCAAAAATCATTATG
* * **
886352 ATGAATAAGAAATTTATGAAAAATCATTA
1 ATGAAAAACAAATTTACCAAAAATCATTA
886381 AAAGATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGAAAAACAAATTTACCAAAAATCATTATG
Found at i:886920 original size:19 final size:20
Alignment explanation
Indices: 886886--886923 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
886876 CAAAATTTCA
*
886886 TTTTGTTTTCCAAAATCAAC
1 TTTTGCTTTCCAAAATCAAC
886906 TTTTGCTTT-CAAAATCAA
1 TTTTGCTTTCCAAAATCAA
886924 ATCATTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTGCTTTCCAAAATCAAC
Found at i:887409 original size:15 final size:15
Alignment explanation
Indices: 887389--887422 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
887379 CAAGGTAACA
* *
887389 CTTTTTTTTTCTTTT
1 CTTTTTTCTTCTCTT
887404 CTTTTTTCTTCTCTT
1 CTTTTTTCTTCTCTT
887419 CTTT
1 CTTT
887423 ATGTTCTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTTTCTTCTCTT
Found at i:888906 original size:2 final size:2
Alignment explanation
Indices: 888901--888927 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
888891 TGTGTGTGTG
888901 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
888928 CTTATTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:889197 original size:2 final size:2
Alignment explanation
Indices: 889190--889214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
889180 ATTAAATTGA
889190 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
889215 CATAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:890096 original size:63 final size:63
Alignment explanation
Indices: 889996--890196 Score: 393
Period size: 63 Copynumber: 3.2 Consensus size: 63
889986 TAACCTAATT
*
889996 TTAGCATTATCATTATCAAAATTGAGCATTATAAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
890059 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
890122 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
890185 TTAGCATTATCA
1 TTAGCATTATCA
890197 AGAAATGACA
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 137 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (63 bp):
TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
Found at i:890203 original size:41 final size:41
Alignment explanation
Indices: 890141--890235 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
890131 TCATTATCAA
890141 AATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATT-AGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
890183 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
1 AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
*
890224 AATGAGCATTAT
1 AATTAGCATTAT
890236 ACAATACTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 48 0.92
42 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.32
Consensus pattern (41 bp):
AATTAGCATTATCAAGAAATGACAATTTACAATGCTAGTTG
Found at i:895664 original size:63 final size:63
Alignment explanation
Indices: 895565--895765 Score: 384
Period size: 63 Copynumber: 3.2 Consensus size: 63
895555 TAACCTAATT
895565 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
895628 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
*
895691 TTAGCATTATCATTATCAAAATTGAGCATTACCAAGAAATGACAATTTACAATGCTAGTTGAA
1 TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
*
895754 TTAACATTATCA
1 TTAGCATTATCA
895766 AGAAATGACA
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 136 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (63 bp):
TTAGCATTATCATTATCAAAATTGAGCATTATCAAGAAATGACAATTTACAATGCTAGTTGAA
Found at i:895774 original size:41 final size:41
Alignment explanation
Indices: 895717--895804 Score: 149
Period size: 41 Copynumber: 2.1 Consensus size: 41
895707 CAAAATTGAG
* *
895717 CATTACCAAGAAATGACAATTTACAATGCTAGTTGAATTAA
1 CATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAA
*
895758 CATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAT
1 CATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAA
895799 CATTAT
1 CATTAT
895805 ACAATACTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (41 bp):
CATTATCAAGAAATGACAATTTACAATGCTAGTTGAATGAA
Found at i:897323 original size:58 final size:58
Alignment explanation
Indices: 897256--897438 Score: 348
Period size: 58 Copynumber: 3.2 Consensus size: 58
897246 GTTATGATGA
*
897256 TATATATATGTAAATATACATATATAATAAATGTATTCTTTGTTTGTATTAATGCATG
1 TATACATATGTAAATATACATATATAATAAATGTATTCTTTGTTTGTATTAATGCATG
897314 TATACATATGTAAATATACATATATAATAAATGTATTCTTTGTTTGTATTAATGCATG
1 TATACATATGTAAATATACATATATAATAAATGTATTCTTTGTTTGTATTAATGCATG
*
897372 TATACATATGTAAATATTCATATATAATAAATGTATTCTTTGTTTGTATTAATGCATG
1 TATACATATGTAAATATACATATATAATAAATGTATTCTTTGTTTGTATTAATGCATG
897430 TATACATAT
1 TATACATAT
897439 ATATAAATTC
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 123 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.46
Consensus pattern (58 bp):
TATACATATGTAAATATACATATATAATAAATGTATTCTTTGTTTGTATTAATGCATG
Found at i:898635 original size:21 final size:19
Alignment explanation
Indices: 898583--898655 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
898573 TTATGAGTGC
* *
898583 AAAA-TTTCGAAACTTTTGT
1 AAAAGTTTCAAAACTCTT-T
*
898602 AAAA-TTTCGAAACTCTTAAT
1 AAAAGTTTCAAAACTCTT--T
898622 AAAAGTTTCAAAACTCTTT
1 AAAAGTTTCAAAACTCTTT
* *
898641 CAAAGTTTCCAAACT
1 AAAAGTTTCAAAACT
898656 ATGAACCGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 30 0.64
20 5 0.11
21 12 0.26
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (19 bp):
AAAAGTTTCAAAACTCTTT
Found at i:898932 original size:14 final size:14
Alignment explanation
Indices: 898915--898945 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
898905 TTTATATACG
898915 TATATACATACTTA
1 TATATACATACTTA
*
898929 TATATAGATACTTA
1 TATATACATACTTA
898943 TAT
1 TAT
898946 GTGTGTGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (14 bp):
TATATACATACTTA
Found at i:899056 original size:2 final size:2
Alignment explanation
Indices: 899045--899090 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
899035 TCATACGTAT
899045 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
899086 TA TA T
1 TA TA T
899091 TATTTTTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:899307 original size:19 final size:19
Alignment explanation
Indices: 899280--899340 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
899270 TTAACTTATA
*
899280 TATATTTATAAGTATAATG
1 TATACTTATAAGTATAATG
899299 TATACTTAT-A-T-T-A--
1 TATACTTATAAGTATAATG
899312 TATACTTATAAGTATAATG
1 TATACTTATAAGTATAATG
*
899331 TATAGTTATA
1 TATACTTATA
899341 TAAACATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
13 9 0.26
14 1 0.03
15 2 0.06
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.50
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (19 bp):
TATACTTATAAGTATAATG
Found at i:899321 original size:32 final size:32
Alignment explanation
Indices: 899278--899341 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
899268 TATTAACTTA
*
899278 TATATATTTATAAGTATAATGTATACTTATAT
1 TATATACTTATAAGTATAATGTATACTTATAT
*
899310 TATATACTTATAAGTATAATGTATAGTTATAT
1 TATATACTTATAAGTATAATGTATACTTATAT
899342 AAACATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (32 bp):
TATATACTTATAAGTATAATGTATACTTATAT
Found at i:899365 original size:30 final size:30
Alignment explanation
Indices: 899329--899402 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
899319 ATAAGTATAA
*
899329 TGTATAGTTATATAAACATATATATAAACT
1 TGTATAGTTATATAAACATACATATAAACT
899359 TGTATAGTTATATAAACATACATATAAACT
1 TGTATAGTTATATAAACATACATATAAACT
*
899389 TTTATA-TATATATA
1 TGTATAGT-TATATA
899403 TATTATATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 1 0.02
30 40 0.98
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (30 bp):
TGTATAGTTATATAAACATACATATAAACT
Found at i:899398 original size:2 final size:2
Alignment explanation
Indices: 899391--899508 Score: 69
Period size: 2 Copynumber: 62.5 Consensus size: 2
899381 TATAAACTTT
*
899391 TA TA TA TA TA TA TA T- TA TA T- TA TA TA T- TA TA -A GTA -A TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
899429 TA T- TA TA TA TA CA TG TA T- TA TCA TA T- TA TCA TA -A CA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA TA TA TA
*
899469 TCA TA CA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
899509 TAATTTTTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
1 11 0.12
2 72 0.80
3 7 0.08
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:900469 original size:64 final size:63
Alignment explanation
Indices: 900400--900520 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 63
900390 TTGGACTCTC
*
900400 AGTGCATCGATGCACTAAG-A-GTACATCGATGCATGAAATGCATTCAATGTTTTGAAAAAGCCT
1 AGTGCATCGATGCA-T-AGTATGTACATCGATGCATAAAATGCATTCAATG-TTTGAAAAAGCCT
900463 G
63 G
* * *
900464 AGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAA
1 AGTGCATCGATGCATAGTATGTACATCGATGCATAAAATGCATTCAATGTTTGAAAA
900521 CTTAATTGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
62 1 0.02
63 10 0.20
64 40 0.78
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (63 bp):
AGTGCATCGATGCATAGTATGTACATCGATGCATAAAATGCATTCAATGTTTGAAAAAGCCTG
Found at i:900533 original size:64 final size:65
Alignment explanation
Indices: 900423--900562 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 65
900413 ACTAAGAGTA
* *
900423 CATCGATGCATGAAATGCATTCAATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGG-TAT-GT
1 CATCGATGCATAAAATGCATTCAATGTTTTGAAAAAGACTGAGTGCATCGATGCATGGAT-TGGT
900486 G
65 G
* *
900487 CATCGATGCATAAAATGCATTCGATG-TTTGAAAACTTA-ATTG-GTGCATCGATGCATGGATTG
1 CATCGATGCATAAAATGCATTCAATGTTTTGAAAA---AGACTGAGTGCATCGATGCATGGATTG
900549 GTG
63 GTG
*
900552 CATCGGTGCAT
1 CATCGATGCAT
900563 CACCTTGAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
63 8 0.12
64 41 0.62
65 16 0.24
66 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
CATCGATGCATAAAATGCATTCAATGTTTTGAAAAAGACTGAGTGCATCGATGCATGGATTGGTG
Found at i:900550 original size:20 final size:20
Alignment explanation
Indices: 900525--900562 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
900515 TGAAAACTTA
900525 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
900545 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
900563 CACCTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:901859 original size:32 final size:32
Alignment explanation
Indices: 901816--901879 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
901806 TATTAACTTA
* * *
901816 TATATATTTATAAGTATAATGTATACTTATAT
1 TATATACTTATAAGTAAAACGTATACTTATAT
*
901848 TATATACTTATAAGTAAAACGTATAGTTATAT
1 TATATACTTATAAGTAAAACGTATACTTATAT
901880 AAACTTGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (32 bp):
TATATACTTATAAGTAAAACGTATACTTATAT
Found at i:901922 original size:2 final size:2
Alignment explanation
Indices: 901915--902031 Score: 74
Period size: 2 Copynumber: 61.5 Consensus size: 2
901905 CATATAAACT
*
901915 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TT TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
901955 -A GTA TA -A TA TA TA T- TA TA TA TA CA TG TA T- TA TCA TA T- TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
* * *
901994 TCA TA -A CA TT TA TCA TA CA TA T- TA TA -A TA TA TA TA TA T
1 T-A TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
902032 TAATTTTTCC
Statistics
Matches: 90, Mismatches: 11, Indels: 28
0.70 0.09 0.22
Matches are distributed among these distances:
1 10 0.11
2 73 0.81
3 7 0.08
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:901964 original size:29 final size:29
Alignment explanation
Indices: 901914--902033 Score: 93
Period size: 29 Copynumber: 4.0 Consensus size: 29
901904 ACATATAAAC
901914 TTATATATATATATATATATATATATTAT
1 TTATATATATATATATATATATATATTAT
901943 TTATATAT-TATA-AGTATAATATATATTAT
1 TTATATATATATATA-TAT-ATATATATTAT
* * * **
901972 ATATACATGTAT-TATCATATTATCATAACAT
1 TTATATATATATATAT-ATA-TAT-ATATTAT
*
902003 TTATCATACATATTATAATATATATATATTA
1 TTAT-ATATATA-TAT-ATATATATATATTA
902034 ATTTTTCCTC
Statistics
Matches: 70, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
27 1 0.01
28 7 0.10
29 27 0.39
30 9 0.13
31 8 0.11
32 8 0.11
33 4 0.06
34 4 0.06
35 2 0.03
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (29 bp):
TTATATATATATATATATATATATATTAT
Found at i:901991 original size:23 final size:25
Alignment explanation
Indices: 901965--902033 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 25
901955 AGTATAATAT
*
901965 ATATTAT-ATATACATGTATTAT-C
1 ATATTATAATATACATATATTATAC
* * *
901988 ATATTATCATA-ACATTTATCATAC
1 ATATTATAATATACATATATTATAC
*
902012 ATATTATAATATATATATATTA
1 ATATTATAATATACATATATTA
902034 ATTTTTCCTC
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 16 0.43
24 14 0.38
25 7 0.19
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.46
Consensus pattern (25 bp):
ATATTATAATATACATATATTATAC
Found at i:904171 original size:153 final size:153
Alignment explanation
Indices: 903847--904162 Score: 632
Period size: 153 Copynumber: 2.1 Consensus size: 153
903837 AAGCAAATTT
903847 TATAAAATAAGAACATATAAAAGTCTAAAATGAGTAGAAACAAAATTTTAATTAAAAATATAAGA
1 TATAAAATAAGAACATATAAAAGTCTAAAATGAGTAGAAACAAAATTTTAATTAAAAATATAAGA
903912 AAATATTTAAAATATATATTAATTTAAAATTTTTGGAGTACGTGACAAGCATCATTTTACTGTCA
66 AAATATTTAAAATATATATTAATTTAAAATTTTTGGAGTACGTGACAAGCATCATTTTACTGTCA
903977 AATAATATCATTAATCTCAAAAA
131 AATAATATCATTAATCTCAAAAA
904000 TATAAAATAAGAACATATAAAAGTCTAAAATGAGTAGAAACAAAATTTTAATTAAAAATATAAGA
1 TATAAAATAAGAACATATAAAAGTCTAAAATGAGTAGAAACAAAATTTTAATTAAAAATATAAGA
904065 AAATATTTAAAATATATATTAATTTAAAATTTTTGGAGTACGTGACAAGCATCATTTTACTGTCA
66 AAATATTTAAAATATATATTAATTTAAAATTTTTGGAGTACGTGACAAGCATCATTTTACTGTCA
904130 AATAATATCATTAATCTCAAAAA
131 AATAATATCATTAATCTCAAAAA
904153 TATAAAATAA
1 TATAAAATAA
904163 AGTAATATAG
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 163 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.33
Consensus pattern (153 bp):
TATAAAATAAGAACATATAAAAGTCTAAAATGAGTAGAAACAAAATTTTAATTAAAAATATAAGA
AAATATTTAAAATATATATTAATTTAAAATTTTTGGAGTACGTGACAAGCATCATTTTACTGTCA
AATAATATCATTAATCTCAAAAA
Found at i:904939 original size:15 final size:15
Alignment explanation
Indices: 904919--904951 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
904909 GAAAACATTT
904919 AAAGAAAAATAAAAG
1 AAAGAAAAATAAAAG
*
904934 AAAGAAAAGTAAAAG
1 AAAGAAAAATAAAAG
904949 AAA
1 AAA
904952 AAGTAAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (15 bp):
AAAGAAAAATAAAAG
Found at i:905084 original size:12 final size:13
Alignment explanation
Indices: 905067--905095 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
905057 ATAAATTACA
905067 TAAAGATAATT-T
1 TAAAGATAATTCT
905079 TAAAGATAATTCT
1 TAAAGATAATTCT
905092 TAAA
1 TAAA
905096 ATTAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (13 bp):
TAAAGATAATTCT
Found at i:906328 original size:15 final size:15
Alignment explanation
Indices: 906308--906336 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
906298 TCTATATCAG
906308 ATAGTAGATTTAGTT
1 ATAGTAGATTTAGTT
906323 ATAGTAGATTTAGT
1 ATAGTAGATTTAGT
906337 ATTGACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
ATAGTAGATTTAGTT
Found at i:911691 original size:36 final size:37
Alignment explanation
Indices: 911610--911691 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
911600 GGTTAATAAT
* * *
911610 AATAATAATAATAAAATAAGTAAAATCATATTAACAGA
1 AATAATAATAAAAAAATAAG-AAAATAATATTAAAAGA
* *
911648 AAGAATAATAAAAAAATAA-AAAATAATATTAAAAGG
1 AATAATAATAAAAAAATAAGAAAATAATATTAAAAGA
*
911684 GATAATAA
1 AATAATAA
911692 AATAATAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
36 20 0.54
38 17 0.46
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (37 bp):
AATAATAATAAAAAAATAAGAAAATAATATTAAAAGA
Found at i:912942 original size:18 final size:19
Alignment explanation
Indices: 912912--912957 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
912902 AGAAGAAGAA
912912 AAAAATAATTTAA-AAAAG
1 AAAAATAATTTAATAAAAG
*
912930 AAAAAT-ATATTAATAAAAT
1 AAAAATAAT-TTAATAAAAG
912949 AATAAATAA
1 AA-AAATAA
912958 ATTGTAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 10 0.43
19 6 0.26
20 4 0.17
21 1 0.04
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATAATTTAATAAAAG
Found at i:913559 original size:22 final size:22
Alignment explanation
Indices: 913542--913608 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
913532 CTCGTATAAA
913542 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
913564 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
913586 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
913608 T
1 T
913609 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:913853 original size:30 final size:30
Alignment explanation
Indices: 913818--913880 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
913808 TCATATCGCG
*
913818 TAGACATAGT-ATTTCCATACCTTTAACACA
1 TAGACATA-TCATTTACATACCTTTAACACA
*
913848 TAGACATATCATTTACATACCTTTATCACA
1 TAGACATATCATTTACATACCTTTAACACA
913878 TAG
1 TAG
913881 TTCATATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (30 bp):
TAGACATATCATTTACATACCTTTAACACA
Found at i:913935 original size:29 final size:29
Alignment explanation
Indices: 913902--913973 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
913892 TTTTCTGCAT
* **
913902 ATTCAAGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
913931 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
913960 ATTCATGTCATGTA
1 ATTCATGTCATGTA
913974 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:914395 original size:68 final size:68
Alignment explanation
Indices: 914276--914427 Score: 200
Period size: 68 Copynumber: 2.2 Consensus size: 68
914266 TTTTTCTCAT
* * *
914276 GGGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAGTCTGGAATTTCATATACG
1 GGGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAA-ATCATATACG
914341 ATGA
65 ATGA
* * * * *
914345 GGGGGTATCGGTTCCCCCCC-TGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATCATATTCGT
1 GGGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAAATCATATACGA
914409 TGA
66 TGA
*
914412 -AGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
914428 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
66 15 0.20
67 11 0.15
68 29 0.39
69 19 0.26
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAAATCATATACGA
TGA
Found at i:914438 original size:21 final size:20
Alignment explanation
Indices: 914408--914449 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
914398 ATCATATTCG
* *
914408 TTGAAGGGTATCGGTTCCCC
1 TTGAAGGGTACCGATTCCCC
914428 TTGAATGGGTACCGATTCCCC
1 TTGAA-GGGTACCGATTCCCC
914449 T
1 T
914450 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.31
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Found at i:914440 original size:66 final size:67
Alignment explanation
Indices: 914282--914449 Score: 180
Period size: 68 Copynumber: 2.5 Consensus size: 67
914272 TCATGGGGGA
* * * *
914282 ATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAGTCTGGAATTTCATATACGATGAGG
1 ATCGGTT-CCCCCC-TGGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGATGAGA
914347 GGGT
64 GGGT
* * * *
914351 ATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTTGA-AG
1 ATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGATGAGAG
914414 GGT
65 GGT
* *
914417 ATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 ATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
914450 AGCCCGAAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
64 6 0.07
66 27 0.31
67 11 0.13
68 29 0.33
69 14 0.16
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (67 bp):
ATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGATGAGAGG
GT
Found at i:920487 original size:22 final size:22
Alignment explanation
Indices: 920462--920512 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
920452 CACCACAGCT
*
920462 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
920484 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
920506 CGTAGAA
1 CGTAGAA
920513 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:920513 original size:22 final size:22
Alignment explanation
Indices: 920470--920514 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
920460 CTCGTATAAA
920470 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
920492 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
920514 T
1 T
920515 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:920759 original size:30 final size:30
Alignment explanation
Indices: 920724--920786 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
920714 TCATATCGCG
*
920724 TAGACATAGT-ATTTCCATACCTTTAACACA
1 TAGACATA-TCATTTACATACCTTTAACACA
*
920754 TAGACATATCATTTACATACCTTTATCACA
1 TAGACATATCATTTACATACCTTTAACACA
920784 TAG
1 TAG
920787 TTCATATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.35
Consensus pattern (30 bp):
TAGACATATCATTTACATACCTTTAACACA
Found at i:920841 original size:29 final size:29
Alignment explanation
Indices: 920808--920879 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
920798 TTTTCTGCAT
* **
920808 ATTCAAGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
920837 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
920866 ATTCATGTCATGTA
1 ATTCATGTCATGTA
920880 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:921330 original size:67 final size:69
Alignment explanation
Indices: 921183--921334 Score: 209
Period size: 68 Copynumber: 2.2 Consensus size: 69
921173 TTTTCTCATG
* * *
921183 GGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAGTCTGGAATTTCATATACGA
1 GGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
*
921248 TGAG
66 TGAA
* * * * *
921252 GGGGTATCGGTTCCCCCCC-TGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGT
1 GGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
921315 TGAA
66 TGAA
921319 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
921335 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
67 27 0.36
68 29 0.39
69 18 0.24
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (69 bp):
GGGGTATCGGTTCCCCCCCTTAGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
TGAA
Found at i:921344 original size:21 final size:21
Alignment explanation
Indices: 921314--921356 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
921304 ATCATATTCG
* *
921314 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
921335 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
921356 T
1 T
921357 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:921346 original size:67 final size:67
Alignment explanation
Indices: 921183--921356 Score: 190
Period size: 67 Copynumber: 2.6 Consensus size: 67
921173 TTTTCTCATG
* * * *
921183 GGGGAATCGGTTCCCCCCCTTAGGGGTATCGATTCCCCTCAAGCAGTCTGGAATTTCATATACGA
1 GGGGTATCGGTT-CCCCCC-TGGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGA
*
921248 TGAG
64 TGAA
* * * *
921252 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGAT
921316 GAA
65 GAA
* *
921319 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
921357 AGCCCGAAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
65 6 0.07
67 39 0.42
68 29 0.32
69 18 0.20
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAGTCTGGAATATCATATACGATG
AA
Found at i:922144 original size:38 final size:38
Alignment explanation
Indices: 922092--922258 Score: 176
Period size: 38 Copynumber: 4.6 Consensus size: 38
922082 GAAAAAATCA
*
922092 TTTTTAAAATTATATATTATATATTTTCAAAAACATTG
1 TTTTTAAAACTATATATTATATATTTTCAAAAACATTG
*
922130 TTTTTAAAACTATATA--ATATATTTTCAAAAATATTG
1 TTTTTAAAACTATATATTATATATTTTCAAAAACATTG
** **
922166 --TCCAAAACTATATATTATATATATTTTTAAAACATT-
1 TTTTTAAAACTATATATTATATAT-TTTCAAAAACATTG
*
922202 TTTTAAAAACTATATATTATATATTATTC--AAA-A-TG
1 TTTTTAAAACTATATATTATATATT-TTCAAAAACATTG
922237 TTTTTAAAA-T-TATATTATATAT
1 TTTTTAAAACTATATATTATATAT
922259 ATATATATAT
Statistics
Matches: 111, Mismatches: 11, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
33 12 0.11
34 14 0.13
35 9 0.08
36 28 0.25
37 11 0.10
38 37 0.33
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.49
Consensus pattern (38 bp):
TTTTTAAAACTATATATTATATATTTTCAAAAACATTG
Found at i:922178 original size:34 final size:35
Alignment explanation
Indices: 922104--922234 Score: 111
Period size: 36 Copynumber: 3.6 Consensus size: 35
922094 TTTAAAATTA
* **
922104 TATATTATATATTTTCAAAAACATTGTTTTTAAAAC
1 TATATAATATATTTTCAAAAACATTG-TTCCAAAAC
*
922140 TATATAATATATTTTCAAAAATATTG-TCCAAAAC
1 TATATAATATATTTTCAAAAACATTGTTCCAAAAC
** * **
922174 TATATATTATATATATTTTTAAAACATTTTTTAAAAAC
1 TATATA--ATATAT-TTTCAAAAACATTGTTCCAAAAC
922212 TATATATTATATATTATTCAAAA
1 TATATA--ATATATT-TTCAAAA
922235 TGTTTTTAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
34 12 0.15
36 30 0.38
37 11 0.14
38 25 0.32
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.46
Consensus pattern (35 bp):
TATATAATATATTTTCAAAAACATTGTTCCAAAAC
Found at i:922259 original size:2 final size:2
Alignment explanation
Indices: 922247--922278 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
922237 TTTTTAAAAT
922247 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
922279 TCAAATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:922296 original size:50 final size:46
Alignment explanation
Indices: 922212--922310 Score: 146
Period size: 49 Copynumber: 2.1 Consensus size: 46
922202 TTTTAAAAAC
922212 TATATATTATATATTATTCAAAATGTTTTTAAAATTATATTATATATA
1 TATATATTATATATTATTCAAAATGTTTTTAAAATTATA-TAT-TATA
922260 TATATATATATATATATATTC-AAATGTTTTTAAAAATTATATATTATA
1 TATATAT-TATATAT-TATTCAAAATGTTTTT-AAAATTATATATTATA
922308 TAT
1 TAT
922311 GTTTTCAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
48 14 0.29
49 20 0.42
50 14 0.29
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (46 bp):
TATATATTATATATTATTCAAAATGTTTTTAAAATTATATATTATA
Found at i:922379 original size:28 final size:26
Alignment explanation
Indices: 922320--922384 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 26
922310 TGTTTTCAAA
922320 ATGTTTTC-AAAACTACATAATATAT
1 ATGTTTTCAAAAACTACATAATATAT
*
922345 ATGTTTTCAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTACATA--ATATAT
*
922373 ATTTTTTCAAAA
1 ATGTTTTCAAAA
922385 TGTTTTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 8 0.23
26 10 0.29
28 17 0.49
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (26 bp):
ATGTTTTCAAAAACTACATAATATAT
Found at i:922389 original size:64 final size:64
Alignment explanation
Indices: 922283--922424 Score: 180
Period size: 62 Copynumber: 2.2 Consensus size: 64
922273 ATATATTCAA
* * * *
922283 ATGTTTTTAAAAATTATATATTATATATGTTTTCAAAATG-TTTTCAAAACTACATA-ATATAT
1 ATGTTTTCAAAAACTATATATTATATATGTTTTCAAAATGTTTTTAAAAACTACATATATATAC
* *
922345 ATGTTTTCAAAAACTATATATTATATATATTTTTTCAAAATGTTTTTTAAAAACTATATATTATA
1 ATGTTTTCAAAAACTATATA-T-TATATATGTTTTCAAAATG-TTTTTAAAAACTACATA-TATA
922410 TAC
62 TAC
922413 ATGTTTTCAAAA
1 ATGTTTTCAAAA
922425 TGTTTTTTAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
62 18 0.26
63 1 0.01
64 18 0.26
66 14 0.21
68 17 0.25
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (64 bp):
ATGTTTTCAAAAACTATATATTATATATGTTTTCAAAATGTTTTTAAAAACTACATATATATAC
Found at i:922399 original size:40 final size:40
Alignment explanation
Indices: 922348--922464 Score: 207
Period size: 40 Copynumber: 2.9 Consensus size: 40
922338 AATATATATG
* *
922348 TTTTCAAAAACTATATATTATATATATTTTTTCAAAATGT
1 TTTTTAAAAACTATATATTATATATATGTTTTCAAAATGT
*
922388 TTTTTAAAAACTATATATTATATACATGTTTTCAAAATGT
1 TTTTTAAAAACTATATATTATATATATGTTTTCAAAATGT
922428 TTTTTAAAAACTATATATTATATATATGTTTTCAAAA
1 TTTTTAAAAACTATATATTATATATATGTTTTCAAAA
922465 CTATATAATA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (40 bp):
TTTTTAAAAACTATATATTATATATATGTTTTCAAAATGT
Found at i:922464 original size:27 final size:27
Alignment explanation
Indices: 922429--922493 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
922419 TCAAAATGTT
*
922429 TTTTAAAAACTATATATTATATATATG
1 TTTTAAAAACTATATAATATATATATG
*
922456 TTTTCAAAACTATATAATATATATATG
1 TTTTAAAAACTATATAATATATATATG
922483 TTTTTAAAAAC
1 -TTTTAAAAAC
922494 CGATTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 25 0.74
28 9 0.26
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (27 bp):
TTTTAAAAACTATATAATATATATATG
Found at i:922556 original size:26 final size:26
Alignment explanation
Indices: 922496--922558 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
922486 TTAAAAACCG
922496 ATTTAAAAAAAAAAAACAAACTGTAT
1 ATTTAAAAAAAAAAAACAAACTGTAT
* *
922522 GTTTCAAAAAAACAAAAACTATAC-G-AT
1 ATTT-AAAAAAA-AAAAAC-AAACTGTAT
922549 ATTTAAAAAA
1 ATTTAAAAAA
922559 CTCCGGACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 9 0.29
27 12 0.39
28 7 0.23
29 3 0.10
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (26 bp):
ATTTAAAAAAAAAAAACAAACTGTAT
Found at i:925679 original size:31 final size:31
Alignment explanation
Indices: 925633--925710 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
925623 TTCAATGTCC
* *
925633 AAGTGACCAAAACTTAATGAAACAATAACGT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
* * *
925664 AAGTTACCAGAACTTAATAAAACGATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
*
925695 AAGAGACCAAAACTTA
1 AAGTGACCAAAACTTA
925711 TGTTTATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.19
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:931144 original size:20 final size:21
Alignment explanation
Indices: 931119--931211 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
931109 TTTTCCCAAT
*
931119 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
931139 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
931160 TCGCAATGTGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
931180 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
931201 TCGCAATGCGA
1 TCGCAATGCGA
931212 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:931164 original size:41 final size:41
Alignment explanation
Indices: 931119--931211 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
931109 TTTTCCCAAT
931119 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
931160 TCGCAATGTGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
931201 TCGCAATGCGA
1 TCGCAATGCGA
931212 TACTGACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:931224 original size:41 final size:41
Alignment explanation
Indices: 931138--931272 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
931128 GAATAAGTAA
* * *
931138 ATCGCAACGCGAATTGGGAAAATCGCAATGTGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGAG-ATACTG-ACT
*
931179 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
* * ** * *
931220 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGAGATACTGACT
*
931261 TTCGCAACGCGA
1 ATCGCAACGCGA
931273 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
Found at i:931225 original size:20 final size:20
Alignment explanation
Indices: 931200--931294 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
931190 AATTGGGAAA
*
931200 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
931220 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
931241 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
931261 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
931281 TTCGCAACGCGATA
1 ATCGCAACGCGATA
931295 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:931510 original size:22 final size:22
Alignment explanation
Indices: 931482--931525 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
931472 CACTCTCTCA
931482 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
931504 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
931526 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:931755 original size:19 final size:19
Alignment explanation
Indices: 931731--931781 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
931721 ATCAACCAAG
931731 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
931750 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
931769 AATCGCAACGCGA
1 AATCGCAACGCGA
931782 TTTTAGTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.41, C:0.27, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGCA
Found at i:931833 original size:20 final size:20
Alignment explanation
Indices: 931808--931845 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
931798 CGATTCTCTC
931808 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
931828 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
931846 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:933180 original size:18 final size:18
Alignment explanation
Indices: 933159--933203 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
933149 TCCACTTCGG
*
933159 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
933177 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
933195 GAGCCATCA
1 GAGCCATCA
933204 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:933739 original size:19 final size:20
Alignment explanation
Indices: 933685--933751 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
933675 TAGTTTACTT
* *
933685 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
933705 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
933725 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
933744 TCGCAACG
1 TCGCAACG
933752 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:933817 original size:14 final size:14
Alignment explanation
Indices: 933798--933919 Score: 109
Period size: 14 Copynumber: 7.9 Consensus size: 14
933788 TTGTGTTTCG
933798 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
933812 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
933828 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
933844 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
933860 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
933876 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
933892 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
933908 CGTTGCGATTTT
1 CGTTGCGATTTT
933920 CATTTCGCAT
Statistics
Matches: 90, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
14 45 0.50
16 12 0.13
18 33 0.37
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:933832 original size:32 final size:32
Alignment explanation
Indices: 933793--933935 Score: 268
Period size: 32 Copynumber: 4.4 Consensus size: 32
933783 GCGATTTGTG
933793 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
933825 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
933857 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
933889 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
*
933922 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
933936 AGCCATTTCC
Statistics
Matches: 109, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 91 0.83
33 18 0.17
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:933954 original size:20 final size:19
Alignment explanation
Indices: 933920--933974 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
933910 TTGCGATTTT
*
933920 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
933939 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
933959 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
933975 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:935861 original size:14 final size:14
Alignment explanation
Indices: 935842--935877 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
935832 ATTGTTTAAT
935842 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
935856 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
935870 TGATTTGT
1 TGATTTGT
935878 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:936003 original size:14 final size:14
Alignment explanation
Indices: 935984--936037 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
935974 CGAAATGGCT
935984 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
935998 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
936017 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
936031 ATCGCAA
1 ATCGCAA
936038 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Done.