Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold262
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: 1141274
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 4 of 8
Found at i:405937 original size:188 final size:188
Alignment explanation
Indices: 405620--405998 Score: 659
Period size: 188 Copynumber: 2.0 Consensus size: 188
405610 TCCAGTTAAG
*
405620 ATAAAAGTTTATAACCTAAATACAAGAAAACTAATTTAAGAATAATTAGCAATTATAGGTTATGC
1 ATAAAAGTTTATAACCTAAACACAAGAAAACTAATTTAAGAATAATTAGCAATTATAGGTTATGC
* *
405685 AATTGACTTAAAAAGATATAGGTTTTAAATGTCCCTTATATTCATATAGAATTGTTGAAGCTAGA
66 AATTGACTTAAAAAGATATAGGTTTTAAATGTCCCTTATATTCATATAAAATTATTGAAGCTAGA
* * *
405750 TATGTTAAGTTTCTTATGGATTGTGAGTCCAGTGGAATTGGTTTTCCTTGAAAGATTA
131 AATGCTAAGTTTCTTATGGATTGTGAGTCCAGTAGAATTGGTTTTCCTTGAAAGATTA
405808 ATAAAAGTTTATAACCTAAACACAAGAAAACTAATTTAAGAATAATTAGCAATTATAGGTTATGC
1 ATAAAAGTTTATAACCTAAACACAAGAAAACTAATTTAAGAATAATTAGCAATTATAGGTTATGC
* * * *
405873 AATTGACTTAAAAGGATATAGGTTTTACATGTTCCTTATATTCGTATAAAATTATTGAAGCTAGA
66 AATTGACTTAAAAAGATATAGGTTTTAAATGTCCCTTATATTCATATAAAATTATTGAAGCTAGA
*
405938 AATGCTAAGTTTCTTATGGATTGTGAGTCCAGTAGAATTGGTTTTCCTTGTAAGATTA
131 AATGCTAAGTTTCTTATGGATTGTGAGTCCAGTAGAATTGGTTTTCCTTGAAAGATTA
405996 ATA
1 ATA
405999 TTGAGAAATA
Statistics
Matches: 180, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
188 180 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (188 bp):
ATAAAAGTTTATAACCTAAACACAAGAAAACTAATTTAAGAATAATTAGCAATTATAGGTTATGC
AATTGACTTAAAAAGATATAGGTTTTAAATGTCCCTTATATTCATATAAAATTATTGAAGCTAGA
AATGCTAAGTTTCTTATGGATTGTGAGTCCAGTAGAATTGGTTTTCCTTGAAAGATTA
Found at i:406865 original size:140 final size:139
Alignment explanation
Indices: 406614--406889 Score: 498
Period size: 140 Copynumber: 2.0 Consensus size: 139
406604 TTGGAAAATC
* *
406614 AATATATGGACTTAAAACAAGCATTGCACTAATGGTATATAAAGTTTCATAATATTGTACATCAT
1 AATATATGGACTAAAAACAAGCATTGCACTAATGCTATATAAAGTTTCATAATATTGTACATCAT
406679 TTGGTTTACTAAAGATGTCATTGATCAGTGTATATACTTTAAAGTCAGTAAGAATAAGTTTCATA
66 TTGGTTTACTAAAGATGTCATTGATCAGTGTATATACTTTAAAGTCAGTAAGAATAAGTTTCATA
406744 ATTTTACTA
131 ATTTTACTA
*
406753 AATATATGGACTAAAAACAAGCATTGCACTAATGCTATATAAAGTTTCATAATGTTGTGACATCA
1 AATATATGGACTAAAAACAAGCATTGCACTAATGCTATATAAAGTTTCATAATATTGT-ACATCA
* *
406818 TTTGGTTTACTAAAGATGTCGTTGATCAGTGTATATACTTTAAAGTCAGTAAGAGTAAGTTTCAT
65 TTTGGTTTACTAAAGATGTCATTGATCAGTGTATATACTTTAAAGTCAGTAAGAATAAGTTTCAT
406883 AATTTTA
130 AATTTTA
406890 GTCTTTTAAG
Statistics
Matches: 131, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
139 55 0.42
140 76 0.58
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (139 bp):
AATATATGGACTAAAAACAAGCATTGCACTAATGCTATATAAAGTTTCATAATATTGTACATCAT
TTGGTTTACTAAAGATGTCATTGATCAGTGTATATACTTTAAAGTCAGTAAGAATAAGTTTCATA
ATTTTACTA
Found at i:408053 original size:15 final size:16
Alignment explanation
Indices: 408035--408066 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
408025 AATTAAGGTG
408035 ATCTTATTT-AAATAA
1 ATCTTATTTAAAATAA
408050 ATCTTATTTAAAATAA
1 ATCTTATTTAAAATAA
408066 A
1 A
408067 ACTCTAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
ATCTTATTTAAAATAA
Found at i:410214 original size:4 final size:4
Alignment explanation
Indices: 410200--410241 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
410190 TGTAAGCATG
*
410200 TGTA CGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
410242 AGCTACCTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.24, C:0.02, G:0.26, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:410509 original size:21 final size:21
Alignment explanation
Indices: 410469--410509 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
410459 TGTTTTTAAA
* * *
410469 AATTTTATTTAAATACATTAT
1 AATTATATTTAAAAAAATTAT
410490 AATTATATTTAAAAAAATTA
1 AATTATATTTAAAAAAATTA
410510 ATTTATTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTATATTTAAAAAAATTAT
Found at i:411579 original size:50 final size:50
Alignment explanation
Indices: 411445--411676 Score: 331
Period size: 50 Copynumber: 4.6 Consensus size: 50
411435 AGTTGTTGTC
* * * * * *
411445 ATTGTTGACTATCCTTCACCAATCTTTGACAATAGAGTGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
411495 ATTGTTGACGA-TCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
411544 ATTGTTGATGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * * *
411594 ATTGTTGACGATTCTTCATCAACCTTTGGCAAATGGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGAC-AATAGAGAGAGGTGGCCATA
*
411645 ATTGTTGACGATTCTTCGCCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
411677 ATGTGGCCAT
Statistics
Matches: 163, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
49 42 0.26
50 76 0.47
51 45 0.28
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:411670 original size:101 final size:99
Alignment explanation
Indices: 411445--411676 Score: 347
Period size: 99 Copynumber: 2.3 Consensus size: 99
411435 AGTTGTTGTC
* * * * * *
411445 ATTGTTGACTATCCTTCACCAATCTTTGACAATAGAGTGAGGTGGTCGTAATTGTTGACGATCTT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATCTT
411510 CACCAACCTTTGACAATAGAGAGAGGTGGCCATT
66 CACCAACCTTTGACAATAGAGAGAGGTGGCCATT
*
411544 ATTGTTGATGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTCT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGA-TCT
* * *
411609 TCATCAACCTTTGGCAAATGGAGAGAGGTGGCCATT
65 TCACCAACCTTTGAC-AATAGAGAGAGGTGGCCATT
*
411645 ATTGTTGACGATTCTTCGCCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
411677 ATGTGGCCAT
Statistics
Matches: 119, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 54 0.45
100 16 0.13
101 49 0.41
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (99 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATCTT
CACCAACCTTTGACAATAGAGAGAGGTGGCCATT
Found at i:416162 original size:50 final size:50
Alignment explanation
Indices: 416087--416316 Score: 379
Period size: 50 Copynumber: 4.6 Consensus size: 50
416077 AGTTGTTGCC
* * * *
416087 ATTGTTGACTATCCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
416137 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
416187 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* * *
416237 ATTGTTGACGATTCTGCACCAACCTTTGACAAATGGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGAC-AATAGAGAGAGGTGGCCATA
416288 ATTGTTGACGATTCTTCACCAACCTTTGA
1 ATTGTTGACGATTCTTCACCAACCTTTGA
416317 TAAATGTGGC
Statistics
Matches: 169, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
50 123 0.73
51 46 0.27
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:418075 original size:32 final size:32
Alignment explanation
Indices: 418039--418100 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
418029 AAAAAAATCA
418039 GCTAACATAGCTTTCAAGTTCCTTAAAGAATG
1 GCTAACATAGCTTTCAAGTTCCTTAAAGAATG
*
418071 GCTAACGTAGCTTTCAAGTTCCTTAAAGAA
1 GCTAACATAGCTTTCAAGTTCCTTAAAGAA
418101 AATATTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (32 bp):
GCTAACATAGCTTTCAAGTTCCTTAAAGAATG
Found at i:418792 original size:25 final size:26
Alignment explanation
Indices: 418743--418826 Score: 88
Period size: 25 Copynumber: 3.3 Consensus size: 26
418733 TACTAATTTT
*
418743 AACAAACAACAAGTTACTATTTTTGACA
1 AACAAA-AACAA-TCACTATTTTTGACA
418771 AACAAAAA-AATCACTATTTTTGACA
1 AACAAAAACAATCACTATTTTTGACA
*
418796 TAA-AAAAACCATCA-T-TTTTT-ACA
1 -AACAAAAACAATCACTATTTTTGACA
418819 AACAAAAA
1 AACAAAAA
418827 TAATGAATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
22 2 0.04
23 8 0.16
24 5 0.10
25 20 0.39
26 8 0.16
27 2 0.04
28 6 0.12
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.27
Consensus pattern (26 bp):
AACAAAAACAATCACTATTTTTGACA
Found at i:418825 original size:23 final size:22
Alignment explanation
Indices: 418761--418826 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 22
418751 ACAAGTTACT
*
418761 ATTTTTGACAAACAAAAAAATC
1 ATTTTTTACAAACAAAAAAATC
*
418783 ACTATTTTTGACATAA-AAAAACCATC
1 A-T-TTTTT-ACA-AACAAAAA-AATC
418809 ATTTTTTACAAACAAAAA
1 ATTTTTTACAAACAAAAA
418827 TAATGAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
22 3 0.08
23 9 0.25
24 9 0.25
25 9 0.25
26 6 0.17
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (22 bp):
ATTTTTTACAAACAAAAAAATC
Found at i:418848 original size:48 final size:49
Alignment explanation
Indices: 418761--418855 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 49
418751 ACAAGTTACT
*
418761 ATTTTTGACAAACAAAAAAATCACTATTTTTGACATAAAAA-AACCATC
1 ATTTTTGACAAACAAAAAAATCAATATTTTTGACATAAAAATAACCATC
* * *
418809 ATTTTTTACAAACAAAAATAATGAAT-TTTATTGA-TTAAAAATAACCA
1 ATTTTTGACAAACAAAAA-AATCAATATTT-TTGACATAAAAATAACCA
418856 CACACCATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
48 26 0.65
49 14 0.35
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.33
Consensus pattern (49 bp):
ATTTTTGACAAACAAAAAAATCAATATTTTTGACATAAAAATAACCATC
Found at i:419379 original size:15 final size:16
Alignment explanation
Indices: 419359--419392 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
419349 TTTTTAAATT
419359 TTTATGTTT-AGATCA
1 TTTATGTTTCAGATCA
*
419374 TTTATGTTTCAGGTCA
1 TTTATGTTTCAGATCA
419390 TTT
1 TTT
419393 TTAATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.56
Consensus pattern (16 bp):
TTTATGTTTCAGATCA
Found at i:419674 original size:5 final size:5
Alignment explanation
Indices: 419664--419712 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
419654 ATTTTTTTCT
*
419664 AATTA AATT- AATGTA AATTA AATTTA AATTA AAATA AATT- AATTA AATT
1 AATTA AATTA AAT-TA AATTA AA-TTA AATTA AATTA AATTA AATTA AATT
419713 TTTTAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 7 0.18
5 23 0.61
6 8 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (5 bp):
AATTA
Found at i:419682 original size:10 final size:9
Alignment explanation
Indices: 419663--419712 Score: 55
Period size: 9 Copynumber: 5.1 Consensus size: 9
419653 AATTTTTTTC
419663 TAATTAAAT
1 TAATTAAAT
419672 TAATGTAAAT
1 TAAT-TAAAT
419682 TAAATTTAAAT
1 T-AA-TTAAAT
*
419693 TAAAATAAAT
1 T-AATTAAAT
419703 TAATTAAAT
1 TAATTAAAT
419712 T
1 T
419713 TTTTAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 12 0.33
10 12 0.33
11 11 0.31
12 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (9 bp):
TAATTAAAT
Found at i:419692 original size:21 final size:19
Alignment explanation
Indices: 419663--419712 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
419653 AATTTTTTTC
**
419663 TAATTAAATTAATGTAAAT
1 TAATTAAATTAAAATAAAT
419682 TAAATTTAAATTAAAATAAAT
1 T-AA-TTAAATTAAAATAAAT
419703 TAATTAAATT
1 TAATTAAATT
419713 TTTTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.30
20 4 0.15
21 15 0.56
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAATTAAATTAAAATAAAT
Found at i:421186 original size:14 final size:14
Alignment explanation
Indices: 421167--421222 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
421157 TATTTTTATC
421167 TTAAATTTAATATA
1 TTAAATTTAATATA
**
421181 TTAAATACGAA-A-A
1 TTAAAT-TTAATATA
421194 TTAAATTTAATATA
1 TTAAATTTAATATA
**
421208 TTAAAAATAATATA
1 TTAAATTTAATATA
421222 T
1 T
421223 ATTTTTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
12 2 0.06
13 8 0.24
14 21 0.64
15 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (14 bp):
TTAAATTTAATATA
Found at i:426622 original size:15 final size:15
Alignment explanation
Indices: 426599--426644 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
426589 ACATCTTCCC
*
426599 ATTAAATATTAATTA
1 ATTATATATTAATTA
*
426614 ATTATATATTATTTA
1 ATTATATATTAATTA
426629 ATCTATA-ATTAATTA
1 AT-TATATATTAATTA
426644 A
1 A
426645 ACCATGATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATATATTAATTA
Found at i:426732 original size:20 final size:18
Alignment explanation
Indices: 426684--426732 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
426674 TCTAGCAATA
426684 AATTTTTTTAAAAAACTT
1 AATTTTTTTAAAAAACTT
*
426702 AATATTTTTAACTAAAA-TT
1 AATTTTTTTAA--AAAACTT
426721 AATTTTTATTAA
1 AATTTTT-TTAA
426733 TTTTAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 10 0.38
19 8 0.31
20 8 0.31
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTTTTTAAAAAACTT
Found at i:426966 original size:12 final size:12
Alignment explanation
Indices: 426949--426973 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
426939 ATCATTACTC
426949 TCTTTTTTTTTT
1 TCTTTTTTTTTT
426961 TCTTTTTTTTTT
1 TCTTTTTTTTTT
426973 T
1 T
426974 TTCAATAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:427191 original size:29 final size:30
Alignment explanation
Indices: 427159--427224 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
427149 ATAATTTTTT
*
427159 AAATAAATTTTTATAT-TTT-TATTACATTA
1 AAATAAATTTTTA-ATCTTTACATTACATTA
* *
427188 AAATAATTTTTTAATCTTTACATTACATTG
1 AAATAAATTTTTAATCTTTACATTACATTA
427218 AAATAAA
1 AAATAAA
427225 CCTTTAATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 2 0.06
29 15 0.48
30 14 0.45
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (30 bp):
AAATAAATTTTTAATCTTTACATTACATTA
Found at i:427231 original size:30 final size:30
Alignment explanation
Indices: 427179--427237 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
427169 TTATATTTTT
***
427179 ATTACATTAAAATAATTTTTTAATCTTTAC
1 ATTACATTAAAATAAACCTTTAATCTTTAC
* *
427209 ATTACATTGAAATAAACCTTTAATGTTTA
1 ATTACATTAAAATAAACCTTTAATCTTTA
427238 AGTTTTATCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (30 bp):
ATTACATTAAAATAAACCTTTAATCTTTAC
Found at i:430403 original size:12 final size:12
Alignment explanation
Indices: 430388--430416 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
430378 CTTTTTCAAC
430388 ATATACATACAT
1 ATATACATACAT
430400 ATATACATACAT
1 ATATACATACAT
430412 ATATA
1 ATATA
430417 TATATATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (12 bp):
ATATACATACAT
Found at i:430411 original size:16 final size:16
Alignment explanation
Indices: 430390--430426 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
430380 TTTTCAACAT
430390 ATACATACATATATAC
1 ATACATACATATATAC
* *
430406 ATACATATATATATAT
1 ATACATACATATATAC
430422 ATACA
1 ATACA
430427 CTTTTTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (16 bp):
ATACATACATATATAC
Found at i:430461 original size:44 final size:44
Alignment explanation
Indices: 430408--430495 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
430398 ATATATACAT
430408 ACATATATATATATATACACTTTTTAACATCACTATAGTATAAA
1 ACATATATATATATATACACTTTTTAACATCACTATAGTATAAA
*
430452 ACATATATATATATATACACTTTTTAACGTCACTATAGTATAAA
1 ACATATATATATATATACACTTTTTAACATCACTATAGTATAAA
430496 TAAACAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.39
Consensus pattern (44 bp):
ACATATATATATATATACACTTTTTAACATCACTATAGTATAAA
Found at i:430946 original size:21 final size:23
Alignment explanation
Indices: 430898--430946 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
430888 ATAAAGTCTT
430898 TTTAAAAAAATTATGATTTAAAA
1 TTTAAAAAAATTATGATTTAAAA
*
430921 -ATAAAAAAATTAT-A-TTAAAA
1 TTTAAAAAAATTATGATTTAAAA
430941 TTTAAA
1 TTTAAA
430947 TATTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.26
21 5 0.22
22 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TTTAAAAAAATTATGATTTAAAA
Found at i:431216 original size:21 final size:21
Alignment explanation
Indices: 431175--431217 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
431165 TTAGTAATTT
* *
431175 TAAATTTTATAAATAAAAAAA
1 TAAATTTTAAAAAAAAAAAAA
431196 TAAA-TTTAAAAAAAAATAAAA
1 TAAATTTTAAAAAAAAA-AAAA
431217 T
1 T
431218 TTGATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAATTTTAAAAAAAAAAAAA
Found at i:431667 original size:11 final size:12
Alignment explanation
Indices: 431642--431678 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
431632 TATTTATTTA
431642 TTAAATAATAAT
1 TTAAATAATAAT
431654 TTAAATAA-AAT
1 TTAAATAATAAT
*
431665 TTAAATTATAAT
1 TTAAATAATAAT
431677 TT
1 TT
431679 TTTTTACTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTAAATAATAAT
Found at i:431863 original size:13 final size:13
Alignment explanation
Indices: 431845--431915 Score: 50
Period size: 13 Copynumber: 5.9 Consensus size: 13
431835 TTATATAATT
431845 TTATATATTATAA
1 TTATATATTATAA
431858 TTATAT-TTA-AA
1 TTATATATTATAA
*
431869 ATA-ATA-TAT-A
1 TTATATATTATAA
*
431879 TT-TATA-TAAAA
1 TTATATATTATAA
431890 TTATTATATTAATAA
1 TTA-TATATT-ATAA
431905 TT-TATATTATA
1 TTATATATTATA
431916 TAAATTTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
10 11 0.24
11 7 0.15
12 6 0.13
13 16 0.35
14 1 0.02
15 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTATATATTATAA
Found at i:431887 original size:15 final size:15
Alignment explanation
Indices: 431832--431922 Score: 59
Period size: 15 Copynumber: 6.3 Consensus size: 15
431822 TCTTTATAAG
*
431832 TATTTATATAAT-TT
1 TATTTATATAATATA
*
431846 TATATATTATAAT-TA
1 TATTTA-TATAATATA
*
431861 TATTTAAAATAATATA
1 TATTT-ATATAATATA
*
431877 TATTTATATAAAAT-
1 TATTTATATAATATA
*
431891 TA-TTATATTA-ATA
1 TATTTATATAATATA
*
431904 -ATTTATATTATATA
1 TATTTATATAATATA
*
431918 AATTT
1 TATTT
431923 TAATATAGTT
Statistics
Matches: 63, Mismatches: 7, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
12 3 0.05
13 15 0.24
14 10 0.16
15 27 0.43
16 8 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTTATATAATATA
Found at i:431924 original size:16 final size:16
Alignment explanation
Indices: 431875--431924 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 16
431865 TAAAATAATA
431875 TATATTTATATAAAATTAT
1 TATA-TTATAT-AAATT-T
431894 TATATTA-AT-AA-TT
1 TATATTATATAAATTT
431907 TATATTATATAAATTT
1 TATATTATATAAATTT
431923 TA
1 TA
431925 ATATAGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 8 0.29
14 3 0.11
15 4 0.14
16 4 0.14
17 2 0.07
18 3 0.11
19 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTATATAAATTT
Found at i:432186 original size:15 final size:14
Alignment explanation
Indices: 432166--432206 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
432156 AAAGTTAATT
432166 AATATATTATTTGTA
1 AATATATTATTT-TA
*
432181 AATATATTATATTA
1 AATATATTATTTTA
*
432195 AATATAATATTT
1 AATATATTATTT
432207 AATAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
AATATATTATTTTA
Found at i:432198 original size:14 final size:15
Alignment explanation
Indices: 432166--432200 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
432156 AAAGTTAATT
*
432166 AATATATTATTTGTA
1 AATATATTATATGTA
432181 AATATATTATAT-TA
1 AATATATTATATGTA
432195 AATATA
1 AATATA
432201 ATATTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
AATATATTATATGTA
Found at i:432868 original size:3 final size:3
Alignment explanation
Indices: 432860--432915 Score: 87
Period size: 3 Copynumber: 18.7 Consensus size: 3
432850 TCAAATCACA
*
432860 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AATT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
432906 AAT AA- AAT AA
1 AAT AAT AAT AA
432916 AATGGGTCTC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:433166 original size:11 final size:11
Alignment explanation
Indices: 433150--433299 Score: 51
Period size: 11 Copynumber: 13.5 Consensus size: 11
433140 ATAATTTATG
433150 TATTTATTTTA
1 TATTTATTTTA
*
433161 TATTTATATTA
1 TATTTATTTTA
* *
433172 TTTTTTAAATATTA
1 -TATTT--ATTTTA
*
433186 TAATTATATTTA
1 TATTTAT-TTTA
** *
433198 -AAATATTATA
1 TATTTATTTTA
**
433208 TATAAATTTTA
1 TATTTATTTTA
*
433219 -ATATATTTATA
1 TATTTATTT-TA
*
433230 TATTTATATTA
1 TATTTATTTTA
433241 TATTTA-TTTA
1 TATTTATTTTA
* * *
433251 TTTTTATATAA
1 TATTTATTTTA
433262 TATTATATTTTA
1 TATT-TATTTTA
433274 -A-TTATTTT-
1 TATTTATTTTA
*
433282 TATATCATATTTA
1 TAT-TTAT-TTTA
433295 TATTT
1 TATTT
433300 TATAAAAATA
Statistics
Matches: 103, Mismatches: 22, Indels: 27
0.68 0.14 0.18
Matches are distributed among these distances:
9 7 0.07
10 19 0.18
11 43 0.42
12 22 0.21
13 6 0.06
14 6 0.06
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTATTTTA
Found at i:433186 original size:19 final size:19
Alignment explanation
Indices: 433164--433270 Score: 76
Period size: 20 Copynumber: 5.4 Consensus size: 19
433154 TATTTTATAT
433164 TTATATTATTTTTTAAATA
1 TTATATTATTTTTTAAATA
* *
433183 TTATAATTATATTTAAAATA
1 TTAT-ATTATTTTTTAAATA
**
433203 TTATATATAAATTTTAATATA
1 TTATAT-TATTTTTTAA-ATA
*
433224 TT-TATATATTTATATTATAT-
1 TTATAT-TATTT-T-TTAAATA
433244 TTAT-TTATTTTTATATAATA
1 TTATATTATTTTT-TA-AATA
433264 TTATATT
1 TTATATT
433271 TTAATTATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
17 1 0.01
18 3 0.04
19 13 0.19
20 39 0.56
21 11 0.16
22 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATATTATTTTTTAAATA
Found at i:433193 original size:31 final size:29
Alignment explanation
Indices: 433158--433286 Score: 97
Period size: 27 Copynumber: 4.4 Consensus size: 29
433148 TGTATTTATT
*
433158 TTATATTTATATTATTT-TTTAAATATTATAA
1 TTATATTTATA-TATTTATATAAAT-TT-TAA
*
433189 TTATATTTAAAATATTATATATAAATTTTAA
1 TTATATTT-ATATATT-TATATAAATTTTAA
* *
433220 -TATATTTATATATTTATAT-TATATTTAT
1 TTATATTTATATATTTATATAAAT-TTTAA
* * *
433248 TTATTTTTATATA-ATAT-TATATTTTAA
1 TTATATTTATATATTTATATAAATTTTAA
*
433275 TTATTTTTATAT
1 TTATATTTATAT
433287 CATATTTATA
Statistics
Matches: 84, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
27 19 0.23
28 15 0.18
29 17 0.20
30 7 0.08
31 15 0.18
32 5 0.06
33 6 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
TTATATTTATATATTTATATAAATTTTAA
Found at i:433230 original size:27 final size:28
Alignment explanation
Indices: 433180--433301 Score: 97
Period size: 27 Copynumber: 4.3 Consensus size: 28
433170 TATTTTTTAA
*
433180 ATATTATAATTATATTTAAAATATTATATAT
1 ATATTTTAATTATATTT---ATATTATATAT
* *
433211 AAATTTTAA-TATATTTATA-TATTTAT
1 ATATTTTAATTATATTTATATTATATAT
* * *
433237 ATTATATTTATTTATTTTTATATAATAT-T
1 A-TAT-TTTAATTATATTTATATTATATAT
* * *
433266 ATATTTTAATTATTTTTATATCATATTT
1 ATATTTTAATTATATTTATATTATATAT
433294 ATATTTTA
1 ATATTTTA
433302 TAAAAATATA
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
26 7 0.09
27 25 0.33
28 16 0.21
29 11 0.14
30 10 0.13
31 7 0.09
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
ATATTTTAATTATATTTATATTATATAT
Found at i:433473 original size:19 final size:20
Alignment explanation
Indices: 433436--433473 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
433426 AAGAGCAGAA
* *
433436 AAAATAAAATTAATTTTTTT
1 AAAATAAAATAAATATTTTT
433456 AAAA-AAAATAAATATTTT
1 AAAATAAAATAAATATTTT
433474 ATTTTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATAAAATAAATATTTTT
Found at i:433478 original size:25 final size:24
Alignment explanation
Indices: 433434--433492 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
433424 ATAAGAGCAG
433434 AAAAAATAAAATTAATTTTTTTAA
1 AAAAAATAAAATTAATTTTTTTAA
*
433458 AAAAAATAAATATT-TTATTTTTTAA
1 AAAAAATAAA-ATTAAT-TTTTTTAA
433483 AATAAAATAA
1 AA-AAAATAA
433493 TTAATCCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 11 0.35
25 13 0.42
26 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAAAATAAAATTAATTTTTTTAA
Found at i:434390 original size:14 final size:14
Alignment explanation
Indices: 434366--434399 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
434356 AAATTTAAAA
*
434366 TCTTTCTTTTTTTT
1 TCTTTCCTTTTTTT
*
434380 TTTTTCCTTTTTTT
1 TCTTTCCTTTTTTT
434394 TCTTTC
1 TCTTTC
434400 TTTGTTAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TCTTTCCTTTTTTT
Found at i:435840 original size:18 final size:18
Alignment explanation
Indices: 435817--435856 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
435807 GACGATAAAC
435817 CAAATGGTGTGGTGAAAT
1 CAAATGGTGTGGTGAAAT
* *
435835 CAAATGGTTTGGTGAATT
1 CAAATGGTGTGGTGAAAT
435853 CAAA
1 CAAA
435857 AGGTAATCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (18 bp):
CAAATGGTGTGGTGAAAT
Found at i:438614 original size:2 final size:2
Alignment explanation
Indices: 438607--438632 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
438597 ACATATCTTC
438607 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
438633 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:438637 original size:2 final size:2
Alignment explanation
Indices: 438632--438658 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
438622 TCTCTCTCTC
438632 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
438659 CAAAAATTTA
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:438934 original size:22 final size:23
Alignment explanation
Indices: 438909--438978 Score: 92
Period size: 22 Copynumber: 3.1 Consensus size: 23
438899 ATAATATTTT
438909 TAATATAATTATAATA-AAAAAA
1 TAATATAATTATAATATAAAAAA
*
438931 TAATATAATTATAATATTAAAAA
1 TAATATAATTATAATATAAAAAA
438954 TAATAT--TTATATATATAATAAAA
1 TAATATAATTATA-ATATAA-AAAA
438977 TA
1 TA
438979 TATTAATCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 5 0.12
22 21 0.49
23 17 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATATAATTATAATATAAAAAA
Found at i:441967 original size:14 final size:15
Alignment explanation
Indices: 441939--441976 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
441929 ACAAAAAATT
441939 ATTAAATTATTAAAA
1 ATTAAATTATTAAAA
441954 ATTAAATT-TTAAAA
1 ATTAAATTATTAAAA
*
441968 AATAAATTA
1 ATTAAATTA
441977 CAAAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTATTAAAA
Found at i:442352 original size:13 final size:13
Alignment explanation
Indices: 442331--442355 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
442321 AAAAATATTT
442331 TTTTAAAATTATC
1 TTTTAAAATTATC
442344 TTTTAAAATTAT
1 TTTTAAAATTAT
442356 GTCTCTTAAA
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:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAAAATTATC
Found at i:444859 original size:26 final size:25
Alignment explanation
Indices: 444777--444860 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 25
444767 TTAAATTATT
*
444777 TTTTAATAATAAAAAATTTTATTTAA-A
1 TTTTAAT-TTAAAAAATTTTA--TAATA
*
444804 TTTT-ATTATAAAAAATATATATAATA
1 TTTTAATT-TAAAAAAT-TTTATAATA
444830 --TTAATTTAAAATAATTTTATAATA
1 TTTTAATTTAAAA-AATTTTATAATA
444854 TTTTAAT
1 TTTTAAT
444861 ATTTTTAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
24 15 0.32
25 9 0.19
26 16 0.34
27 7 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTAATTTAAAAAATTTTATAATA
Found at i:445038 original size:21 final size:20
Alignment explanation
Indices: 445012--445067 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
445002 ATAAATTTAA
445012 ATTAATTTAAATTATTATTTT
1 ATTAATTTAAATTATTA-TTT
*
445033 ATTAA-TAAAATATATTATTT
1 ATTAATTTAAAT-TATTATTT
445053 ATTTAATTT-AATTAT
1 A-TTAATTTAAATTAT
445068 AAAAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 12 0.40
21 17 0.57
22 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTAATTTAAATTATTATTT
Found at i:445623 original size:22 final size:21
Alignment explanation
Indices: 445585--445626 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
445575 TATAGTGGCA
**
445585 GAAAAAAATTAAAAAGAAAAG
1 GAAAAAAAAAAAAAAGAAAAG
445606 GAAAAAAAAAAAAGAAGAAAA
1 GAAAAAAAAAAAA-AAGAAAA
445627 CAACATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (21 bp):
GAAAAAAAAAAAAAAGAAAAG
Found at i:446449 original size:15 final size:15
Alignment explanation
Indices: 446429--446458 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
446419 ATCTAAAAAT
446429 TATTTAAATTTATAA
1 TATTTAAATTTATAA
446444 TATTTAAATTTATAA
1 TATTTAAATTTATAA
446459 AAAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAAATTTATAA
Found at i:453022 original size:43 final size:43
Alignment explanation
Indices: 452960--453041 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
452950 CATCTAAGTC
452960 CGAGTAACATAGTTACTAACTGAAAATTTTAGTGTTTTTCAAT
1 CGAGTAACATAGTTACTAACTGAAAATTTTAGTGTTTTTCAAT
* *
453003 CGAGTATCATAGTTGCTAACTGAAAATTTTAGTGTTTTT
1 CGAGTAACATAGTTACTAACTGAAAATTTTAGTGTTTTT
453042 TCAGTGGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (43 bp):
CGAGTAACATAGTTACTAACTGAAAATTTTAGTGTTTTTCAAT
Found at i:454000 original size:22 final size:22
Alignment explanation
Indices: 453975--454071 Score: 86
Period size: 21 Copynumber: 4.8 Consensus size: 22
453965 AATTAATGTT
*
453975 AATAATATTAAATATTATATAA
1 AATAATATTAAATATAATATAA
*
453997 AATAAT-TAAAATATAATATAA
1 AATAATATTAAATATAATATAA
454018 AA-AATA-T--ATA-AATATAA
1 AATAATATTAAATATAATATAA
*
454035 AAT-ATTTTAAATATAATTATAA
1 AATAATATTAAATATAA-TATAA
*
454057 TATAATA--AAATATAA
1 AATAATATTAAATATAA
454072 AATTTTAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
17 11 0.18
18 4 0.07
20 6 0.10
21 25 0.41
22 13 0.21
23 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATAATATTAAATATAATATAA
Found at i:454012 original size:16 final size:15
Alignment explanation
Indices: 453991--454074 Score: 68
Period size: 15 Copynumber: 5.6 Consensus size: 15
453981 ATTAAATATT
453991 ATATAAAATAATTAAA
1 ATATAAAATAA-TAAA
*
454007 ATATAATATAA-AAA
1 ATATAAAATAATAAA
454021 ATATATAAAT-ATAAA
1 ATATA-AAATAATAAA
*
454036 ATATTTTAAAT-AT-AA
1 ATA--TAAAATAATAAA
* *
454051 TTATAATATAATAAA
1 ATATAAAATAATAAA
454066 ATATAAAAT
1 ATATAAAAT
454075 TTTAATAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
13 4 0.07
14 11 0.20
15 22 0.41
16 16 0.30
17 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATAAAATAATAAA
Found at i:454047 original size:38 final size:37
Alignment explanation
Indices: 453991--454074 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 37
453981 ATTAAATATT
453991 ATATAAAATAATTAAAATATAATATAAAAAAT-ATATAA
1 ATATAAAATAATTAAAATATAAT-TAAAAAATAATA-AA
* * * *
454029 ATATAAAATATTTTAAATATAATTATAATATAATAAA
1 ATATAAAATAATTAAAATATAATTAAAAAATAATAAA
454066 ATATAAAAT
1 ATATAAAAT
454075 TTTAATAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
37 17 0.41
38 24 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (37 bp):
ATATAAAATAATTAAAATATAATTAAAAAATAATAAA
Found at i:454062 original size:5 final size:5
Alignment explanation
Indices: 453985--454071 Score: 54
Period size: 5 Copynumber: 17.4 Consensus size: 5
453975 AATAATATTA
* * * *
453985 AATAT TATAT AAAAT AATTAA AATAT AATAT AA-AA AATAT -ATA- AATAT
1 AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT
* * * *
454033 AAAAT ATTTT AAATAT AATTAT AATAT AATAA AATAT AA
1 AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT AA
454072 AATTTTAATA
Statistics
Matches: 60, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
4 9 0.15
5 40 0.67
6 11 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:454295 original size:30 final size:28
Alignment explanation
Indices: 454243--454365 Score: 107
Period size: 30 Copynumber: 4.4 Consensus size: 28
454233 AGATTTTTTT
*
454243 TAATATAAATTTTTTATATTTATAATAAA
1 TAATATAAATTTTATATATTTATAA-AAA
454272 TAAATAATAAATTTTAT-TATTTATAAAAA
1 T-AAT-ATAAATTTTATATATTTATAAAAA
* * *
454301 TAATATAAATTTAGATAATAAATT-TAAACA
1 TAATATAAATTT-TAT-AT-ATTTATAAAAA
454331 T--T-TAAA-TTTA-ATATTTATAAAAA
1 TAATATAAATTTTATATATTTATAAAAA
454354 TAATATAAATTT
1 TAATATAAATTT
454366 AAATAATAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 24
0.71 0.07 0.22
Matches are distributed among these distances:
22 3 0.04
23 8 0.11
25 2 0.03
26 6 0.08
27 14 0.18
28 6 0.08
29 5 0.07
30 19 0.25
31 13 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
TAATATAAATTTTATATATTTATAAAAA
Found at i:454321 original size:47 final size:48
Alignment explanation
Indices: 454260--454377 Score: 132
Period size: 53 Copynumber: 2.3 Consensus size: 48
454250 AATTTTTTAT
*
454260 ATTTATAATAAATAAATA-A-TAAATTTTATTATTTATAAAAATAATATAA
1 ATTTA-AAT-AATAAATACATTAAA-TTTAATATTTATAAAAATAATATAA
*
454309 ATTTAGATAATAAATTTAAACATTTAAATTTAATATTTATAAAAATAATATAA
1 ATTTAAATAATAAA--T--ACA-TTAAATTTAATATTTATAAAAATAATATAA
454362 ATTTAAATAATAAATA
1 ATTTAAATAATAAATA
454378 TTTAAAAATT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
47 6 0.10
48 2 0.03
49 7 0.12
51 2 0.03
52 1 0.02
53 37 0.63
54 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (48 bp):
ATTTAAATAATAAATACATTAAATTTAATATTTATAAAAATAATATAA
Found at i:454353 original size:53 final size:55
Alignment explanation
Indices: 454279--454395 Score: 175
Period size: 53 Copynumber: 2.1 Consensus size: 55
454269 AAATAAATAA
* * *
454279 TAAATTTTATTATTTATAAAAATAATATAAATTTAGATAAT-AA-ATTTAAACATT
1 TAAA-TTTAATATTTATAAAAATAATATAAATTTAAATAATAAATATTTAAAAATT
454333 TAAATTTAATATTTATAAAAATAATATAAATTTAAATAATAAATATTTAAAAATT
1 TAAATTTAATATTTATAAAAATAATATAAATTTAAATAATAAATATTTAAAAATT
*
454388 TATATTTA
1 TAAATTTA
454396 CATTCTTTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
53 34 0.60
54 6 0.11
55 17 0.30
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (55 bp):
TAAATTTAATATTTATAAAAATAATATAAATTTAAATAATAAATATTTAAAAATT
Found at i:454369 original size:15 final size:15
Alignment explanation
Indices: 454298--454383 Score: 55
Period size: 13 Copynumber: 6.2 Consensus size: 15
454288 TTATTTATAA
454298 AAATAATATAAATTT
1 AAATAATATAAATTT
*
454313 AGAT-A-ATAAATTT
1 AAATAATATAAATTT
* *
454326 AAA-CATTTAAATTT
1 AAATAATATAAATTT
*
454340 -AAT-ATTTATAA---
1 AAATAATATA-AATTT
454351 AAATAATATAAATTT
1 AAATAATATAAATTT
454366 AAATAATA-AATATTT
1 AAATAATATAA-ATTT
454381 AAA
1 AAA
454384 AATTTATATT
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
12 5 0.09
13 22 0.39
14 12 0.21
15 18 0.32
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (15 bp):
AAATAATATAAATTT
Found at i:455149 original size:27 final size:27
Alignment explanation
Indices: 455119--455176 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
455109 CAATTAAATT
* *
455119 AATACATATTTTTTA-TTAATATTAAA
1 AATACATAATATTTATTTAATATTAAA
**
455145 CAATATTTAATATTTATTTAATATTAAA
1 -AATACATAATATTTATTTAATATTAAA
455173 AATA
1 AATA
455177 TTTTTTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (27 bp):
AATACATAATATTTATTTAATATTAAA
Found at i:455193 original size:19 final size:20
Alignment explanation
Indices: 455153--455194 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
455143 AACAATATTT
455153 AATATTTATTTAATATTAAA
1 AATATTTATTTAATATTAAA
455173 AATATTT-TTTAAATATTAAA
1 AATATTTATTT-AATATTAAA
455193 AA
1 AA
455195 AAGAAGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATTTATTTAATATTAAA
Found at i:463783 original size:26 final size:26
Alignment explanation
Indices: 463759--463810 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
463749 TTACGATTAA
*
463759 TTATAATAAATATTAATAATAATTATAC
1 TTATAAT-AATA-AAATAATAATTATAC
*
463787 TTATAATTATAAAATAATAATTAT
1 TTATAATAATAAAATAATAATTAT
463811 GAACGATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 12 0.55
27 3 0.14
28 7 0.32
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TTATAATAATAAAATAATAATTATAC
Found at i:464060 original size:21 final size:23
Alignment explanation
Indices: 464025--464165 Score: 73
Period size: 21 Copynumber: 6.2 Consensus size: 23
464015 AATTAAAATT
* *
464025 AATAATATTAAATATGATA-AAA
1 AATAATATAAAATATAATATAAA
464047 AATAAT-TAAAATATAATATAAA
1 AATAATATAAAATATAATATAAA
* * *
464069 AATATAAATATAATATATATTTAAA
1 AATA-ATATAAAATATA-ATATAAA
464094 AAT-AT-TAAAATTTTTATAATAT-AA
1 AATAATATAAAA----TATAATATAAA
* * *
464118 ATTAATATAAAA-ATATTTTAAA
1 AATAATATAAAATATAATATAAA
* *
464140 TATAAT-TATAATATAATA-AAA
1 AATAATATAAAATATAATATAAA
*
464161 TATAA
1 AATAA
464166 AATTTTAATA
Statistics
Matches: 91, Mismatches: 16, Indels: 25
0.69 0.12 0.19
Matches are distributed among these distances:
21 27 0.30
22 27 0.30
23 2 0.02
24 12 0.13
25 14 0.15
26 9 0.10
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (23 bp):
AATAATATAAAATATAATATAAA
Found at i:464079 original size:19 final size:20
Alignment explanation
Indices: 464028--464085 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
464018 TAAAATTAAT
*
464028 AATATTAAATATGATA-AAA
1 AATATTAAATATAATATAAA
464047 AATAATTAAAATATAATATAAA
1 AAT-ATT-AAATATAATATAAA
464069 AATA-TAAATATAATATA
1 AATATTAAATATAATATA
464086 TATTTAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 15 0.43
20 4 0.11
21 10 0.29
22 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
AATATTAAATATAATATAAA
Found at i:464124 original size:27 final size:28
Alignment explanation
Indices: 464094--464155 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
464084 TATATTTAAA
*
464094 AATATTAAAAT-TTTTATAATATAAAT-T
1 AATATAAAAATATTTTA-AATATAAATAT
*
464121 AATATAAAAATATTTTAAATATAATTAT
1 AATATAAAAATATTTTAAATATAAATAT
464149 AATATAA
1 AATATAA
464156 TAAAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 18 0.58
28 13 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AATATAAAAATATTTTAAATATAAATAT
Found at i:464365 original size:29 final size:28
Alignment explanation
Indices: 464317--464435 Score: 97
Period size: 27 Copynumber: 4.3 Consensus size: 28
464307 TTTCTTTGAG
*
464317 TATAAATTTTTTATATTTATAATAAATAAA
1 TATAAATTTTATATATTTATAA-AAAT-AA
464347 TAATAAATTTTAT-TA-TTATAAAAATAA
1 T-ATAAATTTTATATATTTATAAAAATAA
* ** **
464374 TATAAA-TTTAAATAATAAATTTAAAT-A
1 TATAAATTTTATAT-ATTTATAAAAATAA
*
464401 TTTAAA-TTTA-ATATTTATAAAAATAA
1 TATAAATTTTATATATTTATAAAAATAA
464427 TATAAATTT
1 TATAAATTT
464436 AAATAATAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
25 12 0.17
26 14 0.20
27 16 0.23
28 10 0.14
29 6 0.08
30 3 0.04
31 10 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAAATTTTATATATTTATAAAAATAA
Found at i:464386 original size:15 final size:14
Alignment explanation
Indices: 464368--464446 Score: 71
Period size: 13 Copynumber: 5.9 Consensus size: 14
464358 ATTATTATAA
464368 AAATAATATAAATTT
1 AAAT-ATATAAATTT
464383 AAATA-ATAAATTT
1 AAATATATAAATTT
*
464396 AAATATTTAAATTT
1 AAATATATAAATTT
*
464410 -AATATTTATAA---
1 AAATATATA-AATTT
464421 AAATAATATAAATTT
1 AAAT-ATATAAATTT
464436 AAATA-ATAAAT
1 AAATATATAAAT
464447 ATTTAAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
12 5 0.09
13 31 0.56
14 11 0.20
15 8 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATATAAATTT
Found at i:464419 original size:53 final size:55
Alignment explanation
Indices: 464362--464465 Score: 176
Period size: 53 Copynumber: 1.9 Consensus size: 55
464352 AATTTTATTA
*
464362 TTATAAAAATAATATAAATTTAAATAAT-AA-ATTTAAATATTTAAATTTAATAT
1 TTATAAAAATAATATAAATTTAAATAATAAATATTTAAAAATTTAAATTTAATAT
*
464415 TTATAAAAATAATATAAATTTAAATAATAAATATTTAAAAATTTATATTTA
1 TTATAAAAATAATATAAATTTAAATAATAAATATTTAAAAATTTAAATTTA
464466 CATTCTTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 28 0.60
54 2 0.04
55 17 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (55 bp):
TTATAAAAATAATATAAATTTAAATAATAAATATTTAAAAATTTAAATTTAATAT
Found at i:464436 original size:26 final size:27
Alignment explanation
Indices: 464329--464437 Score: 102
Period size: 26 Copynumber: 4.0 Consensus size: 27
464319 TAAATTTTTT
*
464329 ATATTTATAATAAATAAATAATAAATTTT
1 ATATTTATAA-AAATAAAT-ATAAATTTA
464358 AT-TATTATAAAAAT-AATATAAATTTA
1 ATAT-TTATAAAAATAAATATAAATTTA
* **
464384 A-A-TAATAAATTTAAATATTTAAATTTA
1 ATATTTATAAAAATAAATA--TAAATTTA
464411 ATATTTATAAAAAT-AATATAAATTTA
1 ATATTTATAAAAATAAATATAAATTTA
464437 A
1 A
464438 ATAATAAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
24 7 0.11
25 4 0.06
26 18 0.27
27 12 0.18
28 10 0.15
29 15 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
ATATTTATAAAAATAAATATAAATTTA
Found at i:464450 original size:15 final size:15
Alignment explanation
Indices: 464395--464453 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 15
464385 ATAATAAATT
464395 TAAATATTTAAAT--
1 TAAATATTTAAATAA
* *
464408 TTAATATTTATAAAAA
1 TAAATATTTA-AATAA
464424 TAATATAAATTTAAATAA
1 TAA-AT--ATTTAAATAA
464442 TAAATATTTAAA
1 TAAATATTTAAA
464454 AATTTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
13 9 0.25
14 2 0.06
15 7 0.19
16 2 0.06
17 4 0.11
18 7 0.19
19 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATATTTAAATAA
Found at i:464511 original size:15 final size:15
Alignment explanation
Indices: 464491--464520 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
464481 ATACTAATTT
464491 TATTTAAATTCAAAA
1 TATTTAAATTCAAAA
*
464506 TATTTAAATTTAAAA
1 TATTTAAATTCAAAA
464521 AAAAATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TATTTAAATTCAAAA
Found at i:465714 original size:19 final size:20
Alignment explanation
Indices: 465674--465715 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
465664 AACAATATTT
465674 AATATTTATTTAATATTAAA
1 AATATTTATTTAATATTAAA
465694 AATATTT-TTTAAATATTAAA
1 AATATTTATTT-AATATTAAA
465714 AA
1 AA
465716 AAGAAGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATTTATTTAATATTAAA
Found at i:467221 original size:15 final size:15
Alignment explanation
Indices: 467201--467229 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
467191 ATGTTTGTGA
467201 GAAAAAGTAATAAAG
1 GAAAAAGTAATAAAG
467216 GAAAAAGTAATAAA
1 GAAAAAGTAATAAA
467230 TATTAAAATT
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:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (15 bp):
GAAAAAGTAATAAAG
Found at i:468378 original size:16 final size:16
Alignment explanation
Indices: 468341--468398 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
468331 TAAATATAAT
* *
468341 ATATTTA-AAATTAAA
1 ATATTTATATATTTAA
*
468356 ATTTTTATATATTTAA
1 ATATTTATATATTTAA
468372 ATATTTATATTATATT--
1 ATATTTATA-TAT-TTAA
468388 ATATTTATATA
1 ATATTTATATA
468399 ATTGATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 8 0.22
16 23 0.64
17 3 0.08
18 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTTATATATTTAA
Found at i:468818 original size:17 final size:17
Alignment explanation
Indices: 468782--468814 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
468772 TAAAAATATT
*
468782 TAAATTTAAATTTAAAA
1 TAAATTTAAATTAAAAA
468799 TAAATTT-AATTAAAAA
1 TAAATTTAAATTAAAAA
468815 ATAATCCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTAAAAA
Found at i:470041 original size:64 final size:64
Alignment explanation
Indices: 469902--470051 Score: 159
Period size: 64 Copynumber: 2.3 Consensus size: 64
469892 CAAATTAATT
* ** * *
469902 ATTTAAGTTATTTTAAATTTAAATCATTACGATTTTTATTTATTTCAAGTTCTAATCAATTTAG
1 ATTTAAGTTATTTTAGATTTTGATCATTACGATTTTTATTCATTTCAAGTTCGAATCAATTTAG
469966 ATTT-AGATTATTTTAGATTTTGATCACTGTA-GA-TTTTATTCATTTCAAGTTCGAATC-ATTT
1 ATTTAAG-TTATTTTAGATTTTGATCA-T-TACGATTTTTATTCATTTCAAGTTCGAATCAATTT
470027 CA-
63 -AG
470029 AGTTTAAGTTATTTT-GAGTTTTG
1 A-TTTAAGTTATTTTAGA-TTTTG
470052 GTTGGTCAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
63 9 0.12
64 58 0.78
65 5 0.07
66 2 0.03
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (64 bp):
ATTTAAGTTATTTTAGATTTTGATCATTACGATTTTTATTCATTTCAAGTTCGAATCAATTTAG
Found at i:470915 original size:30 final size:29
Alignment explanation
Indices: 470879--470944 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 29
470869 ATCAATTGTG
*
470879 AAAAATAATAATATTTTGATAA-TATATTT
1 AAAAATAATAATATTTTAATAATTA-ATTT
470908 CAAAAATAATAATATTTTAATAATTAATTT
1 -AAAAATAATAATATTTTAATAATTAATTT
470938 AAAAATA
1 AAAAATA
470945 TTACTTTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 7 0.21
30 25 0.74
31 2 0.06
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (29 bp):
AAAAATAATAATATTTTAATAATTAATTT
Found at i:471137 original size:24 final size:23
Alignment explanation
Indices: 471097--471154 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
471087 AAAAATAATT
*
471097 AATAATAT-TTTAAATTTAATAA
1 AATAATATATTAAAATTTAATAA
**
471119 AATAATATATTAAATATTTTTTAA
1 AATAATATATTAAA-ATTTAATAA
471143 AATAATA-ATTAA
1 AATAATATATTAA
471155 TTAATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.26
23 9 0.29
24 14 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATAATATATTAAAATTTAATAA
Found at i:471161 original size:24 final size:24
Alignment explanation
Indices: 471116--471165 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
471106 TTAAATTTAA
471116 TAAAATAATATATTAAATATTTTT
1 TAAAATAATATATTAAATATTTTT
*
471140 TAAAATAATA-ATTAATTAATTTTT
1 TAAAATAATATATTAAAT-ATTTTT
471164 TA
1 TA
471166 TAAACATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAAATAATATATTAAATATTTTT
Found at i:471162 original size:23 final size:24
Alignment explanation
Indices: 471116--471163 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
471106 TTAAATTTAA
*
471116 TAAAATAATATATTAAATATTTTT
1 TAAAATAATATATTAAATAATTTT
*
471140 TAAAATAATA-ATTAATTAATTTT
1 TAAAATAATATATTAAATAATTTT
471163 T
1 T
471164 TATAAACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAAATAATATATTAAATAATTTT
Found at i:471744 original size:17 final size:16
Alignment explanation
Indices: 471722--471756 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
471712 TTTATTTTAT
471722 TTTTTATATATTTATAA
1 TTTTTATATA-TTATAA
471739 TTTTTATATATTATAA
1 TTTTTATATATTATAA
471755 TT
1 TT
471757 AAATCATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTATATATTATAA
Found at i:472044 original size:3 final size:3
Alignment explanation
Indices: 472036--472086 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
472026 AATTCATCAA
472036 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
472084 AAT
1 AAT
472087 GCAGAGAATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:472243 original size:3 final size:3
Alignment explanation
Indices: 472235--472275 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
472225 CAATAAACAT
472235 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
472276 TGATTTCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:474359 original size:22 final size:21
Alignment explanation
Indices: 474334--474378 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
474324 AAACCTTAAA
*
474334 AAAAAAGAAATTAATTTCAATG
1 AAAAAAGAAACTAA-TTCAATG
* *
474356 AAAAAATAAACTCATTCAATG
1 AAAAAAGAAACTAATTCAATG
474377 AA
1 AA
474379 CTTTCTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.60, C:0.09, G:0.07, T:0.24
Consensus pattern (21 bp):
AAAAAAGAAACTAATTCAATG
Found at i:475532 original size:3 final size:3
Alignment explanation
Indices: 475526--475570 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
475516 AAAAAATTCC
475526 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
475571 ATTCCTAGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:475886 original size:23 final size:23
Alignment explanation
Indices: 475825--475886 Score: 54
Period size: 27 Copynumber: 2.6 Consensus size: 23
475815 AGAATTCTAG
**
475825 TTAAA-TTTAATAAATTTAGTAA
1 TTAAATTTTAATAAATTTAAAAA
*
475847 TTAATTGATATTAAATAAATTTAAAAA
1 TTAA---AT-TTTAATAAATTTAAAAA
475874 TTAAATTTTAATA
1 TTAAATTTTAATA
475887 TTTATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
22 4 0.13
23 6 0.19
24 2 0.06
25 1 0.03
27 18 0.58
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (23 bp):
TTAAATTTTAATAAATTTAAAAA
Found at i:477880 original size:16 final size:16
Alignment explanation
Indices: 477859--477891 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
477849 AAACTAAATG
477859 ACTTTTATCGAAACTT
1 ACTTTTATCGAAACTT
477875 ACTTTTATCGAAACTT
1 ACTTTTATCGAAACTT
477891 A
1 A
477892 TTAACGGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ACTTTTATCGAAACTT
Found at i:479781 original size:14 final size:14
Alignment explanation
Indices: 479764--479792 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
479754 CAATTAATTC
479764 ATATAATATTTTTA
1 ATATAATATTTTTA
479778 ATATAATATTTTTA
1 ATATAATATTTTTA
479792 A
1 A
479793 GATTGAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATAATATTTTTA
Found at i:482766 original size:1 final size:1
Alignment explanation
Indices: 482760--482850 Score: 74
Period size: 1 Copynumber: 91.0 Consensus size: 1
482750 AAATCTTCAC
* * ** * * * **
482760 TTTTTTTTTTTTGTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
482825 TTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
482851 CCAATTGCCA
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:482805 original size:33 final size:33
Alignment explanation
Indices: 482759--482849 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
482749 CAAATCTTCA
482759 CTTTTTTTT-TTTTGTTTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTC
482791 CTTTTTTTTGTTTTG-TTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTC
482823 CTTTTTTTTGTTTTGTTTTTTTCTTTT
1 CTTTTTTTTGTTTTGTTTTTTT-TTTT
482850 TCCAATTGCC
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
32 41 0.73
33 11 0.20
34 4 0.07
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (33 bp):
CTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTC
Found at i:492630 original size:5 final size:5
Alignment explanation
Indices: 492622--492668 Score: 62
Period size: 5 Copynumber: 9.6 Consensus size: 5
492612 GCTTAGCTTT
*
492622 TTTTC TTTTC TTTTC TTTTC TTTTTT TTTTC TTTT- TTTT- TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTT
492669 AGCTTTCAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 8 0.21
5 26 0.68
6 4 0.11
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (5 bp):
TTTTC
Found at i:492662 original size:11 final size:11
Alignment explanation
Indices: 492620--492662 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
492610 GAGCTTAGCT
492620 TTTTTTCTTTTC
1 TTTTTT-TTTTC
*
492632 -TTTTCTTTTC
1 TTTTTTTTTTC
492642 TTTTTTTTTTC
1 TTTTTTTTTTC
492653 TTTTTTTTTT
1 TTTTTTTTTT
492663 TTCTTTAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 5 0.18
11 23 0.82
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:494178 original size:25 final size:23
Alignment explanation
Indices: 494133--494180 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
494123 ATTTTTTTTT
*
494133 ATAAAAAAAATTATGATTTAAAA
1 ATAAAAAAAATTATAATTTAAAA
494156 ATAAAAAAAATTATAAGTATTAAAA
1 ATAAAAAAAATTATAA-T-TTAAAA
494181 TTTAAATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.68
24 1 0.05
25 6 0.27
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (23 bp):
ATAAAAAAAATTATAATTTAAAA
Found at i:494581 original size:41 final size:41
Alignment explanation
Indices: 494521--494613 Score: 168
Period size: 41 Copynumber: 2.2 Consensus size: 41
494511 AATTTATATA
*
494521 TCTCATATTCATATTATCGTATTTAATATTACTAAATCTATC
1 TCTCA-ATACATATTATCGTATTTAATATTACTAAATCTATC
494563 TCTCAATACATATTATCGTATTTAATATTACTAAATCTATC
1 TCTCAATACATATTATCGTATTTAATATTACTAAATCTATC
494604 TCTCAATACA
1 TCTCAATACA
494614 AAAATTTCGA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 45 0.90
42 5 0.10
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.44
Consensus pattern (41 bp):
TCTCAATACATATTATCGTATTTAATATTACTAAATCTATC
Found at i:495126 original size:29 final size:27
Alignment explanation
Indices: 495094--495153 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
495084 TCATGCATTA
* *
495094 TTTTACTATTTTTAAATGAAATTTTTTAT
1 TTTTACTATATTT-AATGAAA-TTTGTAT
* *
495123 TTTTATTATATTTAATTAAATTTGTAT
1 TTTTACTATATTTAATGAAATTTGTAT
495150 TTTT
1 TTTT
495154 TAGTTTATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 10 0.37
28 6 0.22
29 11 0.41
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTTACTATATTTAATGAAATTTGTAT
Found at i:495247 original size:20 final size:20
Alignment explanation
Indices: 495214--495252 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
495204 TTAAGAATTT
*
495214 ATTTAATTATATAAATAAAAA
1 ATTTAATTAGATAAA-AAAAA
495235 ATTT-ATTAGATAAAAAAA
1 ATTTAATTAGATAAAAAAA
495253 TCAATAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
ATTTAATTAGATAAAAAAAA
Found at i:495284 original size:21 final size:23
Alignment explanation
Indices: 495226--495285 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
495216 TTAATTATAT
495226 AAATAAAAAATTTATTAGATAAAA
1 AAATAAAAAATTTA-TAGATAAAA
* * *
495250 AAATCAATAGTTTA-A-ATAAAA
1 AAATAAAAAATTTATAGATAAAA
*
495271 AAATTAAAAATTTAT
1 AAATAAAAAATTTAT
495286 TTAAATGTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 17 0.59
22 1 0.03
24 11 0.38
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (23 bp):
AAATAAAAAATTTATAGATAAAA
Found at i:495290 original size:21 final size:21
Alignment explanation
Indices: 495203--495290 Score: 50
Period size: 21 Copynumber: 3.9 Consensus size: 21
495193 TTTGATTTTT
*
495203 ATTAAGAATTTATTTAATTATATAA
1 ATTAAAAATTTATTTAA--A-A-AA
*
495228 ATAAAAAATTTATTAGATAAAAAA
1 ATTAAAAATTTATT---TAAAAAA
* * * **
495252 ATCAATAGTTTAAATAAAAAA
1 ATTAAAAATTTATTTAAAAAA
495273 ATTAAAAATTTATTTAAA
1 ATTAAAAATTTATTTAAA
495291 TGTGATTTAT
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
21 20 0.42
24 11 0.23
25 13 0.27
26 1 0.02
28 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (21 bp):
ATTAAAAATTTATTTAAAAAA
Found at i:495595 original size:8 final size:8
Alignment explanation
Indices: 495574--495655 Score: 53
Period size: 8 Copynumber: 9.8 Consensus size: 8
495564 AAAAATAATA
495574 ATATAAAT
1 ATATAAAT
495582 AT-TAAAT
1 ATATAAAT
495589 ATATAAAT
1 ATATAAAT
495597 ATATTAAAAT
1 ATA-T-AAAT
*
495607 TTATAAA-
1 ATATAAAT
*
495614 ATTTAAAT
1 ATATAAAT
*
495622 -TATTTAAT
1 ATA-TAAAT
495630 ATATTAATATTT
1 ATA-TAA-A--T
495642 ATATAAAT
1 ATATAAAT
495650 ATATAA
1 ATATAA
495656 TATTTTAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
7 13 0.22
8 24 0.41
9 7 0.12
10 8 0.14
11 3 0.05
12 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
ATATAAAT
Found at i:495612 original size:33 final size:33
Alignment explanation
Indices: 495578--495666 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 33
495568 ATAATAATAT
495578 AAATATTAAA-TATATAAATATATTAAAATTTATA
1 AAAT-TTAAATTAT-TAAATATATTAAAATTTATA
* *
495612 AAATTTAAATTATTTAATATATTAATATTTATA
1 AAATTTAAATTATTAAATATATTAAAATTTATA
495645 TAAATATATAATATT-TTAAATA
1 -AAAT-T-TAA-ATTATTAAATA
495667 CGATTATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
33 23 0.49
34 11 0.23
35 1 0.02
36 9 0.19
37 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
AAATTTAAATTATTAAATATATTAAAATTTATA
Found at i:495657 original size:27 final size:27
Alignment explanation
Indices: 495584--495724 Score: 76
Period size: 33 Copynumber: 5.0 Consensus size: 27
495574 ATATAAATAT
*
495584 TAAATATATAAATATATTAAAATTTATAAAA
1 TAAATATAT-AATATATTAATATTTAT---A
*
495615 TTTAAATTATTTAATATATTAATATTTATA
1 --TAAA-TATATAATATATTAATATTTATA
* *
495645 TAAATATATAATATTTTAAATACGATTATA
1 TAAATATATAATATATT-AATA--TTTATA
* *
495675 -AAATATGAT-ATATATAAATA-TGATA
1 TAAATAT-ATAATATATTAATATTTATA
*
495700 TAAATATACGAAT-TATTAA-ATTTAT
1 TAAATATA-TAATATATTAATATTTAT
495725 CTTATAGATA
Statistics
Matches: 88, Mismatches: 11, Indels: 25
0.71 0.09 0.20
Matches are distributed among these distances:
25 6 0.07
26 14 0.16
27 13 0.15
28 12 0.14
29 11 0.12
30 8 0.09
33 20 0.23
34 4 0.05
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (27 bp):
TAAATATATAATATATTAATATTTATA
Found at i:495695 original size:15 final size:15
Alignment explanation
Indices: 495641--495701 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
495631 TATTAATATT
495641 TATATAAATAT-ATAA
1 TATATAAATATGAT-A
* *
495656 TATTTTAAATACGAT-
1 TA-TATAAATATGATA
495671 TATA-AAATATGATA
1 TATATAAATATGATA
495685 TATATAAATATGATA
1 TATATAAATATGATA
495700 TA
1 TA
495702 AATATACGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 8 0.21
14 5 0.13
15 16 0.42
16 7 0.18
17 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (15 bp):
TATATAAATATGATA
Found at i:495793 original size:5 final size:5
Alignment explanation
Indices: 495772--495898 Score: 50
Period size: 5 Copynumber: 25.8 Consensus size: 5
495762 ATTCATCTCC
* * * * *
495772 TATTA TATT- TA-TA TATTT TATTA TATTA TAATCA TATTTA AAATA TTTTA
1 TATTA TATTA TATTA TATTA TATTA TATTA T-ATTA TA-TTA TATTA TATTA
* * * * *
495822 TATTTA TATTA -ATTT TAATA TATTA -ATAA T-TTA TATTA TA-TA AATTT
1 TA-TTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
** * *
495869 TAAAA AATATA TATTT TATTA TATTA TATT
1 TATTA TAT-TA TATTA TATTA TATTA TATT
495899 TTAATTATTT
Statistics
Matches: 84, Mismatches: 28, Indels: 20
0.64 0.21 0.15
Matches are distributed among these distances:
3 1 0.01
4 16 0.19
5 52 0.62
6 15 0.18
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:495810 original size:21 final size:18
Alignment explanation
Indices: 495772--495906 Score: 59
Period size: 18 Copynumber: 7.3 Consensus size: 18
495762 ATTCATCTCC
495772 TATTATATTTATATATTT
1 TATTATATTTATATATTT
495790 TATTATA-TTATAATCATATT
1 TATTATATTTAT-AT-AT-TT
**
495810 TAAAATATTT-TATATTT
1 TATTATATTTATATATTT
495827 ATATTA-ATTTTAATATATTAAT
1 -TATTATA-TTT-ATATATT--T
* *
495849 AATTTATATTATATAAATTT
1 TA-TTATATT-TATATATTT
* **
495869 TA--AAAAATATATATTT
1 TATTATATTTATATATTT
495885 TATTATA-TTATAT-TTT
1 TATTATATTTATATATTT
*
495901 AATTAT
1 TATTAT
495907 TTTTTACTCT
Statistics
Matches: 88, Mismatches: 14, Indels: 32
0.66 0.10 0.24
Matches are distributed among these distances:
16 18 0.20
17 14 0.16
18 19 0.22
19 4 0.05
20 16 0.18
21 3 0.03
22 12 0.14
23 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATATTTATATATTT
Found at i:495838 original size:17 final size:16
Alignment explanation
Indices: 495816--495870 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 16
495806 TATTTAAAAT
495816 ATTTTATATTTATATTA
1 ATTTTATA-TTATATTA
495833 ATTTTA-A-TATATTA
1 ATTTTATATTATATTA
*
495847 ATAATTTATATTATATAA
1 AT--TTTATATTATATTA
495865 ATTTTA
1 ATTTTA
495871 AAAAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 9 0.27
16 9 0.27
17 7 0.21
18 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTATATTATATTA
Found at i:495838 original size:27 final size:28
Alignment explanation
Indices: 495772--495859 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 28
495762 ATTCATCTCC
*
495772 TATT-ATATTT-ATATATTTTATTATATTA
1 TATTAATATTTAAAATATTTTA-TAT-TTA
* *
495800 TAATCATATTTAAAATATTTTATATTTA
1 TATTAATATTTAAAATATTTTATATTTA
* *
495828 TATTAAT-TTTAATATA-TTAATAATTTA
1 TATTAATATTTAAAATATTTTAT-ATTTA
495855 TATTA
1 TATTA
495860 TATAAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.08
27 18 0.35
28 11 0.22
29 9 0.18
30 9 0.18
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTAATATTTAAAATATTTTATATTTA
Found at i:495887 original size:32 final size:33
Alignment explanation
Indices: 495813--495897 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 33
495803 TCATATTTAA
* * *
495813 AATATTTTATATTTATATTAATTTTAATATATT
1 AATATTTTATATTTATATAAATTTTAAAAAATT
*
495846 AATAATTTATA-TTATATAAATTTTAAAAAA-T
1 AATATTTTATATTTATATAAATTTTAAAAAATT
495877 ATATATTTTATTATATTATAT
1 A-ATATTTTA-TAT-TTATAT
495898 TTTAATTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
31 2 0.05
32 23 0.53
33 12 0.28
35 6 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
AATATTTTATATTTATATAAATTTTAAAAAATT
Found at i:495905 original size:16 final size:16
Alignment explanation
Indices: 495772--495906 Score: 73
Period size: 16 Copynumber: 8.1 Consensus size: 16
495762 ATTCATCTCC
*
495772 TATTATATTTATATATTT
1 TATTATATTT-TA-ATTA
* *
495790 TATTATATTATAATCA
1 TATTATATTTTAATTA
495806 TATTTAAAATATTTTATATTTA
1 TA-TT---ATATTTTA-A-TTA
495828 TATTA-ATTTTAA-TA
1 TATTATATTTTAATTA
*
495842 TATTAATAATTTATATTA
1 TATT-ATATTTTA-ATTA
* *
495860 TA-TAAATTTTAA-AA
1 TATTATATTTTAATTA
*
495874 AATATATATTTT-ATTA
1 TAT-TATATTTTAATTA
495890 TATTATATTTTAATTA
1 TATTATATTTTAATTA
495906 T
1 T
495907 TTTTTACTCT
Statistics
Matches: 90, Mismatches: 13, Indels: 30
0.68 0.10 0.23
Matches are distributed among these distances:
14 8 0.09
15 11 0.12
16 31 0.34
17 12 0.13
18 14 0.16
20 7 0.08
21 3 0.03
22 4 0.04
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATATTTTAATTA
Found at i:496410 original size:40 final size:40
Alignment explanation
Indices: 496365--496445 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
496355 ATTATCTTAA
496365 TTTAATCATAATTATAAAAAACTTTAATCATTGTTTTTTG
1 TTTAATCATAATTATAAAAAACTTTAATCATTGTTTTTTG
496405 TTTAATCATAATTATAAAAAACTTTAATCATTGTTTTTTG
1 TTTAATCATAATTATAAAAAACTTTAATCATTGTTTTTTG
496445 T
1 T
496446 ATGAAGGCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (40 bp):
TTTAATCATAATTATAAAAAACTTTAATCATTGTTTTTTG
Found at i:497529 original size:21 final size:21
Alignment explanation
Indices: 497503--497543 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
497493 CTAACTTTTT
497503 AATTTTTTAAATATTTATGTC
1 AATTTTTTAAATATTTATGTC
*
497524 AATTTTTTAAGTATTTATGT
1 AATTTTTTAAATATTTATGT
497544 GTATCTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (21 bp):
AATTTTTTAAATATTTATGTC
Found at i:499110 original size:2 final size:2
Alignment explanation
Indices: 499103--499140 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
499093 CCATTTTGTC
499103 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
499141 CACATTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:499489 original size:11 final size:11
Alignment explanation
Indices: 499455--499498 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
499445 AATTAATTAA
499455 TTTATATTTAT
1 TTTATATTTAT
*
499466 TTTTTATTT-T
1 TTTATATTTAT
*
499476 TTTGTATTTAT
1 TTTATATTTAT
499487 TTTATATTTAT
1 TTTATATTTAT
499498 T
1 T
499499 AAAATATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTATATTTAT
Found at i:499509 original size:5 final size:5
Alignment explanation
Indices: 499501--499639 Score: 69
Period size: 5 Copynumber: 28.2 Consensus size: 5
499491 TATTTATTAA
* *
499501 AATAT AATAT AAAAT -ATA- ATATAT AATAT ATTAT AATAT AATATT AATAT
1 AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT AATA-T AATAT
* * * * * *
499551 ACGATAT ATTA- AATTT AATAT AATAT AA-AT TAT-T AATAT ATTAA AATTT
1 A--ATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* **
499600 AAATTT AA-AT -ATAT AATAT TTTA- AATAT AATTAT AATAT A
1 -AATAT AATAT AATAT AATAT AATAT AATAT AA-TAT AATAT A
499640 TTTCTTTTTA
Statistics
Matches: 100, Mismatches: 20, Indels: 28
0.68 0.14 0.19
Matches are distributed among these distances:
3 1 0.01
4 15 0.15
5 63 0.63
6 16 0.16
7 5 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.44
Consensus pattern (5 bp):
AATAT
Found at i:499513 original size:12 final size:12
Alignment explanation
Indices: 499498--499544 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
499488 TTATATTTAT
499498 TAAAATATAATA
1 TAAAATATAATA
499510 TAAAATATAATA
1 TAAAATATAATA
*
499522 TATAATAT-AT-
1 TAAAATATAATA
*
499532 TATAATATAATA
1 TAAAATATAATA
499544 T
1 T
499545 TAATATACGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 8 0.25
11 4 0.12
12 20 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TAAAATATAATA
Found at i:499546 original size:47 final size:47
Alignment explanation
Indices: 499495--499639 Score: 116
Period size: 49 Copynumber: 3.0 Consensus size: 47
499485 ATTTTATATT
499495 TATTAAAATATAATATAAAATATAATATATAATATATTATAATATAA
1 TATTAAAATATAATATAAAATATAATATATAATATATTATAATATAA
* * * * * *
499542 TATTAATATACGATATATTAAATTTAATATA-ATATAAATTATTA-AT-A
1 TATTAAAATA-TA-ATATAAAATATAATATATA-ATATATTATAATATAA
* * *
499589 TATTAAAATTTAAATTTAAATATATAATATTTTAAATATAATTATAATATA
1 TATTAAAATAT-AATATAAA-ATATAATA-TAT-AATAT-ATTATAATATA
499640 TTTCTTTTTA
Statistics
Matches: 72, Mismatches: 15, Indels: 17
0.69 0.14 0.16
Matches are distributed among these distances:
46 5 0.07
47 26 0.36
48 5 0.07
49 27 0.38
50 7 0.10
51 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (47 bp):
TATTAAAATATAATATAAAATATAATATATAATATATTATAATATAA
Found at i:499624 original size:16 final size:16
Alignment explanation
Indices: 499495--499628 Score: 83
Period size: 16 Copynumber: 8.7 Consensus size: 16
499485 ATTTTATATT
499495 TATTAAA-ATATAATA
1 TATTAAATATATAATA
*
499510 TAAAATATAATATATAATA
1 T--ATTA-AATATATAATA
*
499529 TATTATA-ATAT-A-A
1 TATTAAATATATAATA
**
499542 TATT-AATATACGATA
1 TATTAAATATATAATA
499557 TATTAAAT-T-TAATA
1 TATTAAATATATAATA
499571 TAATATAAAT-TATTAATA
1 T-AT-TAAATATA-TAATA
*
499589 TATTAAA-ATTTAA-A
1 TATTAAATATATAATA
499603 T-TTAAATATATAATA
1 TATTAAATATATAATA
*
499618 TTTTAAATATA
1 TATTAAATATA
499629 ATTATAATAT
Statistics
Matches: 94, Mismatches: 9, Indels: 31
0.70 0.07 0.23
Matches are distributed among these distances:
12 1 0.01
13 13 0.14
14 13 0.14
15 18 0.19
16 24 0.26
17 8 0.09
18 8 0.09
19 9 0.10
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (16 bp):
TATTAAATATATAATA
Found at i:501952 original size:16 final size:16
Alignment explanation
Indices: 501933--501969 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
501923 TTTAAATTTT
501933 TTAAATTTAAATTAAG
1 TTAAATTTAAATTAAG
* *
501949 TTAAATTTAGATTAAT
1 TTAAATTTAAATTAAG
501965 TTAAA
1 TTAAA
501970 ATTTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (16 bp):
TTAAATTTAAATTAAG
Found at i:502019 original size:22 final size:23
Alignment explanation
Indices: 501985--502044 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
501975 ATTTAATTAT
*
501985 TAATTATATTATTAAAAATTTTTTA
1 TAATTA-A-TATTAAAAATATTTTA
*
502010 T-ATTAATATT-AATATATTTTA
1 TAATTAATATTAAAAATATTTTA
502031 TAATTAA-ATTAAAA
1 TAATTAATATTAAAA
502045 TAAATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
21 13 0.43
22 11 0.37
23 1 0.03
24 4 0.13
25 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTAATATTAAAAATATTTTA
Found at i:503839 original size:12 final size:12
Alignment explanation
Indices: 503822--503856 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
503812 ATTCATGATT
*
503822 ATATGATTTAAA
1 ATATGATATAAA
503834 ATATGATATAAA
1 ATATGATATAAA
*
503846 ATATAATATAA
1 ATATGATATAA
503857 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (12 bp):
ATATGATATAAA
Done.