Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007838.1 Hibiscus syriacus cultivar Beakdansim tig00110187_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: 3429202
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 13
Found at i:684 original size:39 final size:39
Alignment explanation
Indices: 630--705 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
620 TTCTTAGTTA
*
630 CATTAATTGAAATGAATTAATCGAGAATTCATCAACTTT
1 CATTAATTGAAATGAATTAATCAAGAATTCATCAACTTT
669 CATTAATTGAAATGAATTAATCAAGAATTCATCAACT
1 CATTAATTGAAATGAATTAATCAAGAATTCATCAACT
706 GTCTTTAGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (39 bp):
CATTAATTGAAATGAATTAATCAAGAATTCATCAACTTT
Found at i:2655 original size:32 final size:33
Alignment explanation
Indices: 2599--2690 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
2589 AACCCAATAA
*
2599 AATTGACATCAATTAGATATCATAAAACATT-CAT
1 AATTGATATCAATTAG--ATCATAAAACATTGCAT
* * * *
2633 ACATT-TTATCGATTAGATCATAAAACTTTGTAT
1 A-ATTGATATCAATTAGATCATAAAACATTGCAT
2666 AATTGATATCAATTAGATCATAAAA
1 AATTGATATCAATTAGATCATAAAA
2691 AAAATTATAC
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
32 15 0.31
33 21 0.44
34 9 0.19
35 3 0.06
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.36
Consensus pattern (33 bp):
AATTGATATCAATTAGATCATAAAACATTGCAT
Found at i:3748 original size:60 final size:59
Alignment explanation
Indices: 3649--3821 Score: 177
Period size: 60 Copynumber: 2.9 Consensus size: 59
3639 ACCCGAACTC
* * * *
3649 AAACTATAACCCTTGTTCTAAATTGGTTCTTAAACTTTTAAATATTTTAATTTTATCA-A
1 AAACTATGACCCTTGTTCTAAATTGG-TCTCAAACTTTTAAACATTTTAATTTCATCATA
* * *
3708 TAAACTATGACCCTCGTTCTAAATTGGTCGTCAAAGTTTTAAACATTTTAATTTCATCCTA
1 -AAACTATGACCCTTGTTCTAAATTGGTC-TCAAACTTTTAAACATTTTAATTTCATCATA
* * * * * * *
3769 AAAGTATGACCTTTATTCTAAATTGGTCCCCAAACTTTTGAGCATTTCAATTT
1 AAACTATGACCCTTGTTCTAAATTGGT-CTCAAACTTTTAAACATTTTAATTT
3822 TATCCCAAAC
Statistics
Matches: 94, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
59 2 0.02
60 90 0.96
61 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (59 bp):
AAACTATGACCCTTGTTCTAAATTGGTCTCAAACTTTTAAACATTTTAATTTCATCATA
Found at i:6410 original size:2 final size:2
Alignment explanation
Indices: 6403--6431 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6393 TAATTTTAAT
6403 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6432 GAGTTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10563 original size:58 final size:58
Alignment explanation
Indices: 10382--10609 Score: 185
Period size: 58 Copynumber: 3.9 Consensus size: 58
10372 TAAGAATATC
* * ** * * * * * *
10382 ACTTTTGGTTCACTAACCTAAAATAAAGTC-AAGCCAAGCTCGAAATCCAAACGGTGA
1 ACTTTTGGTTGACTACCCTAAAATCGAGTCTAAGTCGAGATCGAAAACCCAACAGTGA
* * * * *
10439 ACTTTTGGTTGACTGACTACCCTAAAATCGAGCCTATGTCGAGCTCGAAAAGCGAACAGTGA
1 ACTTTTGG-T---TGACTACCCTAAAATCGAGTCTAAGTCGAGATCGAAAACCCAACAGTGA
* *
10501 ACTTTTGGTTGACTACCCTAAAATCGAGTCTAAGTCGATATC-AAAACCCCAACGGT-A
1 ACTTTTGGTTGACTACCCTAAAATCGAGTCTAAGTCGAGATCGAAAA-CCCAACAGTGA
* * * *
10558 TACTTTTGGTTAACTACCCTAAAATCGAGTCTATGTCAAGCTCG-AAACCCAA
1 -ACTTTTGGTTGACTACCCTAAAATCGAGTCTAAGTCGAGATCGAAAACCCAA
10610 AAGGTGCACA
Statistics
Matches: 139, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
57 18 0.13
58 76 0.55
61 17 0.12
62 28 0.20
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (58 bp):
ACTTTTGGTTGACTACCCTAAAATCGAGTCTAAGTCGAGATCGAAAACCCAACAGTGA
Found at i:17845 original size:545 final size:535
Alignment explanation
Indices: 16349--18418 Score: 2096
Period size: 545 Copynumber: 3.8 Consensus size: 535
16339 ATGGATTCTT
* * * * * *
16349 ATTTTGAAAACTTTAATCAAGTAATTATATTAGATTTTTCT-CATCACCTTTCTGGATCTTGACA
1 ATTTTGAAAACTTTAATGAAGTAATTACATTAGATTTTT-TGCATCTCATTTCTAGATCATGACA
* * * * * *
16413 TTAATTAATTAGATTTA-AAAGTTTATTATGTGTGTTACTGACAGTTATTCAAACCCATTTTATA
65 TTAATGAATTAGATTTATAAA-TTTATTATTTATGTTACTAACAGTTATTGAAA-CTATTTTATA
** * * * *
16477 A-AATAGAGACGGATAAATAGAGAAAATAATGAATTATATTATTGATTTAAGGACACTGGATTTC
128 ATAA-AGAGACATATAAATAGAGAAAACAATGAA-TATATGATTGATTTAAGGACAATGAATTTC
* * ** *
16541 AGAGATAGTATGAATTGAATAATAAAATATTTAACAA-TGTAATATTCACCAGATCCGTAAATTA
191 AAAAATAGTATGAATTGAATAATAAAATACATAA-AAGTGTAATATTCACCAAATCCGTAAATTA
* * * *
16605 ATTGGATGCCAAATTAATGTTGGGAAAAATGGACTTTTGGTAATTTTGAGGCATATTTTCAATGA
255 ATTAGATGCCGAATTAATGTT-GAAAAAATGGACTTTTGGAAATTTTGAGGCATATTTTCAATGA
* * * *
16670 GTAAAGGTT--G-TCGAGTAATAAAATCATGGTTTTATATTCTACTCAATGAGACCTTTACAATG
319 ATAAAGGTTGAGATCGAATAATAAAATCATGATTTTATATTCTACTCAATGAGACCTTTACAACG
* *
16732 ATATATCATATGCTCAAAAT-GATTGAGTGATGAATGAGAAATTAATGATCAAAGTAAACTACAT
384 ATATATCATATGCTCAAAATAG-TTGAGTGATGAATGAGAAATTAATGCTCAAAGTAAACTACTT
* * * *
16796 GTAAACGAATTGATTATTCAACAATGGCTATTAACC-CTATACCAAGAGAAAAAAGTTACCAAAA
448 GTAAACTAATTGATTATTCAACAATGGCTATTGACCTATATATCAAGAG-AAAAAGTTACCAAAA
* **
16860 ATTATAGTTTTT-AACAGATTCAT
512 ATTATAGTTTTTAAATAGATTCCC
* * *
16883 ATTTTGAAGACTTTAATGAAGTAGTTACATTGGATTTTTTGCATCTCATTTCTAGATC-TCGACA
1 ATTTTGAAAACTTTAATGAAGTAATTACATTAGATTTTTTGCATCTCATTTCTAGATCAT-GACA
* * *
16947 TTAATGAATTAGATTTATAAA--T-TTA-TTATG-TGC-AACAATTATTCGAAACAATTTTATAA
65 TTAATGAATTAGATTTATAAATTTATTATTTATGTTACTAACAGTTATT-GAAACTATTTTATAA
* * * * * *
17006 TATAA-AGACAAATAAATAGAGAAAATAATTAATGATATGATTGGTTTAAGGACATTGAGTTTCA
129 TA-AAGAGACATATAAATAGAGAAAACAATGAAT-ATATGATTGATTTAAGGACAATGAATTTCA
* * * *
17070 GAGAGAGTATGAATTGAATAATAAAATACATAATAGTGTAATATTCACCAAATCCGTAAATTAAT
192 AAAATAGTATGAATTGAATAATAAAATACATAAAAGTGTAATATTCACCAAATCCGTAAATTAAT
* * * *
17135 TGGATGCCGAATTAATGTTGAAAAAATGGACTTTTGGTAATTTTGAAGCATATTTTCAATGAGTA
257 TAGATGCCGAATTAATGTTGAAAAAATGGACTTTTGGAAATTTTGAGGCATATTTTCAATGAATA
* * * *
17200 AAGGTTGAGATTCGAATAATAAAATCATGGTTTTATATTCTACTCCATGCA-TCCTTTACAACGG
322 AAGGTTGAGA-TCGAATAATAAAATCATGATTTTATATTCTACTCAATG-AGACCTTTACAACGA
* * * * *
17264 TATATCATATGCTCAAAATAATTAAGTGGTGAATGAGAAATTAATGCTCAATGTAAGCTACTTGT
385 TATATCATATGCTCAAAATAGTTGAGTGATGAATGAGAAATTAATGCTCAAAGTAAACTACTTGT
17329 AAACTAATTGATTATTCAACAATGGCTATTGACCATATATATATCAAGAGAAAAAGTTACCAAAA
450 AAACTAATTGATTATTCAACAATGGCTATTGACC---TATATATCAAGAGAAAAAGTTACCAAAA
*
17394 CTTATAGTTTTTAAATAGATTCCC
512 ATTATAGTTTTTAAATAGATTCCC
* * * * **
17418 ATTTTGAAAACTTTAATGATGTATTTACATTGGATTTTTTGCATTTCATTTCGGGATCATGACAT
1 ATTTTGAAAACTTTAATGAAGTAATTACATTAGATTTTTTGCATCTCATTTCTAGATCATGACAT
* * * *
17483 TAATGAATTAGATTTATAAATTTATTATTTATGTTACTGACAGTTATATGTAATTGTTTTATAAT
66 TAATGAATTAGATTTATAAATTTATTATTTATGTTACTAACAGTTAT-TGAAACTATTTTATAAT
* * *
17548 ATATA-AGACATATAAATAGAGAAAACAATGAATAATAT-ATTTGATTAAAAGACAATGAATTTT
130 A-A-AGAGACATATAAATAGAGAAAACAATGAAT-ATATGA-TTGATTTAAGGACAATGAATTTC
* * ** * *
17611 AAAAATAGTGTGAATTGAATAATAAAATACTTAAAAGTGTAATATTCATAAAATCCTTAAATCAA
191 AAAAATAGTATGAATTGAATAATAAAATACATAAAAGTGTAATATTCACCAAATCCGTAAATTAA
* * *
17676 TTAGATGCTGATTTAATGTTAGAAAAAAAATGGACTTTTGGAAATTTCGAGGCATATTTTCAATG
256 TTAGATGCCGAATTAATGTT-G--AAAAAATGGACTTTTGGAAATTTTGAGGCATATTTTCAATG
* * * * * *
17741 AATGAAGGTTGAAATTTGAATAATATAATTATGATTTTATATTCTACTCAATGAGACCTTTATAA
318 AATAAAGGTTGAGA-TCGAATAATAAAATCATGATTTTATATTCTACTCAATGAGACCTTTACAA
* * * *
17806 CGGTATATCATATGCTCAAAATAGTTGAGTGACGAATGAGAAATTGATGCTCAAAATAAACTACT
382 CGATATATCATATGCTCAAAATAGTTGAGTGATGAATGAGAAATTAATGCTCAAAGTAAACTACT
*
17871 TGTAAACTAATTGATTATTCAACAATGGCTA-TGAACCCTATATATCAATAGAAAAAGTTACCAA
447 TGTAAACTAATTGATTATTCAACAATGGCTATTG-A-CCTATATATCAAGAGAAAAAGTTACCAA
*
17935 AAATTATAGTTTTTTTAAATAGAATCCC
510 AAATTATAG--TTTTTAAATAGATTCCC
* * * * * * *
17963 ATTTTGAAAACTTTAATGAAGTAATTATAGTAGATATTTCGTATATCATTTCTAGATCAAGACAT
1 ATTTTGAAAACTTTAATGAAGTAATTACATTAGATTTTTTGCATCTCATTTCTAGATCATGACAT
* * * * ** * *
18028 TAATGAATCAGAATTATAAATTTATTACTTT-CGTTATTAAC-GATTATCTTTAATTGTTTTATA
66 TAATGAATTAGATTTATAAATTTATTA-TTTATGTTACTAACAG-TTAT-TGAAACTATTTTATA
* ** * * *
18091 ATAAAGTGACAGT-TAGGTGGAGAAAACAAT-AAGCTATATGATTGATTTAAGGA-TATTATATT
128 ATAAAGAGACA-TATAAATAGAGAAAACAATGAA--TATATGATTGATTTAAGGACAATGA-ATT
* * * * * * * * *
18153 TTAAAATTAGTGT-AATCTAAATGATAAAATAAATAAAACTTTAATATTCATCAAATCCGTAAAT
189 TCAAAAATAGTATGAAT-TGAATAATAAAATACATAAAAGTGTAATATTCACCAAATCCGTAAAT
* * ** * * * * * *
18217 AAATTAGGTATCTATTTAATGTTAGAAAAAATGGA-TTGTTAGAACTTTTGAGCCATATTTTCTA
253 TAATTAGATGCCGAATTAATGTT-GAAAAAATGGACTT-TTGGAAATTTTGAGGCATATTTTCAA
* * * * * * *
18281 TGGATAAAGGTGGAGATTC-AAGCAATAAAAAT-ATTATTTTATATTCTATTCTATGAGATCTTT
316 TGAATAAAGGTTGAGA-TCGAA-TAAT-AAAATCATGATTTTATATTCTACTCAATGAGACCTTT
* * ** * ** *
18344 AAAACGATATACCATATATTCAAAATGGTTGAGTGATGAATGAGAAATTAAAACTCAAAGTAAGC
378 ACAACGATATATCATATGCTCAAAATAGTTGAGTGATGAATGAGAAATTAATGCTCAAAGTAAAC
18409 TACTTGTAAA
443 TACTTGTAAA
18419 TTTTGTTGAG
Statistics
Matches: 1305, Mismatches: 182, Indels: 90
0.83 0.12 0.06
Matches are distributed among these distances:
527 52 0.04
528 143 0.11
529 8 0.01
530 4 0.00
531 138 0.11
532 2 0.00
533 2 0.00
534 94 0.07
535 98 0.08
536 1 0.00
537 1 0.00
538 3 0.00
539 5 0.00
540 2 0.00
541 27 0.02
542 258 0.20
543 47 0.04
544 110 0.08
545 305 0.23
546 5 0.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (535 bp):
ATTTTGAAAACTTTAATGAAGTAATTACATTAGATTTTTTGCATCTCATTTCTAGATCATGACAT
TAATGAATTAGATTTATAAATTTATTATTTATGTTACTAACAGTTATTGAAACTATTTTATAATA
AAGAGACATATAAATAGAGAAAACAATGAATATATGATTGATTTAAGGACAATGAATTTCAAAAA
TAGTATGAATTGAATAATAAAATACATAAAAGTGTAATATTCACCAAATCCGTAAATTAATTAGA
TGCCGAATTAATGTTGAAAAAATGGACTTTTGGAAATTTTGAGGCATATTTTCAATGAATAAAGG
TTGAGATCGAATAATAAAATCATGATTTTATATTCTACTCAATGAGACCTTTACAACGATATATC
ATATGCTCAAAATAGTTGAGTGATGAATGAGAAATTAATGCTCAAAGTAAACTACTTGTAAACTA
ATTGATTATTCAACAATGGCTATTGACCTATATATCAAGAGAAAAAGTTACCAAAAATTATAGTT
TTTAAATAGATTCCC
Found at i:21307 original size:21 final size:21
Alignment explanation
Indices: 21283--21333 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
21273 TGAACACAAC
*
21283 ATAATATACATACACTTTCAT
1 ATAATATACATACACGTTCAT
21304 ATAATATACATACACGTTCAT
1 ATAATATACATACACGTTCAT
21325 ATATATATA
1 ATA-ATATA
21334 TATGCAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAATATACATACACGTTCAT
Found at i:28322 original size:2 final size:2
Alignment explanation
Indices: 28311--28346 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
28301 AGTCATCTTT
28311 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28347 TGGGAATCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31408 original size:2 final size:2
Alignment explanation
Indices: 31403--31466 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
31393 ATGAGCGCGC
31403 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
31445 AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
31467 AAAGATAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39697 original size:16 final size:16
Alignment explanation
Indices: 39666--39705 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
39656 TTTACTTCAA
*
39666 AATGATT-AAGTGCTG
1 AATGATTCAAATGCTG
39681 AATGATTCAAATGCTG
1 AATGATTCAAATGCTG
*
39697 AATAATTCA
1 AATGATTCA
39706 GGAACTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (16 bp):
AATGATTCAAATGCTG
Found at i:41117 original size:2 final size:2
Alignment explanation
Indices: 41110--41147 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
41100 ATGATTTAGA
41110 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
41148 GTGTGTGATT
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:42617 original size:60 final size:60
Alignment explanation
Indices: 42543--42679 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
42533 AACTTTTGGA
* * * *
42543 AAAAGTATAC-AAATGATTC-ATTGACTATAATATATTATTTTGTTGAGTTCATCGATTATT
1 AAAAGT-TACAAAATGATTCAATTGACTATAAGATATTACTTTGTTGAG-TCATCGACTATC
* * * *
42603 AAAAGTTACAAAATG-GTCAATTGACTATAAGATGTTGCTTTGTTGAGTCATTGACTATC
1 AAAAGTTACAAAATGATTCAATTGACTATAAGATATTACTTTGTTGAGTCATCGACTATC
42662 AAAAGTTACAAAATGATT
1 AAAAGTTACAAAATGATT
42680 ACTCAACTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 29 0.45
60 36 0.55
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (60 bp):
AAAAGTTACAAAATGATTCAATTGACTATAAGATATTACTTTGTTGAGTCATCGACTATC
Found at i:45661 original size:13 final size:13
Alignment explanation
Indices: 45643--45669 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
45633 GTGCTGGAAT
45643 TTATAGACTTCTC
1 TTATAGACTTCTC
45656 TTATAGACTTCTC
1 TTATAGACTTCTC
45669 T
1 T
45670 GTCACTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (13 bp):
TTATAGACTTCTC
Found at i:63200 original size:153 final size:150
Alignment explanation
Indices: 62925--63207 Score: 381
Period size: 153 Copynumber: 1.9 Consensus size: 150
62915 CAAGGTGCCA
* * *
62925 GATGTTGGTTGGGATGCTTCTGCGTGGAACAAAAATGCTGAAAATGGTGACAAATTTGCAGCAGC
1 GATGTTGGTTGGGATGCTTCTGCATGGAACAAAAATGCAGAAAACGGTGACAAATTTGCAGCAGC
** ** *
62990 TGCGACCAGTCCGAAGAAGCAAAACGAGTGGTCTGGTTGGGGGGCGAGCAAATCTAAATCGCAAG
66 TGCGACCAGTCCGAAGAAGCAAAACGAGTGGTCTGACTGGGGCACGAGCAAATCTAAATCACAAG
63055 ATGTTGTTCCTCCAAAAGTG
131 ATGTTGTTCCTCCAAAAGTG
* * ** *
63075 GATGTTGGTTGGGATGCTTCGTCTGCATTGAATAAAAATGCAGAGGACGGTGACAATTTTGCAGC
1 GATGTTGGTTGGGATGC-T--TCTGCATGGAACAAAAATGCAGAAAACGGTGACAAATTTGCAGC
*
63140 AGCTGC-ATCCAG-CTCGAAGAAGCAAAATGAGTGGTCTGACTGGGGCACGAGCAAATCTAAATC
63 AGCTGCGA-CCAGTC-CGAAGAAGCAAAACGAGTGGTCTGACTGGGGCACGAGCAAATCTAAATC
63203 ACAAG
126 ACAAG
63208 GTGGCTCCAC
Statistics
Matches: 114, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
150 17 0.15
151 1 0.01
152 2 0.02
153 94 0.82
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.23
Consensus pattern (150 bp):
GATGTTGGTTGGGATGCTTCTGCATGGAACAAAAATGCAGAAAACGGTGACAAATTTGCAGCAGC
TGCGACCAGTCCGAAGAAGCAAAACGAGTGGTCTGACTGGGGCACGAGCAAATCTAAATCACAAG
ATGTTGTTCCTCCAAAAGTG
Found at i:63811 original size:36 final size:36
Alignment explanation
Indices: 63795--64038 Score: 276
Period size: 36 Copynumber: 6.8 Consensus size: 36
63785 GTATACAATG
* *
63795 AATAGTTCCTGGGACCATCAAAAGTCACCTGCAACT
1 AATAGTTCTTGGGACCAACAAAAGTCACCTGCAACT
* * * *
63831 AATAGTTATTGGGACCAACAGAAGTCACCTGCGACG
1 AATAGTTCTTGGGACCAACAAAAGTCACCTGCAACT
63867 AATAGTTCTTGGGACCAACAAAAGTCACCTGCAACT
1 AATAGTTCTTGGGACCAACAAAAGTCACCTGCAACT
* ** *
63903 AATAGTTCTTGGGACCAACAGAAGTCACCTGTGACA
1 AATAGTTCTTGGGACCAACAAAAGTCACCTGCAACT
* * * **
63939 AATAGTTCTTGGAACCAGCAAAAGTCACCTAC-GGT
1 AATAGTTCTTGGGACCAACAAAAGTCACCTGCAACT
* * *
63974 GAATAGTTCATGGGACCAACAAAAGTCACCTACAGC-
1 -AATAGTTCTTGGGACCAACAAAAGTCACCTGCAACT
* *
64010 GATGAGTTCTTGGGATCAACAAAAGTCAC
1 AAT-AGTTCTTGGGACCAACAAAAGTCAC
64039 AAGAAAGTTT
Statistics
Matches: 176, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
35 2 0.01
36 173 0.98
37 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (36 bp):
AATAGTTCTTGGGACCAACAAAAGTCACCTGCAACT
Found at i:63916 original size:108 final size:107
Alignment explanation
Indices: 63771--64038 Score: 311
Period size: 108 Copynumber: 2.5 Consensus size: 107
63761 TAATTCTTCA
*** * * * *
63771 GACCAACAAAAGTCGTATACAATGAATAGTTCCTGGGACCATCAAAAGTCACCTGCAACTAATAG
1 GACCAACAAAAGTCACCTACAA-CAATAGTTCTTGGGACCAACAAAAGTCACCTGCAACAAATAG
* * * *
63836 TTATTGGGACCAACAGAAGTCACCTGCGACGAATAGTTCTTGG
65 TTATTGGAACCAACAAAAGTCACCTACGACGAATAGTTCATGG
* * **
63879 GACCAACAAAAGTCACCTGCAACTAATAGTTCTTGGGACCAACAGAAGTCACCTGTGACAAATAG
1 GACCAACAAAAGTCACCTACAAC-AATAGTTCTTGGGACCAACAAAAGTCACCTGCAACAAATAG
* * **
63944 TTCTTGGAACCAGCAAAAGTCACCTACGGTGAATAGTTCATGG
65 TTATTGGAACCAACAAAAGTCACCTACGACGAATAGTTCATGG
* * *
63987 GACCAACAAAAGTCACCTACAGCGATGAGTTCTTGGGATCAACAAAAGTCAC
1 GACCAACAAAAGTCACCTACAACAAT-AGTTCTTGGGACCAACAAAAGTCAC
64039 AAGAAAGTTT
Statistics
Matches: 134, Mismatches: 24, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
107 2 0.01
108 132 0.99
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (107 bp):
GACCAACAAAAGTCACCTACAACAATAGTTCTTGGGACCAACAAAAGTCACCTGCAACAAATAGT
TATTGGAACCAACAAAAGTCACCTACGACGAATAGTTCATGG
Found at i:66147 original size:39 final size:39
Alignment explanation
Indices: 66093--66223 Score: 208
Period size: 39 Copynumber: 3.4 Consensus size: 39
66083 CTCGTTTTGG
*
66093 AGGGAATCGTGAGCGAAGTGTTGCTCCGGAGAATTCTCA
1 AGGGAACCGTGAGCGAAGTGTTGCTCCGGAGAATTCTCA
** * *
66132 AGGGAACCGTGAGCGAAGCATTGGTCCGAAGAATTCTCA
1 AGGGAACCGTGAGCGAAGTGTTGCTCCGGAGAATTCTCA
*
66171 AGTGAACCGTGAGCGAAGTGTTGCTCCGGAGAATTCTCA
1 AGGGAACCGTGAGCGAAGTGTTGCTCCGGAGAATTCTCA
66210 AGGGAACCGTGAGC
1 AGGGAACCGTGAGC
66224 AACACTGGAA
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (39 bp):
AGGGAACCGTGAGCGAAGTGTTGCTCCGGAGAATTCTCA
Found at i:66262 original size:57 final size:57
Alignment explanation
Indices: 66174--66282 Score: 173
Period size: 57 Copynumber: 1.9 Consensus size: 57
66164 ATTCTCAAGT
* * * *
66174 GAACCGTGAGCGAAGTGTTGCTCCGGAGAATTCTCAAGGGAACCGTGAGCAACACTG
1 GAACCATGAGCAAAGCGTTGCTCCAGAGAATTCTCAAGGGAACCGTGAGCAACACTG
*
66231 GAACCATGAGCAAAGCGTTGCTCCAGAGAATTCTCAAGGGAACGGTGAGCAA
1 GAACCATGAGCAAAGCGTTGCTCCAGAGAATTCTCAAGGGAACCGTGAGCAA
66283 AGCGCTGCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.31, C:0.22, G:0.30, T:0.17
Consensus pattern (57 bp):
GAACCATGAGCAAAGCGTTGCTCCAGAGAATTCTCAAGGGAACCGTGAGCAACACTG
Found at i:77055 original size:15 final size:17
Alignment explanation
Indices: 77030--77062 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
77020 GTTTCTCTGT
77030 TTTTCGTTAATTT-CTC
1 TTTTCGTTAATTTACTC
77046 TTTT-GTTAATTTACTC
1 TTTTCGTTAATTTACTC
77062 T
1 T
77063 CATACCGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.64
Consensus pattern (17 bp):
TTTTCGTTAATTTACTC
Found at i:77439 original size:2 final size:2
Alignment explanation
Indices: 77432--77466 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
77422 GCATCTTCTC
77432 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
77467 TTTCCGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:79730 original size:20 final size:20
Alignment explanation
Indices: 79700--79751 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
79690 TGCGATTTTC
*
79700 CAAATTCGCAACGCGAATCTG
1 CAAA-TCGCAACGCGAATATG
*
79721 TAAATCGCAACGCGAATATG
1 CAAATCGCAACGCGAATATG
79741 CAAATCGCAAC
1 CAAATCGCAAC
79752 ACAGAAGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.17
Consensus pattern (20 bp):
CAAATCGCAACGCGAATATG
Found at i:79828 original size:20 final size:18
Alignment explanation
Indices: 79805--79851 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
79795 GATTTTCGAA
79805 TTCGCAACAAGAATTTTAAT
1 TTCGCAACAAG--TTTTAAT
* *
79825 TTCGCAACATGTTTTATT
1 TTCGCAACAAGTTTTAAT
79843 TTCGCAACA
1 TTCGCAACA
79852 CAAATGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.60
20 10 0.40
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (18 bp):
TTCGCAACAAGTTTTAAT
Found at i:80010 original size:16 final size:16
Alignment explanation
Indices: 79989--80028 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
79979 TCCCCATCTC
*
79989 TAATTTTTTTTTTACA
1 TAATTTTTTTTCTACA
* *
80005 TAATTTTATTTCTATA
1 TAATTTTTTTTCTACA
80021 TAATTTTT
1 TAATTTTT
80029 CAATGATTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TAATTTTTTTTCTACA
Found at i:80804 original size:24 final size:24
Alignment explanation
Indices: 80751--80797 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
80741 GTATTCAAAA
*
80751 TTTGATCTTGGTCAATACCTGGAC
1 TTTGATCTTGGTCAATACCAGGAC
80775 TTTGATCTTGGTCAATACTCAGG
1 TTTGATCTTGGTCAATAC-CAGG
80798 TTTTGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGGAC
Found at i:83088 original size:18 final size:18
Alignment explanation
Indices: 83065--83100 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
83055 AAGGAAAAGG
*
83065 AAATCAAAATTGCAATCA
1 AAATCAAAATTCCAATCA
83083 AAATCAAAATTCCAATCA
1 AAATCAAAATTCCAATCA
83101 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.19, G:0.03, T:0.22
Consensus pattern (18 bp):
AAATCAAAATTCCAATCA
Found at i:83348 original size:29 final size:29
Alignment explanation
Indices: 83306--83378 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
83296 AATTCGCAAC
**
83306 GCGAAAGTCAAATTCACATTGTGATTGTT
1 GCGAAAGTCAAATTCACATTACGATTGTT
* *
83335 GCGAAAGTCAAATTCGCGTTACGATTGTT
1 GCGAAAGTCAAATTCACATTACGATTGTT
* *
83364 GCAAAAATCAAATTC
1 GCGAAAGTCAAATTC
83379 GAAACGCGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (29 bp):
GCGAAAGTCAAATTCACATTACGATTGTT
Found at i:84870 original size:42 final size:42
Alignment explanation
Indices: 84795--84893 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
84785 GTGATAGAAT
* * * * *
84795 AGGTGATGGCTCTCGTTGTGGAGGTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAAAATCGGCTCAATC
* *
84837 ATGTGATGGCTCTGGGTGTCGAGCTGTAAAATCGGCTCAATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAAAATCGGCTCAATC
84879 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
84894 AAGTGGGGGG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTGTAAAATCGGCTCAATC
Found at i:86454 original size:20 final size:20
Alignment explanation
Indices: 86429--86479 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
86419 GAAACTAAAA
*
86429 TCGCGTTGCTATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
86449 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
*
86469 TCGTGTTGCGA
1 TCGCGTTGCGA
86480 ATTTAAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.49
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:86490 original size:20 final size:20
Alignment explanation
Indices: 86447--86490 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
86437 CTATTTTCAT
* * *
86447 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
*
86467 TTTCGTGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
86487 TTTC
1 TTTC
86491 AAAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:87029 original size:20 final size:20
Alignment explanation
Indices: 87004--87052 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
86994 TAAACGCGCT
87004 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
* *
87024 TTGCGAATTTGATTTCTGTG
1 TTGCGAATTTGACTTATGTG
87044 TTGCGAATT
1 TTGCGAATT
87053 ACAAATTCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.10, G:0.24, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:94803 original size:23 final size:21
Alignment explanation
Indices: 94742--94795 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
94732 ACCGAGAAAG
*
94742 AAGAC-AAAAAACGTGTCATA
1 AAGACAAAAAAACGTGTCACA
94762 AAGACAAAAAAACGTGTCACA
1 AAGACAAAAAAACGTGTCACA
*
94783 AAGGCAAAGAAAA
1 AAGACAAA-AAAA
94796 ACATGTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 5 0.17
21 21 0.70
22 4 0.13
ACGTcount: A:0.59, C:0.15, G:0.17, T:0.09
Consensus pattern (21 bp):
AAGACAAAAAAACGTGTCACA
Found at i:95522 original size:25 final size:26
Alignment explanation
Indices: 95467--95527 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
95457 TATTAAAATT
* *
95467 ATTATTTTATATATTAAAAATAGGAA
1 ATTATTTTATATAATAAAAATAGAAA
* *
95493 A-TATTTTATA-AATAAAATTATAAA
1 ATTATTTTATATAATAAAAATAGAAA
95517 ATTATTGTTAT
1 ATTATT-TTAT
95528 CCATTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 11 0.38
25 13 0.45
26 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (26 bp):
ATTATTTTATATAATAAAAATAGAAA
Found at i:96037 original size:50 final size:50
Alignment explanation
Indices: 95983--96090 Score: 117
Period size: 50 Copynumber: 2.1 Consensus size: 50
95973 CAGTAAAGCA
** * * * *
95983 CGCCCCTTGAACCGCGTTATACGTTGATTTGGCATCACGTGGGTATAGTG
1 CGCCCCTTGAACCGCGACATACGGTGATTTGACACCACGTGGGTATAGCG
* ** *
96033 CGCCCCCTGCCCCGCGACATACGGTGATTTGACGCCACGTGGGTATAGCG
1 CGCCCCTTGAACCGCGACATACGGTGATTTGACACCACGTGGGTATAGCG
96083 CGTCCCCT
1 CG-CCCCT
96091 GATTCGCATT
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
50 42 0.91
51 4 0.09
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (50 bp):
CGCCCCTTGAACCGCGACATACGGTGATTTGACACCACGTGGGTATAGCG
Found at i:98535 original size:29 final size:29
Alignment explanation
Indices: 98493--98549 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
98483 ATGTCATTCC
*
98493 CCCGTTTGTTTGGCAAACATTCTCAGTCT
1 CCCGTTTGGTTGGCAAACATTCTCAGTCT
98522 CCCGTTTGGTTGGCAAACATTCTCAGTC
1 CCCGTTTGGTTGGCAAACATTCTCAGTC
98550 CCCTGTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (29 bp):
CCCGTTTGGTTGGCAAACATTCTCAGTCT
Found at i:99082 original size:18 final size:18
Alignment explanation
Indices: 99055--99100 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
99045 AATATTCTCA
99055 GTAATTTTATTCCTACTG
1 GTAATTTTATTCCTACTG
*
99073 GTAATCTTATTCCTACTG
1 GTAATTTTATTCCTACTG
*
99091 ATAATTTTAT
1 GTAATTTTAT
99101 ATTTTGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (18 bp):
GTAATTTTATTCCTACTG
Found at i:102780 original size:3 final size:3
Alignment explanation
Indices: 102772--102806 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
102762 GTCATTTTGT
102772 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
102807 CTATGATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:105150 original size:31 final size:33
Alignment explanation
Indices: 105108--105182 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
105098 ATAATTCTAA
* * *
105108 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
* *
105140 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
105171 ATAAAAAATAAT
1 ATAAAAAATAAT
105183 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 18 0.51
32 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAAATATATTAAT
Found at i:105150 original size:34 final size:31
Alignment explanation
Indices: 105105--105193 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
105095 TTAATAATTC
*
105105 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
105139 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
105170 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
105194 AAAATAAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 2 0.04
34 22 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:112235 original size:24 final size:24
Alignment explanation
Indices: 112208--112282 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
112198 TATGGTACTC
112208 AACTACTACCAAACCTTTAAAGTA
1 AACTACTACCAAACCTTTAAAGTA
* ** **
112232 AACT-CCAAAAAACTACGGT--AGTA
1 AACTACTACCAAAC--CTTTAAAGTA
112255 AACTACTACCAAACCTTTAAAGTA
1 AACTACTACCAAACCTTTAAAGTA
112279 AACT
1 AACT
112283 CCGAAACCTT
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
22 2 0.06
23 14 0.39
24 18 0.50
25 2 0.06
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.23
Consensus pattern (24 bp):
AACTACTACCAAACCTTTAAAGTA
Found at i:112245 original size:47 final size:47
Alignment explanation
Indices: 112191--112284 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
112181 TTAAAAAAGA
* *
112191 AAAAAACTATGGTACTCAACTACTACCAAACCTTTAAAGTAAACTCC
1 AAAAAACTACGGTACTAAACTACTACCAAACCTTTAAAGTAAACTCC
*
112238 AAAAAACTACGGTAGTAAACTACTACCAAACCTTTAAAGTAAACTCC
1 AAAAAACTACGGTACTAAACTACTACCAAACCTTTAAAGTAAACTCC
112285 GAAACCTTCT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (47 bp):
AAAAAACTACGGTACTAAACTACTACCAAACCTTTAAAGTAAACTCC
Found at i:115431 original size:3 final size:3
Alignment explanation
Indices: 115423--115479 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
115413 TGGTTTCATT
* *
115423 TTA TTA TTA TTA CTA TTA -TA TTA TTA TTTA TTT TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
115468 TTA TTA TTA TTA
1 TTA TTA TTA TTA
115480 CAAACAGACC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:116906 original size:21 final size:23
Alignment explanation
Indices: 116850--116907 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 23
116840 TCATTTTTTG
* *
116850 TTATTTTTAAATAAATAAATATT
1 TTATTTTTAGATAAATAAATATA
*
116873 TTATTTTT-G-TAAAT-TATA-A
1 TTATTTTTAGATAAATAAATATA
116892 TTATTTTTAGATAAAT
1 TTATTTTTAGATAAAT
116908 GTTTTATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.27
20 4 0.13
21 10 0.33
23 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (23 bp):
TTATTTTTAGATAAATAAATATA
Found at i:117003 original size:131 final size:127
Alignment explanation
Indices: 116781--117137 Score: 481
Period size: 131 Copynumber: 2.8 Consensus size: 127
116771 TATCTAAGTA
* *
116781 TTTTAATATTTATTTATTTTTTAATATTAAGAAATAGCAGTCTTAAAGCAACTGGATGTTCATTT
1 TTTTAATATTTATTTACTTTTTAATATTAAGAAATAGCAGTCTTAAAGCAACTGAATG-TCATTT
* *
116846 TTTGTTATTTTTAAATAAATAAATATTTTATTTTTGTAAATTATAAT-TATTTTTAGATAAATG
65 TTTGATATTTTTAAATAAATAAATATTTTATTTTTGTAAATTAT-ATCTATTTTTAAATAAATG
*
116909 TTTTATTAATATTTATTTA-TTTTTAATATTAAGAAA-GGACAGTCTTAAAGCAACTGAATGTCC
1 --TT-TTAATATTTATTTACTTTTTAATATTAAGAAATAG-CAGTCTTAAAGCAACTGAATGT-C
**
116972 ATTTTTCTGATATTTTTAAATAAATAAATATTTTACATTTGTAAATTATATCTATTTTTAAATAA
61 ATTTTT-TGATATTTTTAAATAAATAAATATTTTATTTTTGTAAATTATATCTATTTTTAAATAA
117037 ATG
125 ATG
* *
117040 TTTTAATATTTATTTACTTTTTAATATTAAGAAAATAGCTA-TTTTAAAGCACCTAGAA-GTCAT
1 TTTTAATATTTATTTACTTTTTAATATTAAG-AAATAGC-AGTCTTAAAGCAACT-GAATGTCAT
* *
117103 TTTATGATATTTTTAAATAAATAAATATCTTATTT
63 TTTTTGATATTTTTAAATAAATAAATATTTTATTT
117138 ATATATATAA
Statistics
Matches: 204, Mismatches: 13, Indels: 22
0.85 0.05 0.09
Matches are distributed among these distances:
128 42 0.21
129 24 0.12
130 65 0.32
131 73 0.36
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.49
Consensus pattern (127 bp):
TTTTAATATTTATTTACTTTTTAATATTAAGAAATAGCAGTCTTAAAGCAACTGAATGTCATTTT
TTGATATTTTTAAATAAATAAATATTTTATTTTTGTAAATTATATCTATTTTTAAATAAATG
Found at i:121446 original size:60 final size:59
Alignment explanation
Indices: 121289--121455 Score: 165
Period size: 60 Copynumber: 2.8 Consensus size: 59
121279 TATAGTTTGT
* * * *
121289 GATGAAATTGGAATATTTAAAAAATTTAGAAACCAATTTAGAATAAAAGTAATAGTCTAG
1 GATGAAATTGAAATATTT-AAAAGTTTAGAAACCAATTTAGAATGAAAGTAATAGTCTAA
* * * * ** * *
121349 GATGAAATTGAAATATTCAAAAGTTTA-ATGACTAATTTAGAATGAGAGTCTTATTTTATA
1 GATGAAATTGAAATATTTAAAAGTTTAGA-AACCAATTTAGAATGAAAGTAATAGTCTA-A
* * *
121409 GATGAAATTAAAATATTTAAAAGTTTAGACACCAATTTAAAATGAAA
1 GATGAAATTGAAATATTTAAAAGTTTAGAAACCAATTTAGAATGAAA
121456 TACATACTTG
Statistics
Matches: 86, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
58 1 0.01
59 29 0.34
60 55 0.64
61 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (59 bp):
GATGAAATTGAAATATTTAAAAGTTTAGAAACCAATTTAGAATGAAAGTAATAGTCTAA
Found at i:134912 original size:24 final size:24
Alignment explanation
Indices: 134885--134975 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
134875 TTCATTTGAT
* *
134885 TTCTGATCTGATACTTGACATAAA
1 TTCTGATATGATACTTGACATAGA
134909 TTCTGATATGATA-TATGACATAGA
1 TTCTGATATGATACT-TGACATAGA
* * *
134933 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATAGA
*
134957 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
134976 GTGAATTATG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATAGA
Found at i:134987 original size:24 final size:24
Alignment explanation
Indices: 134885--134992 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
134875 TTCATTTGAT
* *
134885 TTCTGATCTGATACTTGACATAAA
1 TTCTGATATGATACTTGACATGAA
134909 TTCTGATATGATA-TATGACAT-AGA
1 TTCTGATATGATACT-TGACATGA-A
* * *
134933 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGAA
* *
134957 TTTTGATATGATACTTGACGTGAA
1 TTCTGATATGATACTTGACATGAA
* *
134981 TTATGATTTGAT
1 TTCTGATATGAT
134993 TTTTGATATA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.03
24 67 0.96
25 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.41
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGAA
Found at i:136586 original size:56 final size:55
Alignment explanation
Indices: 136495--136603 Score: 130
Period size: 56 Copynumber: 2.0 Consensus size: 55
136485 CTTGGGTCCG
* * *
136495 AGACACTGGTGCAAGTGTCCGACAGAGAGGTTCAAGATAGAGGATCGGGCTTGCTA
1 AGACACTGGTGCAAGAGTCCGAAAGAGAGATTCAAGATAG-GGATCGGGCTTGCTA
* * **
136551 AGACATTGGTGCAAGAGTCCGAAAGGGA-ATCTCAAGATAGTTATCGGGCTTGC
1 AGACACTGGTGCAAGAGTCCGAAAGAGAGAT-TCAAGATAGGGATCGGGCTTGC
136604 CAAAGCCACC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
55 12 0.27
56 33 0.73
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.21
Consensus pattern (55 bp):
AGACACTGGTGCAAGAGTCCGAAAGAGAGATTCAAGATAGGGATCGGGCTTGCTA
Found at i:138719 original size:51 final size:51
Alignment explanation
Indices: 138661--139069 Score: 253
Period size: 51 Copynumber: 7.7 Consensus size: 51
138651 CCGCCATTGT
138661 CACTTCCACTTTCAGTTCCAGAAGCACCCCATCCACCCCCACCACCCTTGC
1 CACTTCCACTTTCAGTTCCAGAAGCACCCCATCCACCCCCACCACCCTTGC
*
138712 CACTTCCACTTTCAGTTCCAGAAGCACCCCATCCGCCGCCACCGCCACCCCAACCAC-TGCC
1 CACTTCCACTTTCAGTTCCAGAAGCACCCCAT------CCACC-CC-CACC-ACC-CTTG-C
* * *
138773 GCTACTCTTTCCACTTCCACTATCAATTCTAGAAGCACCCCATCCACCACCACCACCCTTGC
1 -C-A--C-TTCCACTTTCAGT-TC----C-AGAAGCACCCCATCCACCCCCACCACCCTTGC
* * *
138835 CACTTCCAC--T---TT-CAGAAGCACCCCATCCGCCGCCGCCACCCTTGC
1 CACTTCCACTTTCAGTTCCAGAAGCACCCCATCCACCCCCACCACCCTTGC
*** *** * * * * *
138880 CACTTCCACTTTCAGAAGCA-TCCCATCCGCC-GCCGCCGCCGCCCCCCTTGC
1 CACTTCCACTTTCAGTTCCAGAAGCA-CC-CCATCCACCCCCACCACCCTTGC
* * * *
138931 CAGTTCCACTTTTAGTTCCATAAGCACCCCATCC-CCCACCACCACCCTTCC
1 CACTTCCACTTTCAGTTCCAGAAGCACCCCATCCACCC-CCACCACCCTTGC
* * * ***
138982 CATTTCCACTTTCAGTTCCAGAAGCACCCCATCCACCACCACCACCATAAA
1 CACTTCCACTTTCAGTTCCAGAAGCACCCCATCCACCCCCACCACCCTTGC
* *
139033 CACTGCCACTTTCAGTTCCCGAAGCACCCCATCCACC
1 CACTTCCACTTTCAGTTCCAGAAGCACCCCATCCACC
139070 AGTACCACCG
Statistics
Matches: 283, Mismatches: 40, Indels: 70
0.72 0.10 0.18
Matches are distributed among these distances:
45 38 0.13
46 1 0.00
47 1 0.00
50 6 0.02
51 158 0.56
52 7 0.02
57 11 0.04
58 3 0.01
59 3 0.01
60 6 0.02
61 3 0.01
62 3 0.01
63 6 0.02
64 3 0.01
65 2 0.01
66 16 0.06
67 2 0.01
71 1 0.00
72 13 0.05
ACGTcount: A:0.22, C:0.49, G:0.10, T:0.20
Consensus pattern (51 bp):
CACTTCCACTTTCAGTTCCAGAAGCACCCCATCCACCCCCACCACCCTTGC
Found at i:138761 original size:72 final size:72
Alignment explanation
Indices: 138685--138826 Score: 176
Period size: 72 Copynumber: 2.0 Consensus size: 72
138675 GTTCCAGAAG
* * * * *
138685 CACCCCATCCACCCCCACCACCCTTGCCACTTCCACTTTCAGTTCCAGAAGCACCCCATCCGCCG
1 CACCCCAACCACCCCCACCACCCTTGCCACTTCCACTATCAATTCCAGAAGCACCCCATCCACCA
138750 CCACCGC
66 CCACCGC
** * * * * *
138757 CACCCCAACCACTGCCGCTACTCTTTCCACTTCCACTATCAATTCTAGAAGCACCCCATCCACCA
1 CACCCCAACCACCCCCACCACCCTTGCCACTTCCACTATCAATTCCAGAAGCACCCCATCCACCA
138822 CCACC
66 CCACC
138827 ACCCTTGCCA
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.23, C:0.52, G:0.08, T:0.18
Consensus pattern (72 bp):
CACCCCAACCACCCCCACCACCCTTGCCACTTCCACTATCAATTCCAGAAGCACCCCATCCACCA
CCACCGC
Found at i:138854 original size:45 final size:45
Alignment explanation
Indices: 138803--139112 Score: 176
Period size: 51 Copynumber: 6.4 Consensus size: 45
138793 TATCAATTCT
138803 AGAAGCACCCCATCCACCACCACCACCCTTGCCACTTCCACTTTC
1 AGAAGCACCCCATCCACCACCACCACCCTTGCCACTTCCACTTTC
* * *
138848 AGAAGCACCCCATCCGCCGCCGCCACCCTTGCCACTTCCACTTTC
1 AGAAGCACCCCATCCACCACCACCACCCTTGCCACTTCCACTTTC
* * * * * *
138893 AGAAGCATCCCATCCGCCGCCGCCGCCGCCCCCCTTGCCAGTTCCACTTTTAGTTCC
1 AGAAGCACCCCAT------CCACCACCACCACCCTTGCCACTTCCAC---T--TT-C
* * * *
138950 ATAAGCACCCCATCCCCCACCACCACCCTTCCCATTTCCACTTTCAGTTCC
1 AGAAGCACCCCATCCACCACCACCACCCTTGCCACTTCCAC--T---TT-C
* * * *
139001 AGAAGCACCCCATCCACCACCACCACCATAAACACTGCCACTTTCAGTTCC
1 AGAAGCACCCCATCCACCACCACCACC-----C-TTGCCACTTCCACTTTC
* ** * * *
139052 CGAAGCACCCCATCCACCAGTACCA-CC--GCCACTTTCAGTTCC
1 AGAAGCACCCCATCCACCACCACCACCCTTGCCACTTCCACTTTC
139094 AGAAGCACCCCATCCACCA
1 AGAAGCACCCCATCCACCA
139113 GGGAAAGCTT
Statistics
Matches: 220, Mismatches: 26, Indels: 41
0.77 0.09 0.14
Matches are distributed among these distances:
42 33 0.15
45 55 0.25
50 4 0.02
51 102 0.46
52 1 0.00
54 1 0.00
55 1 0.00
56 3 0.01
57 20 0.09
ACGTcount: A:0.23, C:0.49, G:0.10, T:0.18
Consensus pattern (45 bp):
AGAAGCACCCCATCCACCACCACCACCCTTGCCACTTCCACTTTC
Found at i:138882 original size:123 final size:123
Alignment explanation
Indices: 138630--138868 Score: 339
Period size: 123 Copynumber: 2.0 Consensus size: 123
138620 GTTAGTACCA
* * *
138630 CCACCCCAACCACTGCCGCCTCCGCCATTGTCACTTCCACTTTCAGTTCCAGAAGCACCCCATCC
1 CCACCCCAACCACTGCCGCCTACGCCATTGTCACTTCCACTATCAATTCCAGAAGCACCCCATCC
*
138695 ACCCCCACCACCCTTGCCACTTCCACTTTCAGTTCCAGAAGCACCCCATCCGCCGCCACCG
66 ACCACCACCACCCTTGCCACTTCCAC-TT-A-TTCCAGAAGCACCCCATCCGCCGCCACCG
* *
138756 CCACCCCAACCACTGCCG-CTAC-TC-TT-TCCACTTCCACTATCAATTCTAGAAGCACCCCATC
1 CCACCCCAACCACTGCCGCCTACGCCATTGT-CACTTCCACTATCAATTCCAGAAGCACCCCATC
138817 CACCACCACCACCCTTGCCACTTCCAC-T-TT-CAGAAGCACCCCATCCGCCGCC
65 CACCACCACCACCCTTGCCACTTCCACTTATTCCAGAAGCACCCCATCCGCCGCC
138869 GCCACCCTTG
Statistics
Matches: 106, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
117 22 0.21
118 2 0.02
121 1 0.01
122 1 0.01
123 58 0.55
124 1 0.01
125 3 0.03
126 18 0.17
ACGTcount: A:0.21, C:0.50, G:0.10, T:0.19
Consensus pattern (123 bp):
CCACCCCAACCACTGCCGCCTACGCCATTGTCACTTCCACTATCAATTCCAGAAGCACCCCATCC
ACCACCACCACCCTTGCCACTTCCACTTATTCCAGAAGCACCCCATCCGCCGCCACCG
Found at i:139070 original size:51 final size:51
Alignment explanation
Indices: 138936--139112 Score: 183
Period size: 51 Copynumber: 3.6 Consensus size: 51
138926 CTTGCCAGTT
* * * * *** * *
138936 CCACTTTTAGTTCCATAAGCACCCCATCCCCCACCACCACCCTTCCCATTT
1 CCACTTTCAGTTCCAGAAGCACCCCATCCACCACCACCACCATAAACACTG
138987 CCACTTTCAGTTCCAGAAGCACCCCATCCACCACCACCACCATAAACACTG
1 CCACTTTCAGTTCCAGAAGCACCCCATCCACCACCACCACCATAAACACTG
* **
139038 CCACTTTCAGTTCCCGAAGCACCCCAT---CCACCAGTACC----AC-C-G
1 CCACTTTCAGTTCCAGAAGCACCCCATCCACCACCACCACCATAAACACTG
139080 CCACTTTCAGTTCCAGAAGCACCCCATCCACCA
1 CCACTTTCAGTTCCAGAAGCACCCCATCCACCA
139113 GGGAAAGCTT
Statistics
Matches: 110, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
42 27 0.25
43 1 0.01
44 2 0.02
45 3 0.03
48 9 0.08
51 68 0.62
ACGTcount: A:0.26, C:0.47, G:0.08, T:0.19
Consensus pattern (51 bp):
CCACTTTCAGTTCCAGAAGCACCCCATCCACCACCACCACCATAAACACTG
Found at i:146689 original size:12 final size:12
Alignment explanation
Indices: 146672--146698 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
146662 AAATATTAAC
146672 TTCTTCTTTCTT
1 TTCTTCTTTCTT
146684 TTCTTCTTTCTT
1 TTCTTCTTTCTT
146696 TTC
1 TTC
146699 CGCCTCTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTCTTCTTTCTT
Found at i:177523 original size:7 final size:7
Alignment explanation
Indices: 177506--177536 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
177496 AGTATTCGTC
177506 CTGCA-T
1 CTGCATT
177512 CTGCATT
1 CTGCATT
177519 CTGCATT
1 CTGCATT
177526 CTGCATT
1 CTGCATT
177533 CTGC
1 CTGC
177537 CTATGATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.13, C:0.32, G:0.16, T:0.39
Consensus pattern (7 bp):
CTGCATT
Found at i:183353 original size:21 final size:22
Alignment explanation
Indices: 183302--183353 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
183292 ATCTAATATT
*
183302 AAAATTATAGATTTTTTTATCAA
1 AAAATTATAGATTCTTTTA-CAA
183325 AAACATTATAGATTCTTTTA-AA
1 AAA-ATTATAGATTCTTTTACAA
*
183347 ATAATTA
1 AAAATTA
183354 AAATCTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 4 0.15
23 3 0.12
24 15 0.58
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (22 bp):
AAAATTATAGATTCTTTTACAA
Found at i:184868 original size:42 final size:42
Alignment explanation
Indices: 184821--184901 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
184811 CAAAATGTAT
* *
184821 CACCGATGGATGCACATGGTAATCAAGGACAAAAACCGGTTA
1 CACCGACGGAGGCACATGGTAATCAAGGACAAAAACCGGTTA
* **
184863 CACCGACGGAGGCACGTGGTAATCAAGGACCGAAACCGG
1 CACCGACGGAGGCACATGGTAATCAAGGACAAAAACCGG
184902 ATGCACATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.35, C:0.25, G:0.28, T:0.12
Consensus pattern (42 bp):
CACCGACGGAGGCACATGGTAATCAAGGACAAAAACCGGTTA
Found at i:187362 original size:192 final size:192
Alignment explanation
Indices: 186874--187381 Score: 462
Period size: 192 Copynumber: 2.7 Consensus size: 192
186864 GATTCACTTT
* * * * * * * * * ** *
186874 TCTTCCTTTCCCTCCTACCAGCAGAGTCAGAGTCATCCTCATTTGAGTCGTTTCTATGAGGACCT
1 TCTTCTTTTCCCTCCCACCATCAGAATCAGAGTAATCCTCACTGGAATCATGCCTATGACGA-CT
* * * * * ** * *
186939 T-TCTTAACTGTGTCCTTTTTACGATCTCTCATTCTGTCCGCATCAGAATCAGATTCAC--CGC-
65 TCTCTCAACTATCTCCTTTTTACAACCTCTCACCCTATCTGCATCAGAATCAGATTCACTAC-CT
* *
187000 -TGATGTCCCTCTCTCTCCTCTGGCTCACAGTCAACTCATTCTTTCGTTTATGAACTTCACCTC
129 ATGTTGTCCCTCTCTCTCCTCTGCCTCACAGTCAACTCATTCTTTCGTTTATGAACTTCACCTC
** * * * * * *
187063 TCTTCTTTTCCCTCCCATGATCAGAATCAGTGTCATCCTCACTGGAGTCATGTCTGTTACGACTT
1 TCTTCTTTTCCCTCCCACCATCAGAATCAGAGTAATCCTCACTGGAATCATGCCTATGACGACTT
* ** ** * *
187128 CTCTCAACTATTTCCTTTTTACGTCCTCTTGCTCTATCTGCATCATAATCAGATTCACTACCTAT
66 CTCTCAACTATCTCCTTTTTACAACCTCTCACCCTATCTGCATCAGAATCAGATTCACTACCTAT
* *
187193 GTTGTCCCTCTTTCTCCTCTGCCTCCCAGTCAACTCGA-TC-TTCTGTTT-TCGAACTTCACCTC
131 GTTGTCCCTCTCTCTCCTCTGCCTCACAGTCAACTC-ATTCTTTC-GTTTAT-GAACTTCACCTC
*
187255 TCTTCTTTTGCCC-CCCACCATCAGAATCAGAGTAATCCTCACTTGAATCATGCCTATGACGACT
1 TCTTCTTTT-CCCTCCCACCATCAGAATCAGAGTAATCCTCACTGGAATCATGCCTATGACGACT
* * * *
187319 TTTCTTAA-TAATCT-CTCTTTTACAACCTCTCACCCTGTCTGCATCAGAATCATATTCACTACC
65 TCTCTCAACT-ATCTCCT-TTTTACAACCTCTCACCCTATCTGCATCAGAATCAGATTCACTACC
187382 CTGCAATATC
Statistics
Matches: 259, Mismatches: 49, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
188 3 0.01
189 94 0.36
190 1 0.00
191 8 0.03
192 149 0.58
193 4 0.02
ACGTcount: A:0.19, C:0.32, G:0.11, T:0.37
Consensus pattern (192 bp):
TCTTCTTTTCCCTCCCACCATCAGAATCAGAGTAATCCTCACTGGAATCATGCCTATGACGACTT
CTCTCAACTATCTCCTTTTTACAACCTCTCACCCTATCTGCATCAGAATCAGATTCACTACCTAT
GTTGTCCCTCTCTCTCCTCTGCCTCACAGTCAACTCATTCTTTCGTTTATGAACTTCACCTC
Found at i:195073 original size:25 final size:25
Alignment explanation
Indices: 195045--195106 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
195035 ACCAAAGTGT
195045 CGCGTAGAAATTTGTCCCGAAGGAC
1 CGCGTAGAAATTTGTCCCGAAGGAC
* *
195070 CGCGTAG-AACTTGTCCCGAATGAC
1 CGCGTAGAAATTTGTCCCGAAGGAC
* *
195094 CACATAGAAATTT
1 CGCGTAGAAATTT
195107 CTTAAGAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 20 0.65
25 11 0.35
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (25 bp):
CGCGTAGAAATTTGTCCCGAAGGAC
Found at i:200071 original size:25 final size:25
Alignment explanation
Indices: 200017--200100 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
200007 TGTAATGCCA
*
200017 CGTAGAATTTTG-CACCGAAGTG-CCG
1 CGTAGAAATTTGTC-CCGAAG-GACCG
200042 CGTAGAAATTTGTCCCGAAGGACCG
1 CGTAGAAATTTGTCCCGAAGGACCG
* * *
200067 TGTAG-AATTTGTCCCGAAAGACCA
1 CGTAGAAATTTGTCCCGAAGGACCG
*
200091 CATAGAAATT
1 CGTAGAAATT
200101 CCTTAAGAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
24 21 0.42
25 28 0.56
26 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (25 bp):
CGTAGAAATTTGTCCCGAAGGACCG
Found at i:200080 original size:24 final size:24
Alignment explanation
Indices: 200017--200089 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
200007 TGTAATGCCA
200017 CGTAGAATTT-TGCACCGAAGTG-CCG
1 CGTAGAATTTGT-C-CCGAAG-GACCG
200042 CGTAGAAATTTGTCCCGAAGGACCG
1 CGTAG-AATTTGTCCCGAAGGACCG
* *
200067 TGTAGAATTTGTCCCGAAAGACC
1 CGTAGAATTTGTCCCGAAGGACC
200090 ACATAGAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 18 0.42
25 18 0.42
26 6 0.14
27 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.23
Consensus pattern (24 bp):
CGTAGAATTTGTCCCGAAGGACCG
Found at i:200096 original size:24 final size:24
Alignment explanation
Indices: 200048--200097 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
200038 GCCGCGTAGA
* ***
200048 AATTTGTCCCGAAGGACCGTGTAG
1 AATTTGTCCCGAAAGACCACATAG
200072 AATTTGTCCCGAAAGACCACATAG
1 AATTTGTCCCGAAAGACCACATAG
200096 AA
1 AA
200098 ATTCCTTAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (24 bp):
AATTTGTCCCGAAAGACCACATAG
Found at i:203603 original size:29 final size:29
Alignment explanation
Indices: 203571--203635 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
203561 TTTATGAAGT
203571 TTATGTAAAATGAAATTTGACGTGAGAAA
1 TTATGTAAAATGAAATTTGACGTGAGAAA
203600 TTATGTAAAATGAAATTTGACGTGAGAAA
1 TTATGTAAAATGAAATTTGACGTGAGAAA
203629 TTATGTA
1 TTATGTA
203636 TGATTTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (29 bp):
TTATGTAAAATGAAATTTGACGTGAGAAA
Found at i:215983 original size:18 final size:19
Alignment explanation
Indices: 215946--215983 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
215936 TGAGATACGT
*
215946 TTAATTAAATAATGTAACA
1 TTAATTAAATAATATAACA
*
215965 TTAATTTAA-AATATAACA
1 TTAATTAAATAATATAACA
215983 T
1 T
215984 AATATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (19 bp):
TTAATTAAATAATATAACA
Found at i:216158 original size:52 final size:52
Alignment explanation
Indices: 216058--216160 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
216048 TATTTCTTTA
* * *
216058 GGTCGTGAGTTCTAAACCGACTAAGAGTACTCTCCTTCCTTCCCATCAAGTT
1 GGTCGTGAGTTCTAAACCAACTAAGAGCACTCTCCTTCCTTCACATCAAGTT
* * * * *
216110 GGTCGTGTGTTTTAGACCAACTAAGAGCACTCTCCTTCCTTTATATCAAGT
1 GGTCGTGAGTTCTAAACCAACTAAGAGCACTCTCCTTCCTTCACATCAAGT
216161 GATATTAAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.33
Consensus pattern (52 bp):
GGTCGTGAGTTCTAAACCAACTAAGAGCACTCTCCTTCCTTCACATCAAGTT
Found at i:222096 original size:30 final size:30
Alignment explanation
Indices: 222055--222112 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
222045 GTTTAGTACC
*
222055 TAAATTATTTTTAAGTTTTGAAAAAAATAT
1 TAAACTATTTTTAAGTTTTGAAAAAAATAT
222085 TAAACTATTTTTAAGTTTTGAAAAAAAT
1 TAAACTATTTTTAAGTTTTGAAAAAAAT
222113 GAAAGTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (30 bp):
TAAACTATTTTTAAGTTTTGAAAAAAATAT
Found at i:222141 original size:30 final size:30
Alignment explanation
Indices: 222102--222160 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
222092 TTTTTAAGTT
*
222102 TTGAAAAAAA-TGAAAGTTTATATACTAAAA
1 TTGAAAAAAACT-AAAGTTTAAATACTAAAA
* *
222132 TTGACAAAAACTATAGTTTAAATACTAAA
1 TTGAAAAAAACTAAAGTTTAAATACTAAA
222161 TGTGTTAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.54, C:0.07, G:0.08, T:0.31
Consensus pattern (30 bp):
TTGAAAAAAACTAAAGTTTAAATACTAAAA
Found at i:222815 original size:41 final size:41
Alignment explanation
Indices: 222758--222839 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
222748 TTTGTTTGTC
*
222758 ATTGTTGGTGAGGTTACACTACCATTCGAATCTCTAGTCGT
1 ATTGTTGGTGAGGTTACACTACCATTCGAATCTCTAATCGT
*
222799 ATTGTTGGTGAGGTTACATTACCATTCGAATCTCTAATCGT
1 ATTGTTGGTGAGGTTACACTACCATTCGAATCTCTAATCGT
222840 CATCGCTGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (41 bp):
ATTGTTGGTGAGGTTACACTACCATTCGAATCTCTAATCGT
Found at i:222945 original size:24 final size:24
Alignment explanation
Indices: 222887--222936 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
222877 GGATTTGGAG
*
222887 ATTAAAGA-TTTCGGTTATAAGAA
1 ATTAAAGATTTTGGGTTATAAGAA
222910 ATTAAAGATTTTGGGTTATAAGAA
1 ATTAAAGATTTTGGGTTATAAGAA
222934 ATT
1 ATT
222937 TAGTGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (24 bp):
ATTAAAGATTTTGGGTTATAAGAA
Found at i:223174 original size:7 final size:7
Alignment explanation
Indices: 223162--223217 Score: 103
Period size: 7 Copynumber: 7.9 Consensus size: 7
223152 TATCTTATAT
223162 AATTTTG
1 AATTTTG
223169 AATTTTTG
1 AA-TTTTG
223177 AATTTTG
1 AATTTTG
223184 AATTTTG
1 AATTTTG
223191 AATTTTG
1 AATTTTG
223198 AATTTTG
1 AATTTTG
223205 AATTTTG
1 AATTTTG
223212 AATTTT
1 AATTTT
223218 TTTATTAGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
7 41 0.85
8 7 0.15
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
AATTTTG
Found at i:228110 original size:15 final size:15
Alignment explanation
Indices: 228087--228117 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
228077 CAACACAACA
228087 AAAACGTGCCTAACT
1 AAAACGTGCCTAACT
*
228102 AAAATGTGCCTAACT
1 AAAACGTGCCTAACT
228117 A
1 A
228118 CTTTCCCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
AAAACGTGCCTAACT
Found at i:241281 original size:13 final size:13
Alignment explanation
Indices: 241242--241285 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
241232 AAAATTTCTC
241242 ATTTATATCATCA
1 ATTTATATCATCA
*
241255 ATTCTTTATC-TCA
1 ATT-TATATCATCA
*
241268 ATTTATACCATCA
1 ATTTATATCATCA
241281 ATTTA
1 ATTTA
241286 CCTACTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 4 0.15
13 17 0.65
14 5 0.19
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTATATCATCA
Found at i:251612 original size:23 final size:24
Alignment explanation
Indices: 251586--251631 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
251576 TTTTTTAAAT
*
251586 ATTATAAT-ATATAAAATATATCA
1 ATTAAAATAATATAAAATATATCA
*
251609 ATTAAAATAAATATACAATATAT
1 ATTAAAAT-AATATAAAATATAT
251632 ATTTTCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
25 12 0.63
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
ATTAAAATAATATAAAATATATCA
Found at i:256838 original size:22 final size:23
Alignment explanation
Indices: 256810--256853 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
256800 TTCTTTTTAT
256810 TTTATTA-TCTTGGTTTTATTCC
1 TTTATTATTCTTGGTTTTATTCC
*
256832 TTTATTATTTTTTGGTTTTATT
1 TTTATTA-TTCTTGGTTTTATT
256854 TTATTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.14, C:0.07, G:0.09, T:0.70
Consensus pattern (23 bp):
TTTATTATTCTTGGTTTTATTCC
Found at i:266591 original size:31 final size:31
Alignment explanation
Indices: 266553--266706 Score: 265
Period size: 31 Copynumber: 5.0 Consensus size: 31
266543 CCCGAAGGAC
* *
266553 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
266584 CAGTCCATATGTCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
266615 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
266646 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
266677 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
266707 CCCTCGACCC
Statistics
Matches: 118, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:270956 original size:31 final size:31
Alignment explanation
Indices: 270918--271102 Score: 327
Period size: 31 Copynumber: 6.0 Consensus size: 31
270908 CCCGAAGGAC
* *
270918 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
270949 CAGTCCATATGTCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
270980 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
271011 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
271042 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
271073 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
271103 CCCTCGACCC
Statistics
Matches: 149, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 148 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:276510 original size:19 final size:19
Alignment explanation
Indices: 276473--276510 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
276463 CAAAATCTAT
*
276473 TTTTTAAATTCTTTTTAAA
1 TTTTTAAATTCTTTATAAA
276492 TTTTTAAATT-TCTTATAAA
1 TTTTTAAATTCT-TTATAAA
276511 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTAAATTCTTTATAAA
Found at i:277300 original size:426 final size:426
Alignment explanation
Indices: 276507--277358 Score: 1695
Period size: 426 Copynumber: 2.0 Consensus size: 426
276497 AAATTTCTTA
276507 TAAAACAATTAATTTTGTTTTTAAAATTTTACAAACCTAGATAAAAACGGATTTTTCCTGAAATT
1 TAAAACAATTAATTTTGTTTTTAAAATTTTACAAACCTAGATAAAAACGGATTTTTCCTGAAATT
276572 TCTCATTCATACACAGTAAAATTTGCCCAATTTTTTTCTTTCAGAATCTCATAATCTACTTTCTC
66 TCTCATTCATACACAGTAAAATTTGCCCAATTTTTTTCTTTCAGAATCTCATAATCTACTTTCTC
276637 ATTCTCATTTATTTATGATTTTTTAATTAAATCTCTTTACCACTCGCCTAACAACCTTCATTTTC
131 ATTCTCATTTATTTATGATTTTTTAATTAAATCTCTTTACCACTCGCCTAACAACCTTCATTTTC
276702 AACTCGGCTGTGTGAATCATTTTGACTCGTCGTCAACTCAGCTCTCACTGTGAATGCCATGATGT
196 AACTCGGCTGTGTGAATCATTTTGACTCGTCGTCAACTCAGCTCTCACTGTGAATGCCATGATGT
*
276767 TCTTTTTTCCCCTCTTGTCTTGCTCTCAGGTACTTATAATCCTCTTTTTGATTCTGGGTCTTTTT
261 TCTTTTTTCCCCTCTTGTCTTACTCTCAGGTACTTATAATCCTCTTTTTGATTCTGGGTCTTTTT
276832 TTCCCATTTAGAATGTTTTAGATTTTTTTTATGAATGGCGTTTGAATTATTTTCTTTATCAGATG
326 TTCCCATTTAGAATGTTTTAGATTTTTTTTATGAATGGCGTTTGAATTATTTTCTTTATCAGATG
276897 CTTAGAGAACAGTGATAATGGAGAACCCTAAAACCC
391 CTTAGAGAACAGTGATAATGGAGAACCCTAAAACCC
276933 TAAAACAATTAATTTTGTTTTTAAAATTTTACAAACCTAGATAAAAACGGATTTTTCCTGAAATT
1 TAAAACAATTAATTTTGTTTTTAAAATTTTACAAACCTAGATAAAAACGGATTTTTCCTGAAATT
276998 TCTCATTCATACACAGTAAAATTTGCCCAATTTTTTTCTTTCAGAATCTCATAATCTACTTTCTC
66 TCTCATTCATACACAGTAAAATTTGCCCAATTTTTTTCTTTCAGAATCTCATAATCTACTTTCTC
277063 ATTCTCATTTATTTATGATTTTTTAATTAAATCTCTTTACCACTCGCCTAACAACCTTCATTTTC
131 ATTCTCATTTATTTATGATTTTTTAATTAAATCTCTTTACCACTCGCCTAACAACCTTCATTTTC
277128 AACTCGGCTGTGTGAATCATTTTGACTCGTCGTCAACTCAGCTCTCACTGTGAATGCCATGATGT
196 AACTCGGCTGTGTGAATCATTTTGACTCGTCGTCAACTCAGCTCTCACTGTGAATGCCATGATGT
277193 TCTTTTTTCCCCTCTTGTCTTACTCTCAGGTACTTATAATCCTCTTTTTGATTCTGGGTCTTTTT
261 TCTTTTTTCCCCTCTTGTCTTACTCTCAGGTACTTATAATCCTCTTTTTGATTCTGGGTCTTTTT
277258 TTCCCATTTAGAATGTTTTAGATTTTTTTTATGAATGGCGTTTGAATTATTTTCTTTATCAGATG
326 TTCCCATTTAGAATGTTTTAGATTTTTTTTATGAATGGCGTTTGAATTATTTTCTTTATCAGATG
277323 CTTAGAGAACAGTGATAATGGAGAACCCTAAAACCC
391 CTTAGAGAACAGTGATAATGGAGAACCCTAAAACCC
277359 CAGAAAGTTT
Statistics
Matches: 425, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
426 425 1.00
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.42
Consensus pattern (426 bp):
TAAAACAATTAATTTTGTTTTTAAAATTTTACAAACCTAGATAAAAACGGATTTTTCCTGAAATT
TCTCATTCATACACAGTAAAATTTGCCCAATTTTTTTCTTTCAGAATCTCATAATCTACTTTCTC
ATTCTCATTTATTTATGATTTTTTAATTAAATCTCTTTACCACTCGCCTAACAACCTTCATTTTC
AACTCGGCTGTGTGAATCATTTTGACTCGTCGTCAACTCAGCTCTCACTGTGAATGCCATGATGT
TCTTTTTTCCCCTCTTGTCTTACTCTCAGGTACTTATAATCCTCTTTTTGATTCTGGGTCTTTTT
TTCCCATTTAGAATGTTTTAGATTTTTTTTATGAATGGCGTTTGAATTATTTTCTTTATCAGATG
CTTAGAGAACAGTGATAATGGAGAACCCTAAAACCC
Found at i:280491 original size:19 final size:19
Alignment explanation
Indices: 280467--280511 Score: 81
Period size: 19 Copynumber: 2.3 Consensus size: 19
280457 GTCAGCAATG
280467 ATAAAATTGTAAAGTAAGA
1 ATAAAATTGTAAAGTAAGA
280486 ATAAAATTGTAAAGTAAGA
1 ATAAAATTGTAAAGTAAGA
280505 AGTAAAA
1 A-TAAAA
280512 GAAAACATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (19 bp):
ATAAAATTGTAAAGTAAGA
Found at i:291001 original size:41 final size:41
Alignment explanation
Indices: 290939--291057 Score: 193
Period size: 41 Copynumber: 2.9 Consensus size: 41
290929 ACGTTGCATT
*
290939 TCGCGTTGCGTTTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
* * *
290980 TCGCATTGCGATTTTCCATTTCGCGTTACGATAGTTGAAAT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
291021 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTTG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTG
291058 TGATAGTCTG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:291023 original size:21 final size:21
Alignment explanation
Indices: 290958--291032 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
290948 GTTTTTCCAT
290958 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
* * * ** *
290979 ATCGCATTGCGAT-TTTCCAT
1 TTCGCGTTGCGATAGTTGAAA
*
290999 TTCGCGTTACGATAGTTGAAA
1 TTCGCGTTGCGATAGTTGAAA
291020 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
291033 TTTCCATTTC
Statistics
Matches: 39, Mismatches: 14, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 13 0.33
21 26 0.67
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTTGAAA
Found at i:291051 original size:20 final size:20
Alignment explanation
Indices: 290935--291052 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 20
290925 ATTCACGTTG
*
290935 CATTTCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATTTTC
* *
290955 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
290976 AAAATCGCATTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* * *
290996 CATTTCGCGTTACGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* *
291017 AAATTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
*
291037 CATTTCGCATTGCGAT
1 CATTTCGCGTTGCGAT
291053 AGTTGTGATA
Statistics
Matches: 72, Mismatches: 24, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 43 0.60
21 29 0.40
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:291658 original size:5 final size:5
Alignment explanation
Indices: 291652--291707 Score: 76
Period size: 5 Copynumber: 10.8 Consensus size: 5
291642 TCCGTCTCGG
* *
291652 GTCGG GTCGG GTCGT GGTCGT GGTCGT GTCGT GTCGT GTCGT GTCGT GTCGT
1 GTCGT GTCGT GTCGT -GTCGT -GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT
291704 GTCG
1 GTCG
291708 ATACGTGTCT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
5 38 0.78
6 11 0.22
ACGTcount: A:0.00, C:0.20, G:0.46, T:0.34
Consensus pattern (5 bp):
GTCGT
Found at i:291714 original size:15 final size:15
Alignment explanation
Indices: 291668--291716 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
291658 TCGGGTCGTG
*
291668 GTCGTGGTCGTGTCGT
1 GTCGT-GTCGTGACGT
*
291684 GTCGTGTCGTGTCGT
1 GTCGTGTCGTGACGT
291699 GTCGTGTCGAT-ACGT
1 GTCGTGTCG-TGACGT
291714 GTC
1 GTC
291717 TTCGACACGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
15 25 0.81
16 6 0.19
ACGTcount: A:0.04, C:0.20, G:0.39, T:0.37
Consensus pattern (15 bp):
GTCGTGTCGTGACGT
Found at i:291807 original size:19 final size:19
Alignment explanation
Indices: 291783--291845 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
291773 CTTTTTTTTT
291783 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
291802 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
291824 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
291843 CAA
1 CAA
291846 AGACAACTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 16 0.48
20 2 0.06
21 2 0.06
22 13 0.39
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:291825 original size:22 final size:22
Alignment explanation
Indices: 291798--291869 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
291788 AATTTGGAAA
291798 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
291820 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
291839 ATCGCAAAGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
291861 ATCGCAACG
1 ATCGCAACG
291870 CGAAATGGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 2 0.05
22 21 0.57
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:291829 original size:41 final size:41
Alignment explanation
Indices: 291783--291889 Score: 171
Period size: 41 Copynumber: 2.6 Consensus size: 41
291773 CTTTTTTTTT
291783 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
1 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
*
291824 CAACGAATTTGGAAAATCGCAAAGACAACTGTAGACTATCG
1 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
*
291865 CAACGCGAA-ATGGAAAATCGCAACG
1 CAA--CGAATTTGGAAAATCGCAACG
291890 CGAATTTGCG
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
41 43 0.70
42 14 0.23
43 4 0.07
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (41 bp):
CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCG
Found at i:300689 original size:178 final size:178
Alignment explanation
Indices: 300390--300746 Score: 705
Period size: 178 Copynumber: 2.0 Consensus size: 178
300380 TTACCAGTGA
300390 AATATTTTACTTCTCACAGTTTGAAATCAGCGAAACTTGAATTTATTGTTTTTAGTAGTGTTACA
1 AATATTTTACTTCTCACAGTTTGAAATCAGCGAAACTTGAATTTATTGTTTTTAGTAGTGTTACA
300455 AAATTGAAGCGTGCTGAACAGACTTATTTATGAAGAATGCAAGTTTATTCTTTCGTTGTACTGAT
66 AAATTGAAGCGTGCTGAACAGACTTATTTATGAAGAATGCAAGTTTATTCTTTCGTTGTACTGAT
300520 AATTTTCAGGGGATAAACTTTATAAAAAATTTAACCTGTGGTTGATTT
131 AATTTTCAGGGGATAAACTTTATAAAAAATTTAACCTGTGGTTGATTT
300568 AATATTTTACTTCTCACAGTTTGAAATCAGCGAAACTTGAATTTATTGTTTTTAGTAGTGTTACA
1 AATATTTTACTTCTCACAGTTTGAAATCAGCGAAACTTGAATTTATTGTTTTTAGTAGTGTTACA
300633 AAATTGAAGCGTGCTGAACAGACTTATTTATGAAGAATGCAAGTTTATTCTTTCGTTGTACTGAT
66 AAATTGAAGCGTGCTGAACAGACTTATTTATGAAGAATGCAAGTTTATTCTTTCGTTGTACTGAT
*
300698 AATTTTCAGGGGATAAACTTTATAAAAAATTTAACCTGTGTTTGATTT
131 AATTTTCAGGGGATAAACTTTATAAAAAATTTAACCTGTGGTTGATTT
300746 A
1 A
300747 TAGTATATTC
Statistics
Matches: 178, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
178 178 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (178 bp):
AATATTTTACTTCTCACAGTTTGAAATCAGCGAAACTTGAATTTATTGTTTTTAGTAGTGTTACA
AAATTGAAGCGTGCTGAACAGACTTATTTATGAAGAATGCAAGTTTATTCTTTCGTTGTACTGAT
AATTTTCAGGGGATAAACTTTATAAAAAATTTAACCTGTGGTTGATTT
Found at i:303426 original size:23 final size:24
Alignment explanation
Indices: 303384--303431 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
303374 GCTCTTCAAA
*
303384 ATATTTATATAATATATAAAAAAT
1 ATATTTATATAAAATATAAAAAAT
*
303408 ATATTT-TATAAAATTTAAAAAAT
1 ATATTTATATAAAATATAAAAAAT
303431 A
1 A
303432 ATAAAAGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATATTTATATAAAATATAAAAAAT
Found at i:303707 original size:11 final size:11
Alignment explanation
Indices: 303693--303723 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
303683 TGAGCACTAC
303693 CCGACTCGCAA
1 CCGACTCGCAA
303704 CCGACTCGCAA
1 CCGACTCGCAA
303715 CCGACTCGC
1 CCGACTCGC
303724 TTGATTAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.23, C:0.48, G:0.19, T:0.10
Consensus pattern (11 bp):
CCGACTCGCAA
Found at i:307995 original size:296 final size:299
Alignment explanation
Indices: 307347--308097 Score: 768
Period size: 296 Copynumber: 2.5 Consensus size: 299
307337 ACTTTCGTTC
* * * * ** * * * *
307347 ACCTTATCATCATTGGTCGAAGAAACGAGAAATCTCGTATGGTCTACCTCAAACACATCTTTA-T
1 ACCTTATCATCACTGGTAGAAGAAACAAGAAATCTCGGATCATCTACCTCAAATACGTATTCAGT
* * * ** * ** *
307411 TCGTTTCTGGTTCTTGTGCTTTAAACCTAACAGATTGTCTTCTTAAACACGCCCTGC-AATCAAA
66 T-GCTTCTGGTTCTTGGGATTTACTCCTAACAGATTGCCTTCTTAAACACAACCTGCTAA-GAAA
* ** * *
307475 ACAAAAAAAGAAACCACATATTTTTCCTTTGTCATTGTGAAGTTTTCACATAATAATAAAACTAA
129 AC-ATAAAAGAAA-C-CATAAATTTCCCTTGTCATTATGAAGTTTTCACATAATAATAAAACTAA
* * * *
307540 AGATGATTGAGAATGATTTGCACTGAGCAATTAGAAATGTGCAAAAAAACCTTTTGTTGCCAATC
191 AGAAGATCGAGAATGATTTGCACTGAGCAATAAAAAATGT-CAAAAAAACCTTTTGTTGCCAATC
* * *
307605 CCCTCCTTGGATTGGACTGGTTTGATATCAGGGCCACTCTCATAC
255 CCCTCCTTGGATTGGACTGGTTTGATATAAGGGCCACACTCATAA
* ** *
307650 ACCTTATCATCACTGGTTGAAGAAACAAGAAATCTCGTTTTATCTACCTCAAATACGTATTCAGT
1 ACCTTATCATCACTGGTAGAAGAAACAAGAAATCTCGGATCATCTACCTCAAATACGTATTCAGT
* * * * *
307715 TGCTTCTGGTTCTTGGGATTTA-TGCCTAACAGATTGTCTTCTTGAACATAACTTGCT-GGATAA
66 TGCTTCTGGTTCTTGGGATTTACT-CCTAACAGATTGCCTTCTTAAACACAACCTGCTAAGA-AA
* * *
307778 ACATAAAGGAAACCATAAATTTCCCTTGTCATTATGAAGTTTTCA-A-ATTAA-AAAACTAACGA
129 ACATAAAAGAAACCATAAATTTCCCTTGTCATTATGAAGTTTTCACATAATAATAAAACTAAAGA
* * ** *
307840 AGA-CGA-AATGATTTGTACTGAGCAATAAAAAATGT-ACAAAAACCTTTTGTTTTCGATCCCCT
194 AGATCGAGAATGATTTGCACTGAGCAATAAAAAATGTCAAAAAAACCTTTTGTTGCCAATCCCCT
* *
307902 CCTTGGCTTTGACTGGTTTGATATTAGAAGGGCCACACTCA-AGA
259 CCTTGGATTGGACTGGTTTGATA-T--AAGGGCCACACTCATA-A
* * * * *
307946 ACCTTATCATCACTGGTAGAAGAAGCAAGAAATTTTGGATCATCTACCTCGAATACGTCTTCAGT
1 ACCTTATCATCACTGGTAGAAGAAACAAGAAATCTCGGATCATCTACCTCAAATACGTATTCAGT
* * * * *
308011 TGTTTCTGGTTCTTGTGTTTTACTCCTAGCAGATTGCCTTCTTAAACACACCCTGCTAAGAAAAC
66 TGCTTCTGGTTCTTGGGATTTACTCCTAACAGATTGCCTTCTTAAACACAACCTGCTAAGAAAAC
*
308076 ATAAAAGAACCCATAAATTTCC
131 ATAAAAGAAACCATAAATTTCC
308098 TTATAAGTTT
Statistics
Matches: 374, Mismatches: 64, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
293 44 0.12
294 1 0.00
295 27 0.07
296 140 0.37
297 15 0.04
298 4 0.01
299 1 0.00
300 28 0.07
301 1 0.00
302 9 0.02
303 102 0.27
304 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (299 bp):
ACCTTATCATCACTGGTAGAAGAAACAAGAAATCTCGGATCATCTACCTCAAATACGTATTCAGT
TGCTTCTGGTTCTTGGGATTTACTCCTAACAGATTGCCTTCTTAAACACAACCTGCTAAGAAAAC
ATAAAAGAAACCATAAATTTCCCTTGTCATTATGAAGTTTTCACATAATAATAAAACTAAAGAAG
ATCGAGAATGATTTGCACTGAGCAATAAAAAATGTCAAAAAAACCTTTTGTTGCCAATCCCCTCC
TTGGATTGGACTGGTTTGATATAAGGGCCACACTCATAA
Found at i:310033 original size:2 final size:2
Alignment explanation
Indices: 310026--310068 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
310016 TAAAAATTTA
310026 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
310068 A
1 A
310069 ATTTATGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:317199 original size:13 final size:13
Alignment explanation
Indices: 317181--317205 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
317171 TAGTTTTTTT
317181 TAAAATCAATTTA
1 TAAAATCAATTTA
317194 TAAAATCAATTT
1 TAAAATCAATTT
317206 TGTTAAAAAC
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAAATCAATTTA
Found at i:319526 original size:37 final size:37
Alignment explanation
Indices: 319450--319526 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
319440 TTTTTATATT
*
319450 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
319487 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
319524 TTT
1 TTT
319527 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:319708 original size:20 final size:20
Alignment explanation
Indices: 319672--319709 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
319662 ATCCTATTAA
**
319672 CTGATAATCTTTTATTCCCG
1 CTGATAATCTTACATTCCCG
319692 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
319710 GTGAACCAAA
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:0.24, C:0.26, G:0.08, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCG
Found at i:322578 original size:147 final size:145
Alignment explanation
Indices: 322206--322644 Score: 427
Period size: 147 Copynumber: 3.0 Consensus size: 145
322196 TCTTTCTTTT
* * * * * *
322206 CTACATCAACTTTATCTTCCACAAACCCAGAATCATCCATTTCGGCAACTTCCTCATTCAGTTCA
1 CTACATAAACCTTATCTTCC-CAACCCCAGAATCATCCATTTCAGTAACTTCCTCATTCAGATCA
* ** * *
322271 GAAGTCAGGTTATCTTCCTTAATTGTATTTTCACCATCTCCAATGTTCGACGAAATGTCAGGCTG
65 GAA-TCAGGTTATCTTCCTTAATTGCATTTTCTGCATCTCCAATGTTCGATGAAATGTCAGACTG
* *
322336 AAC-AATAGTCGACTTGG
129 AACTACT-GTCGACTTGA
* * * *
322353 CTGCA-ATAA-CTTCAT-TTCCCACTACCCCAGAATCATCCATTTCAGTAACCTCCTCCTTCAGC
1 CTACATA-AACCTT-ATCTTCCCA--ACCCCAGAATCATCCATTTCAGTAACTTCCTCATTCAGA
* * * * * * *
322415 TCAGATGTTAGTTTATCTCCCATAATTGCGTTTTCTGCATCTGCAATGTTCGATGAAATGTCAGA
62 TCAGA-ATCAGGTTATCTTCCTTAATTGCATTTTCTGCATCTCCAATGTTCGATGAAATGTCAGA
*
322480 TTGAACTACTGTCGACTTGA
126 CTGAACTACTGTCGACTTGA
* * * *
322500 CTACATAAACCTTATCTTCCTCAACCCCAGAATCATCCATTTCAGTAACTTCCACTTTAAGATCG
1 CTACATAAACCTTATCTTCC-CAACCCCAGAATCATCCATTTCAGTAACTTCCTCATTCAGATCA
* ** * * * *
322565 GACATGAGGTTATCTTCCTTGGTTGCATTTTCTGCATCTTCACTGTTCGATGAAATGCCGGACTG
65 GA-ATCAGGTTATCTTCCTTAATTGCATTTTCTGCATCTCCAATGTTCGATGAAATGTCAGACTG
*
322630 AACTACAGTCGACTT
129 AACTACTGTCGACTT
322645 AGTTTCAAAA
Statistics
Matches: 236, Mismatches: 46, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
145 2 0.01
146 6 0.03
147 216 0.92
148 10 0.04
149 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (145 bp):
CTACATAAACCTTATCTTCCCAACCCCAGAATCATCCATTTCAGTAACTTCCTCATTCAGATCAG
AATCAGGTTATCTTCCTTAATTGCATTTTCTGCATCTCCAATGTTCGATGAAATGTCAGACTGAA
CTACTGTCGACTTGA
Found at i:323995 original size:227 final size:227
Alignment explanation
Indices: 323617--324032 Score: 649
Period size: 227 Copynumber: 1.8 Consensus size: 227
323607 TAATTATGTC
* * * * *
323617 TATAAAGCATACATTATTAATTGTTTAAGAAATTTTTAAATAAATATTATATTATAATCATTCGA
1 TATAAAGCATACATTATCAATTGATTAAAAAATTTCTAAATAAATATTATATTATAATCATTCAA
323682 TATTAAAATAGATAAATTATATAAAGGTGGTTGTTTTGTTTCATTTTCTAACCCTAATAAACTTT
66 TATTAAAATAGATAAATTATATAAAGGTGGTTGTTTTGTTTCATTTTCTAACCCTAATAAACTTT
*
323747 TTTCTTATAATAACATAAAAGATTAATTTGAAAATGT-ATTAATCTTCAGTAATTAATATAGATA
131 TTTCTTATAATAACATAAAAGATTAATTTGAAAATGTAATAAATCTTCAGTAATTAATATAGATA
323811 TCTAAAAGGATTTAAATCCGAGTATTTGTGTT
196 TCTAAAAGGATTTAAATCCGAGTATTTGTGTT
* * *
323843 TATAAAGCATATATTATCAATTGATTAAAAAATTTCTAAATAAATATT-TACCTTATAATGATTT
1 TATAAAGCATACATTATCAATTGATTAAAAAATTTCTAAATAAATATTATA--TTATAATCATTC
* *
323907 AATATTAAAATAGATAAATTATATAAAGGTGGTTGTTTTGTTT-ATTTTCTAATCCTAATAAGCT
64 AATATTAAAATAGATAAATTATATAAAGGTGGTTGTTTTGTTTCATTTTCTAACCCTAATAAACT
* * * *
323971 TTTTTCCTTGTAATAATATAAAAGATTAATTTGAAAATTTAATAAATTTTCAGTAATTAATA
129 TTTTT-CTTATAATAACATAAAAGATTAATTTGAAAATGTAATAAATCTTCAGTAATTAATA
324033 ATATATATAT
Statistics
Matches: 171, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
225 2 0.01
226 67 0.39
227 83 0.49
228 19 0.11
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (227 bp):
TATAAAGCATACATTATCAATTGATTAAAAAATTTCTAAATAAATATTATATTATAATCATTCAA
TATTAAAATAGATAAATTATATAAAGGTGGTTGTTTTGTTTCATTTTCTAACCCTAATAAACTTT
TTTCTTATAATAACATAAAAGATTAATTTGAAAATGTAATAAATCTTCAGTAATTAATATAGATA
TCTAAAAGGATTTAAATCCGAGTATTTGTGTT
Found at i:324469 original size:25 final size:28
Alignment explanation
Indices: 324419--324474 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
324409 TGACTTAATA
*
324419 TATTAATATATTAATATTTCATTTTTAT
1 TATTAATATATTAATACTTCATTTTTAT
324447 TATTAATATATT-ATACTT-ATTTTATAT
1 TATTAATATATTAATACTTCATTTT-TAT
324474 T
1 T
324475 TTTTTTCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.19
27 9 0.35
28 12 0.46
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TATTAATATATTAATACTTCATTTTTAT
Found at i:329080 original size:20 final size:20
Alignment explanation
Indices: 329020--329106 Score: 77
Period size: 21 Copynumber: 4.0 Consensus size: 20
329010 AGATTCAATC
329020 AGAACAAAAAGGAAAAAAAGAA
1 AGAACAAAAA-G-AAAAAAGAA
* * *
329042 AAAAGAAAATAAGCAAAAAAAAA
1 AGAA-CAAA-AAG-AAAAAAGAA
329065 AGAA-AACAGAAGAAAAAAGAA
1 AGAACAA-A-AAGAAAAAAGAA
329086 AGAACAAAAAGAAAAAAGAA
1 AGAACAAAAAGAAAAAAGAA
329106 A
1 A
329107 AAAGGACAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
20 13 0.24
21 15 0.28
22 9 0.17
23 15 0.28
24 2 0.04
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.01
Consensus pattern (20 bp):
AGAACAAAAAGAAAAAAGAA
Found at i:329084 original size:37 final size:35
Alignment explanation
Indices: 329025--329118 Score: 102
Period size: 37 Copynumber: 2.6 Consensus size: 35
329015 CAATCAGAAC
* *
329025 AAAAAGGAAAAAAAGAAAAAAGAAAATAAGC-AAAA-
1 AAAAAAGAAAAAAAGAAAAAAG-AAAGAA-CAAAAAG
329060 AAAAAAGAAAACAGAAGAAAAAAGAAAGAACAAAAAG
1 AAAAAAGAAAA-A-AAGAAAAAAGAAAGAACAAAAAG
*
329097 AAAAAAGAAAAAAGGACAAAAA
1 AAAAAAGAAAAAAAGA-AAAAA
329119 AGCACATGCA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
35 14 0.27
36 16 0.31
37 21 0.41
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.01
Consensus pattern (35 bp):
AAAAAAGAAAAAAAGAAAAAAGAAAGAACAAAAAG
Found at i:329118 original size:9 final size:7
Alignment explanation
Indices: 329033--329110 Score: 72
Period size: 7 Copynumber: 11.0 Consensus size: 7
329023 ACAAAAAGGA
329033 AAAAAAG
1 AAAAAAG
329040 AAAAAAG
1 AAAAAAG
329047 AAAATAAG
1 AAAA-AAG
329055 CAAAAAA-
1 -AAAAAAG
329062 AAAAGAA-
1 AAAA-AAG
*
329069 AACAGAAG
1 AA-AAAAG
329077 AAAAAAG
1 AAAAAAG
*
329084 AAAGAA-
1 AAAAAAG
*
329090 CAAAAAG
1 AAAAAAG
329097 AAAAAAG
1 AAAAAAG
329104 AAAAAAG
1 AAAAAAG
329111 GACAAAAAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
6 8 0.14
7 39 0.66
8 8 0.14
9 4 0.07
ACGTcount: A:0.81, C:0.04, G:0.14, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:329772 original size:22 final size:22
Alignment explanation
Indices: 329744--329794 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
329734 CCACATCAAT
* *
329744 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAACATCAAATACAAAA
*
329766 CCTTTGAACATCAAATGCAAAA
1 CCTTTGAACATCAAATACAAAA
329788 CCTTTGA
1 CCTTTGA
329795 CCAAACACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.25
Consensus pattern (22 bp):
CCTTTGAACATCAAATACAAAA
Found at i:330642 original size:106 final size:106
Alignment explanation
Indices: 330501--331531 Score: 1735
Period size: 106 Copynumber: 9.7 Consensus size: 106
330491 TTTGCTCGAG
*
330501 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
* *
330566 GCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGAC
66 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
* * *
330607 AACTCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
330672 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
66 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
* *
330713 AACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
*
330778 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCTGAC
66 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
* * *
330819 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAATAAACAACTTCCCAATTTTAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
* * * * *
330884 GCCAATTTCAAATTCCCAGTGAATGATATTGGACTCAAGAC
66 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
*
330925 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
*
330990 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC
66 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
* *
331031 AACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCAACAAACGACTTCCCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
* *
331096 GCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGAC
66 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
* * *
331137 AACGCAAGTTCAACTTCACGACGAA-GGACCGATGGTTGTCAATAAACAATTTCCCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
331201 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
66 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
*
331242 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
331307 GCCAATTTCAACTTCACAGCGAAGGATATTGGACT-CATGAC
66 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA-GAC
*
331348 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
* * * *
331413 GCCAATTTCAAATTCCCAGCGAATGATATTGGACTCAAGAC
66 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
*
331454 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAA-AACTTCTCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
331518 GCCAATTTCAACTT
66 GCCAATTTCAACTT
331532 TGTCAACTTC
Statistics
Matches: 867, Mismatches: 55, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
105 130 0.15
106 736 0.85
107 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAC
Found at i:331500 original size:529 final size:529
Alignment explanation
Indices: 330501--331531 Score: 1956
Period size: 529 Copynumber: 1.9 Consensus size: 529
330491 TTTGCTCGAG
*
330501 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
*
330566 GCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACTCAAGTTCAACTTCACGACGA
66 GCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
330631 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAG
131 AGGGACCGATGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAG
*
330696 GATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAAC
196 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
*
330761 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCTGACAACGCAA
261 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCATGACAACGCAA
*
330826 GTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAATAAACAACTTCCCAATTTTAGAGCCAATT
326 GTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAATAAACAACTTCCCAATTTCAGAGCCAATT
*
330891 TCAAATTCCCAGTGAATGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
391 TCAAATTCCCAGCGAATGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
330956 GCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
456 GCTGGTTGTCAACAAA-AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
331021 GACTCCAGAC
520 GACTCCAGAC
* *
331031 AACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCAACAAACGACTTCCCAATTTCAGA
1 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
331096 GCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
66 GCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
331161 A-GGACCGATGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAG
131 AGGGACCGATGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAG
331225 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
196 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
331290 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCATGACAACGCAA
261 AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCATGACAACGCAA
*
331355 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATT
326 GTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAATAAACAACTTCCCAATTTCAGAGCCAATT
331420 TCAAATTCCCAGCGAATGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
391 TCAAATTCCCAGCGAATGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
331485 GCTGGTTGTCAACAAAAACTTCTCAATTTCAGAGCCAATTTCAACTT
456 GCTGGTTGTCAACAAAAACTTCTCAATTTCAGAGCCAATTTCAACTT
331532 TGTCAACTTC
Statistics
Matches: 491, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
528 31 0.06
529 333 0.68
530 127 0.26
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (529 bp):
AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGATGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAG
GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
AACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCATGACAACGCAA
GTTCAACTTCACGACGAAGGGACCGCTGGCTGTCAATAAACAACTTCCCAATTTCAGAGCCAATT
TCAAATTCCCAGCGAATGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
GCTGGTTGTCAACAAAAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
ACTCCAGAC
Found at i:331593 original size:16 final size:16
Alignment explanation
Indices: 331572--331606 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
331562 TTTTTTTGTC
331572 TTTGTCTTTGTCCTAT
1 TTTGTCTTTGTCCTAT
331588 TTTGTCTTTGTCCTAT
1 TTTGTCTTTGTCCTAT
331604 TTT
1 TTT
331607 TCGTTCCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.06, C:0.17, G:0.11, T:0.66
Consensus pattern (16 bp):
TTTGTCTTTGTCCTAT
Found at i:331719 original size:25 final size:28
Alignment explanation
Indices: 331669--331724 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
331659 TGACTTAATA
*
331669 TATTAATATATTAATATTTCATTTTTAT
1 TATTAATATATTAATACTTCATTTTTAT
331697 TATTAATATATT-ATACTT-ATTTTATAT
1 TATTAATATATTAATACTTCATTTT-TAT
331724 T
1 T
331725 TTTTTTCCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.19
27 9 0.35
28 12 0.46
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TATTAATATATTAATACTTCATTTTTAT
Found at i:364916 original size:80 final size:86
Alignment explanation
Indices: 364821--364977 Score: 227
Period size: 89 Copynumber: 1.9 Consensus size: 86
364811 CGAATTTAAG
*
364821 AAAATTTGAATTCAAATTTTAAATAC-ATATA-A-AT-T-TA-ATATATTATTTTTTAAAATTAG
1 AAAATTCGAATTCAAATTTTAAATACAATATATATATATATATATATATTATTTTTTAAAATTAG
364880 ATATTTAATTCAACTGAAGTT
66 ATATTTAATTCAACTGAAGTT
*
364901 AAAATTCGAATTCAAATTTTAAATACATATATATATATATATATATATATATTATTTTTTTAAAT
1 AAAATTCGAATTCAAATTTTAAATAC--A-ATATATATATATATATATATATTATTTTTTAAAAT
364966 TAGATATTTAAT
63 TAGATATTTAAT
364978 ATCTCATTTC
Statistics
Matches: 66, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
80 25 0.38
84 5 0.08
85 1 0.02
86 2 0.03
87 1 0.02
88 2 0.03
89 30 0.45
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (86 bp):
AAAATTCGAATTCAAATTTTAAATACAATATATATATATATATATATATTATTTTTTAAAATTAG
ATATTTAATTCAACTGAAGTT
Found at i:364934 original size:2 final size:2
Alignment explanation
Indices: 364927--364952 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
364917 TTTTAAATAC
364927 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
364953 TATTTTTTTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:367753 original size:30 final size:30
Alignment explanation
Indices: 367719--367806 Score: 149
Period size: 30 Copynumber: 2.9 Consensus size: 30
367709 GATTTTATTT
* * *
367719 TGACAGTTATATCCATTCTTTTTGGTTCCA
1 TGACAGTTATGTCCTTTCTTTGTGGTTCCA
367749 TGACAGTTATGTCCTTTCTTTGTGGTTCCA
1 TGACAGTTATGTCCTTTCTTTGTGGTTCCA
367779 TGACAGTTATGTCCTTTCTTTGTGGTTC
1 TGACAGTTATGTCCTTTCTTTGTGGTTC
367807 ATAATCATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.15, C:0.19, G:0.18, T:0.48
Consensus pattern (30 bp):
TGACAGTTATGTCCTTTCTTTGTGGTTCCA
Found at i:371605 original size:31 final size:31
Alignment explanation
Indices: 371570--371631 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
371560 TCGCGAGCCT
* *
371570 AAAATTTTCAAGCTCGACTCGAACTCGAAAA
1 AAAATATTCAAACTCGACTCGAACTCGAAAA
*
371601 AAAATATTGAAACTCGACTCGAACTCGAAAA
1 AAAATATTCAAACTCGACTCGAACTCGAAAA
371632 TGCTCGAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (31 bp):
AAAATATTCAAACTCGACTCGAACTCGAAAA
Found at i:371780 original size:36 final size:36
Alignment explanation
Indices: 371680--371783 Score: 113
Period size: 36 Copynumber: 2.8 Consensus size: 36
371670 CTCGAGACTC
* **
371680 AAGCTCGATTAAAGCTCGATTTTGAGCTCGATTGAAA
1 AAGCTCGATTCAAGCTCGA-TTCAAGCTCGATTGAAA
* *
371717 AA-CTCGATGCAAGCTCGATTGAGAAGCTCGATT-AAA
1 AAGCTCGATTCAAGCTCGATT--CAAGCTCGATTGAAA
371753 AAGCTCGATTTCAAGCTCGATTCAAGCTCGA
1 AAGCTCGA-TTCAAGCTCGATTCAAGCTCGA
371784 AAATGAGTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
35 2 0.04
36 27 0.47
37 16 0.28
38 12 0.21
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (36 bp):
AAGCTCGATTCAAGCTCGATTCAAGCTCGATTGAAA
Found at i:372505 original size:3 final size:3
Alignment explanation
Indices: 372497--372530 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
372487 TTCCCCTTGC
372497 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
372531 TACTTGATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:373796 original size:22 final size:22
Alignment explanation
Indices: 373779--373843 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
373769 CTCGTATAAA
373779 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
373801 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
373823 TGCACCGTAGTGCCCGTAGAA
1 TGCACCGAAGTGCCCGTAGAA
373844 GATGTCCATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:375544 original size:21 final size:21
Alignment explanation
Indices: 375514--375558 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
375504 TTCTTTTCGT
* *
375514 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
375535 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
375556 TTG
1 TTG
375559 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:376544 original size:7 final size:7
Alignment explanation
Indices: 376532--376568 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
376522 CATAATCGGA
376532 TTTAGGG
1 TTTAGGG
376539 TTTAGGG
1 TTTAGGG
*
376546 TTTAGGT
1 TTTAGGG
376553 TTTAGGG
1 TTTAGGG
*
376560 TTTAAGG
1 TTTAGGG
376567 TT
1 TT
376569 CATTACAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:376743 original size:25 final size:23
Alignment explanation
Indices: 376714--376765 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
376704 AAAAATTAGT
376714 TATTAAAATATTATCATTAGA-AATA
1 TATT-AAAT-TTATCATTAGATAA-A
*
376739 TATTAAATTTGTCATTAGATAAA
1 TATTAAATTTATCATTAGATAAA
376762 TATT
1 TATT
376766 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 15 0.60
24 6 0.24
25 4 0.16
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (23 bp):
TATTAAATTTATCATTAGATAAA
Found at i:378925 original size:235 final size:236
Alignment explanation
Indices: 378514--378985 Score: 928
Period size: 235 Copynumber: 2.0 Consensus size: 236
378504 ATTATCATCG
378514 AGAAAACAAGTGGTGTCAACTTGCTGAGAATTAATGTTGTTGGGTTCTTTCGATTGAGTCATTTC
1 AGAAAACAAGTGGTGTCAACTTGCTGAGAATTAATGTTGTTGGGTTCTTTCGATTGAGTCATTTC
378579 CAATATAATGGCTACCAAGTTGGCTTGTTGGCATTGCATTGTGACGGTCTCGGCTTGCGCTTTGG
66 CAATATAATGGCTACCAAGTTGGCTTGTTGGCATTGCATTGTGACGGTCTCGGCTTGCGCTTTGG
*
378644 CGAGTTGGGCTTGGAGTTCACTCACTTTTTTTTGAAGCTGGCATATGGCCCCGGCGCAACCGTAC
131 CGAGTTGGGCTTGGAGTTCACTCACTTGTTTTTGAAGCTGGCATATGGCCCCGGCGCAACCGTAC
378709 ACAGGG-CGCGGATTCGAGCACTCGCCTCGTACACCATGCT
196 ACAGGGTCGCGGATTCGAGCACTCGCCTCGTACACCATGCT
378749 AGAAAACAAGTGGTGTCAACTTGCTGAGAATTAATGTTGTTGGGTTCTTTCGATTGAGTCATTTC
1 AGAAAACAAGTGGTGTCAACTTGCTGAGAATTAATGTTGTTGGGTTCTTTCGATTGAGTCATTTC
378814 CAATATAATGGCTACCAAGTTGGCTTGTTGGCATTGCATTGTGACGGTCTCGGCTTGCGCTTTGG
66 CAATATAATGGCTACCAAGTTGGCTTGTTGGCATTGCATTGTGACGGTCTCGGCTTGCGCTTTGG
378879 CGAGTTGGGCTTGGAGTTCACTCACTTGTTTTTGAAGCTGGCATATGGCCCCGGCGCAACCGTAC
131 CGAGTTGGGCTTGGAGTTCACTCACTTGTTTTTGAAGCTGGCATATGGCCCCGGCGCAACCGTAC
378944 ACAGGGTCGCGGATTCGAGCACTCGCCTCGTACACCATGCT
196 ACAGGGTCGCGGATTCGAGCACTCGCCTCGTACACCATGCT
378985 A
1 A
378986 CTTTCAAGTT
Statistics
Matches: 235, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
235 200 0.85
236 35 0.15
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (236 bp):
AGAAAACAAGTGGTGTCAACTTGCTGAGAATTAATGTTGTTGGGTTCTTTCGATTGAGTCATTTC
CAATATAATGGCTACCAAGTTGGCTTGTTGGCATTGCATTGTGACGGTCTCGGCTTGCGCTTTGG
CGAGTTGGGCTTGGAGTTCACTCACTTGTTTTTGAAGCTGGCATATGGCCCCGGCGCAACCGTAC
ACAGGGTCGCGGATTCGAGCACTCGCCTCGTACACCATGCT
Found at i:381423 original size:157 final size:157
Alignment explanation
Indices: 381129--381444 Score: 616
Period size: 157 Copynumber: 2.0 Consensus size: 157
381119 CTATTTACTT
381129 ACTAAAATTTCGATTTGTTCCGATTTTGATCATATTGTTGCTGAATATTTAACATCCTTATGACT
1 ACTAAAATTTCGATTTGTTCCGATTTTGATCATATTGTTGCTGAATATTTAACATCCTTATGACT
381194 AGACATTTGACTTTTACAAATTATGAAATAACCCAAAATGTTTACTATATTTTTATGAAAACCCC
66 AGACATTTGACTTTTACAAATTATGAAATAACCCAAAATGTTTACTATATTTTTATGAAAACCCC
381259 TTATTTTGGATTTTTTTTTAATTTCTCG
131 TTATTTTGGA-TTTTTTTTAATTTCTCG
381287 ACTAAAA-TTCGATTTGTTCCGATTTTGATCATATTGTTGCTGAATATTTAACATCCTTATGACT
1 ACTAAAATTTCGATTTGTTCCGATTTTGATCATATTGTTGCTGAATATTTAACATCCTTATGACT
381351 AGACATTTGACTTTTACAAATTATGAAATAACCCAAAATGTTTACTATATTTTTATGAAAACCCC
66 AGACATTTGACTTTTACAAATTATGAAATAACCCAAAATGTTTACTATATTTTTATGAAAACCCC
381416 TTATTTTGGATTTTTTTTAATTTCTCG
131 TTATTTTGGATTTTTTTTAATTTCTCG
381443 AC
1 AC
381445 GATGTACCAT
Statistics
Matches: 158, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
156 19 0.12
157 132 0.84
158 7 0.04
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (157 bp):
ACTAAAATTTCGATTTGTTCCGATTTTGATCATATTGTTGCTGAATATTTAACATCCTTATGACT
AGACATTTGACTTTTACAAATTATGAAATAACCCAAAATGTTTACTATATTTTTATGAAAACCCC
TTATTTTGGATTTTTTTTAATTTCTCG
Found at i:382807 original size:2 final size:2
Alignment explanation
Indices: 382800--382868 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
382790 CATATTACTC
382800 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
382842 AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
382869 GCACGCTAAG
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:383613 original size:35 final size:35
Alignment explanation
Indices: 383574--383642 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
383564 TCTTGACATT
383574 TTAAGTTTGAGTAGCTGCGTCTGTAGGATGTGCGC
1 TTAAGTTTGAGTAGCTGCGTCTGTAGGATGTGCGC
*
383609 TTAAGTTTGAGTAGTTGCGTCTGTAGGATGTGCG
1 TTAAGTTTGAGTAGCTGCGTCTGTAGGATGTGCG
383643 TGCATTATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.17, C:0.12, G:0.35, T:0.36
Consensus pattern (35 bp):
TTAAGTTTGAGTAGCTGCGTCTGTAGGATGTGCGC
Found at i:388398 original size:36 final size:36
Alignment explanation
Indices: 388330--388399 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
388320 GAAATGAACT
**
388330 TCATCATCCTCATCAGAAGCAGGTCCACCATCATCC
1 TCATCATCCTCATCAGAAGCACATCCACCATCATCC
* *
388366 TCATCATCCTCATCAGAATCACATCCATCATCAT
1 TCATCATCCTCATCAGAAGCACATCCACCATCAT
388400 GATTCTCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.30, C:0.37, G:0.07, T:0.26
Consensus pattern (36 bp):
TCATCATCCTCATCAGAAGCACATCCACCATCATCC
Done.