Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 26
Found at i:356537 original size:15 final size:15
Alignment explanation
Indices: 356505--356537 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
356495 ACTCTATTTT
*
356505 CCCTCACCGTCATTC
1 CCCTCACCGTCATCC
356520 CCCTCACCGTCATCC
1 CCCTCACCGTCATCC
356535 CCC
1 CCC
356538 AATACAACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.61, G:0.06, T:0.21
Consensus pattern (15 bp):
CCCTCACCGTCATCC
Found at i:364173 original size:33 final size:33
Alignment explanation
Indices: 364131--364206 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 33
364121 TGTAAGTAGG
* ***
364131 ACAATTAGTACAGATGGTGCTCCTTCAAGCAGC
1 ACAAGTAGTACAGATGAAACTCCTTCAAGCAGC
* * *
364164 ACAAGTAGTACGGATGAAACTCCTTTAAGCAGG
1 ACAAGTAGTACAGATGAAACTCCTTCAAGCAGC
*
364197 AGAAGTAGTA
1 ACAAGTAGTA
364207 GGGATGTATC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (33 bp):
ACAAGTAGTACAGATGAAACTCCTTCAAGCAGC
Found at i:364212 original size:33 final size:33
Alignment explanation
Indices: 364150--364212 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
364140 ACAGATGGTG
364150 CTCCTTCAAGCAGCACAAGTAGTACGGATGAAA
1 CTCCTTCAAGCAGCACAAGTAGTACGGATGAAA
* * * *
364183 CTCCTTTAAGCAGGAGAAGTAGTAGGGATG
1 CTCCTTCAAGCAGCACAAGTAGTACGGATG
364213 TATCTATAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (33 bp):
CTCCTTCAAGCAGCACAAGTAGTACGGATGAAA
Found at i:367609 original size:31 final size:32
Alignment explanation
Indices: 367547--367611 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
367537 CAAGTAATGG
367547 AAGCTGAAAACAGATGATAATCACAAAATTTA
1 AAGCTGAAAACAGATGATAATCACAAAATTTA
367579 AAGCTGAAAACAGATGATAATCA-AAAATTTA
1 AAGCTGAAAACAGATGATAATCACAAAATTTA
367610 AA
1 AA
367612 CAGAATGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.55, C:0.11, G:0.12, T:0.22
Consensus pattern (32 bp):
AAGCTGAAAACAGATGATAATCACAAAATTTA
Found at i:374030 original size:31 final size:31
Alignment explanation
Indices: 373992--374085 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
373982 AGGGTCGAGG
*
373992 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
374023 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
374054 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
374085 G
1 G
374086 GTCCTTCGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:376698 original size:31 final size:31
Alignment explanation
Indices: 376660--376753 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
376650 AGGGTCGAGG
376660 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
376691 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
376722 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
376753 G
1 G
376754 GTCCTTCGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:380775 original size:31 final size:31
Alignment explanation
Indices: 380737--380830 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
380727 AGGGTCGAGG
*
380737 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
380768 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
380799 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
380830 G
1 G
380831 GTCCTTCGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:394028 original size:3 final size:3
Alignment explanation
Indices: 394020--394049 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
394010 ATATGAATTA
394020 AAT AAT AAT AAAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
394050 AAAGGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:396607 original size:20 final size:20
Alignment explanation
Indices: 396582--396661 Score: 61
Period size: 20 Copynumber: 3.7 Consensus size: 20
396572 TAATTAAAAT
396582 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
** *
396602 GCATGAACGGATGCCATATTTAAAAT
1 GCATGAAATGATG-C--A-TT--AAG
*
396628 ACATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
*
396648 GCATGAAAAGATGC
1 GCATGAAATGATGC
396662 CATAACTAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
20 25 0.56
21 1 0.02
22 2 0.04
23 2 0.04
24 2 0.04
25 1 0.02
26 12 0.27
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (20 bp):
GCATGAAATGATGCATTAAG
Found at i:396625 original size:46 final size:46
Alignment explanation
Indices: 396569--396673 Score: 165
Period size: 46 Copynumber: 2.3 Consensus size: 46
396559 TTAAACGAAT
* **
396569 CCATAATTAAAATGCATGAAATGATGCATTAAGGCATGAACGGATG
1 CCATAATTAAAATACATGAAATGATGCATTAAGGCATGAAAAGATG
*
396615 CCATATTTAAAATACATGAAATGATGCATTAAGGCATGAAAAGATG
1 CCATAATTAAAATACATGAAATGATGCATTAAGGCATGAAAAGATG
*
396661 CCATAACTAAAAT
1 CCATAATTAAAAT
396674 TTACAAGAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (46 bp):
CCATAATTAAAATACATGAAATGATGCATTAAGGCATGAAAAGATG
Found at i:402563 original size:20 final size:20
Alignment explanation
Indices: 402538--402584 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
402528 TCTTGAGTTG
402538 AGATGTTCCATGAAGATGTT
1 AGATGTTCCATGAAGATGTT
402558 AGATGTTCCATGAAGATGTT
1 AGATGTTCCATGAAGATGTT
402578 AGATGTT
1 AGATGTT
402585 AAAGGGGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.36
Consensus pattern (20 bp):
AGATGTTCCATGAAGATGTT
Found at i:402961 original size:96 final size:94
Alignment explanation
Indices: 402843--403021 Score: 209
Period size: 96 Copynumber: 1.9 Consensus size: 94
402833 TGAGGGGAAA
* * * * *
402843 TATCGATACCATGGATCCAGAATGTCA-AAATAGTATCAATACTAAAAATG-GGTATCGATACCA
1 TATCGATACCATGCAACCAGAATAT-AGAAATAGCATCAATACT-AAAAGGAGGTATCGATACCA
* *
402906 TAGTATAGTAGTATCGATACTGAGAGAAGGG
64 TAGTATAGAAGTATCAATACTGAGAGAAGGG
* * * *
402937 TATCGATACCATGCCAACACAGAATATAGAAATGGCATCGATACTGAAAGGAGGTATCGGTACCA
1 TATCGATACCATG-CAAC-CAGAATATAGAAATAGCATCAATACTAAAAGGAGGTATCGATACCA
403002 TAGTATAGAAGTATCAATAC
64 TAGTATAGAAGTATCAATAC
403022 CAGGGTAGTA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
94 13 0.19
95 7 0.10
96 50 0.71
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (94 bp):
TATCGATACCATGCAACCAGAATATAGAAATAGCATCAATACTAAAAGGAGGTATCGATACCATA
GTATAGAAGTATCAATACTGAGAGAAGGG
Found at i:403520 original size:46 final size:46
Alignment explanation
Indices: 403435--403730 Score: 387
Period size: 46 Copynumber: 6.5 Consensus size: 46
403425 ACTGCTCTTA
*
403435 AACGAAT-CCATAATTAAAATGCATGAAAGGAGGCATTAAGGCATG
1 AACGAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATG
* ** * * * * *
403480 AACAAATGATATTATTAATATACATGAAAAGATGCTTTAAGGCATG
1 AACGAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATG
* *
403526 AACGAATGCCATAATTAAAATGCATGAAAGGATACATTAAGGCACG
1 AACGAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATG
* *
403572 AACGAATGCCATAATTAAAATGCACGAAAGGATGCATTAAGACATG
1 AACGAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATG
* * *
403618 AACGGATGCCATAATTAAAATGCATGAAATGATTCATTAAGGCATG
1 AACGAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATG
* *
403664 AAAGGATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATG
1 AACGAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATG
* * * *
403710 AAAGGATGTCATAACTAAAAT
1 AACGAATGCCATAATTAAAAT
403731 TTACAAGAAA
Statistics
Matches: 217, Mismatches: 33, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
45 6 0.03
46 211 0.97
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (46 bp):
AACGAATGCCATAATTAAAATGCATGAAAGGATGCATTAAGGCATG
Found at i:403689 original size:26 final size:26
Alignment explanation
Indices: 403521--403698 Score: 113
Period size: 26 Copynumber: 7.5 Consensus size: 26
403511 ATGCTTTAAG
* *
403521 GCATGAACGAATGCCATAATTAAAAT
1 GCATGAAAGGATGCCATAATTAAAAT
* *
403547 GCATGAAAGGAT---A-CATT--AAG
1 GCATGAAAGGATGCCATAATTAAAAT
* * *
403567 GCACGAACGAATGCCATAATTAAAAT
1 GCATGAAAGGATGCCATAATTAAAAT
* *
403593 GCACGAAAGGATG-C---ATTAAGA-
1 GCATGAAAGGATGCCATAATTAAAAT
*
403614 -CATGAACGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCCATAATTAAAAT
* * *
403639 GCATGAAATGAT----TCATT--AAG
1 GCATGAAAGGATGCCATAATTAAAAT
403659 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCCATAATTAAAAT
403685 GCATGAAAGGATGC
1 GCATGAAAGGATGC
403699 ATTAAGGCAT
Statistics
Matches: 112, Mismatches: 22, Indels: 36
0.66 0.13 0.21
Matches are distributed among these distances:
20 34 0.30
21 1 0.01
22 13 0.12
23 2 0.02
24 13 0.12
25 1 0.01
26 48 0.43
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAATTAAAAT
Found at i:403710 original size:20 final size:20
Alignment explanation
Indices: 403597--403717 Score: 80
Period size: 20 Copynumber: 5.5 Consensus size: 20
403587 TAAAATGCAC
*
403597 GAAAGGATGCATTAAGACAT
1 GAAAGGATGCATTAAGGCAT
* *
403617 GAACGGATGCCATAATTAAAATGCAT
1 GAAAGGATG-C---ATT--AAGGCAT
* *
403643 GAAATGATTCATTAAGGCAT
1 GAAAGGATGCATTAAGGCAT
*
403663 GAAAGGATGCCATAATTAAAATGCAT
1 GAAAGGATG-C---ATT--AAGGCAT
403689 GAAAGGATGCATTAAGGCAT
1 GAAAGGATGCATTAAGGCAT
403709 GAAAGGATG
1 GAAAGGATG
403718 TCATAACTAA
Statistics
Matches: 78, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
20 36 0.46
21 2 0.03
22 6 0.08
24 6 0.08
25 2 0.03
26 26 0.33
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (20 bp):
GAAAGGATGCATTAAGGCAT
Found at i:406602 original size:15 final size:15
Alignment explanation
Indices: 406582--406610 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
406572 GAACTAGGTT
406582 TTATTATTGTTTTAA
1 TTATTATTGTTTTAA
406597 TTATTATTGTTTTA
1 TTATTATTGTTTTA
406611 TTTTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
TTATTATTGTTTTAA
Found at i:407971 original size:27 final size:27
Alignment explanation
Indices: 407933--407987 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
407923 CATACATTAC
407933 GGTGATGTCGGACTATGAGCAGTGGAG
1 GGTGATGTCGGACTATGAGCAGTGGAG
407960 GGTGATGTCGGACTATGAGCAGTGGAG
1 GGTGATGTCGGACTATGAGCAGTGGAG
407987 G
1 G
407988 CACACTCGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.11, G:0.45, T:0.22
Consensus pattern (27 bp):
GGTGATGTCGGACTATGAGCAGTGGAG
Found at i:416557 original size:16 final size:15
Alignment explanation
Indices: 416531--416629 Score: 94
Period size: 16 Copynumber: 6.4 Consensus size: 15
416521 ATTATGCTTG
416531 AAGAGAAAAAAAGAAA
1 AAGA-AAAAAAAGAAA
416547 AAGAAACAAAAAGAACA
1 AAGAAA-AAAAAGAA-A
*
416564 GAGAAAAAAAAGAGAA
1 AAGAAAAAAAAGA-AA
416580 AA-AAAAGAAAAGAAA
1 AAGAAAA-AAAAGAAA
*
416595 AAGAAACAAAAG-AA
1 AAGAAAAAAAAGAAA
* * *
416609 AATACAAAAGAGAAA
1 AAGAAAAAAAAGAAA
416624 AAGAAA
1 AAGAAA
416630 GAGAAAATTA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.15
15 21 0.31
16 30 0.44
17 7 0.10
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.01
Consensus pattern (15 bp):
AAGAAAAAAAAGAAA
Found at i:416578 original size:42 final size:43
Alignment explanation
Indices: 416539--416631 Score: 114
Period size: 48 Copynumber: 2.0 Consensus size: 43
416529 TGAAGAGAAA
* *
416539 AAAAGAAAAAGAAACAAAAAGAACAGAGAAAAAAAAGAGAAAAAAAAG
1 AAAAGAAAAAGAAAC-AAAAG-A-A-A-ATACAAAAGAGAAAAAAAAG
416587 AAAAGAAAAAGAAACAAAAGAAAATACAAAAGAGAAAAAGAAAG
1 AAAAGAAAAAGAAACAAAAGAAAATACAAAAGAGAAAAA-AAAG
416631 A
1 A
416632 GAAAATTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
43 14 0.33
44 6 0.14
45 1 0.02
46 1 0.02
47 5 0.12
48 15 0.36
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.01
Consensus pattern (43 bp):
AAAAGAAAAAGAAACAAAAGAAAATACAAAAGAGAAAAAAAAG
Found at i:416590 original size:20 final size:20
Alignment explanation
Indices: 416531--416636 Score: 83
Period size: 20 Copynumber: 5.0 Consensus size: 20
416521 ATTATGCTTG
416531 AAGAG-AAAAAAAGAAAAAGA
1 AAGAGAAAAAAAAGAAAAA-A
*
416551 AACA-AAAAGAACAGAGAAAAAA
1 AAGAGAAAA-AA-A-AGAAAAAA
416573 AAGAGAAAAAAAAGAAAAGAA
1 AAGAGAAAAAAAAGAAAA-AA
*
416594 AA-AGAAACAAAAGAAAATACAA
1 AAGAGAAAAAAAAG-AAA-A-AA
416616 AAGAGAAAAAGAAAGAGAAAA
1 AAGAGAAAAA-AAAGA-AAAA
416637 TTAAAAATTA
Statistics
Matches: 70, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
20 22 0.31
21 10 0.14
22 13 0.19
23 19 0.27
24 6 0.09
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.01
Consensus pattern (20 bp):
AAGAGAAAAAAAAGAAAAAA
Found at i:416657 original size:7 final size:8
Alignment explanation
Indices: 416633--416666 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
416623 AAAGAAAGAG
*
416633 AAAATTAA
1 AAAATAAA
*
416641 AAATTAAA
1 AAAATAAA
416649 AAAATAAA
1 AAAATAAA
416657 AAAATAAA
1 AAAATAAA
416665 AA
1 AA
416667 GGGGTTCAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (8 bp):
AAAATAAA
Found at i:417362 original size:16 final size:17
Alignment explanation
Indices: 417336--417410 Score: 86
Period size: 16 Copynumber: 4.5 Consensus size: 17
417326 ACCACATTTT
417336 AAAAGAAAAGAAATAAG
1 AAAAGAAAAGAAATAAG
*
417353 AAGA-AAAAGAAATAAG
1 AAAAGAAAAGAAATAAG
417369 AAAAGAAAAGAAATGGAA-
1 AAAAGAAAAGAAAT--AAG
*
417387 AAAAGGAAAGAAA-AAG
1 AAAAGAAAAGAAATAAG
417403 AAAA-AAAA
1 AAAAGAAAA
417411 CAGAAGAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
15 5 0.10
16 19 0.38
17 12 0.24
18 12 0.24
19 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (17 bp):
AAAAGAAAAGAAATAAG
Found at i:417379 original size:23 final size:24
Alignment explanation
Indices: 417353--417407 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
417343 AAGAAATAAG
*
417353 AAGAAAAAGAAATAAGAAAAG-AA
1 AAGAAAAAGAAAAAAGAAAAGAAA
** *
417376 AAGAAATGGAAAAAAGGAAAGAAA
1 AAGAAAAAGAAAAAAGAAAAGAAA
417400 AAGAAAAA
1 AAGAAAAA
417408 AAACAGAAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (24 bp):
AAGAAAAAGAAAAAAGAAAAGAAA
Found at i:418039 original size:43 final size:43
Alignment explanation
Indices: 417914--418171 Score: 146
Period size: 43 Copynumber: 5.9 Consensus size: 43
417904 AGTGTCAATC
* * * * * *
417914 TTTTGCTCTATTCTTCATAGAAGGAGTTGAATCAGCA-TAACTTTA
1 TTTTGCTCGATTCTTCACAAAAGGAGTTGGATCAACATTGAC---A
* * *
417959 TTTTGCTCGATTCTATCACAGAAGGAG-GGAGACCAACATTGACA
1 TTTTGCTCGATTCT-TCACAAAAGGAGTTG-GATCAACATTGACA
* * * * *
418003 TTTTGTTTGATCCTTCACAAAAGGAGTTGGATCAACAATGTCA
1 TTTTGCTCGATTCTTCACAAAAGGAGTTGGATCAACATTGACA
* * * * * *
418046 TTTCGCTCGATTCTTCACAGAATGAGTTGAATC-A-GTGTAACCTTA
1 TTTTGCTCGATTCTTCACAAAAGGAGTTGGATCAACAT-TGA-C--A
* * * * * *
418091 TTTTGCTCAATTTTATCTCAAAAGGAGGTAGATCAACATCGACA
1 TTTTGCTCGATTCT-TCACAAAAGGAGTTGGATCAACATTGACA
* *
418135 TTTTGTTTGATTCTTCACAAAAGGAGTTGGATCAACA
1 TTTTGCTCGATTCTTCACAAAAGGAGTTGGATCAACA
418172 GTGTTATTCC
Statistics
Matches: 157, Mismatches: 45, Indels: 24
0.69 0.20 0.11
Matches are distributed among these distances:
42 2 0.01
43 69 0.44
44 24 0.15
45 26 0.17
46 30 0.19
47 5 0.03
48 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (43 bp):
TTTTGCTCGATTCTTCACAAAAGGAGTTGGATCAACATTGACA
Found at i:418128 original size:132 final size:132
Alignment explanation
Indices: 417918--418303 Score: 463
Period size: 132 Copynumber: 2.9 Consensus size: 132
417908 TCAATCTTTT
* * * * *
417918 GCTCTATTCTTCATAGAAGGAGTTGAATCAGCATAACTTTATTTTGCTCGATTCTATCACAGAAG
1 GCTCGATTCTTCACAGAAGGAGTTGAATCAGCATAACCTTATTTTGCTCGATTCTATCTCAAAAG
* * *
417983 GAGGGAGACCAACATTGACATTTTGTTTGATCCTTCACAAAAGGAGTTGGATCAACAATGTCATT
66 GAGGTAGATCAACATTGACATTTTGTTTGATTCTTCACAAAAGGAGTTGGATCAACAATGTCATT
*
418048 TC
131 CC
* ** * *
418050 GCTCGATTCTTCACAGAATGAGTTGAATCAGTGTAACCTTATTTTGCTCAATTTTATCTCAAAAG
1 GCTCGATTCTTCACAGAAGGAGTTGAATCAGCATAACCTTATTTTGCTCGATTCTATCTCAAAAG
* * *
418115 GAGGTAGATCAACATCGACATTTTGTTTGATTCTTCACAAAAGGAGTTGGATCAACAGTGTTATT
66 GAGGTAGATCAACATTGACATTTTGTTTGATTCTTCACAAAAGGAGTTGGATCAACAATGTCATT
418180 CC
131 CC
* * * * * *
418182 GCTTGATTCTTAACAGAAGGATTTGAATCAGCCTAATCTTATGTTGCTCGATTCTATCAT-AGAA
1 GCTCGATTCTTCACAGAAGGAGTTGAATCAGCATAACCTTATTTTGCTCGATTCTATC-TCA-AA
*** * **
418246 A-GAGGTAGATTGGCATTGGCAAATTGTTTGATTCTTCACAGAAA-GAGTTGGATCAACA
64 AGGAGGTAGATCAACATTGACATTTTGTTTGATTCTTCACA-AAAGGAGTTGGATCAACA
418304 TTTTTCATGT
Statistics
Matches: 217, Mismatches: 34, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
132 210 0.97
133 7 0.03
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (132 bp):
GCTCGATTCTTCACAGAAGGAGTTGAATCAGCATAACCTTATTTTGCTCGATTCTATCTCAAAAG
GAGGTAGATCAACATTGACATTTTGTTTGATTCTTCACAAAAGGAGTTGGATCAACAATGTCATT
CC
Found at i:425153 original size:2 final size:2
Alignment explanation
Indices: 425148--425191 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
425138 TCCTCAAATT
425148 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
425190 TA
1 TA
425192 AGTTAAAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:426386 original size:2 final size:2
Alignment explanation
Indices: 426379--426440 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
426369 TAGAATGATC
426379 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
426421 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
426441 CTGAAGATCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:428437 original size:23 final size:23
Alignment explanation
Indices: 428407--428530 Score: 131
Period size: 23 Copynumber: 5.4 Consensus size: 23
428397 CCCTTTTATT
* **
428407 CTAAACGAGCACGTTCGTAAACG
1 CTAAACGAACACGTTCACAAACG
*
428430 CTAAACGAACATGTTCACAAACG
1 CTAAACGAACACGTTCACAAACG
* * *
428453 CTAAACAAACATGTTCACAAACA
1 CTAAACGAACACGTTCACAAACG
* *
428476 CTAAACGAACATGTTTACAAACG
1 CTAAACGAACACGTTCACAAACG
* * **
428499 ATAAACAAACATATTCACAAACG
1 CTAAACGAACACGTTCACAAACG
428522 CTAAACGAA
1 CTAAACGAA
428531 TGCTAAATGA
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 86 1.00
ACGTcount: A:0.47, C:0.24, G:0.11, T:0.18
Consensus pattern (23 bp):
CTAAACGAACACGTTCACAAACG
Found at i:428482 original size:46 final size:46
Alignment explanation
Indices: 428425--428530 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
428415 GCACGTTCGT
* *
428425 AAACGCTAAACGAACATGTTCACAAACGCTAAACAAACATGTTCAC
1 AAACGCTAAACGAACATGTTCACAAACGATAAACAAACATATTCAC
* *
428471 AAACACTAAACGAACATGTTTACAAACGATAAACAAACATATTCAC
1 AAACGCTAAACGAACATGTTCACAAACGATAAACAAACATATTCAC
428517 AAACGCTAAACGAA
1 AAACGCTAAACGAA
428531 TGCTAAATGA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.50, C:0.24, G:0.09, T:0.17
Consensus pattern (46 bp):
AAACGCTAAACGAACATGTTCACAAACGATAAACAAACATATTCAC
Found at i:428550 original size:34 final size:33
Alignment explanation
Indices: 428495--428598 Score: 93
Period size: 34 Copynumber: 3.1 Consensus size: 33
428485 CATGTTTACA
* *
428495 AACGATAAACAAACATATTCACAAACGCTAAACG
1 AACG-TAAACGAACATGTTCACAAACGCTAAACG
* * * * *
428529 AATGCTAAATGAACATGTTCACGAACGATAAATG
1 AACG-TAAACGAACATGTTCACAAACGCTAAACG
* *
428563 AACGTAAACGAATATGTTCATGAAA-GCTAAACG
1 AACGTAAACGAACATGTTCA-CAAACGCTAAACG
428596 AAC
1 AAC
428599 ATATAAATAA
Statistics
Matches: 54, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
33 23 0.43
34 31 0.57
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.19
Consensus pattern (33 bp):
AACGTAAACGAACATGTTCACAAACGCTAAACG
Found at i:428621 original size:24 final size:23
Alignment explanation
Indices: 428594--428656 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
428584 GAAAGCTAAA
428594 CGAACATATAAATAAACATGTTCG
1 CGAACAT-TAAATAAACATGTTCG
* *
428618 CGAACATTTAAACAAGCATGTTCG
1 CGAACA-TTAAATAAACATGTTCG
*
428642 CGAACGTTAAATAAA
1 CGAACATTAAATAAA
428657 TGAACATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 7 0.21
24 25 0.76
25 1 0.03
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.24
Consensus pattern (23 bp):
CGAACATTAAATAAACATGTTCG
Found at i:429206 original size:20 final size:20
Alignment explanation
Indices: 429168--429206 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
429158 CCGAAAATAA
*
429168 ATCCCCAACGGCTACAAATT
1 ATCCCCAACGACTACAAATT
* *
429188 ATCCCCATCGACTAGAAAT
1 ATCCCCAACGACTACAAAT
429207 GACCACAAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (20 bp):
ATCCCCAACGACTACAAATT
Found at i:433515 original size:20 final size:20
Alignment explanation
Indices: 433490--433529 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
433480 CTGAGCAATG
433490 GTGTAACTACCATGGCCACC
1 GTGTAACTACCATGGCCACC
433510 GTGTAACTACCATGGCCACC
1 GTGTAACTACCATGGCCACC
433530 TTATAACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.35, G:0.20, T:0.20
Consensus pattern (20 bp):
GTGTAACTACCATGGCCACC
Found at i:433536 original size:20 final size:20
Alignment explanation
Indices: 433493--433536 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
433483 AGCAATGGTG
*
433493 TAACTACCATGGCCACCGTG
1 TAACTACCATGGCCACCGTA
*
433513 TAACTACCATGGCCACCTTA
1 TAACTACCATGGCCACCGTA
433533 TAAC
1 TAAC
433537 AACAGTGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.23
Consensus pattern (20 bp):
TAACTACCATGGCCACCGTA
Found at i:440181 original size:21 final size:21
Alignment explanation
Indices: 440155--440209 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
440145 ATCGTGATTG
*
440155 CGGCCGTCACGGGCGCTATTA
1 CGGCCGTCGCGGGCGCTATTA
**
440176 CGGCCGTCGCGGATGCTATTA
1 CGGCCGTCGCGGGCGCTATTA
*
440197 CGGCTGTCGCGGG
1 CGGCCGTCGCGGG
440210 TAACTCTGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.11, C:0.31, G:0.38, T:0.20
Consensus pattern (21 bp):
CGGCCGTCGCGGGCGCTATTA
Found at i:444724 original size:124 final size:122
Alignment explanation
Indices: 444517--444754 Score: 343
Period size: 124 Copynumber: 1.9 Consensus size: 122
444507 AAACTTTCAG
*
444517 TTTTTTCAAAATCACTCATAATGTTTAGTTTTTATTTTATTTTAGTACCCAACATTAAAAACTTA
1 TTTTTTCAAAACCACTCATAATGTTTAGTTTTTATTTTATTTTAGTACCCAACATTAAAAACTTA
*
444582 ACGCTTTTAGTACCTAAAATATCAGTTTTAATCTGTTTTAGTACCTAAAGTTTTAAT
66 ACGCGTTTAGTACCTAAAATATCAGTTTTAATCTGTTTTAGTACCTAAAGTTTTAAT
* * **
444639 TTTTTTCAAAACCA-TACCTAATTTTTAGTTTTTTATTTTATTTTAGTACCACGTCATTAAAAAC
1 TTTTTTCAAAACCACT-CATAATGTTTAG-TTTTTATTTTATTTTAGTACC-CAACATTAAAAAC
* * * * *
444703 TTTATGCGTTTAGTACCTAAAATATCAGTTTTGATTTGTTTTAGTATCTAAA
63 TTAACGCGTTTAGTACCTAAAATATCAGTTTTAATCTGTTTTAGTACCTAAA
444755 AAATTCAAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
121 1 0.01
122 23 0.23
123 21 0.21
124 57 0.56
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (122 bp):
TTTTTTCAAAACCACTCATAATGTTTAGTTTTTATTTTATTTTAGTACCCAACATTAAAAACTTA
ACGCGTTTAGTACCTAAAATATCAGTTTTAATCTGTTTTAGTACCTAAAGTTTTAAT
Found at i:448972 original size:31 final size:30
Alignment explanation
Indices: 448908--448982 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
448898 ACAAAATTCG
* *
448908 TTTCAAGGGAAACGACTCAAAGATAGTTTTA
1 TTTCAAGAGAAACAACTCAAAGATA-TTTTA
448939 TTTCAAGAGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGAGAAAC-AACTCAAAGATATTT-TA
**
448970 TTTTTAGAGAAAC
1 TTTCAAGAGAAAC
448983 TGCCTTAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 25 0.66
32 10 0.26
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (30 bp):
TTTCAAGAGAAACAACTCAAAGATATTTTA
Found at i:449552 original size:37 final size:37
Alignment explanation
Indices: 449511--449582 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
449501 AAGAGACAAA
*
449511 ATTTTGTTTCCAA-AGAAACATACTCAAAGATTTTTTC
1 ATTTTGTTT-CAAGAGAAACAAACTCAAAGATTTTTTC
* *
449548 ATTTTGTTTTAAGTGAAACAAACTCAAAGATTTTT
1 ATTTTGTTTCAAGAGAAACAAACTCAAAGATTTTT
449583 CAAGAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 2 0.06
37 29 0.94
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (37 bp):
ATTTTGTTTCAAGAGAAACAAACTCAAAGATTTTTTC
Found at i:449610 original size:166 final size:163
Alignment explanation
Indices: 449292--449655 Score: 380
Period size: 166 Copynumber: 2.2 Consensus size: 163
449282 TGATTTTGTT
* * *
449292 AAAAGAAACAAACTCAAAGATTTTTTTCAAAAAACTGTTTCAAGAGAGACAAAACTTTGTTTCAA
1 AAAAGAAACAGACTCAAAGATTTTTTTCAAAAAACTGTCTCAAAAGAGACAAAACTTTGTTTCAA
** ** * *
449357 AAGAAAAATAATCAAAATTGGGTTTTGTTTCAAGGGAAACATGCTCACATATATTTGTTTTAAGA
66 AAGAAAAATAATCAAAATTGCATTTTGTTTCAAGGGAAACAAACTCACATAGATTTGTTTCAAGA
449422 GAAATTGTCTCAAAAGAGACAAACCTTTGTTTTC
131 GAAATTGTCTCAAAAGAGACAAACCTTTG-TTTC
* * *
449456 ATAA-AAACAGACTTAAAGATTTTTCTTCAAAAGGAACTGTCTCAAAAGAGACAAAATTTTGTTT
1 AAAAGAAACAGACTCAAAGATTTTT-TTCAAAA--AACTGTCTCAAAAGAGACAAAACTTTGTTT
* * * * * *
449520 CCAAAGAAACATACTCAAAGATTTTTTCATTTTGTTTTAAGTGAAACAAACTCA-A-AGA-TT-T
63 CAAAAGAAAAATAATCAAA-A---TTGCATTTTGTTTCAAGGGAAACAAACTCACATAGATTTGT
* **
449581 TTCAAGA-AAATCTGTCTCAAGAGAGACAAAGTTTTGTTTC
124 TTCAAGAGAAAT-TGTCTCAAAAGAGACAAACCTTTGTTTC
*
449621 AAAAGAAATAGACTCAAAGATCATTTGTTTCAAAA
1 AAAAGAAACAGACTCAAAGAT--TTT-TTTCAAAA
449656 GAAATGACTC
Statistics
Matches: 164, Mismatches: 24, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
163 18 0.11
164 10 0.06
165 11 0.07
166 85 0.52
167 3 0.02
168 12 0.07
169 2 0.01
170 23 0.14
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (163 bp):
AAAAGAAACAGACTCAAAGATTTTTTTCAAAAAACTGTCTCAAAAGAGACAAAACTTTGTTTCAA
AAGAAAAATAATCAAAATTGCATTTTGTTTCAAGGGAAACAAACTCACATAGATTTGTTTCAAGA
GAAATTGTCTCAAAAGAGACAAACCTTTGTTTC
Found at i:449667 original size:30 final size:31
Alignment explanation
Indices: 449613--449671 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
449603 GAGACAAAGT
449613 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCA
449644 TTTGTTTCAAAAGAAAT-GACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
449672 GATGTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 11 0.39
31 17 0.61
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCA
Found at i:449749 original size:36 final size:36
Alignment explanation
Indices: 449709--449846 Score: 181
Period size: 36 Copynumber: 3.8 Consensus size: 36
449699 ATAATTTGGA
*
449709 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * * *
449745 AAATTGTCTCAAACGACACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
449781 AAATTGTCTCAAGCGAGACAACATTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* *
449816 AAAATGATCTCAAGTGAGATCAAC-TTTGTTT
1 AAATTG-TCTCAAGCGAGA-CAACATTTGTTT
449847 AATATGAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
35 8 0.09
36 77 0.87
37 4 0.04
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:449968 original size:107 final size:103
Alignment explanation
Indices: 449785--450136 Score: 385
Period size: 107 Copynumber: 3.3 Consensus size: 103
449775 TTAGAGAAAT
* * *
449785 TGTCTCAAGCGAGAC-AACATTTGTTTTTGAGAAAAT--GATCTCAAGTGAGATCAACTTTGTTT
1 TGTCTCAAACAAGACGAA-ATTTG-TTTTGAAAAAATACGATCTCAAGTGAGATCAACTTTGTTT
*
449847 AATATGAAAACAAATTTGAAATTTGTATTCTCAAAGGAAAAA
64 AATGTG-AAACAAATTTGAAATTTGTA-TCTCAAAGGAAAAA
* *
449889 TGTCTCAAACAAGACGAAATTTGTTTTGAAAAGAATAAC-AGTCTCAAGTGAGATTAATTTTTGT
1 TGTCTCAAACAAGACGAAATTTGTTTTGAAAA-AAT-ACGA-TCTCAAGTGAGATCAA-CTTTG-
* * *
449953 TTTAA-GTGAATCAAATTCGAAATTTGTATATCAAAGGAAAAAAAA
61 TTTAATGTGAAACAAATTTGAAATTTGTATCTCAAAGG---AAAAA
* * *
449998 TGTCTCAAGCAAGACGAAGTTTGTTTT-AAGAAAATACGATCTCAAATGAGATCAACTTTGTTTA
1 TGTCTCAAACAAGACGAAATTTGTTTTGAA-AAAATACGATCTCAAGTGAGATCAACTTTGTTTA
*
450062 ATGTGAAACAAA-TTCAAATTTTGTATCTCAAAGGAAAAA
65 ATGTGAAACAAATTTGAAA-TTTGTATCTCAAAGGAAAAA
**
450101 TGTCTCAAATGAGACGAAATTTGTTTTGAAAGAAAT
1 TGTCTCAAACAAGACGAAATTTGTTTTGAAA-AAAT
450137 TGTCTCAAGC
Statistics
Matches: 209, Mismatches: 22, Indels: 34
0.79 0.08 0.13
Matches are distributed among these distances:
103 37 0.18
104 27 0.13
105 11 0.05
106 36 0.17
107 49 0.23
108 12 0.06
109 37 0.18
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (103 bp):
TGTCTCAAACAAGACGAAATTTGTTTTGAAAAAATACGATCTCAAGTGAGATCAACTTTGTTTAA
TGTGAAACAAATTTGAAATTTGTATCTCAAAGGAAAAA
Found at i:451804 original size:24 final size:25
Alignment explanation
Indices: 451760--451806 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
451750 TCTTTTTTGT
451760 TCTTTGCTTTTTCTTTGCTCTTTTC
1 TCTTTGCTTTTTCTTTGCTCTTTTC
451785 TCTTTG-TTTTTC-TTGTCTCTTT
1 TCTTTGCTTTTTCTTTG-CTCTTT
451807 GCTTTGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 12 0.57
25 6 0.29
ACGTcount: A:0.00, C:0.21, G:0.09, T:0.70
Consensus pattern (25 bp):
TCTTTGCTTTTTCTTTGCTCTTTTC
Found at i:458804 original size:43 final size:41
Alignment explanation
Indices: 458745--458831 Score: 111
Period size: 43 Copynumber: 2.1 Consensus size: 41
458735 TAAATTTATG
*
458745 ATAAAAGATTATTGAAACAATTAACCATCGTTAAGATTCGA
1 ATAAAAGATTATTGAAACAATTAACCATAGTTAAGATTCGA
* * * *
458786 ATAAAAGAAATTATTGAAACAGTTAATCGTAGTTGAGATTCGA
1 ATAAAAG--ATTATTGAAACAATTAACCATAGTTAAGATTCGA
458829 ATA
1 ATA
458832 GAATCAATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 7 0.18
43 32 0.82
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (41 bp):
ATAAAAGATTATTGAAACAATTAACCATAGTTAAGATTCGA
Found at i:460956 original size:15 final size:16
Alignment explanation
Indices: 460932--460961 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
460922 CTTATTGAAA
460932 AAAAATAATACAATAT
1 AAAAATAATACAATAT
460948 AAAAA-AATACAATA
1 AAAAATAATACAATA
460962 AAGAATACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAATAATACAATAT
Found at i:461114 original size:3 final size:3
Alignment explanation
Indices: 461106--461202 Score: 194
Period size: 3 Copynumber: 32.3 Consensus size: 3
461096 ATCTACCATA
461106 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
461154 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
461202 T
1 T
461203 TACAAACCAA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:463036 original size:22 final size:21
Alignment explanation
Indices: 463006--463046 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
462996 CGATACTGTA
*
463006 ATAGAGTATCGGTACCATGAT
1 ATAGAGTATCGATACCATGAT
463027 ATAGTAGTATCGATACCATG
1 ATAG-AGTATCGATACCATG
463047 GTAGGGGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (21 bp):
ATAGAGTATCGATACCATGAT
Found at i:463483 original size:56 final size:56
Alignment explanation
Indices: 463392--463748 Score: 520
Period size: 56 Copynumber: 6.3 Consensus size: 56
463382 TGACACTATA
* *
463392 TGTGTGCAAAAAAATTAAGAAATTCATAATGAGTTTATAAATTTTCGTATGGGCACTT
1 TGTGTGC--AAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTT
* *
463450 TGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTTTCGTATGGGCTCTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAA-TTTTCGTATGGGCACTT
* * *
463507 TGTGTGTAAAAATTAAGAAATTCATAATGAGTTTATGAATTTTTGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTT
* *
463563 TGTGTGCAAAAACTAAGAAATTCATAATGAGATTATGAATTTTCGTATGGACACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTT
* *** *
463619 TGTGTGTAAAAACTAAGAAATTCATAGCAAGTTTATGAATTTCCGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTT
* *
463675 TGTGTGCAAAAACTAAGAAATTCATAACGAGTTTATGAA-TTTCAGTATGAGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTTC-GTATGGGCACTT
463731 TGTGTGC-AAAACTAAGAA
1 TGTGTGCAAAAACTAAGAA
463749 GTAAGAAGTT
Statistics
Matches: 271, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
55 14 0.05
56 198 0.73
57 52 0.19
58 7 0.03
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35
Consensus pattern (56 bp):
TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTTCGTATGGGCACTT
Found at i:464941 original size:76 final size:76
Alignment explanation
Indices: 464790--464997 Score: 274
Period size: 76 Copynumber: 2.7 Consensus size: 76
464780 CAAAGCCAAA
* ** * **
464790 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
464855 TTTGGCTCCGAG
65 TTTGGCTCCGAG
* *
464867 ATTTCCAGAATGCTCGGAGGGAACCAATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
464932 TTTGTTCCGAG
66 TTGGCTCCGAG
* * * *
464943 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
464998 TTGTACAACG
Statistics
Matches: 115, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 17 0.15
76 74 0.64
77 24 0.21
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:470806 original size:21 final size:21
Alignment explanation
Indices: 470769--470829 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
470759 TTTTGGTGCA
*
470769 GAGGGAATCGA-TCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
470789 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
470810 GAAGGAGAACCGATTCCCCC
1 G-AGG-GAACCGATTCCCCC
470830 TACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.29
21 8 0.23
22 3 0.09
23 14 0.40
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:473613 original size:74 final size:75
Alignment explanation
Indices: 473431--473638 Score: 260
Period size: 75 Copynumber: 2.8 Consensus size: 75
473421 CAAAGCCAAA
** * **
473431 AATTCCAGATTGCTCATAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGG
1 AATTCCAGA-TGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
473495 TTTGGCTCCGAG
64 TTTGGCTCCGAG
*
473507 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
473571 TTTGTTCCGAG
65 TTGGCTCCGAG
* * *
473582 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
473639 TGTACAACGG
Statistics
Matches: 116, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
74 21 0.18
75 64 0.55
76 30 0.26
77 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:479789 original size:19 final size:22
Alignment explanation
Indices: 479765--479815 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 22
479755 TACAGAAATT
*
479765 GTATCGATACCGT-A-ATAG-A
1 GTATCGATACCATAATATAGTA
*
479784 GTATCGGTACCATAATATAGTA
1 GTATCGATACCATAATATAGTA
479806 GTATCGATAC
1 GTATCGATAC
479816 TATTGAGCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 11 0.42
20 1 0.04
21 4 0.15
22 10 0.38
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (22 bp):
GTATCGATACCATAATATAGTA
Found at i:480219 original size:56 final size:56
Alignment explanation
Indices: 480144--480555 Score: 700
Period size: 56 Copynumber: 7.3 Consensus size: 56
480134 TGGCATTATA
* *
480144 TGTGTGCAAAAAAATTAAGAAATTCATAATGAGTTTATGAATTTCCATATGGGCACTT
1 TGTGTGC--AAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* *
480202 TGTATGCAAAAACTAAGAAATTCATAATGAGTTCATGAATTTCCGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
*
480258 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCATTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* *
480314 TGTGTACAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCATATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
480370 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* *
480426 TGTGTGCAAAAACTAAGAAATTCATAACGAGTTTATAAATTTCCGTATGGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
* *
480482 TGTGTGCAAAAACTAAGAAATTCATGATGAGTTTATGAATTTCCGTATTGGCACTT
1 TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
480538 TGTGTGC-AAAACTAAGAA
1 TGTGTGCAAAAACTAAGAA
480556 GTAAGAAGTT
Statistics
Matches: 336, Mismatches: 18, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
55 11 0.03
56 319 0.95
58 6 0.02
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (56 bp):
TGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTTCCGTATGGGCACTT
Found at i:484248 original size:19 final size:22
Alignment explanation
Indices: 484204--484254 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 22
484194 GTATGAACAA
484204 TATCGATACCATATGGTAGAGG
1 TATCGATACCATATGGTAGAGG
*
484226 TATCGATACC-TAT-G-AGGGG
1 TATCGATACCATATGGTAGAGG
484245 TATCGATACC
1 TATCGATACC
484255 CGGGGAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.50
20 1 0.04
21 3 0.11
22 10 0.36
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (22 bp):
TATCGATACCATATGGTAGAGG
Found at i:492525 original size:110 final size:109
Alignment explanation
Indices: 492327--492772 Score: 610
Period size: 110 Copynumber: 4.0 Consensus size: 109
492317 CCAAACGACA
* * *
492327 TGATGTTTTCAAAAGAATTTTTAGAGAAACTAAGCCTGGTTTTTAGGGGTTTCTTGATGATAATT
1 TGATGTTTTCAAAAGAGTTTTT--AGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATT
* *
492392 TCAAATGAATTTTTAAGATAAGCTAAGCCTAATTTTTAGGGGTTTCT
64 TCCAATGAATTTTTAA-AGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * *
492439 TGATGTTTTCAAACGAGTTTTTAGAAACTAAGTCTGATTTTTAGGGGTTTCTTGATGATGGTTTC
1 TGATGTTTTCAAAAGAGTTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTC
492504 CAATGAATTTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
66 CAATGAA-TTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * * *
492549 TGA--TTTTCAAAAGAGTTTTTAGAGACTAAGCCTGATTTTTAGGGGTTTCTTAATAATGATTTT
1 TGATGTTTTCAAAAGAGTTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTC
*
492612 CAATTAATTTTTTAAAAAAGAAGCTAAGCCTAA-TTTTAGGGGTTTCT
66 CAATGAA-TTTTT---AAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * * * * * *
492659 TTATGTTCTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTGAAGGGTTTCTTGAAGATTATTTC
1 TGATGTTTTCAAAAGAGTTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTC
*
492724 CAAAGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
66 CAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
492768 TGATG
1 TGATG
492773 ATAACTGAAA
Statistics
Matches: 297, Mismatches: 30, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
108 82 0.28
109 18 0.06
110 93 0.31
111 29 0.10
112 75 0.25
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (109 bp):
TGATGTTTTCAAAAGAGTTTTTAGAAACTAAGCCTGATTTTTAGGGGTTTCTTGATGATGATTTC
CAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
Found at i:492812 original size:115 final size:108
Alignment explanation
Indices: 492345--492828 Score: 427
Period size: 110 Copynumber: 4.4 Consensus size: 108
492335 TCAAAAGAAT
* * * * * *
492345 TTTTAGAGAAACTAAGCCTGGTTTTTAGGGGTTTCTTGATGATAATTT-CAAATGAATTTTTAAG
1 TTTTA-AGAAACTAAGCCTGATTTTCAAGGATTTCTTGAAGATTATTTCCAAA-GAATTTTTAA-
* ** *
492409 ATAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAACGAG
63 AGAAGCTAAGCCTAA-TTTTAGGGGTTTCTTGATGTACTAAAACGAG
* * * * * * ** *
492456 TTTTTAGAAACTAAGTCTGATTTTTAGGGGTTTCTTGATGATGGTTTCCAATGAATTTTTTAAAG
1 TTTTAAGAAACTAAGCCTGATTTTCAAGGATTTCTTGAAGATTATTTCCAAAGAA-TTTTTAAAG
* *
492521 AAGCTAAGCCTAATTTTTAGGGGTTTCTTGATTTTC-AAAA-GAG
65 AAGCTAAGCCTAA-TTTTAGGGGTTTCTTGATGTACTAAAACGAG
* * * * * * * * **
492564 TTTTTAGAGACTAAGCCTGATTTTTAGGGGTTTCTT-AATAATGATTTTCAATTAATTTTTTAAA
1 TTTTAAGAAACTAAGCCTGATTTTCAAGGATTTCTTGAA-GATTATTTCCAAAGAA-TTTTT---
* * * *
492628 AAAGAAGCTAAGCCTAATTTTAGGGGTTTCTTTATGTTCTCAAATGAG
61 AAAGAAGCTAAGCCTAATTTTAGGGGTTTCTTGATGTACTAAAACGAG
* * *
492676 TTTTTAGAAACTAAGCCTGATTTTGAAGGGTTTCTTGAAGATTATTTCCAAAGAATTTTTAAAGA
1 TTTTAAGAAACTAAGCCTGATTTTCAAGGATTTCTTGAAGATTATTTCCAAAGAATTTTTAAAGA
492741 AGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAACTGAAAACGAAAG
66 AGCTAAGCCTAA-TTTTAGGGGTTTCTTGATG-T-ACT-AAAACG--AG
*
492790 ATTTTAAGAAACTAAGCTTGATTTTCAAGGATTTCTTGA
1 -TTTTAAGAAACTAAGCCTGATTTTCAAGGATTTCTTGA
492829 TGAGTAAGTC
Statistics
Matches: 321, Mismatches: 36, Indels: 28
0.83 0.09 0.07
Matches are distributed among these distances:
107 1 0.00
108 72 0.22
109 21 0.07
110 97 0.30
111 41 0.13
112 51 0.16
113 2 0.01
114 2 0.01
115 34 0.11
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (108 bp):
TTTTAAGAAACTAAGCCTGATTTTCAAGGATTTCTTGAAGATTATTTCCAAAGAATTTTTAAAGA
AGCTAAGCCTAATTTTAGGGGTTTCTTGATGTACTAAAACGAG
Found at i:492939 original size:41 final size:41
Alignment explanation
Indices: 492827--492955 Score: 161
Period size: 42 Copynumber: 3.1 Consensus size: 41
492817 AGGATTTCTT
* *
492827 GATGAGTAAGTCCTTCGGGCCAT-CAGTAAGTCTTTCGAGCAT
1 GATGA-TAAGTCCTTCGGGTCATCCA-TAAGTCTTTCGAGCAA
* * *
492869 GATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAA
1 GATG-ATAAGTCCTTCGGGTCATCCATAAGTCTTTCGAGCAA
* *
492911 GATGATAAGTCCTTCGGGTCATCCATAAGACCTTCGAGCAA
1 GATGATAAGTCCTTCGGGTCATCCATAAGTCTTTCGAGCAA
492952 GATG
1 GATG
492956 TTTTCAACAT
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
41 36 0.48
42 38 0.51
43 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (41 bp):
GATGATAAGTCCTTCGGGTCATCCATAAGTCTTTCGAGCAA
Found at i:493116 original size:60 final size:59
Alignment explanation
Indices: 492961--493117 Score: 269
Period size: 59 Copynumber: 2.6 Consensus size: 59
492951 AGATGTTTTC
*
492961 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCATCAACGCCCCACCAGAGGGGTT
1 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTT
* *
493020 AACATTTTCTTTGTTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTT
1 AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTT
*
493079 AATATTTCCTATTGCTCGATTCACAACACTTCGAATCAG
1 AACATTTCCT-TTGCTCGATTCACAACACTTCGAATCAG
493118 TTTAAGTCCT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 64 0.70
60 27 0.30
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (59 bp):
AACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTT
Found at i:495204 original size:17 final size:18
Alignment explanation
Indices: 495168--495213 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
495158 GGTCATTGTA
495168 TTTATGTTTATGTTTATT
1 TTTATGTTTATGTTTATT
*
495186 TTTAT-TTTATGTTGTTTT
1 TTTATGTTTATGTT-TATT
495204 TTTACTGTTT
1 TTTA-TGTTT
495214 TTATTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.33
18 12 0.50
19 1 0.04
20 3 0.12
ACGTcount: A:0.13, C:0.02, G:0.11, T:0.74
Consensus pattern (18 bp):
TTTATGTTTATGTTTATT
Found at i:495243 original size:27 final size:27
Alignment explanation
Indices: 495184--495236 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
495174 TTTATGTTTA
* *
495184 TTTTTATTTTATGTTGTTTTTTTACTG
1 TTTTTATTTTATGTTGTTATTTTAATG
495211 TTTTTATTATTAT-TTGTTATTTTAAT
1 TTTTTATT-TTATGTTGTTATTTTAAT
495237 TATTTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.74
Consensus pattern (27 bp):
TTTTTATTTTATGTTGTTATTTTAATG
Found at i:497750 original size:7 final size:7
Alignment explanation
Indices: 497738--497775 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
497728 AAGACTCGGG
497738 AAAAGTA
1 AAAAGTA
497745 AAAAGTA
1 AAAAGTA
497752 AAAAGTA
1 AAAAGTA
497759 AAAAGTA
1 AAAAGTA
497766 AAAAGTA
1 AAAAGTA
497773 AAA
1 AAA
497776 GAAAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAAGTA
Found at i:501572 original size:157 final size:159
Alignment explanation
Indices: 501303--501667 Score: 452
Period size: 162 Copynumber: 2.3 Consensus size: 159
501293 TGATGTTACC
* *** *
501303 TATGTATTCTATTG-TGGTATATGAGCATGTTGTTCAAATTT-AGTAAAAGGTGGACTTAAAATA
1 TATGTATTCTA-TGATGGTTTATGAGCATGTTGTTCAAATTTGA-TAAAAGACAGACTTAAAAAA
* * *
501366 AAGGATGAATTGAAGAAATAAGGAAAATATGAAAGATTAAGGGACTAAATT-GAAAAAT-AAAAA
64 AAGGATGAATTGAAGAAATAAAGAAAATATGAAAAATTAAGGGACTAAATTAAAAAAATAAAAAA
*
501429 ATTGTTATCTAAAAGAGAAATTGAAAGTACA
129 ATTGTTATCAAAAAGAGAAATTGAAAGTACA
* *
501460 TATGTATTCTACGATGGTTTATGCGCATGTTGTTCAAATTTGATAAAAGACAGACTTAAAACAAA
1 TATGTATTCTATGATGGTTTATGAGCATGTTGTTCAAATTTGATAAAAGACAGACTTAAAA-AAA
* * *
501525 ATGATGAATTGAAGAGATAAAGAAAATATGAAAAATTAA-GGATTAAATTAAAAAAATAAAAAAA
65 AGGATGAATTGAAGAAATAAAGAAAATATGAAAAATTAAGGGACTAAATTAAAAAAAT---AAAA
* * *
501589 AAATTGTTATCAAAAAGAGGAGTTGAAAGTATA
127 AAATTGTTATCAAAAAGAGAAATTGAAAGTACA
* * * *
501622 TATGTATTCTATGATGGTTTATAAGTATGTGGTCCAAATTTGATAA
1 TATGTATTCTATGATGGTTTATGAGCATGTTGTTCAAATTTGATAA
501668 TAAAAAAAGA
Statistics
Matches: 177, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
156 1 0.01
157 60 0.34
158 44 0.25
162 72 0.41
ACGTcount: A:0.46, C:0.05, G:0.18, T:0.30
Consensus pattern (159 bp):
TATGTATTCTATGATGGTTTATGAGCATGTTGTTCAAATTTGATAAAAGACAGACTTAAAAAAAA
GGATGAATTGAAGAAATAAAGAAAATATGAAAAATTAAGGGACTAAATTAAAAAAATAAAAAAAT
TGTTATCAAAAAGAGAAATTGAAAGTACA
Found at i:502475 original size:24 final size:24
Alignment explanation
Indices: 502448--502493 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
502438 AAACAAATGA
*
502448 AAATAAAAGTCTTAATATAAAAAT
1 AAATAAAAGGCTTAATATAAAAAT
502472 AAATAAAAGGCTTAATATAAAA
1 AAATAAAAGGCTTAATATAAAA
502494 TAAGTGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATAAAAGGCTTAATATAAAAAT
Found at i:502804 original size:18 final size:19
Alignment explanation
Indices: 502781--502817 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
502771 TTCATTGAAA
*
502781 AACCGATAAAC-CGAACCG
1 AACCGAAAAACTCGAACCG
502799 AACCGAAAAACTCGAACCG
1 AACCGAAAAACTCGAACCG
502818 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.46, C:0.32, G:0.16, T:0.05
Consensus pattern (19 bp):
AACCGAAAAACTCGAACCG
Found at i:503434 original size:16 final size:16
Alignment explanation
Indices: 503410--503443 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
503400 CGATTGCGGC
503410 AAAGAGGGGAAGAAGA
1 AAAGAGGGGAAGAAGA
* *
503426 AAAGTGGGGAAGGAGA
1 AAAGAGGGGAAGAAGA
503442 AA
1 AA
503444 GGGGAAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (16 bp):
AAAGAGGGGAAGAAGA
Found at i:509154 original size:3 final size:3
Alignment explanation
Indices: 509146--509187 Score: 66
Period size: 3 Copynumber: 13.3 Consensus size: 3
509136 CGGGTCTTTT
509146 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T
509188 GTTTATTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:509199 original size:16 final size:15
Alignment explanation
Indices: 509145--509195 Score: 70
Period size: 16 Copynumber: 3.5 Consensus size: 15
509135 CCGGGTCTTT
509145 TTTATTATTATT-TA
1 TTTATTATTATTATA
509159 -TTATTATTATTATTA
1 TTTATTATTATTA-TA
*
509174 TTTATTATTATTATG
1 TTTATTATTATTATA
509189 TTTATTA
1 TTTATTA
509196 ATTACATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
13 11 0.33
15 10 0.30
16 12 0.36
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTATTATTATTATA
Found at i:509199 original size:19 final size:19
Alignment explanation
Indices: 509146--509187 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
509136 CGGGTCTTTT
509146 TTATTATTATTTATTATTA
1 TTATTATTATTTATTATTA
509165 TTATTATTATTTATTATTA
1 TTATTATTATTTATTATTA
509184 TTAT
1 TTAT
509188 GTTTATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTATTATTTATTATTA
Found at i:509331 original size:25 final size:25
Alignment explanation
Indices: 509302--509374 Score: 128
Period size: 25 Copynumber: 2.9 Consensus size: 25
509292 ACCAACCCAT
*
509302 CAGATTAGGGTTTTAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
509327 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
*
509352 CAAATTAGGGTTTCAAACCCTAA
1 CAGATTAGGGTTTCAAACCCTAA
509375 TCCCCTAATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAA
Found at i:511197 original size:22 final size:22
Alignment explanation
Indices: 511172--511215 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
511162 TCAAACGATG
*
511172 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
511194 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
511216 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:512758 original size:31 final size:32
Alignment explanation
Indices: 512722--512783 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
512712 ATTTTACATG
*
512722 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCATTTGTTTGTGTA
512753 TACTAACTTATTTCTTCTCATTTGTTTGTGT
1 TACTAACTTATTTCTTCTCATTTGTTTGTGT
512784 CAATTTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.16, C:0.15, G:0.10, T:0.60
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCATTTGTTTGTGTA
Found at i:515650 original size:17 final size:16
Alignment explanation
Indices: 515630--515664 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
515620 AGATCATATT
*
515630 AAAGCGAAGAGAAAAGA
1 AAAGCAAAGAG-AAAGA
515647 AAAGCAAAGAGAAAGA
1 AAAGCAAAGAGAAAGA
515663 AA
1 AA
515665 CAAAGTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.69, C:0.06, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAGCAAAGAGAAAGA
Found at i:516865 original size:4 final size:4
Alignment explanation
Indices: 516856--516915 Score: 93
Period size: 4 Copynumber: 15.0 Consensus size: 4
516846 AAAAGTATAC
* * *
516856 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT ATAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
516904 ACAT ACAT ACAT
1 ACAT ACAT ACAT
516916 GATACATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:517513 original size:105 final size:103
Alignment explanation
Indices: 517372--517611 Score: 299
Period size: 105 Copynumber: 2.3 Consensus size: 103
517362 TGAGAATTTT
* * *
517372 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
*
517436 TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 TT-AAACAAAATTAATCTCACCTTGAGATCG-T-TTTC--TCA
* * *
517477 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* * *
517542 TTAAACAAAGTTGATCTCACTTTGAGATCGTTTTCTCA
66 TTAAACAAAATTAATCTCACCTTGAGATCGTTTTCTCA
*
517580 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
517612 TCTAGAAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
102 2 0.02
103 26 0.22
104 7 0.06
105 77 0.65
106 7 0.06
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (103 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TTAAACAAAATTAATCTCACCTTGAGATCGTTTTCTCA
Found at i:517621 original size:36 final size:34
Alignment explanation
Indices: 517573--517676 Score: 111
Period size: 36 Copynumber: 3.0 Consensus size: 34
517563 TTGAGATCGT
*
517573 TTTCTCAAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAACAAA-TTTGTCTCGCTTGAGACAA
** *
517608 TTTCTCTAGAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTA-AAACAAA-TTTGTCTCGCTTGAGACAA
* *
517644 TATCT-TAAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAACAAATTT-GTCTCGCTTGAGACA
517677 TCATTTTCTC
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
33 3 0.05
34 18 0.32
35 9 0.16
36 27 0.47
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (34 bp):
TTTCTCTAAAACAAATTTGTCTCGCTTGAGACAA
Found at i:517951 original size:27 final size:27
Alignment explanation
Indices: 517924--518042 Score: 152
Period size: 27 Copynumber: 4.3 Consensus size: 27
517914 ACAGTTTCTC
*
517924 TTGAAAAAATCTTTGAGTTTGTTCCTC
1 TTGAAAAAATCTTTGAGTTTGTTCCTT
*
517951 TTGAAAAAATC-TTGAAGTTTGCTCCTT
1 TTGAAAAAATCTTTG-AGTTTGTTCCTT
*
517978 TTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTG-A-AAAAATCTTTGAGTTTGTTCCTT
*
518007 TTGAATAAAATCTTTGAG-TTGTTTCTT
1 TTGAA-AAAATCTTTGAGTTTGTTCCTT
518034 TTGAAAAAA
1 TTGAAAAAA
518043 AAAACTTTGA
Statistics
Matches: 81, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.09
27 38 0.47
28 13 0.16
29 21 0.26
30 2 0.02
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (27 bp):
TTGAAAAAATCTTTGAGTTTGTTCCTT
Found at i:517990 original size:56 final size:57
Alignment explanation
Indices: 517927--518054 Score: 163
Period size: 56 Copynumber: 2.3 Consensus size: 57
517917 GTTTCTCTTG
517927 AAAAAATCTTTGAGTTTGTTCCTCTTGAA-AAAATC-TTGAAGTTTGCTCCTTTTG-AA
1 AAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAATCTTTG-AG-TTGCTCCTTTTGAAA
* * * * *
517983 TAAAAATCTTGGAGTTTGTTCCTTTTGAATAAAATCTTTGAGTTGTTTCTTTTGAAA
1 AAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAATCTTTGAGTTGCTCCTTTTGAAA
*
518040 AAAAAAACTTTGAGT
1 AAAAAATCTTTGAGT
518055 CTATTTATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
56 36 0.59
57 22 0.36
58 3 0.05
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (57 bp):
AAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAATCTTTGAGTTGCTCCTTTTGAAA
Found at i:518068 original size:30 final size:29
Alignment explanation
Indices: 518013--518069 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
518003 CCTTTTGAAT
* * *
518013 AAAATCTTTGAGTTGTTTCTTTTGAAAAA
1 AAAAACTTTGAGTTATTTATTTTGAAAAA
518042 AAAAACTTTGAGTCTATTTATTTTGAAA
1 AAAAACTTTGAGT-TATTTATTTTGAAA
518070 CAAAGTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (29 bp):
AAAAACTTTGAGTTATTTATTTTGAAAAA
Found at i:518123 original size:52 final size:52
Alignment explanation
Indices: 518063--518219 Score: 287
Period size: 52 Copynumber: 3.0 Consensus size: 52
518053 GTCTATTTAT
518063 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAATCTTTGAG
1 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAATCTTTGAG
518115 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAATCTTTGAG
1 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAATCTTTGAG
* *
518167 TCTGAAACAAAGTGTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAG
1 TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAG
518220 ATTGTTTTTT
Statistics
Matches: 102, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 89 0.87
53 13 0.13
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (52 bp):
TTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAATCTTTGAG
Found at i:518243 original size:29 final size:30
Alignment explanation
Indices: 518207--518269 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 30
518197 AATTTCGTGA
*
518207 AAAAATCTTTGAGATTGTTT-TTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
*
518236 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
518266 AAAA
1 AAAA
518270 TTTTGTCTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:518789 original size:31 final size:30
Alignment explanation
Indices: 518713--518797 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 30
518703 ATTTTGACTC
* *
518713 CTTTGAGGCAGTTTCTCTAGAAATACAAAAT
1 CTTTGAGTC-GTTTCTCTTGAAATACAAAAT
*
518744 CTTTGAGTTTGTTTCTCTTGAAATA-AAACCAT
1 CTTTGAG-TCGTTTCTCTTGAAATACAAA--AT
*
518776 CTTTGAGTCGTTTCCCTTGAAA
1 CTTTGAGTCGTTTCTCTTGAAA
518798 CGAATTTTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 3 0.07
31 34 0.74
32 9 0.20
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (30 bp):
CTTTGAGTCGTTTCTCTTGAAATACAAAAT
Found at i:519468 original size:28 final size:28
Alignment explanation
Indices: 519436--519489 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
519426 TCAAAATCCA
*
519436 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTTCTATTGAAACAC
*
519464 ATCTTTGAGTTGGTTTCTCTTGAAAC
1 ATCTTTGAGTTGGTTTCTATTGAAAC
519490 CATAGCTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTTCTATTGAAACAC
Found at i:519656 original size:46 final size:45
Alignment explanation
Indices: 519601--519795 Score: 153
Period size: 46 Copynumber: 4.5 Consensus size: 45
519591 CCAGCCGTCC
*
519601 TCATCACGTAGGAACCGTGTTATCACCTTAAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTCATCACCTT-AGATGGCCAGAACTCT
* * *
519647 TCATCACGTATGAGCCGTGTCATTC-CC--AGA---CCAGATCTCT
1 TCATCACGTAGGAACCGTGTCA-TCACCTTAGATGGCCAGAACTCT
* * ** * *
519687 T-ATCACGTAGG-AGCGTGTCA--ACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTCATCACCTTAGATGGCCAGAAC-TCT
*
519728 TCATCACGTAGGAA-CGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTCATCACC-TTAGATGGCCAGAACTCT
* *
519773 TCATCACGTATGAGCCGTGTCAT
1 TCATCACGTAGGAACCGTGTCAT
519796 TCCCCGACCA
Statistics
Matches: 116, Mismatches: 18, Indels: 30
0.71 0.11 0.18
Matches are distributed among these distances:
36 2 0.02
38 10 0.09
39 9 0.08
40 11 0.09
41 7 0.06
42 16 0.14
43 4 0.03
44 3 0.03
45 23 0.20
46 29 0.25
47 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (45 bp):
TCATCACGTAGGAACCGTGTCATCACCTTAGATGGCCAGAACTCT
Found at i:519785 original size:126 final size:129
Alignment explanation
Indices: 519501--519825 Score: 514
Period size: 126 Copynumber: 2.5 Consensus size: 129
519491 ATAGCTCCTA
* * * * * * *
519501 AAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATTTCCTTATCAC
1 AAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCAC
519565 GTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
65 GTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
519630 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCT-CTTATCACG
1 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
519694 TAGGAG-CGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAA-CGTGTTATCACCTT
66 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
* * * *
519756 TAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCCGACCAGATGTCCTCATCACG
1 AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
519821 TAGGA
66 TAGGA
519826 ACCGCGTTAA
Statistics
Matches: 183, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
126 66 0.36
127 55 0.30
128 15 0.08
129 46 0.25
130 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (129 bp):
AAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACG
TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTT
Found at i:520051 original size:16 final size:18
Alignment explanation
Indices: 520012--520058 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 18
520002 GTCCGGGTCT
520012 TTTTTATT-TTATATATA
1 TTTTTATTATTATATATA
520029 TTATTTATTATTAT-TATA
1 TT-TTTATTATTATATATA
520047 -TTTTATTATTAT
1 TTTTTATTATTAT
520059 GTTTATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 10 0.36
19 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTTATTATTATATATA
Found at i:520210 original size:25 final size:25
Alignment explanation
Indices: 520172--520242 Score: 119
Period size: 24 Copynumber: 2.9 Consensus size: 25
520162 ACCAAACCAT
520172 CAGATTAGGG-TTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
*
520196 TAGATTAGGGTTTCAAA-CCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
520220 CAGATTAGGGTTTCAAACCCTAA
1 CAGATTAGGGTTTCAAACCCTAA
520243 TCCCCTAATG
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
24 32 0.74
25 11 0.26
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAA
Found at i:521994 original size:22 final size:22
Alignment explanation
Indices: 521969--522012 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
521959 TCAAACGATG
*
521969 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
521991 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
522013 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:524735 original size:6 final size:6
Alignment explanation
Indices: 524724--527526 Score: 4351
Period size: 6 Copynumber: 481.3 Consensus size: 6
524714 TACATGTATG
524724 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
524772 TAC--A TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
524818 TACATA TACATA TATATACA TACATA TAC--A TACATA TACATA TACATA
1 TACATA TACATA TACAT--A TACATA TACATA TACATA TACATA TACATA
524866 TACATA TAC--A TACATA TACATA TACATA T--ATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
524910 TAC--A TACATA TACATA TACATA TACATA TACATA TACATA -ACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
524955 TACATA TAC--A TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525001 TACATA T--ATA -ACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
* *
525046 TAAATA TACATA TACA-A TACATA TACATA TACATA TACATA TATATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525093 TACATA TACATA TACATA TACATA TACAT- TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525140 TACATA T--ATA TACATA TACATA TACATA TACATA TACATA TAC--A
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525184 TACATA TACATA TAC-TA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525231 TACATA TACATA TACATATA TACATA TACATA TAC-TA T--ATA TACATA
1 TACATA TACATA TAC--ATA TACATA TACATA TACATA TACATA TACATA
525278 TACATA TACATA TACATA TAC--A TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
525324 TACATA TACATA TACATA TACATA TACATA TACCTA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
* *
525372 TACATA TACATA CATATA TACATA TACATA TACATA TACATA TA-ATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
525419 TATATA TACATA TACATA TACATA TAC--A TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525465 TAC--A TACATA TACATA TACATA TACATA TAC-TA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525510 TACATA TACA-A TACATA TACATA TACATA TAC-TA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525556 TACATA TACATA TACATA TAC--A TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525602 TACATA TACATATA TACATA TACATA TACATA TACATA TAC--A TACATA
1 TACATA TAC--ATA TACATA TACATA TACATA TACATA TACATA TACATA
*
525650 TAC--A TACACA TAC-TA TACATA TACATA TA-ATA TACATA TAC-TA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
525693 TACATA TACAATA TACATA TACATA TACATA GACATA TAC-TA TACATA
1 TACATA TAC-ATA TACATA TACATA TACATA TACATA TACATA TACATA
525741 TACATA TACATA TACATA TACATA TACATA TACATA TAC-TA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525788 TACATA T-CATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525835 TACATA TACA-A TTACATA TACATA TAC--A TACAT- TACATA TACATATA
1 TACATA TACATA -TACATA TACATA TACATA TACATA TACATA TAC--ATA
* *
525882 TACATA TACATATA TATATA TACATA TACATA TACATA TACATC TACATA
1 TACATA TAC--ATA TACATA TACATA TACATA TACATA TACATA TACATA
525932 TAC-TA TACATA TACATA TACATA TACATA TACATA -A-ATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
525977 TACATA TACA-A TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
526024 TACATA TACATA TACATA TACATA TACATA TACA-A TACATA T--ATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
526069 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
526117 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
526165 TACATA TACATA TACATA TAC--A TACAT- TA-ATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
526209 TACATA TACATA TACATA TATATACA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACAT--A TACATA TACATA TACATA TACATA
526259 TACATA TACATA TAC--A TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
526305 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
526353 TACATA TAC-TA TACATA TACATA TAC--A TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
526398 TA-ACA TACATA TACATA TAC-TA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
526444 TACATA TACATA TACATATA TACATA TAC--A TACATA TACATA TACTACA
1 TACATA TACATA TAC--ATA TACATA TACATA TACATA TACATA TAC-ATA
526493 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
526541 TACATA TAC--A TACATA TACATA T--ATA TACATA TAC-TA TACATACA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACAT--A
526586 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
526634 TACATA TACATA TAC--A TACATA TACATA TACATA TACATA -ACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
* *
526679 -AC--A TACATA TATACA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
526724 CTAACATA TACATA TACATACA TACATA TACATA -ACATA TACATA TACATA
1 -T-ACATA TACATA TACAT--A TACATA TACATA TACATA TACATA TACATA
526775 TACATA TACATA TAC--A TACATA TACATA TACATA TAC-TA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
526820 TACATA TACATA TACATA TACATA TACATA TACATA TAC--A TACATT
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
526866 TACATA TACATA TACATA TACATA TAC--A TAC-TA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
526911 TACATA TATATA TACATA TACATA TACATA T--ATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
526957 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
527005 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
527053 TACATA TACATA TACATA TACATACA TACATA TACATA TACA-A TACATA
1 TACATA TACATA TACATA TACAT--A TACATA TACATA TACATA TACATA
*
527102 TACATA TACATA TACATA T--ATA TATATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
527148 TACATA TACATA TACATA TACATA TACATA TAC--A TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
527194 TACATA TACATA TACATA -ACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
527241 TACATA TACATA TAC--A TACATA TAC--A TACA-A TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
527284 TACATATA TACATA TACATA TAC--A TACATA TAC--A TACATA TACATA
1 TAC--ATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
*
527330 TACATA TACATA TACATA TACATA TCCATA TAC--A TACATA T-CATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
527375 TACATA TACTATA TACATA TACATA TAC--A TACATA TA-ATA TACATA
1 TACATA TAC-ATA TACATA TACATA TACATA TACATA TACATA TACATA
527421 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
527469 TACATA TACATA TACATA TACATA TACATACA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACAT--A TACATA TACATA TACATA
527519 TACATA TA
1 TACATA TA
527527 AAGGAAAATT
Statistics
Matches: 2618, Mismatches: 37, Indels: 284
0.89 0.01 0.10
Matches are distributed among these distances:
3 1 0.00
4 153 0.06
5 167 0.06
6 2203 0.84
7 20 0.01
8 74 0.03
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TACATA
Found at i:528961 original size:11 final size:11
Alignment explanation
Indices: 528947--528998 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
528937 TTATTACATT
528947 ATTATAAAATA
1 ATTATAAAATA
528958 ATTATTAAAAT-
1 ATTA-TAAAATA
* *
528969 -TTATCAAATT
1 ATTATAAAATA
528979 ATTATAAAATA
1 ATTATAAAATA
528990 ATTAGTAAA
1 ATTA-TAAA
528999 TTTATCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 5 0.15
10 3 0.09
11 16 0.47
12 10 0.29
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
ATTATAAAATA
Found at i:528977 original size:21 final size:20
Alignment explanation
Indices: 528948--528988 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
528938 TATTACATTA
528948 TTATAAAATAATTATTAAAAT
1 TTATAAAATAATTA-TAAAAT
* *
528969 TTATCAAATTATTATAAAAT
1 TTATAAAATAATTATAAAAT
528989 AATTAGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATAAAATAATTATAAAAT
Found at i:528985 original size:32 final size:31
Alignment explanation
Indices: 528916--529007 Score: 123
Period size: 32 Copynumber: 3.0 Consensus size: 31
528906 AAAATAATTA
* * * *
528916 TATTTTAAAATAATAATTAAA-TTATTACAT
1 TATTATAAAATAATTATTAAATTTATCAAAT
528946 TATTATAAAATAATTATTAAAATTTATCAAAT
1 TATTATAAAATAATTATT-AAATTTATCAAAT
*
528978 TATTATAAAATAATTAGTAAATTTATCAAA
1 TATTATAAAATAATTATTAAATTTATCAAA
529008 CTTTACTATA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
30 16 0.29
31 15 0.27
32 24 0.44
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
TATTATAAAATAATTATTAAATTTATCAAAT
Found at i:529082 original size:17 final size:18
Alignment explanation
Indices: 529032--529090 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
529022 CATAATTGTT
* *
529032 ATTTTATAATAATTTGGTA
1 ATTTCATAAT-ATTTAGTA
*
529051 ATTTTACATATTATTTA-TA
1 A-TTT-CATAATATTTAGTA
529070 ATTTCATAATATTTAGTA
1 ATTTCATAATATTTAGTA
529088 ATT
1 ATT
529091 AAAATTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 10 0.30
18 8 0.24
19 4 0.12
20 7 0.21
21 4 0.12
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.54
Consensus pattern (18 bp):
ATTTCATAATATTTAGTA
Found at i:529148 original size:33 final size:33
Alignment explanation
Indices: 529110--529176 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
529100 ATTTAATCAT
529110 AATTTAAATATCTCTATTTTATTATATTATATA
1 AATTTAAATATCTCTATTTTATTATATTATATA
529143 AATTTAAATATCTCTATTTTATTATATTATATA
1 AATTTAAATATCTCTATTTTATTATATTATATA
529176 A
1 A
529177 TAAAATTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (33 bp):
AATTTAAATATCTCTATTTTATTATATTATATA
Found at i:529731 original size:21 final size:20
Alignment explanation
Indices: 529704--529801 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
529694 AATCAGTGTC
529704 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
529725 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
529745 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
529765 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
529786 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
529802 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:529754 original size:41 final size:41
Alignment explanation
Indices: 529645--529801 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
529635 AAATGACCAA
* **
529645 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
529684 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
529725 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
529766 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
529802 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:529811 original size:20 final size:20
Alignment explanation
Indices: 529788--529958 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
529778 GCGAATATGA
529788 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
529808 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
529828 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
529848 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
529868 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
529888 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
529908 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
529928 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
529948 AAATCGCAACG
1 AAATCGCAACG
529959 AGAATCTGTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 127 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:529853 original size:60 final size:58
Alignment explanation
Indices: 529768--529977 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 58
529758 CGATTTTCCA
* ** * *
529768 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGT
* ** *
529828 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGT
* *
529888 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGT
* * *
529948 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
529978 ACTGAAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 120 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGT
Found at i:529959 original size:20 final size:20
Alignment explanation
Indices: 529822--529977 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
529812 CGCAATGCGT
*
529822 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
529842 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
529862 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
529882 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
529902 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
529922 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
529942 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
529962 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
529978 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:529959 original size:40 final size:40
Alignment explanation
Indices: 529788--529977 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
529778 GCGAATATGA
* *
529788 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
529828 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
529868 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
529908 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
529948 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
529978 ACTGAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:530693 original size:24 final size:24
Alignment explanation
Indices: 530654--530700 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
530644 AAATTTGGTC
530654 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
530678 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
530701 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:533262 original size:20 final size:19
Alignment explanation
Indices: 533210--533315 Score: 96
Period size: 19 Copynumber: 5.7 Consensus size: 19
533200 GCAACGAGAG
*
533210 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
533229 AATCGCAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
*
533243 AATCACAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* *
533263 TATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* * *
533283 TATCGTAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
533302 AATCGCAACGCGAA
1 AATCGCAACGCGAA
533316 TTTAGTTTCG
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 26 0.37
20 26 0.37
21 3 0.04
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:533333 original size:19 final size:19
Alignment explanation
Indices: 533311--533353 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
533301 AAATCGCAAC
*
533311 GCGA-ATTTAGTTTCGCGTT
1 GCGATATTTA-TTTCGCATT
*
533330 GCGATTTTTATTTCGCATT
1 GCGATATTTATTTCGCATT
533349 GCGAT
1 GCGAT
533354 TCTCTCGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (19 bp):
GCGATATTTATTTCGCATT
Found at i:533354 original size:19 final size:19
Alignment explanation
Indices: 533316--533386 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
533306 GCAACGCGAA
*
533316 TTTAGTTTCGCGTTGCGATT
1 TTTA-TTTCGCATTGCGATT
533336 TTTATTTCGCATTGCGA--
1 TTTATTTCGCATTGCGATT
* *
533353 -TTCTCTCG--TTGCGATT
1 TTTATTTCGCATTGCGATT
*
533369 TTCATTTCGCATTGCGAT
1 TTTATTTCGCATTGCGAT
533387 AGTCATTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
14 6 0.15
16 6 0.15
17 5 0.12
19 19 0.47
20 4 0.10
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.48
Consensus pattern (19 bp):
TTTATTTCGCATTGCGATT
Found at i:533510 original size:14 final size:14
Alignment explanation
Indices: 533491--533527 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
533481 CATCAATTAA
533491 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
533505 ACAAATCATCTTTT
1 ACAAATCAACTTTT
533519 ACAAATCAA
1 ACAAATCAA
533528 TTAAAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:534922 original size:21 final size:20
Alignment explanation
Indices: 534898--534984 Score: 54
Period size: 21 Copynumber: 4.3 Consensus size: 20
534888 GTGGGAGGGA
534898 CCTCTTCAACGATGACAGTGG
1 CCTCTTCAACGATGA-AGTGG
* * * *
534919 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTCAACGAT-GAAGTGG
* *
534940 ACTC-TCGA-GATGATAG-GG
1 CCTCTTCAACGATGA-AGTGG
534958 CCTCTTCAACGATAGAAGTGG
1 CCTCTTCAACGAT-GAAGTGG
*
534979 ACTCTT
1 CCTCTT
534985 GAGGGATGAC
Statistics
Matches: 48, Mismatches: 12, Indels: 12
0.67 0.17 0.17
Matches are distributed among these distances:
18 6 0.12
19 7 0.15
20 7 0.15
21 27 0.56
22 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.24
Consensus pattern (20 bp):
CCTCTTCAACGATGAAGTGG
Found at i:535429 original size:14 final size:14
Alignment explanation
Indices: 535410--535496 Score: 57
Period size: 14 Copynumber: 5.5 Consensus size: 14
535400 AAAAATGACT
535410 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
535424 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
535443 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
* *
535457 ATCGCAACACAAAATGAAA
1 ATCGC-A-AC--GA-GAGA
535476 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
535490 ATCGCAA
1 ATCGCAA
535497 TGCGAAATGA
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 25 0.44
15 3 0.05
16 4 0.07
17 4 0.07
18 3 0.05
19 18 0.32
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:535447 original size:19 final size:18
Alignment explanation
Indices: 535423--535516 Score: 69
Period size: 19 Copynumber: 5.5 Consensus size: 18
535413 GCAACGAGAG
535423 AATCGCAACGCGAAATGAA
1 AATCGCAAC-CGAAATGAA
*
535442 AATCGCAA-CG--A-GAG
1 AATCGCAACCGAAATGAA
*
535456 AATCGCAACACAAAATGAA
1 AATCGCAAC-CGAAATGAA
*
535475 AATCGCAA-CG--A-GAG
1 AATCGCAACCGAAATGAA
*
535489 AATCGCAATGCGAAATGAA
1 AATCGCAA-CCGAAATGAA
535508 AATCGCAAC
1 AATCGCAAC
535517 ACGATTATAG
Statistics
Matches: 58, Mismatches: 7, Indels: 21
0.67 0.08 0.24
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 28 0.48
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (18 bp):
AATCGCAACCGAAATGAA
Found at i:535447 original size:33 final size:33
Alignment explanation
Indices: 535410--535516 Score: 187
Period size: 33 Copynumber: 3.2 Consensus size: 33
535400 AAAAATGACT
535410 ATCGCAACGAGAGAATCGCAACGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACGCGAAATGAAA
* *
535443 ATCGCAACGAGAGAATCGCAACACAAAATGAAA
1 ATCGCAACGAGAGAATCGCAACGCGAAATGAAA
*
535476 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACGCGAAATGAAA
535509 ATCGCAAC
1 ATCGCAAC
535517 ACGATTATAG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.10
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAACGCGAAATGAAA
Found at i:535564 original size:33 final size:33
Alignment explanation
Indices: 535527--535638 Score: 174
Period size: 33 Copynumber: 3.5 Consensus size: 33
535517 ACGATTATAG
* *
535527 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
* *
535560 TTTCGCGTTGCGATTCTCTAGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
535593 TTTCGCGTTGCGATTATCTCGTTGCGA--TTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
535624 TTTCGCGTTGCGATT
1 TTTCGCGTTGCGATT
535639 CATTTCGCGT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
31 19 0.26
33 55 0.74
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
Found at i:535634 original size:17 final size:17
Alignment explanation
Indices: 535527--535654 Score: 114
Period size: 17 Copynumber: 7.8 Consensus size: 17
535517 ACGATTATAG
535527 TTTCGCGTTGCGA-T--
1 TTTCGCGTTGCGATTCA
535541 TTT-GTCGTTGCGATTTTCA
1 TTTCG-CGTTGCGA--TTCA
535560 TTTCGCGTTGCGATTC-
1 TTTCGCGTTGCGATTCA
**
535576 --TCTAGTTGCGATTTTCA
1 TTTCGCGTTGCGA--TTCA
535593 TTTCGCGTTGCGATT-A
1 TTTCGCGTTGCGATTCA
*
535609 --TCTCGTTGCGATTCA
1 TTTCGCGTTGCGATTCA
535624 TTTCGCGTTGCGATTCA
1 TTTCGCGTTGCGATTCA
535641 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
535655 AGTCATTTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.01
14 32 0.34
15 1 0.01
16 4 0.04
17 34 0.37
19 20 0.22
20 1 0.01
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (17 bp):
TTTCGCGTTGCGATTCA
Found at i:535916 original size:94 final size:94
Alignment explanation
Indices: 535750--536114 Score: 607
Period size: 94 Copynumber: 3.9 Consensus size: 94
535740 CATTACTTCA
* *
535750 CAAAAGACAAAACAAAGA-AGAATACTAACTTCAGAGTATTAAAGAATACACAGTTTAGCAGAAT
1 CAAAAGACAAAACAAAGACA-AATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
535814 TGGCAGCAACCGAACAAATTTACTTTCAAC
65 TGGCAGCAACCGAACAAATTTACTTTCAAC
535844 CAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATT
1 CAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATT
*
535909 GGTAGCAACCGAACAAATTTACTTTCAAC
66 GGCAGCAACCGAACAAATTTACTTTCAAC
535938 CAAAAGACAAAAC-AAGACAAATACTAACTTCACA-TGTTAAAGAATACACAGTTTAGCA-AATT
1 CAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATT
536000 GGCAGCAACCGAACAAATTTAC-TTCAAC
66 GGCAGCAACCGAACAAATTTACTTTCAAC
* * * *
536028 C-AAAGATAAAACAAAAACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGTATT
1 CAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATT
*
536092 GGCAGCAACCGAATAAATTTACT
66 GGCAGCAACCGAACAAATTTACT
536115 AAGCAATCTA
Statistics
Matches: 257, Mismatches: 9, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
89 10 0.04
90 27 0.11
91 48 0.19
92 48 0.19
93 21 0.08
94 102 0.40
95 1 0.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.21
Consensus pattern (94 bp):
CAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATT
GGCAGCAACCGAACAAATTTACTTTCAAC
Found at i:536063 original size:183 final size:188
Alignment explanation
Indices: 535750--536114 Score: 607
Period size: 183 Copynumber: 2.0 Consensus size: 188
535740 CATTACTTCA
*
535750 CAAAAGACAAAACAAAGAAGAATACTAACTTCAGAGTATTAAAGAATACACAGTTTAGCAGAATT
1 CAAAAGACAAAACAAAGAAGAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAGAATT
*
535815 GGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAG
66 GGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAAACAAATACTAACTTCACAG
* *
535880 TGTTAAAGAATACACAGTTTAGCAGAATTGGTAGCAACCGAACAAATTTACTTTCAAC
131 TGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAAC
*
535938 CAAAAGACAAAAC-AAGACA-AATACTAACTTCACA-TGTTAAAGAATACACAGTTTAGCA-AAT
1 CAAAAGACAAAACAAAGA-AGAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAGAAT
*
535999 TGGCAGCAACCGAACAAATTTAC-TTCAACC-AAAGATAAAACAAAAACAAATACTAACTTCACA
65 TGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAAACAAATACTAACTTCACA
* *
536062 GTGTTAAAGAATAAACAGTTTAGCAGTATTGGCAGCAACCGAATAAATTTACT
130 GTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
536115 AAGCAATCTA
Statistics
Matches: 168, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
183 80 0.48
184 7 0.04
185 26 0.15
186 23 0.14
187 18 0.11
188 14 0.08
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.21
Consensus pattern (188 bp):
CAAAAGACAAAACAAAGAAGAATACTAACTTCACAGTATTAAAGAATACACAGTTTAGCAGAATT
GGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAAACAAATACTAACTTCACAG
TGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAAC
Found at i:537794 original size:19 final size:19
Alignment explanation
Indices: 537730--537847 Score: 146
Period size: 19 Copynumber: 6.1 Consensus size: 19
537720 TCTTTTGGTT
*
537730 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
537749 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
537769 AGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
537789 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
537808 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
537827 GAAATGAAAATTGCAATGC
1 GAAATGAAAATCGCAACGC
537846 GA
1 GA
537848 TTTTGGTTTC
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 55 0.62
20 31 0.35
21 2 0.02
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:537962 original size:20 final size:19
Alignment explanation
Indices: 537860--537964 Score: 94
Period size: 20 Copynumber: 5.6 Consensus size: 19
537850 TTGGTTTCGC
*
537860 GTTGCGATTTTCATTTTTT
1 GTTGCGATTTTCATTTTCT
*
537879 GTTGCGA--TTC--TCTC-
1 GTTGCGATTTTCATTTTCT
537893 GTTGCGATTTTCATTTCTCT
1 GTTGCGATTTTCATTT-TCT
* **
537913 CATTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTC-T
537934 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTC-T
537954 GTTGCGATTTT
1 GTTGCGATTTT
537965 AAGTTTAGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
14 7 0.10
15 2 0.03
16 3 0.04
17 3 0.04
18 1 0.01
19 9 0.13
20 29 0.43
21 14 0.21
ACGTcount: A:0.12, C:0.17, G:0.18, T:0.52
Consensus pattern (19 bp):
GTTGCGATTTTCATTTTCT
Found at i:538547 original size:20 final size:19
Alignment explanation
Indices: 538522--538694 Score: 168
Period size: 20 Copynumber: 8.6 Consensus size: 19
538512 CTTTAAAAAT
538522 CGCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTAC-GATA
538542 CGCGTTGCGATTTTACG-TA
1 CGCGTTGCGA-TTTACGATA
* *
538561 TTGTCGTTGCGATTTACGGATT
1 -CG-CGTTGCGATTTAC-GATA
* *
538583 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACG-ATA
*
538603 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTAC-GATA
*
538623 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACG-ATA
*
538643 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTAC-GATA
538663 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTAC-GATA
*
538684 CTCGTTGCGAT
1 CGCGTTGCGAT
538695 AGTCAGAATC
Statistics
Matches: 130, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
19 4 0.03
20 89 0.68
21 36 0.28
22 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (19 bp):
CGCGTTGCGATTTACGATA
Found at i:538608 original size:40 final size:41
Alignment explanation
Indices: 538524--538694 Score: 265
Period size: 40 Copynumber: 4.2 Consensus size: 41
538514 TTAAAAATCG
*
538524 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
* * *
538565 CGTTGCGATTTACGGATTCGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
538605 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
* * *
538645 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
538686 CGTTGCGAT
1 CGTTGCGAT
538695 AGTCAGAATC
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
40 75 0.63
41 44 0.37
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCT
Found at i:538651 original size:60 final size:61
Alignment explanation
Indices: 538521--538694 Score: 210
Period size: 60 Copynumber: 2.9 Consensus size: 61
538511 GCTTTAAAAA
* * *
538521 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTAC-G-TATTGTCGTTGCGATTTACGGAT
1 TCGCATTGCGATTTACGGATACGCGTTGCGATTTTACAGATA-CG-CGTTGCGATTTACGGAT
* * * *
538582 TCGCATTGCGATTTACGTATTCTCGTTGCGA-TTTACAGATACGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGGATACGCGTTGCGATTTTACAGATACGCGTTGCGATTTACGGAT
* * * *
538642 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 TCGCATTGCGATTTACGGATACGCGTTGCGATTTTACAGATACGCGTTGCGAT
538695 AGTCAGAATC
Statistics
Matches: 96, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
60 47 0.49
61 47 0.49
62 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (61 bp):
TCGCATTGCGATTTACGGATACGCGTTGCGATTTTACAGATACGCGTTGCGATTTACGGAT
Found at i:538678 original size:81 final size:81
Alignment explanation
Indices: 538524--538694 Score: 281
Period size: 81 Copynumber: 2.1 Consensus size: 81
538514 TTAAAAATCG
* *
538524 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATTCGCATT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCATT
* *
538589 GCGATTTACGTATTCT
66 GCGATTTACGGATACT
*
538605 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCGTT
1 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCATT
538669 GCGATTTTACGGATACT
66 GCGA-TTTACGGATACT
538686 CGTTGCGAT
1 CGTTGCGAT
538695 AGTCAGAATC
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
80 37 0.44
81 47 0.56
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (81 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGCATT
GCGATTTACGGATACT
Found at i:538708 original size:81 final size:80
Alignment explanation
Indices: 538524--538717 Score: 266
Period size: 81 Copynumber: 2.4 Consensus size: 80
538514 TTAAAAATCG
* * *
538524 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATTCGCATT
1 CGTTGCGATGTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCATT
* *
538589 GCGATTTACGTATTCT
65 GCGATTTACGGATACT
* *
538605 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTG
1 CGTTGCGATGTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTG
538670 CGATTTTACGGATACT
66 CGA-TTTACGGATACT
*
538686 CGTTGCGATAGT-CAGA-ATCGCGTTGCAATTTA
1 CGTTGCGAT-GTACAGATA-CGCGTTGCGATTTA
538718 TATGTTCGTG
Statistics
Matches: 103, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
80 38 0.37
81 64 0.62
82 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (80 bp):
CGTTGCGATGTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTG
CGATTTACGGATACT
Found at i:538838 original size:20 final size:19
Alignment explanation
Indices: 538785--538838 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
538775 ATTCTTCATA
538785 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* ** *
538804 AACTGATTTGTGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
538825 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
538839 TTTATTTCGC
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Done.