Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 12 of 27
Found at i:1831566 original size:34 final size:36
Alignment explanation
Indices: 1831526--1831599 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
1831516 ATTTTATCTA
*
1831526 ATTTAAA-TT-ATTATTTAATAATTAAAATA-TTTTT
1 ATTTAAATTTAATTA-TAAATAATTAAAATATTTTTT
*
1831560 ATTTAAATTTAATTATAAATATTTAAAATATTTTTT
1 ATTTAAATTTAATTATAAATAATTAAAATATTTTTT
1831596 ATTT
1 ATTT
1831600 TTATTAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 7 0.20
35 15 0.43
36 13 0.37
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (36 bp):
ATTTAAATTTAATTATAAATAATTAAAATATTTTTT
Found at i:1831574 original size:39 final size:36
Alignment explanation
Indices: 1831517--1831599 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 36
1831507 TTTAATACGA
*
1831517 TTTTATCTAATTTAAATTATTATTTAATAATTAAAATA-T
1 TTTTATTTAATTTAAATTA-TA---AATAATTAAAATATT
*
1831556 TTTTATTTAAATTT-AATTATAAATATTTAAAATATT
1 TTTTATTT-AATTTAAATTATAAATAATTAAAATATT
1831592 TTTTATTT
1 TTTTATTT
1831600 TTATTAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 12 0.30
36 9 0.22
38 2 0.05
39 12 0.30
40 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (36 bp):
TTTTATTTAATTTAAATTATAAATAATTAAAATATT
Found at i:1831607 original size:35 final size:36
Alignment explanation
Indices: 1831542--1831618 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
1831532 ATTATTATTT
*
1831542 AATAATTAAAATATTTTTATTTAAATTTAAT-TATA
1 AATAATTAAAATATTTTTATTTAAATTTAATATACA
* **
1831577 AATATTTAAAATATTTTTTATTTTTA-TTAATATACA
1 AATAATTAAAATA-TTTTTATTTAAATTTAATATACA
1831613 AATAAT
1 AATAAT
1831619 AATTTAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
35 17 0.49
36 18 0.51
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (36 bp):
AATAATTAAAATATTTTTATTTAAATTTAATATACA
Found at i:1833848 original size:59 final size:58
Alignment explanation
Indices: 1833655--1833863 Score: 261
Period size: 55 Copynumber: 3.7 Consensus size: 58
1833645 ATATGTAAAC
* * * * * *
1833655 ATGTATGCATGTATAACGTTGATTGTTTACCTTTT-A-TTT--TTCTTTGCATGTATGC
1 ATGTATGCATTTATAACATTGATAGTTTA-CTTTTCATTTTGCTTTTTTGTATGTATGT
* *
1833710 ATGTATGTATTTATAACATTGATAGTTTACTTTTCATTTTGC--TTTT-TATGTATCT
1 ATGTATGCATTTATAACATTGATAGTTTACTTTTCATTTTGCTTTTTTGTATGTATGT
1833765 ATGTATGCATTTATAACATTGATAGTTTACTTTTCATTTTGCTTTTTATGTATGTATGT
1 ATGTATGCATTTATAACATTGATAGTTTACTTTTCATTTTGCTTTTT-TGTATGTATGT
* *
1833824 ATGTATGCATTTATAACATTGATAGTTTACCTTTCGTTTT
1 ATGTATGCATTTATAACATTGATAGTTTACTTTTCATTTT
1833864 TCCTTTTAAG
Statistics
Matches: 134, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
54 5 0.04
55 73 0.54
56 6 0.04
57 3 0.02
58 1 0.01
59 46 0.34
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.53
Consensus pattern (58 bp):
ATGTATGCATTTATAACATTGATAGTTTACTTTTCATTTTGCTTTTTTGTATGTATGT
Found at i:1836974 original size:22 final size:22
Alignment explanation
Indices: 1836939--1836991 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1836929 GCAAACCTTT
* * *
1836939 TATATATATTTATATGTACATA
1 TATATACATGTATATGCACATA
* *
1836961 TATATACATGTATATGCATATG
1 TATATACATGTATATGCACATA
1836983 TATATACAT
1 TATATACAT
1836992 ACACTTATAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (22 bp):
TATATACATGTATATGCACATA
Found at i:1837611 original size:14 final size:14
Alignment explanation
Indices: 1837592--1837620 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1837582 ATATATGTAA
1837592 TCTAAATTAATGAT
1 TCTAAATTAATGAT
1837606 TCTAAATTAATGAT
1 TCTAAATTAATGAT
1837620 T
1 T
1837621 AATTGATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TCTAAATTAATGAT
Found at i:1840979 original size:3 final size:3
Alignment explanation
Indices: 1840971--1841006 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1840961 CCTCAAGGCT
1840971 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1841007 GCTCTGACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1842006 original size:2 final size:2
Alignment explanation
Indices: 1841999--1842031 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1841989 TAAGGGATTG
1841999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1842032 ATAATGCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1843399 original size:33 final size:33
Alignment explanation
Indices: 1843337--1843405 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1843327 CCGTTACAAG
*
1843337 CAATGTATCGATACAATTCATCATATATCGATA
1 CAATGTATCGATACAATTCACCATATATCGATA
* *
1843370 CAATGTATCGATAC-ATTGTACCATGTATCGATA
1 CAATGTATCGATACAATT-CACCATATATCGATA
1843403 CAA
1 CAA
1843406 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATTCACCATATATCGATA
Found at i:1843478 original size:19 final size:20
Alignment explanation
Indices: 1843434--1843489 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1843424 TTACTAATTT
* *
1843434 CATGTATCGATACAATTATC
1 CATGTATCGATACAATGATA
1843454 CATGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
*
1843473 CATGTATCGATGCAATG
1 CATGTATCGATACAATG
1843490 TATTGATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:1844599 original size:2 final size:2
Alignment explanation
Indices: 1844553--1844584 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1844543 GTACTTGTTG
1844553 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
1844585 ATCAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1845076 original size:17 final size:18
Alignment explanation
Indices: 1845054--1845103 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
1845044 TACCAATCGC
1845054 ATAAA-TATAAATATATT
1 ATAAATTATAAATATATT
1845071 ATAAATTATTAAATA-ATT
1 ATAAATTA-TAAATATATT
1845089 A-AAATTATAAATATA
1 ATAAATTATAAATATA
1845104 AATATGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.20
17 12 0.40
18 6 0.20
19 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAATTATAAATATATT
Found at i:1845252 original size:39 final size:38
Alignment explanation
Indices: 1845192--1845273 Score: 89
Period size: 39 Copynumber: 2.1 Consensus size: 38
1845182 ATTTTGTATA
* *
1845192 TATATATATGTTAAACATATT-ATTTTAATATTATATTTT
1 TATATATATGTTAAACATATTAAATTTAAT-TT-TAATTT
1845231 TATATCATAT-TTAAA-ATTATTAAATTTAATTTTAATTT
1 TATAT-ATATGTTAAACA-TATTAAATTTAATTTTAATTT
1845269 TATAT
1 TATAT
1845274 TATACTATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
38 11 0.29
39 16 0.42
40 11 0.29
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (38 bp):
TATATATATGTTAAACATATTAAATTTAATTTTAATTT
Found at i:1845469 original size:31 final size:30
Alignment explanation
Indices: 1845441--1845496 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
1845431 TTAAATTTAG
*
1845441 TTATAAATATAT-AAAAATATTTTTAATTT
1 TTATAAATATATAAAAAATAATTTTAATTT
*
1845470 TTATTAATATATAAAAAATAATTTTAA
1 TTATAAATATATAAAAAATAATTTTAA
1845497 ATTAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TTATAAATATATAAAAAATAATTTTAATTT
Found at i:1845506 original size:30 final size:29
Alignment explanation
Indices: 1845446--1845506 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
1845436 TTTAGTTATA
* * **
1845446 AATATATAAAAATATTTTTAATTTTTATT
1 AATATATAAAAATAATTTTAAATTAAATT
1845475 AATATATAAAAAATAATTTTAAATTAAATT
1 AATATAT-AAAAATAATTTTAAATTAAATT
1845505 AA
1 AA
1845507 ATTTTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
AATATATAAAAATAATTTTAAATTAAATT
Found at i:1845861 original size:5 final size:5
Alignment explanation
Indices: 1845845--1845874 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1845835 CTTGCCATTA
*
1845845 TCTTT TCCTT TCTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT
1845875 GAAAACAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:1847580 original size:55 final size:55
Alignment explanation
Indices: 1847494--1847660 Score: 235
Period size: 55 Copynumber: 3.0 Consensus size: 55
1847484 ATATGTAAAC
* *
1847494 ATGTATGTATGTAATGTATGTATAACGTTGATAGTTTACCTTTCATTTTTCTTTTT
1 ATGTATGTATGT-ATGTATTTATAACATTGATAGTTTACCTTTCATTTTTCTTTTT
* * * *
1847550 ATGTATGCATGTATGTATTTATAACATTGATAGTTTACTTTTCATTTTGCTTTTC
1 ATGTATGTATGTATGTATTTATAACATTGATAGTTTACCTTTCATTTTTCTTTTT
* * * *
1847605 ATTTATGTATGTATGCATTTATAACATTGGTAGTTTACCTTTCGTTTTTCTTTTT
1 ATGTATGTATGTATGTATTTATAACATTGATAGTTTACCTTTCATTTTTCTTTTT
1847660 A
1 A
1847661 AGCTGAGATG
Statistics
Matches: 97, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
55 86 0.89
56 11 0.11
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (55 bp):
ATGTATGTATGTATGTATTTATAACATTGATAGTTTACCTTTCATTTTTCTTTTT
Found at i:1863799 original size:3 final size:3
Alignment explanation
Indices: 1863771--1863817 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
1863761 AAGTAAAGAA
* * * *
1863771 ATT A-T ATT GTT ATT ATA ATT AAT ATT ATT ATT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1863818 CATAAAATAG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1864683 original size:3 final size:3
Alignment explanation
Indices: 1864677--1864723 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1864667 AGAAGACAAG
1864677 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1864724 TTCACATAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1868366 original size:33 final size:33
Alignment explanation
Indices: 1868321--1868386 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1868311 ATTTGCCTGC
* *
1868321 ATGTATCGATACAAAGA-TCAGTGTATCGATACA
1 ATGTATCAATACAAAGAGT-AATGTATCGATACA
*
1868354 ATGTATCAATACAATGAGTAATGTATCGATACA
1 ATGTATCAATACAAAGAGTAATGTATCGATACA
1868387 TTTTCTTGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (33 bp):
ATGTATCAATACAAAGAGTAATGTATCGATACA
Found at i:1868431 original size:19 final size:19
Alignment explanation
Indices: 1868407--1868470 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
1868397 AGTAGTTTCA
1868407 TATGTATCGATACAACACT
1 TATGTATCGATACAACACT
1868426 TATGTATCGAT---ACA--
1 TATGTATCGATACAACACT
*
1868440 T-TGTATCGATACAGCACT
1 TATGTATCGATACAACACT
1868458 TATGTATCGATAC
1 TATGTATCGATAC
1868471 TATCGTTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 5 0.13
18 1 0.03
19 22 0.58
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (19 bp):
TATGTATCGATACAACACT
Found at i:1868446 original size:13 final size:13
Alignment explanation
Indices: 1868428--1868452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1868418 ACAACACTTA
1868428 TGTATCGATACAT
1 TGTATCGATACAT
1868441 TGTATCGATACA
1 TGTATCGATACA
1868453 GCACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1868450 original size:32 final size:32
Alignment explanation
Indices: 1868409--1868470 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1868399 TAGTTTCATA
1868409 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
*
1868441 TGTATCGATACAGCACTTATGTATCGATAC
1 TGTATCGATACAACACTTATGTATCGATAC
1868471 TATCGTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:1869682 original size:92 final size:93
Alignment explanation
Indices: 1869551--1869737 Score: 349
Period size: 92 Copynumber: 2.0 Consensus size: 93
1869541 TATAACTTAT
*
1869551 TTGGCTTTCGAGTAAAACGTAGCTCTAGCTAAATTGAGTCATAGATTCTTTAATATTCACCATTG
1 TTGGCTTTCGAGTAAAACGTAGCTCTAGCTAAATTGAGTCATAGATTCTTTAATATTCACCATTA
1869616 AAGTTCATATATTGAAGGGTTATGTTTA
66 AAGTTCATATATTGAAGGGTTATGTTTA
*
1869644 TTGGCTTTCGAGTAAAA-GTAGGTCTAGCTAAATTGAGTCATAGATTCTTTAATATTCACCATTA
1 TTGGCTTTCGAGTAAAACGTAGCTCTAGCTAAATTGAGTCATAGATTCTTTAATATTCACCATTA
1869708 AAGTTCATATATTGAAGGGTTATGTTTA
66 AAGTTCATATATTGAAGGGTTATGTTTA
1869736 TT
1 TT
1869738 ATTCATCAAT
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 75 0.82
93 17 0.18
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (93 bp):
TTGGCTTTCGAGTAAAACGTAGCTCTAGCTAAATTGAGTCATAGATTCTTTAATATTCACCATTA
AAGTTCATATATTGAAGGGTTATGTTTA
Found at i:1870334 original size:16 final size:17
Alignment explanation
Indices: 1870313--1870345 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1870303 ACAAACATCT
1870313 CAAATCCCA-CCAAACC
1 CAAATCCCACCCAAACC
*
1870329 CAAATCTCACCCAAACC
1 CAAATCCCACCCAAACC
1870346 TCTGAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.48, G:0.00, T:0.09
Consensus pattern (17 bp):
CAAATCCCACCCAAACC
Found at i:1875287 original size:2 final size:2
Alignment explanation
Indices: 1875280--1875304 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1875270 ACCTAAACCT
1875280 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1875305 GGGGTGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1878594 original size:35 final size:35
Alignment explanation
Indices: 1878548--1878618 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1878538 AAGGAGTAAG
1878548 TATTGAATGATATCAAATGGAATATGTATTAAAAT
1 TATTGAATGATATCAAATGGAATATGTATTAAAAT
1878583 TATTGAATGATATCAAATGGAATATGTATTAAAAT
1 TATTGAATGATATCAAATGGAATATGTATTAAAAT
1878618 T
1 T
1878619 TTGCTGCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.45, C:0.03, G:0.14, T:0.38
Consensus pattern (35 bp):
TATTGAATGATATCAAATGGAATATGTATTAAAAT
Found at i:1878990 original size:2 final size:2
Alignment explanation
Indices: 1878983--1879020 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1878973 TCTTAATATT
1878983 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1879021 CTTGGACTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1879705 original size:2 final size:2
Alignment explanation
Indices: 1879692--1879754 Score: 72
Period size: 2 Copynumber: 31.5 Consensus size: 2
1879682 TTGGTGTGAG
* * * * * *
1879692 TA TA TA TC TA TA TA TA TA TC TA TA TC TA TA TC TG TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1879734 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1879755 TATTTATTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1879709 original size:12 final size:12
Alignment explanation
Indices: 1879692--1879754 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
1879682 TTGGTGTGAG
1879692 TATATATCTATA
1 TATATATCTATA
1879704 TATATATCTATA
1 TATATATCTATA
* *
1879716 TCTATATCTGTA
1 TATATATCTATA
* *
1879728 TCTATATATATA
1 TATATATCTATA
*
1879740 TATATATATATA
1 TATATATCTATA
1879752 TAT
1 TAT
1879755 TATTTATTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.51
Consensus pattern (12 bp):
TATATATCTATA
Found at i:1882112 original size:2 final size:2
Alignment explanation
Indices: 1882107--1882142 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1882097 TCTCTCTCTT
1882107 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
1882143 CACTATAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1883424 original size:42 final size:42
Alignment explanation
Indices: 1883377--1883505 Score: 106
Period size: 42 Copynumber: 3.1 Consensus size: 42
1883367 TTACATGTAT
*
1883377 ATATATTATGTTAATATTTTTGTATCGATTGTAAAAGCATAA
1 ATATATTATATTAATATTTTTGTATCGATTGTAAAAGCATAA
* * * * * ** *
1883419 ATATATTAAAATTATAAATATTT-AAT-GATT-T--ACGTGTAT
1 ATATATT-ATATTA-ATATTTTTGTATCGATTGTAAAAGCATAA
* *
1883458 ATATATTATTTTAATATTTTTGTATCGCTTGTAAAAGCATAA
1 ATATATTATATTAATATTTTTGTATCGATTGTAAAAGCATAA
1883500 ATATAT
1 ATATAT
1883506 CATAAATTAT
Statistics
Matches: 61, Mismatches: 19, Indels: 14
0.65 0.20 0.15
Matches are distributed among these distances:
37 6 0.10
38 6 0.10
39 14 0.23
40 1 0.02
41 1 0.02
42 21 0.34
43 6 0.10
44 6 0.10
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.47
Consensus pattern (42 bp):
ATATATTATATTAATATTTTTGTATCGATTGTAAAAGCATAA
Found at i:1883482 original size:81 final size:83
Alignment explanation
Indices: 1883357--1883527 Score: 274
Period size: 81 Copynumber: 2.1 Consensus size: 83
1883347 ATTTAATTAA
*
1883357 ATTTGATGATTTACATGTATATATATTATGTTAATATTTTTGTATCGATTGTAAAAGCATAAATA
1 ATTTAATGATTTACATGTATATATATTATGTTAATATTTTTGTATCGATTGTAAAAGCATAAATA
*
1883422 TATTA-AAATTA-TAAAT
66 TATCATAAATTATTAAAT
* * *
1883438 ATTTAATGATTTACGTGTATATATATTATTTTAATATTTTTGTATCGCTTGTAAAAGCATAAATA
1 ATTTAATGATTTACATGTATATATATTATGTTAATATTTTTGTATCGATTGTAAAAGCATAAATA
1883503 TATCATAAATTATTAAAT
66 TATCATAAATTATTAAAT
1883521 ATATTAA
1 AT-TTAA
1883528 AATTATAAAT
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
81 65 0.79
82 6 0.07
83 7 0.09
84 4 0.05
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (83 bp):
ATTTAATGATTTACATGTATATATATTATGTTAATATTTTTGTATCGATTGTAAAAGCATAAATA
TATCATAAATTATTAAAT
Found at i:1883519 original size:19 final size:17
Alignment explanation
Indices: 1883496--1883540 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 17
1883486 TTGTAAAAGC
1883496 ATAAATATATCATAAATT
1 ATAAATATATCA-AAATT
*
1883514 ATTAAATATATTAAAATT
1 A-TAAATATATCAAAATT
1883532 ATAAATATA
1 ATAAATATA
1883541 AATATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 10 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAATATATCAAAATT
Found at i:1883528 original size:17 final size:18
Alignment explanation
Indices: 1883496--1883540 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
1883486 TTGTAAAAGC
1883496 ATAAATATATCAT-AAATT
1 ATAAATATAT-ATAAAATT
1883514 ATTAAATATAT-TAAAATT
1 A-TAAATATATATAAAATT
1883532 ATAAATATA
1 ATAAATATA
1883541 AATATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.36
18 7 0.28
19 9 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAATATATATAAAATT
Found at i:1885969 original size:46 final size:47
Alignment explanation
Indices: 1885902--1885995 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 47
1885892 ATATGTACGC
* *
1885902 ATGTATGTATGTATAACATTGATAGCTTACCTTTCATTTTTCTTTTT
1 ATGTATGCATGTATAACATTGATAGCTTACATTTCATTTTTCTTTTT
*
1885949 ATGTATGCAT-TATAACATTGATAGTTTACATTTCATTTTTCTTTTT
1 ATGTATGCATGTATAACATTGATAGCTTACATTTCATTTTTCTTTTT
1885995 A
1 A
1885996 GGCTGAGATG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 35 0.80
47 9 0.20
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.53
Consensus pattern (47 bp):
ATGTATGCATGTATAACATTGATAGCTTACATTTCATTTTTCTTTTT
Found at i:1886671 original size:4 final size:4
Alignment explanation
Indices: 1886623--1886685 Score: 63
Period size: 4 Copynumber: 15.8 Consensus size: 4
1886613 ACTAGATTCG
* * * * * * *
1886623 TATA TACA TATA TACA TACA TACA TAAA TATA TGTA TACA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
1886671 TATA TATA TATA TAT
1 TATA TATA TATA TAT
1886686 CACCTCAACT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (4 bp):
TATA
Found at i:1886685 original size:8 final size:8
Alignment explanation
Indices: 1886623--1886684 Score: 70
Period size: 8 Copynumber: 7.8 Consensus size: 8
1886613 ACTAGATTCG
1886623 TATATACA
1 TATATACA
1886631 TATATACA
1 TATATACA
*
1886639 TACATACA
1 TATATACA
* *
1886647 TAAATATA
1 TATATACA
*
1886655 TGTATACA
1 TATATACA
*
1886663 TATATATA
1 TATATACA
*
1886671 TATATATA
1 TATATACA
1886679 TATATA
1 TATATA
1886685 TCACCTCAAC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 46 1.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (8 bp):
TATATACA
Found at i:1895649 original size:2 final size:2
Alignment explanation
Indices: 1895644--1895680 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1895634 CGCGCGTGTG
*
1895644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1895681 TAAAATGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1898087 original size:2 final size:2
Alignment explanation
Indices: 1898080--1898105 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1898070 AAAAGTAAGA
1898080 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
1898106 TGTATCAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1899338 original size:21 final size:21
Alignment explanation
Indices: 1899313--1899364 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1899303 TACTATTTAA
*
1899313 ATATTAATAAAAATTTATTTT
1 ATATTAATAAAAATATATTTT
**
1899334 ATATTAATATTAATATATTTT
1 ATATTAATAAAAATATATTTT
*
1899355 -TATAAATAAA
1 ATATTAATAAA
1899365 TTTAAATAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTAATAAAAATATATTTT
Found at i:1902142 original size:18 final size:18
Alignment explanation
Indices: 1902100--1902135 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1902090 ATATATATAT
1902100 ATATATATTTGTTGTATTC
1 ATAT-TATTTGTTGTATTC
*
1902119 GTATTATTTGTTGTATT
1 ATATTATTTGTTGTATT
1902136 ATAATTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.61
Consensus pattern (18 bp):
ATATTATTTGTTGTATTC
Found at i:1909923 original size:2 final size:2
Alignment explanation
Indices: 1909916--1909946 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1909906 ATTCTTGTAT
1909916 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1909947 TTTCATTGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1917602 original size:12 final size:12
Alignment explanation
Indices: 1917578--1917616 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1917568 ATGAAAAGAA
1917578 AATAATAAA-TAT
1 AATAA-AAATTAT
1917590 AATAAAAATTAT
1 AATAAAAATTAT
*
1917602 ATTAAAAATTAT
1 AATAAAAATTAT
1917614 AAT
1 AAT
1917617 GTTTGAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AATAAAAATTAT
Found at i:1919604 original size:26 final size:26
Alignment explanation
Indices: 1919553--1919606 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1919543 AAAGTATACG
*
1919553 ATAAATATTAAACTTATTTAATATTA
1 ATAAATATTAAACTTATTTAAAATTA
* *
1919579 ATAAAT-TTAAAGTTTTTTATAAATTA
1 ATAAATATTAAACTTATTTA-AAATTA
1919605 AT
1 AT
1919607 CAGTTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
ATAAATATTAAACTTATTTAAAATTA
Found at i:1919804 original size:17 final size:18
Alignment explanation
Indices: 1919782--1919817 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1919772 ATATTTTATT
1919782 AATTTAA-AATAATATAA
1 AATTTAATAATAATATAA
1919799 AATTTAATTAATAATATAA
1 AATTTAA-TAATAATATAA
1919818 TCTTATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AATTTAATAATAATATAA
Found at i:1919857 original size:44 final size:45
Alignment explanation
Indices: 1919766--1919863 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
1919756 GTCTTTTAAC
* * * *
1919766 AATATAATATTTTATTAATTTAAAATAATATAAAATTTAATTAAT
1 AATATAATATTATATTAATTCAAAATAATATAAAATATAATAAAT
*
1919811 AATATAATCTTATATTAATTCAAAA-AATAT-AAATATAATAATAT
1 AATATAATATTATATTAATTCAAAATAATATAAAATATAATAA-AT
1919855 AATATAATA
1 AATATAATA
1919864 ATAATAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 9 0.20
44 15 0.33
45 22 0.48
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (45 bp):
AATATAATATTATATTAATTCAAAATAATATAAAATATAATAAAT
Found at i:1919860 original size:19 final size:19
Alignment explanation
Indices: 1919836--1919872 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1919826 TAATTCAAAA
1919836 AATATAA-ATATAATAATAT
1 AATATAATA-ATAATAATAT
1919855 AATATAATAATAATAATA
1 AATATAATAATAATAATA
1919873 ATAGTTGGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AATATAATAATAATAATAT
Found at i:1920064 original size:14 final size:13
Alignment explanation
Indices: 1920045--1920098 Score: 63
Period size: 13 Copynumber: 3.9 Consensus size: 13
1920035 TATCAATTAA
1920045 AATAATAATATTTT
1 AATAAT-ATATTTT
*
1920059 AATAATTTATTTT
1 AATAATATATTTT
1920072 AAATTAATATATTTT
1 -AA-TAATATATTTT
*
1920087 AATAATTTATTT
1 AATAATATATTT
1920099 AAAAATTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 15 0.43
14 10 0.29
15 10 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATAATATATTTT
Found at i:1920071 original size:13 final size:13
Alignment explanation
Indices: 1920053--1920098 Score: 65
Period size: 13 Copynumber: 3.4 Consensus size: 13
1920043 AAAATAATAA
1920053 TATTTTAATAATT
1 TATTTTAATAATT
*
1920066 TATTTTAAATTAATA
1 TATTTT-AA-TAATT
1920081 TATTTTAATAATT
1 TATTTTAATAATT
1920094 TATTT
1 TATTT
1920099 AAAAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 15 0.52
14 4 0.14
15 10 0.34
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTTAATAATT
Found at i:1920075 original size:28 final size:30
Alignment explanation
Indices: 1920043--1920119 Score: 115
Period size: 28 Copynumber: 2.7 Consensus size: 30
1920033 TTTATCAATT
1920043 AAAA-TAATAATATTTTAATAATTTATTT-
1 AAAATTAATAATATTTTAATAATTTATTTA
*
1920071 TAAATTAAT-ATATTTTAATAATTTATTTA
1 AAAATTAATAATATTTTAATAATTTATTTA
*
1920100 AAAATTAATAATAATTTAAT
1 AAAATTAATAATATTTTAAT
1920120 GTGCTAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 22 0.51
29 12 0.28
30 9 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
AAAATTAATAATATTTTAATAATTTATTTA
Found at i:1920077 original size:34 final size:33
Alignment explanation
Indices: 1920022--1920114 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 33
1920012 GTGAACTTAA
* *
1920022 TTTAATAAGTTT-TTATCAATTAAAATAATAATAT
1 TTTAATAA-TTTATTTTAAATTAAAATAAT-ATAT
1920056 TTTAATAATTTATTTTAAA-T----TAATATAT
1 TTTAATAATTTATTTTAAATTAAAATAATATAT
*
1920084 TTTAATAATTTATTTAAAAATTAATAATAAT
1 TTTAATAATTTATTT-TAAATTAA-AATAAT
1920115 TTAATGTGCT
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
28 19 0.40
29 7 0.15
30 1 0.02
33 4 0.08
34 13 0.27
35 4 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (33 bp):
TTTAATAATTTATTTTAAATTAAAATAATATAT
Found at i:1928945 original size:2 final size:2
Alignment explanation
Indices: 1928938--1928972 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1928928 AGTCATTGGT
1928938 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1928973 TGAATGTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1932442 original size:14 final size:16
Alignment explanation
Indices: 1932423--1932508 Score: 63
Period size: 14 Copynumber: 5.2 Consensus size: 16
1932413 AACGAATAAG
1932423 TTTAATATTTA-AA-T
1 TTTAATATTTATAATT
1932437 TTTAATATTTATAATT
1 TTTAATATTTATAATT
*
1932453 TTTAATAATATATAATTAT
1 TTTAAT-ATTTATAA-T-T
*
1932472 TTTATGTTAAATTTA-AATT
1 TTTA----ATATTTATAATT
1932491 TTT-ATATTTATAATT
1 TTTAATATTTATAATT
1932506 TTT
1 TTT
1932509 TATTTATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
14 17 0.29
15 9 0.16
16 7 0.12
17 7 0.12
18 1 0.02
19 9 0.16
20 1 0.02
21 2 0.03
22 4 0.07
23 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (16 bp):
TTTAATATTTATAATT
Found at i:1932510 original size:16 final size:16
Alignment explanation
Indices: 1932427--1932511 Score: 57
Period size: 16 Copynumber: 5.1 Consensus size: 16
1932417 AATAAGTTTA
*
1932427 ATATTTA-AA-TTTTA
1 ATATTTATAATTTTTT
*
1932441 ATATTTATAATTTTTA
1 ATATTTATAATTTTTT
*
1932457 ATAATATATAATTATTTT
1 AT-ATTTATAATT-TTTT
* * *
1932475 ATGTTAAATTTAAATTTTT
1 ATATT---TATAATTTTTT
1932494 ATATTTATAATTTTTT
1 ATATTTATAATTTTTT
1932510 AT
1 AT
1932512 TTATTTTTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 7 0.13
15 2 0.04
16 18 0.33
17 10 0.18
18 5 0.09
19 8 0.15
20 5 0.09
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (16 bp):
ATATTTATAATTTTTT
Found at i:1932512 original size:14 final size:15
Alignment explanation
Indices: 1932427--1932515 Score: 58
Period size: 15 Copynumber: 5.5 Consensus size: 15
1932417 AATAAGTTTA
*
1932427 ATATTTA-AATTTTA
1 ATATTTATAATTTTT
1932441 ATATTTATAATTTTT
1 ATATTTATAATTTTT
*
1932456 AATAATATATAATTATTT
1 -AT-ATTTATAATT-TTT
1932474 -TATGTTAAATTTAAATTTTT
1 ATAT-TT--A--T-AATTTTT
1932494 ATATTTATAATTTTT
1 ATATTTATAATTTTT
1932509 -TATTTAT
1 ATATTTAT
1932516 TTTTTAAATA
Statistics
Matches: 61, Mismatches: 3, Indels: 22
0.71 0.03 0.26
Matches are distributed among these distances:
14 14 0.23
15 15 0.25
16 5 0.08
17 9 0.15
18 5 0.08
20 6 0.10
21 7 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (15 bp):
ATATTTATAATTTTT
Found at i:1932571 original size:25 final size:25
Alignment explanation
Indices: 1932543--1932617 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
1932533 TATTTTTTAT
*
1932543 AATTAAAGT-AAATAATATTTTAAAA
1 AATTAAA-TAAAATAATATATTAAAA
*
1932568 AATTTAATAAAATAATATATTAAAA
1 AATTAAATAAAATAATATATTAAAA
*
1932593 GTAA-AAAATTAAAATAATA-ATTAAA
1 --AATTAAA-TAAAATAATATATTAAA
1932618 TAAGAGTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 1 0.02
25 21 0.50
26 8 0.19
27 12 0.29
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (25 bp):
AATTAAATAAAATAATATATTAAAA
Found at i:1932620 original size:11 final size:12
Alignment explanation
Indices: 1932575--1932617 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
1932565 AAAAATTTAA
1932575 TAAAATAATATAT
1 TAAAATAATA-AT
*
1932588 TAAAAGTAAAAAAT
1 TAAAA-T-AATAAT
1932602 TAAAATAATAAT
1 TAAAATAATAAT
1932614 TAAA
1 TAAA
1932618 TAAGAGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.35
13 6 0.23
14 8 0.31
15 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
TAAAATAATAAT
Found at i:1932828 original size:5 final size:5
Alignment explanation
Indices: 1932820--1932844 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1932810 AAAATTACAC
1932820 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
1932845 TTCTCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:1936631 original size:54 final size:54
Alignment explanation
Indices: 1936549--1936656 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
1936539 CTGAATGTAA
1936549 CACGATAATTTGCAATTGCAAATATTCTTGATGCACTAAGCATTATGCTTTTAT
1 CACGATAATTTGCAATTGCAAATATTCTTGATGCACTAAGCATTATGCTTTTAT
1936603 CACGATAATTTGCAATTGCAAATATTCTTGATGCACTAAGCATTATGCTTTTAT
1 CACGATAATTTGCAATTGCAAATATTCTTGATGCACTAAGCATTATGCTTTTAT
1936657 TTTTAGCTAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (54 bp):
CACGATAATTTGCAATTGCAAATATTCTTGATGCACTAAGCATTATGCTTTTAT
Found at i:1941529 original size:16 final size:19
Alignment explanation
Indices: 1941500--1941535 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
1941490 ACAATTAGGA
1941500 ATAGAAGCATAAAA-TAAT
1 ATAGAAGCATAAAATTAAT
1941518 ATAGAA-CA-AAAATTAAT
1 ATAGAAGCATAAAATTAAT
1941535 A
1 A
1941536 AAATTAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.24
17 7 0.41
18 6 0.35
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (19 bp):
ATAGAAGCATAAAATTAAT
Found at i:1947604 original size:16 final size:18
Alignment explanation
Indices: 1947585--1947617 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1947575 TTAATTCATT
1947585 AAAT-ATTTATT-TTATA
1 AAATAATTTATTATTATA
1947601 AAATAATTTATTATTAT
1 AAATAATTTATTATTAT
1947618 TTTATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATAATTTATTATTATA
Found at i:1947607 original size:28 final size:28
Alignment explanation
Indices: 1947576--1947630 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1947566 CGTAATTATT
1947576 TAATTCATTAA-ATATTTATTTTATAAAA
1 TAATTCATTAATAT-TTTATTTTATAAAA
* * *
1947604 TAATTTATTATTATTTTATTTTTTAAA
1 TAATTCATTAATATTTTATTTTATAAA
1947631 GTTTTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
TAATTCATTAATATTTTATTTTATAAAA
Found at i:1947795 original size:19 final size:20
Alignment explanation
Indices: 1947771--1947808 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1947761 TAAAGTACTG
1947771 TTAT-AATTATTTTATTTTA
1 TTATAAATTATTTTATTTTA
*
1947790 TTATAAATTTTTTTATTTT
1 TTATAAATTATTTTATTTT
1947809 TGTAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATAAATTATTTTATTTTA
Found at i:1951456 original size:12 final size:12
Alignment explanation
Indices: 1951439--1951469 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1951429 AAGCTTTAGC
1951439 TTTATATATATA
1 TTTATATATATA
1951451 TTTATATATATA
1 TTTATATATATA
*
1951463 TATATAT
1 TTTATAT
1951470 GGGACAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTATATATATA
Found at i:1952925 original size:27 final size:28
Alignment explanation
Indices: 1952895--1952948 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
1952885 TTTATGAAAT
*
1952895 AAAAAGTAAAAAATTGAAAAA-AAAAAG
1 AAAAAATAAAAAATTGAAAAATAAAAAG
*
1952922 AAAAAATAAAAATTTGAAAAATAAAAA
1 AAAAAATAAAAAATTGAAAAATAAAAA
1952949 CTGAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (28 bp):
AAAAAATAAAAAATTGAAAAATAAAAAG
Found at i:1952966 original size:2 final size:2
Alignment explanation
Indices: 1952959--1952987 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1952949 CTGAAATTAA
1952959 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1952988 AGGAAATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1953111 original size:24 final size:23
Alignment explanation
Indices: 1953083--1953142 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
1953073 TTTCCTTTTA
1953083 TTTTTTTAAAATTTAAATTTCCAG
1 TTTTTTTAAAATTTAAATTT-CAG
* * * *
1953107 TTTTTTTTAATTTTTAATTTTAG
1 TTTTTTTAAAATTTAAATTTCAG
*
1953130 TTTTTATAAAATT
1 TTTTTTTAAAATT
1953143 GTAATTTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.63
Consensus pattern (23 bp):
TTTTTTTAAAATTTAAATTTCAG
Found at i:1953131 original size:23 final size:23
Alignment explanation
Indices: 1953078--1953151 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
1953068 TCTCTTTTCC
1953078 TTTTA-TTTTTTTAAAATTTAAA
1 TTTTAGTTTTTTTAAAATTTAAA
* * * *
1953100 TTTCCAGTTTTTTTTAATTTTTAA
1 TTT-TAGTTTTTTTAAAATTTAAA
*
1953124 TTTTAGTTTTTATAAAATTGT-AA
1 TTTTAGTTTTTTTAAAATT-TAAA
1953147 TTTTA
1 TTTTA
1953152 AAAATAAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
22 3 0.07
23 20 0.49
24 18 0.44
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.64
Consensus pattern (23 bp):
TTTTAGTTTTTTTAAAATTTAAA
Found at i:1964441 original size:1 final size:1
Alignment explanation
Indices: 1964435--1964461 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1964425 GTCATCCTCG
1964435 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1964462 CCCCCCTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1974737 original size:25 final size:24
Alignment explanation
Indices: 1974700--1974746 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
1974690 TATTAAAATA
1974700 TTTTATATATTTAATTATATTTATT
1 TTTTATATATTTAATTA-ATTTATT
1974725 TTTTATACT-TTTAATTAATTTA
1 TTTTATA-TATTTAATTAATTTA
1974747 ATTCTTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.24
25 15 0.71
26 1 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTTTATATATTTAATTAATTTATT
Found at i:1975048 original size:15 final size:14
Alignment explanation
Indices: 1975025--1975060 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 14
1975015 AAAAAATATT
1975025 TTAATATTAAATTAAA
1 TTAA-ATTAAATT-AA
1975041 TTAAATTAAATTAA
1 TTAAATTAAATTAA
1975055 TTAAAT
1 TTAAAT
1975061 GTATGAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 8 0.40
16 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAAATTAAATTAA
Found at i:1975058 original size:4 final size:5
Alignment explanation
Indices: 1975025--1975060 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
1975015 AAAAAATATT
1975025 TTAATA TTAAA TTAAA TTAAA TTAAA TT-AA TTAAA T
1 TTAA-A TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T
1975061 GTATGAGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.14
5 21 0.72
6 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:1976030 original size:2 final size:2
Alignment explanation
Indices: 1976023--1976059 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1976013 TTTCTAGGAA
1976023 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1976060 GTAAATATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1985302 original size:17 final size:17
Alignment explanation
Indices: 1985278--1985395 Score: 68
Period size: 17 Copynumber: 6.9 Consensus size: 17
1985268 TTACGTGAAT
*
1985278 ATATATTTAAATTTTTTAA
1 ATAT-TTTAAA-TATTTAA
*
1985297 ATATTTTATATATTTAA
1 ATATTTTAAATATTTAA
* *
1985314 ATTTTTTAAATATTT-T
1 ATATTTTAAATATTTAA
*
1985330 ATATATTTAAA-AATT-A
1 ATAT-TTTAAATATTTAA
* *
1985346 TTATTTTATAATATATAA
1 ATATTTTA-AATATTTAA
1985364 ATATATATTAAATA--TAA
1 ATAT-T-TTAAATATTTAA
1985381 ATA-TTTAATATATTT
1 ATATTTTAA-ATATTT
1985396 CAAAAAAATA
Statistics
Matches: 78, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
14 4 0.05
15 8 0.10
16 11 0.14
17 34 0.44
18 9 0.12
19 9 0.12
20 3 0.04
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTTAAATATTTAA
Found at i:1985313 original size:26 final size:26
Alignment explanation
Indices: 1985277--1985340 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
1985267 CTTACGTGAA
1985277 TATATATTTAAATTTTTTAAATATTT
1 TATATATTTAAATTTTTTAAATATTT
1985303 TATATATTTAAATTTTTTAAATATTT
1 TATATATTTAAATTTTTTAAATATTT
1985329 TATATATTTAAA
1 TATATATTTAAA
1985341 AATTATTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TATATATTTAAATTTTTTAAATATTT
Found at i:1985335 original size:9 final size:9
Alignment explanation
Indices: 1985278--1985337 Score: 68
Period size: 9 Copynumber: 6.7 Consensus size: 9
1985268 TTACGTGAAT
1985278 ATATATTTAA
1 ATAT-TTTAA
*
1985288 ATTTTTTAA
1 ATATTTTAA
*
1985297 ATATTTTAT
1 ATATTTTAA
1985306 ATA-TTTAA
1 ATATTTTAA
*
1985314 ATTTTTTAA
1 ATATTTTAA
*
1985323 ATATTTTAT
1 ATATTTTAA
1985332 ATATTT
1 ATATTT
1985338 AAAAATTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
8 6 0.14
9 33 0.79
10 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
ATATTTTAA
Found at i:1985599 original size:28 final size:27
Alignment explanation
Indices: 1985571--1985621 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1985561 TGATTTATAA
*
1985571 AAAAATAGAT-ATA-TAAATTATAATTT
1 AAAAATATATAATATTAAATT-TAATTT
1985597 AAAAATATATAATATTAAATTTAAT
1 AAAAATATATAATATTAAATTTAAT
1985622 GGTTTTTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 9 0.41
27 7 0.32
28 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
AAAAATATATAATATTAAATTTAATTT
Found at i:1985606 original size:22 final size:22
Alignment explanation
Indices: 1985579--1985620 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1985569 AAAAAAATAG
1985579 ATATATAA-ATTATAATTTAAAA
1 ATATATAATATTA-AATTTAAAA
1985601 ATATATAATATTAAATTTAA
1 ATATATAATATTAAATTTAA
1985621 TGGTTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATATAATATTAAATTTAAAA
Found at i:1990800 original size:35 final size:32
Alignment explanation
Indices: 1990761--1990829 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
1990751 CTAATAATAT
1990761 TTAATATATTATATACTTAAAATAAATTTT-ACATA
1 TTAATA-ATT-TATA-TTAAAA-AAATTTTAACATA
*
1990796 TTAATAATTTATATTATAAAAATTTTAACATA
1 TTAATAATTTATATTAAAAAAATTTTAACATA
1990828 TT
1 TT
1990830 TTATGCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 7 0.22
32 12 0.38
33 4 0.12
34 3 0.09
35 6 0.19
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (32 bp):
TTAATAATTTATATTAAAAAAATTTTAACATA
Found at i:1990882 original size:24 final size:22
Alignment explanation
Indices: 1990854--1990900 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
1990844 TATGTTTGTA
* *
1990854 TTAATTTTTATCTAATATTATATT
1 TTAATTATTAT-TAA-AATATATT
1990878 TTAATTATTATTAAAATATATT
1 TTAATTATTATTAAAATATATT
1990900 T
1 T
1990901 ATATTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 3 0.14
24 10 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTAATTATTATTAAAATATATT
Found at i:1996886 original size:3 final size:3
Alignment explanation
Indices: 1996878--1996926 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1996868 AACTTGTTAA
1996878 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1996926 A
1 A
1996927 CACGCAATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1997130 original size:2 final size:2
Alignment explanation
Indices: 1997123--1997151 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1997113 TAAAGAGATA
1997123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1997152 AATGTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1999258 original size:18 final size:19
Alignment explanation
Indices: 1999226--1999261 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1999216 CTATAATCAG
1999226 TAAATTTTAAAAATTTTAT
1 TAAATTTTAAAAATTTTAT
*
1999245 TAAA-TTTAATAATTTTA
1 TAAATTTTAAAAATTTTA
1999262 AATATGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAATTTTAAAAATTTTAT
Found at i:2000041 original size:16 final size:16
Alignment explanation
Indices: 2000009--2000054 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1999999 ATAATATTAA
2000009 AATATTATTTTAAATT
1 AATATTATTTTAAATT
*
2000025 AATA-TATTTATATATT
1 AATATTATTT-TAAATT
2000041 -ATAATTATTTTAAA
1 AAT-ATTATTTTAAA
2000055 GATATCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 7 0.28
16 13 0.52
17 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AATATTATTTTAAATT
Found at i:2000093 original size:15 final size:14
Alignment explanation
Indices: 2000062--2000104 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
2000052 AAAGATATCT
2000062 TTTAATTAATTAATAA
1 TTTAATTAA--AATAA
2000078 TTTCAATTAAAATAA
1 TTT-AATTAAAATAA
2000093 TTTAATTAAAAT
1 TTTAATTAAAAT
2000105 TTAAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.35
15 8 0.31
16 3 0.12
17 6 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTAATTAAAATAA
Found at i:2000596 original size:18 final size:18
Alignment explanation
Indices: 2000541--2000597 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
2000531 TATTTTAATT
2000541 TTAT-TTAATATATTTATA
1 TTATATTAATA-ATTTATA
2000559 TTA-A-T-ATAAATTT-TA
1 TTATATTAAT-AATTTATA
*
2000574 ATATATTAATAATTTATA
1 TTATATTAATAATTTATA
2000592 TTATAT
1 TTATAT
2000598 ATTTTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
15 4 0.13
16 7 0.23
17 8 0.26
18 12 0.39
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATATTAATAATTTATA
Found at i:2000597 original size:20 final size:20
Alignment explanation
Indices: 2000524--2000635 Score: 59
Period size: 20 Copynumber: 6.0 Consensus size: 20
2000514 TTATTTCTTT
* *
2000524 TATTATATATTTTA-ATTTTA
1 TATTA-ATAATTTATATTATA
2000544 T-TTAATATATTTATATTA-A
1 TATTAATA-ATTTATATTATA
2000563 TA-T-A-AATTT-TA--ATA
1 TATTAATAATTTATATTATA
2000577 TATTAATAATTTATATTATA
1 TATTAATAATTTATATTATA
*
2000597 TATTTTAA-AATTTATATATTTA
1 TA--TTAATAATTTATAT-TATA
*
2000619 TATT-ATATTTTA-ATTAT
1 TATTAATAATTTATATTAT
2000636 TTTTATTATT
Statistics
Matches: 73, Mismatches: 5, Indels: 30
0.68 0.05 0.28
Matches are distributed among these distances:
13 1 0.01
14 3 0.04
15 3 0.04
16 5 0.07
17 6 0.08
18 8 0.11
19 13 0.18
20 16 0.22
21 9 0.12
22 9 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTAATAATTTATATTATA
Found at i:2001809 original size:2 final size:2
Alignment explanation
Indices: 2001802--2001831 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2001792 TTGGAGTTGA
*
2001802 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2001832 GCGCATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2004113 original size:34 final size:34
Alignment explanation
Indices: 2004045--2004227 Score: 201
Period size: 34 Copynumber: 5.4 Consensus size: 34
2004035 ATATGCAAAG
* * *
2004045 TGTTGATTAAAT-GGAGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
* **
2004078 TGTTGATTAAATGGGTGATTTGGTGGTTTGTCAT
1 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
* * *
2004112 TGTTGACTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
* *
2004146 TATTGATTAAATGGGTGATTTTGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
* **
2004180 TGTTGACTAAAT-GGTAGATTTGGTAGG-TTGTCAT
1 TGTTGATTAAATGGGT-GATTTGGT-GGCTTACCAT
2004214 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2004228 TGGTTTTTAC
Statistics
Matches: 125, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
33 15 0.12
34 107 0.86
35 3 0.02
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.42
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
Found at i:2004137 original size:68 final size:68
Alignment explanation
Indices: 2004045--2004227 Score: 260
Period size: 68 Copynumber: 2.7 Consensus size: 68
2004035 ATATGCAAAG
* * * **
2004045 TGTTGATTAAAT-GGAGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGT
1 TGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
2004109 CAT
66 CAT
* *
2004112 TGTTGACTAAATGGGAGATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTTGTGGCTTAC
1 TGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
2004177 CAT
66 CAT
* * **
2004180 TGTTGACTAAATGGTAGATTTGGTAGGTTGTCATTGTTGATTAAATGG
1 TGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGG
2004228 TGGTTTTTAC
Statistics
Matches: 103, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
67 11 0.11
68 92 0.89
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.42
Consensus pattern (68 bp):
TGTTGACTAAATGGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
CAT
Found at i:2008695 original size:34 final size:34
Alignment explanation
Indices: 2008638--2008822 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
2008628 AAGTGGGAGA
*
2008638 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2008671 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
2008705 ATTGTTGACTAAATGAGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2008739 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
2008773 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTACC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
2008807 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2008823 TGGTTTTTAC
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
33 17 0.13
34 113 0.86
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:2008738 original size:68 final size:67
Alignment explanation
Indices: 2008638--2008822 Score: 289
Period size: 68 Copynumber: 2.7 Consensus size: 67
2008628 AAGTGGGAGA
* * * * *
2008638 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
2008703 CC
66 CC
*
2008705 ATTGTTGACTAAATGAGAGATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGACTAAATG-GAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
2008770 ACC
65 ACC
*
2008773 ATTGTTGACTAAATGGTAGATTTGGTAGGTTACCATTGTTGATTAAATGG
1 ATTGTTGACTAAATGG-AGATTTGGTAGCTTACCATTGTTGATTAAATGG
2008823 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
67 15 0.14
68 93 0.86
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (67 bp):
ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
CC
Found at i:2009873 original size:17 final size:17
Alignment explanation
Indices: 2009829--2009873 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2009819 TATTACTTAA
2009829 ATTTAAAATATAAATAT
1 ATTTAAAATATAAATAT
***
2009846 ATTTTTTATATAAATAT
1 ATTTAAAATATAAATAT
2009863 ATTTAAAATAT
1 ATTTAAAATAT
2009874 TTTATTTTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAAAATATAAATAT
Found at i:2010756 original size:13 final size:13
Alignment explanation
Indices: 2010738--2010762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2010728 CTCAAAATCA
2010738 TATTTCTTTTTTT
1 TATTTCTTTTTTT
2010751 TATTTCTTTTTT
1 TATTTCTTTTTT
2010763 CAATTAGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (13 bp):
TATTTCTTTTTTT
Found at i:2011654 original size:26 final size:25
Alignment explanation
Indices: 2011598--2011656 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
2011588 TGTTTAATAA
*
2011598 TTAAAATTTTAATTTTTTTCATATT
1 TTAAAATTATAATTTTTTTCATATT
*
2011623 TATAAAATTATAATTTTATATTTATA-T
1 T-TAAAATTATAATTTT-T-TTCATATT
2011650 TTAAAAT
1 TTAAAAT
2011657 ATGTGTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 1 0.03
26 20 0.69
27 3 0.10
28 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TTAAAATTATAATTTTTTTCATATT
Found at i:2013725 original size:14 final size:14
Alignment explanation
Indices: 2013706--2013733 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2013696 TTTTTTCAAA
2013706 TATGAAGTATGAAC
1 TATGAAGTATGAAC
2013720 TATGAAGTATGAAC
1 TATGAAGTATGAAC
2013734 AAAGGTTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (14 bp):
TATGAAGTATGAAC
Found at i:2015663 original size:14 final size:14
Alignment explanation
Indices: 2015604--2015665 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 14
2015594 AGAATTTTAA
2015604 AATTGTGTTTAAGATT
1 AATT-TGTTTAA-ATT
2015620 AATTTGTTTAGAATT
1 AATTTGTTTA-AATT
* **
2015635 AAGTGTGTTCGAATT
1 AA-TTTGTTTAAATT
*
2015650 TATTTGTTTAAATT
1 AATTTGTTTAAATT
2015664 AA
1 AA
2015666 ATAAACTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
14 10 0.28
15 16 0.44
16 10 0.28
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (14 bp):
AATTTGTTTAAATT
Found at i:2016258 original size:21 final size:21
Alignment explanation
Indices: 2016219--2016259 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2016209 CCTATATGAT
*
2016219 ATATTTATTTAATTATTAATA
1 ATATTTATCTAATTATTAATA
* *
2016240 ATATTTATCTAGTTTTTAAT
1 ATATTTATCTAATTATTAAT
2016260 TAAAAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
ATATTTATCTAATTATTAATA
Found at i:2016470 original size:2 final size:2
Alignment explanation
Indices: 2016463--2016503 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2016453 TTCATTGGTT
2016463 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2016504 CTTATGTTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2019033 original size:2 final size:2
Alignment explanation
Indices: 2019028--2019055 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2019018 ACACACACAC
2019028 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
2019056 TCAGTCACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2025054 original size:50 final size:50
Alignment explanation
Indices: 2024974--2025072 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
2024964 GATCACTTGG
* *
2024974 ATTCGCTCTAGTTGCTTTTTTTAATTTTTTGTGTGCACTTAACAACAAAA
1 ATTCACTCTAGTTGCTTTTTTTAATTTTTTGTGTGCACTCAACAACAAAA
2025024 ATTCACTCTAGTTGCTTTTTTTAATTTTTTGTGTGCACTCAACAACAAA
1 ATTCACTCTAGTTGCTTTTTTTAATTTTTTGTGTGCACTCAACAACAAA
2025073 GTGAGTTGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.45
Consensus pattern (50 bp):
ATTCACTCTAGTTGCTTTTTTTAATTTTTTGTGTGCACTCAACAACAAAA
Found at i:2026347 original size:11 final size:11
Alignment explanation
Indices: 2026331--2026355 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2026321 TTCAATATAA
2026331 TTAAAGTATTT
1 TTAAAGTATTT
2026342 TTAAAGTATTT
1 TTAAAGTATTT
2026353 TTA
1 TTA
2026356 CAATATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
TTAAAGTATTT
Found at i:2030572 original size:144 final size:144
Alignment explanation
Indices: 2030312--2030605 Score: 570
Period size: 144 Copynumber: 2.0 Consensus size: 144
2030302 CTATTCACAC
*
2030312 AATATTAATGGAGAACAGGTAAGGCTTGAGTTTAGAAAAAAACCTAAATTACTTGCCATGCCACC
1 AATATTAATGGAGAACAAGTAAGGCTTGAGTTTAGAAAAAAACCTAAATTACTTGCCATGCCACC
*
2030377 ATCATTACAACTGCCCCTTTAGCCATATAGCGACCCAAAACTACTGAGTTGCATTTGCCCACTTG
66 ATCATTACAACTGCCCCTTTAGCCATATAGCGACCCAAAACTACTGAGTTGCATTCGCCCACTTG
2030442 GACTAGGGCAAGCA
131 GACTAGGGCAAGCA
2030456 AATATTAATGGAGAACAAGTAAGGCTTGAGTTTAGAAAAAAACCTAAATTACTTGCCATGCCACC
1 AATATTAATGGAGAACAAGTAAGGCTTGAGTTTAGAAAAAAACCTAAATTACTTGCCATGCCACC
2030521 ATCATTACAACTGCCCCTTTAGCCATATAGCGACCCAAAACTACTGAGTTGCATTCGCCCACTTG
66 ATCATTACAACTGCCCCTTTAGCCATATAGCGACCCAAAACTACTGAGTTGCATTCGCCCACTTG
2030586 GACTAGGGCAAGCA
131 GACTAGGGCAAGCA
2030600 AATATT
1 AATATT
2030606 GAATTAATAA
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 148 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (144 bp):
AATATTAATGGAGAACAAGTAAGGCTTGAGTTTAGAAAAAAACCTAAATTACTTGCCATGCCACC
ATCATTACAACTGCCCCTTTAGCCATATAGCGACCCAAAACTACTGAGTTGCATTCGCCCACTTG
GACTAGGGCAAGCA
Found at i:2034051 original size:12 final size:12
Alignment explanation
Indices: 2034034--2034058 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2034024 CATTGAGTCC
2034034 TTTATTTATTTT
1 TTTATTTATTTT
2034046 TTTATTTATTTT
1 TTTATTTATTTT
2034058 T
1 T
2034059 CCTATTAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTTATTTT
Found at i:2035451 original size:21 final size:21
Alignment explanation
Indices: 2035418--2035460 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2035408 ATATTATGTA
* *
2035418 ATGTTTATGATGTAAAAGTAT
1 ATGTATATAATGTAAAAGTAT
* *
2035439 ATGTATATAATGTTATAGTAT
1 ATGTATATAATGTAAAAGTAT
2035460 A
1 A
2035461 AATATTAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (21 bp):
ATGTATATAATGTAAAAGTAT
Found at i:2035989 original size:7 final size:8
Alignment explanation
Indices: 2035965--2035993 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2035955 ATAGTTTTTT
2035965 AAATATAA
1 AAATATAA
2035973 AAATATAA
1 AAATATAA
2035981 AAATA-AA
1 AAATATAA
2035988 AAATAT
1 AAATAT
2035994 CTTTAGTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATATAA
Found at i:2042306 original size:147 final size:147
Alignment explanation
Indices: 2042029--2042323 Score: 376
Period size: 147 Copynumber: 2.0 Consensus size: 147
2042019 ACTTGTCTAA
**
2042029 ATACACCACAACAGAATAGTGTTGCAGAGAGAAAAAACAAGCATCTGGTAGAAGTATATCGGAGT
1 ATACACCACAACAGAATAGTGTTGCAGAGAGAAAAAACAAGCATCTGACAGAAGTATATCGGAGT
* * * *
2042094 ATAATGCATGCTAAGGATGTCCTTAAGAGATTTTGGGTTGAGTGCATGAGAACAGTAGCTCATAT
66 ATAATGCATGCTAAGAATGTCCTTAAGAAATTTTGGGTTGAATGCATGAGAACAGCAGCTCATAT
2042159 CATAAACAGACTTCCAC
131 CATAAACAGACTTCCAC
* * * * * *
2042176 ATACACCACAGCAGCATGGTGTTGCAGAGAGAAAGAACAAGCATTTGACAGAAGTATGTCGGAGT
1 ATACACCACAACAGAATAGTGTTGCAGAGAGAAAAAACAAGCATCTGACAGAAGTATATCGGAGT
* * ** * * * *
2042241 ATGATGCATGCTAAGAATGT-TTCTGGGAAATTTTGGGTTGAATGTATGAGAATAGCAGTTTATA
66 ATAATGCATGCTAAGAATGTCCT-TAAGAAATTTTGGGTTGAATGCATGAGAACAGCAGCTCATA
* *
2042305 TCATAAATAGACTTTCAC
130 TCATAAACAGACTTCCAC
2042323 A
1 A
2042324 ATCGAAAATT
Statistics
Matches: 125, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
146 1 0.01
147 124 0.99
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (147 bp):
ATACACCACAACAGAATAGTGTTGCAGAGAGAAAAAACAAGCATCTGACAGAAGTATATCGGAGT
ATAATGCATGCTAAGAATGTCCTTAAGAAATTTTGGGTTGAATGCATGAGAACAGCAGCTCATAT
CATAAACAGACTTCCAC
Found at i:2043529 original size:174 final size:174
Alignment explanation
Indices: 2043239--2043590 Score: 695
Period size: 174 Copynumber: 2.0 Consensus size: 174
2043229 TTGATCGAAA
2043239 TGTGTACATGGAACAACCAAAAGGATTCGAGAATAAGATCCATCCTGATTATGTTTGCAAGCTGA
1 TGTGTACATGGAACAACCAAAAGGATTCGAGAATAAGATCCATCCTGATTATGTTTGCAAGCTGA
2043304 AGAAAGCGCTCTATGGGTTGTAACAAGCTCCTAGAGTTTGGTATGGCAAAATTGAAGAGTTTCTC
66 AGAAAGCGCTCTATGGGTTGTAACAAGCTCCTAGAGTTTGGTATGGCAAAATTGAAGAGTTTCTC
2043369 ATTAATAGTGGCTATGTAGTTGCACCAGCTGATTCTAGTTTATT
131 ATTAATAGTGGCTATGTAGTTGCACCAGCTGATTCTAGTTTATT
2043413 TGTGTACATGGAACAACCAAAAGGATTCGAGAATAAGATCCATCCTGATTATGTTTGCAAGCTGA
1 TGTGTACATGGAACAACCAAAAGGATTCGAGAATAAGATCCATCCTGATTATGTTTGCAAGCTGA
2043478 AGAAAGCGCTCTATGGGTTGTAACAAGCTCCTAGAGTTTGGTATGGCAAAATTGAAGAGTTTCTC
66 AGAAAGCGCTCTATGGGTTGTAACAAGCTCCTAGAGTTTGGTATGGCAAAATTGAAGAGTTTCTC
*
2043543 ATTAATAGTGGCTATGTAGTTGCACCAGCTGATTTTAGTTTATT
131 ATTAATAGTGGCTATGTAGTTGCACCAGCTGATTCTAGTTTATT
2043587 TGTG
1 TGTG
2043591 AAAGTTAGAA
Statistics
Matches: 177, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
174 177 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (174 bp):
TGTGTACATGGAACAACCAAAAGGATTCGAGAATAAGATCCATCCTGATTATGTTTGCAAGCTGA
AGAAAGCGCTCTATGGGTTGTAACAAGCTCCTAGAGTTTGGTATGGCAAAATTGAAGAGTTTCTC
ATTAATAGTGGCTATGTAGTTGCACCAGCTGATTCTAGTTTATT
Found at i:2044323 original size:18 final size:18
Alignment explanation
Indices: 2044300--2044334 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2044290 GTTAGTGCAG
*
2044300 TTGATGGGGAATTTACAA
1 TTGATGGAGAATTTACAA
2044318 TTGATGGAGAATTTACA
1 TTGATGGAGAATTTACA
2044335 TCAACCAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (18 bp):
TTGATGGAGAATTTACAA
Found at i:2055334 original size:18 final size:16
Alignment explanation
Indices: 2055288--2055367 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 16
2055278 TATATTATAA
2055288 TTATA-TTTA-AAATAT
1 TTATATTTTATAAAT-T
2055303 TTAATATTTATATAAATT
1 TT-ATATTT-TATAAATT
2055321 TTGATATATTTAT-AA-T
1 TT-ATAT-TTTATAAATT
*
2055337 TTATATTATATAAATT
1 TTATATTTTATAAATT
*
2055353 TTA-A-ATTATAAATT
1 TTATATTTTATAAATT
2055367 T
1 T
2055368 ATAATATATT
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
14 13 0.24
15 9 0.17
16 10 0.19
17 4 0.07
18 12 0.22
19 6 0.11
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (16 bp):
TTATATTTTATAAATT
Found at i:2055348 original size:14 final size:14
Alignment explanation
Indices: 2055325--2055376 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 14
2055315 TAAATTTTGA
2055325 TATATT-TATAATT
1 TATATTATATAATT
2055338 TATATTATATAAATTT
1 TATATTATAT-AA-TT
*
2055354 TAAATTATA-AATT
1 TATATTATATAATT
*
2055367 TATAATATAT
1 TATATTATAT
2055377 TATATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 15 0.47
14 5 0.16
15 2 0.06
16 10 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATATTATATAATT
Found at i:2055349 original size:32 final size:31
Alignment explanation
Indices: 2055301--2055409 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 31
2055291 TATTTAAAAT
2055301 ATTTAATATTTATATAAATTTTGATATATTTATA
1 ATTT-ATA-TTATATAAATTTT-ATATATTTATA
2055335 ATTTATATTATATAAATTTTA-A-A-TTATAA
1 ATTTATATTATATAAATTTTATATATTTAT-A
* *
2055364 ATTTATAATATATTATATTTTA-ATTATTT-T-
1 ATTTATATTATA-TAAATTTTATA-TATTTATA
*
2055394 ATTTATATAAT-TAAAT
1 ATTTATATTATATAAAT
2055410 ATGAGGTGTA
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
28 8 0.12
29 13 0.20
30 19 0.29
31 1 0.02
32 15 0.23
33 5 0.08
34 4 0.06
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (31 bp):
ATTTATATTATATAAATTTTATATATTTATA
Found at i:2055376 original size:29 final size:30
Alignment explanation
Indices: 2055311--2055400 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 30
2055301 ATTTAATATT
*
2055311 TATATAAATTTTGATATATT-TATAATTTATAT
1 TATATAAATTTT-A-A-ATTATATAATTTATAA
2055343 TATATAAATTTTAAATTATA-AATTTATAA
1 TATATAAATTTTAAATTATATAATTTATAA
* * *
2055372 TATATTATATTTT-AATTATTTTATTTATA
1 TATA-TAAATTTTAAATTATATAATTTATA
2055401 TAATTAAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
29 21 0.41
30 17 0.33
31 1 0.02
32 12 0.24
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
TATATAAATTTTAAATTATATAATTTATAA
Found at i:2055396 original size:14 final size:16
Alignment explanation
Indices: 2055267--2055400 Score: 62
Period size: 16 Copynumber: 8.9 Consensus size: 16
2055257 TTTTGTACAG
* *
2055267 TATATTTTATTTATAT
1 TATATTATATTTATAA
*
2055283 TATAATTATATTTAAAA
1 TAT-ATTATATTTATAA
2055300 TAT-TTAATATTTAT-A
1 TATATT-ATATTTATAA
2055315 TA-A--AT-TTTGAT-A
1 TATATTATATTT-ATAA
*
2055327 TAT-TTATAATTTATAT
1 TATATTAT-ATTTATAA
*
2055343 TATA-TAAATTT-TAA
1 TATATTATATTTATAA
*
2055357 -AT-TATAAATTTATAA
1 TATAT-TATATTTATAA
2055372 TATATTATATTT-TAA
1 TATATTATATTTATAA
*
2055387 T-TATTTTATTTATA
1 TATATTATATTTATA
2055401 TAATTAAATA
Statistics
Matches: 92, Mismatches: 9, Indels: 35
0.68 0.07 0.26
Matches are distributed among these distances:
11 3 0.03
12 7 0.08
13 2 0.02
14 20 0.22
15 20 0.22
16 26 0.28
17 14 0.15
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (16 bp):
TATATTATATTTATAA
Found at i:2056130 original size:3 final size:3
Alignment explanation
Indices: 2056122--2056159 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2056112 CTAGAAATAA
2056122 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2056160 GGTTGATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2064750 original size:20 final size:20
Alignment explanation
Indices: 2064718--2064787 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
2064708 GTAACTTAAA
*
2064718 GTATTGATACATTTATGGAT
1 GTATCGATACATTTATGGAT
* * *
2064738 GTATCGATGCA-TTGTGTATT
1 GTATCGATACATTTATGGA-T
2064758 GTATCGATACATTTAAT-G-T
1 GTATCGATACATTT-ATGGAT
2064777 GTATCGATACA
1 GTATCGATACA
2064788 AATGAAGGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
19 17 0.43
20 20 0.50
21 2 0.05
22 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (20 bp):
GTATCGATACATTTATGGAT
Found at i:2064923 original size:92 final size:92
Alignment explanation
Indices: 2064757--2064935 Score: 229
Period size: 92 Copynumber: 1.9 Consensus size: 92
2064747 CATTGTGTAT
* ** * * *
2064757 TGTATCGATACATTTAATGTGTATCGATACAAATGAAGGTTTCAGGGTTTCTTTATCTATTGCCG
1 TGTATCGATACATTTAATGTGTATCGATAAAAATGAAGGTTTCAGCATTTCTTTAGCTACTGCCA
*
2064822 ACCAGATGTATCGATATATTCACATAA
66 ACCAGATGTATCGATACATTCACATAA
*
2064849 TGTATCGATACATTTTCAAT-TGTCTCGATAAAAAT-AAGGGTTTCAGCATTTC-TTAGCTACTG
1 TGTATCGATACA-TTT-AATGTGTATCGATAAAAATGAA-GGTTTCAGCATTTCTTTAGCTACTG
*
2064911 CCAACCATATGTATCGATACATTCA
63 CCAACCAGATGTATCGATACATTCA
2064936 ATCTTGAACT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
92 44 0.59
93 28 0.37
94 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (92 bp):
TGTATCGATACATTTAATGTGTATCGATAAAAATGAAGGTTTCAGCATTTCTTTAGCTACTGCCA
ACCAGATGTATCGATACATTCACATAA
Found at i:2074118 original size:2 final size:2
Alignment explanation
Indices: 2074111--2074138 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2074101 CTTTATTTAA
2074111 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
2074139 TGTTCCAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2074957 original size:18 final size:19
Alignment explanation
Indices: 2074920--2074965 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
2074910 AATATTCAAA
*
2074920 AAATTTTAATAAAAATATT
1 AAATTTAAATAAAAATATT
*
2074939 AAATTTAAATAATAA-ATT
1 AAATTTAAATAAAAATATT
*
2074957 AATTTTAAA
1 AAATTTAAA
2074966 ATTTAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTTAAATAAAAATATT
Done.