Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 6 of 173
Found at i:1608443 original size:18 final size:17
Alignment explanation
Indices: 1608420--1608492 Score: 65
Period size: 18 Copynumber: 4.1 Consensus size: 17
1608410 TTAAAATTTC
1608420 TTTTTAAACTTTTATAAA
1 TTTTTAAA-TTTTATAAA
* * *
1608438 TTTTTAAAATATATAAG
1 TTTTTAAATTTTATAAA
* *
1608455 TTTTGGAATTTTTATAAA
1 TTTT-TAAATTTTATAAA
*
1608473 TATTTTGAATTTTATAAA
1 T-TTTTAAATTTTATAAA
1608491 TT
1 TT
1608493 ATTTTGATTT
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
17 11 0.26
18 28 0.67
19 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTTTAAATTTTATAAA
Found at i:1608484 original size:19 final size:20
Alignment explanation
Indices: 1608455--1608504 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1608445 AATATATAAG
1608455 TTTTGGAATTTTTATAAA-TA
1 TTTT-GAATTTTTATAAATTA
1608475 TTTTGAA-TTTTATAAATTA
1 TTTTGAATTTTTATAAATTA
1608494 TTTTG-ATTTTT
1 TTTTGAATTTTT
1608505 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.36
19 14 0.50
20 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTGAATTTTTATAAATTA
Found at i:1608502 original size:18 final size:18
Alignment explanation
Indices: 1608429--1608503 Score: 66
Period size: 18 Copynumber: 4.2 Consensus size: 18
1608419 CTTTTTAAAC
*
1608429 TTTTATAAAT-TTTTAAA
1 TTTTATAAATATTTTGAA
* * * *
1608446 ATATATAAGT-TTTGGAA
1 TTTTATAAATATTTTGAA
1608463 TTTTTATAAATATTTTGAA
1 -TTTTATAAATATTTTGAA
1608482 TTTTATAAATTATTTTG-A
1 TTTTATAAA-TATTTTGAA
1608500 TTTT
1 TTTT
1608504 TTTTGTAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
17 12 0.26
18 21 0.46
19 13 0.28
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (18 bp):
TTTTATAAATATTTTGAA
Found at i:1609002 original size:19 final size:18
Alignment explanation
Indices: 1608978--1609024 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
1608968 TTATTATCTT
1608978 ATAACTTTTA-AAAATAATA
1 ATAACTTTTACAAAA-AA-A
1608997 ATAACTTCTTACAAAAAAA
1 ATAACTT-TTACAAAAAAA
*
1609016 AAAACTTTT
1 ATAACTTTT
1609025 CACACCAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 14 0.56
20 5 0.20
21 4 0.16
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAACTTTTACAAAAAAA
Found at i:1622402 original size:12 final size:12
Alignment explanation
Indices: 1622384--1622413 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1622374 TATCGCAAAG
1622384 AAAATAGAAATA
1 AAAATAGAAATA
*
1622396 GAAATAGAAATA
1 AAAATAGAAATA
1622408 AAAATA
1 AAAATA
1622414 AAGAACACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (12 bp):
AAAATAGAAATA
Found at i:1630597 original size:37 final size:37
Alignment explanation
Indices: 1630547--1630620 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
1630537 TTAGTTTTTC
**
1630547 GTGACATTTTATAAATGCCACGGGCTAGAAAATATTT
1 GTGACATTTTATAAATGCCACGAACTAGAAAATATTT
* *
1630584 GTGACATTTTATAAATGTCATGAACTAGAAAATATTT
1 GTGACATTTTATAAATGCCACGAACTAGAAAATATTT
1630621 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (37 bp):
GTGACATTTTATAAATGCCACGAACTAGAAAATATTT
Found at i:1641802 original size:27 final size:27
Alignment explanation
Indices: 1641770--1641823 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1641760 TTATTTTTTA
1641770 AAATAAAATTATTT-ATTAAATTAATTT
1 AAATAAAATTATTTAATTAAA-TAATTT
*
1641797 AAATAAAATTTTTTAATTAAATAATTT
1 AAATAAAATTATTTAATTAAATAATTT
1641824 TCCCAACTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AAATAAAATTATTTAATTAAATAATTT
Found at i:1643215 original size:14 final size:14
Alignment explanation
Indices: 1643198--1643249 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
1643188 TAGAACATAT
*
1643198 AACATTAAATCCTA
1 AACACTAAATCCTA
1643212 AACACTAAATCCTA
1 AACACTAAATCCTA
1643226 AAC-CTAGAAT-CTCA
1 AACACTA-AATCCT-A
*
1643240 AACCCTAAAT
1 AACACTAAAT
1643250 AAAAATATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 5 0.15
14 26 0.76
15 3 0.09
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (14 bp):
AACACTAAATCCTA
Found at i:1643686 original size:21 final size:21
Alignment explanation
Indices: 1643649--1643689 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1643639 CTCAAACACA
*
1643649 TTAAACCCATATATCTTAAAC
1 TTAAACCCATACATCTTAAAC
1643670 TTAAACCC-TACACTCTTAAA
1 TTAAACCCATACA-TCTTAAA
1643690 TATATAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAACCCATACATCTTAAAC
Found at i:1643996 original size:83 final size:83
Alignment explanation
Indices: 1643820--1643981 Score: 200
Period size: 83 Copynumber: 2.0 Consensus size: 83
1643810 ATAAACCCTG
* * **
1643820 AACACTACACTTTAAATCTAAAATCTCAAACCTTAAACCCAAAACATAAAAACTTAAACCCTAAA
1 AACACTAAACCTTAAATCTAAAATCTCAAACCTTAAACCCAAAACATAAAAACCCAAACCCTAAA
*
1643885 GTAAAAAATATAACCCCA
66 CTAAAAAATATAACCCCA
* * * * *
1643903 AATACTAAACCTTAAATCTAGAATCTCAAACAC-TAAACCCAAAACATAAAAGCCCAAATCTTAA
1 AACACTAAACCTTAAATCTAAAATCTCAAAC-CTTAAACCCAAAACATAAAAACCCAAACCCTAA
* *
1643967 ACTCAAACATATAAC
65 ACTAAAAAATATAAC
1643982 TTTAAACCCT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
83 65 0.98
84 1 0.02
ACGTcount: A:0.52, C:0.25, G:0.02, T:0.20
Consensus pattern (83 bp):
AACACTAAACCTTAAATCTAAAATCTCAAACCTTAAACCCAAAACATAAAAACCCAAACCCTAAA
CTAAAAAATATAACCCCA
Found at i:1644000 original size:20 final size:19
Alignment explanation
Indices: 1643977--1644035 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1643967 ACTCAAACAT
1643977 ATAACTTTAAACCCTAAACC
1 ATAA-TTTAAACCCTAAACC
1643997 ATAATCTTAAACCCTAAACC
1 ATAAT-TTAAACCCTAAACC
* **
1644017 TTAAGTACAAACCCTAAAC
1 ATAA-TTTAAACCCTAAAC
1644036 TCGAACCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.24
Consensus pattern (19 bp):
ATAATTTAAACCCTAAACC
Found at i:1644192 original size:21 final size:21
Alignment explanation
Indices: 1644168--1644241 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
1644158 CATAACCTTG
1644168 AATCTTAAACCACAAACCCTA
1 AATCTTAAACCACAAACCCTA
* * *
1644189 AATCTAAAAACATAAACCCTA
1 AATCTTAAACCACAAACCCTA
* *
1644210 AA-CTCAAA-CACATAACACTA
1 AATCTTAAACCACA-AACCCTA
*
1644230 AACCCTTAAACC
1 AA-TCTTAAACC
1644242 TTATACCCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.07
20 13 0.31
21 20 0.48
22 5 0.12
23 1 0.02
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18
Consensus pattern (21 bp):
AATCTTAAACCACAAACCCTA
Found at i:1644311 original size:7 final size:7
Alignment explanation
Indices: 1644301--1644327 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1644291 ATAAACCCAT
1644301 AAACCTA
1 AAACCTA
1644308 AAACCTA
1 AAACCTA
1644315 AAACCTA
1 AAACCTA
1644322 AAACCT
1 AAACCT
1644328 TAAATCCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.30, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCTA
Found at i:1644311 original size:15 final size:15
Alignment explanation
Indices: 1644282--1644326 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1644272 AAATTAATAA
1644282 CCATAAA-CTATAAAC
1 CCATAAACCTA-AAAC
1644297 CCATAAACCTAAAAC
1 CCATAAACCTAAAAC
*
1644312 CTA-AAACCTAAAAC
1 CCATAAACCTAAAAC
1644326 C
1 C
1644327 TTAAATCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 12 0.43
15 13 0.46
16 3 0.11
ACGTcount: A:0.53, C:0.31, G:0.00, T:0.16
Consensus pattern (15 bp):
CCATAAACCTAAAAC
Found at i:1644331 original size:15 final size:14
Alignment explanation
Indices: 1644250--1644327 Score: 63
Period size: 14 Copynumber: 5.4 Consensus size: 14
1644240 CCTTATACCC
1644250 AAACTCTAAAACCTA
1 AAAC-CTAAAACCTA
* *
1644265 AACCCTAAAA-TTA
1 AAACCTAAAACCTA
1644278 ATAACC-ATAAA-CTA
1 A-AACCTA-AAACCTA
*
1644292 TAAACCCATAAACCTA
1 -AAACCTA-AAACCTA
1644308 AAACCTAAAACCTA
1 AAACCTAAAACCTA
1644322 AAACCT
1 AAACCT
1644328 TAAATCCTAC
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
13 4 0.08
14 31 0.58
15 15 0.28
16 3 0.06
ACGTcount: A:0.54, C:0.27, G:0.00, T:0.19
Consensus pattern (14 bp):
AAACCTAAAACCTA
Found at i:1644336 original size:29 final size:29
Alignment explanation
Indices: 1644250--1644336 Score: 67
Period size: 29 Copynumber: 3.0 Consensus size: 29
1644240 CCTTATACCC
* *
1644250 AAACTCTAAAACCTAAACCCTAAAAT--TA
1 AAAC-CTAAAACCTAAAACCTTAAATCCTA
*
1644278 ATAACC-ATAAA-CTATAAACCCATAAA-CCTA
1 A-AACCTA-AAACCTA-AAA-CCTTAAATCCTA
1644308 AAACCTAAAACCTAAAACCTTAAATCCTA
1 AAACCTAAAACCTAAAACCTTAAATCCTA
1644337 CTCCTAAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
27 4 0.09
28 13 0.28
29 22 0.48
30 7 0.15
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (29 bp):
AAACCTAAAACCTAAAACCTTAAATCCTA
Found at i:1644783 original size:35 final size:34
Alignment explanation
Indices: 1644683--1644797 Score: 110
Period size: 35 Copynumber: 3.3 Consensus size: 34
1644673 GAACACATTC
* *
1644683 AACCATAAACCCAAACCTTGAATCCTAAACTCAT
1 AACCATAAACCCAAACCTTTAAACCTAAACTCAT
* *
1644717 AACTCAT-AACCCTAAACCATTATACCTTAAACTCA-
1 AAC-CATAAACCC-AAACCTTTAAACC-TAAACTCAT
*
1644752 AACCATAAATCCCAAACCTTTAAACCATAAAC-CTT
1 AACCATAAA-CCCAAACCTTTAAACC-TAAACTCAT
*
1644787 AACCTTAAACC
1 AACCATAAACC
1644798 ATAAACCCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
34 14 0.21
35 41 0.62
36 11 0.17
ACGTcount: A:0.44, C:0.32, G:0.01, T:0.23
Consensus pattern (34 bp):
AACCATAAACCCAAACCTTTAAACCTAAACTCAT
Found at i:1644810 original size:20 final size:20
Alignment explanation
Indices: 1644751--1644815 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
1644741 CCTTAAACTC
1644751 AAACCATAAATCCCAAACCTTT
1 AAACCATAAA-CCCAAACC-TT
**
1644773 AAACCATAAACCTTAACCTT
1 AAACCATAAACCCAAACCTT
*
1644793 AAACCATAAACCCAAACCCT
1 AAACCATAAACCCAAACCTT
1644813 AAA
1 AAA
1644816 TCTAAAATCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 22 0.58
21 6 0.16
22 10 0.26
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.18
Consensus pattern (20 bp):
AAACCATAAACCCAAACCTT
Found at i:1645999 original size:21 final size:22
Alignment explanation
Indices: 1645958--1646000 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1645948 TTAACTATTC
*
1645958 AAATATGATTTATGAGTATTTT
1 AAATATGATTTATGAGAATTTT
1645980 AAATATG-TTTATTGA-AATTTT
1 AAATATGATTTA-TGAGAATTTT
1646001 GTGTATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
AAATATGATTTATGAGAATTTT
Found at i:1646320 original size:33 final size:31
Alignment explanation
Indices: 1646278--1646356 Score: 106
Period size: 30 Copynumber: 2.5 Consensus size: 31
1646268 TAAATTGTTT
1646278 TTGTATTGGTTATTGTCTATCATGTTGTATTAAA
1 TTGT-TTGGTTATTGTCT-T-ATGTTGTATTAAA
*
1646312 TTGTTTGGTCATT-TCTTATGTTGTATTAAA
1 TTGTTTGGTTATTGTCTTATGTTGTATTAAA
*
1646342 TTGTTTGGTTGTTGT
1 TTGTTTGGTTATTGT
1646357 TTGCTTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 24 0.59
31 2 0.05
32 3 0.07
33 8 0.20
34 4 0.10
ACGTcount: A:0.18, C:0.05, G:0.20, T:0.57
Consensus pattern (31 bp):
TTGTTTGGTTATTGTCTTATGTTGTATTAAA
Found at i:1648818 original size:21 final size:21
Alignment explanation
Indices: 1648792--1648843 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1648782 CAAGTGGTTG
1648792 CCCCAACTCAGCAACAGACTA
1 CCCCAACTCAGCAACAGACTA
* * * *
1648813 CCCCAAATCAGTAAGAGACTG
1 CCCCAACTCAGCAACAGACTA
1648834 CCCCAACTCA
1 CCCCAACTCA
1648844 ATAGGAGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.40, G:0.12, T:0.12
Consensus pattern (21 bp):
CCCCAACTCAGCAACAGACTA
Found at i:1649983 original size:15 final size:15
Alignment explanation
Indices: 1649963--1649993 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1649953 TCTCTTCTCT
*
1649963 TCCTCCTTCTCCTTC
1 TCCTCCTCCTCCTTC
1649978 TCCTCCTCCTCCTTC
1 TCCTCCTCCTCCTTC
1649993 T
1 T
1649994 TTTTCTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (15 bp):
TCCTCCTCCTCCTTC
Found at i:1649999 original size:21 final size:22
Alignment explanation
Indices: 1649949--1649999 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1649939 ACATCTCCAT
*
1649949 TTTTTCTCTTCTCTTCCTCCTTC
1 TTTTTCTC-TCTCCTCCTCCTTC
**
1649972 TCCTTCTC-CTCCTCCTCCTTC
1 TTTTTCTCTCTCCTCCTCCTTC
1649993 TTTTTCT
1 TTTTTCT
1650000 TCTTCTTCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 17 0.74
23 6 0.26
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTCTCTCTCCTCCTCCTTC
Found at i:1652609 original size:28 final size:28
Alignment explanation
Indices: 1652559--1652613 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1652549 TAGAATTTAA
*
1652559 TTATTATAAAAATAGTTTAAATTAAATT
1 TTATTATAAAAATAATTTAAATTAAATT
*
1652587 TTATTAT-ATAATAATTTATAATTAAAT
1 TTATTATAAAAATAATTTA-AATTAAAT
1652614 AGACGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
TTATTATAAAAATAATTTAAATTAAATT
Found at i:1652754 original size:21 final size:20
Alignment explanation
Indices: 1652728--1652771 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1652718 TATAAATCAA
1652728 ATTATTAAAAATAATAAAAAT
1 ATTATTAAAAATAA-AAAAAT
* *
1652749 ATTATTTAAAATAAAAATAT
1 ATTATTAAAAATAAAAAAAT
1652769 ATT
1 ATT
1652772 GAATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTATTAAAAATAAAAAAAT
Found at i:1657112 original size:15 final size:15
Alignment explanation
Indices: 1657094--1657125 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1657084 GAAATTGTTC
*
1657094 TAGATGAATTATATA
1 TAGATGAATTACATA
1657109 TAGATGAATTACATA
1 TAGATGAATTACATA
1657124 TA
1 TA
1657126 ATATCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (15 bp):
TAGATGAATTACATA
Found at i:1658016 original size:17 final size:16
Alignment explanation
Indices: 1657976--1658008 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1657966 AACATTTAGC
1657976 AAAAAGAGA-AAACCAA
1 AAAAAGA-ATAAACCAA
1657992 AAAAAGAATAAACCAA
1 AAAAAGAATAAACCAA
1658008 A
1 A
1658009 TTAAAGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.76, C:0.12, G:0.09, T:0.03
Consensus pattern (16 bp):
AAAAAGAATAAACCAA
Found at i:1659825 original size:19 final size:19
Alignment explanation
Indices: 1659798--1659840 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1659788 ATATGTGTTT
* *
1659798 TAATTATAATAAAATAAAG
1 TAATAATAATAAAAGAAAG
1659817 TAATAATAATAAAAGAAAG
1 TAATAATAATAAAAGAAAG
1659836 -AATAA
1 TAATAA
1659841 AGAAAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (19 bp):
TAATAATAATAAAAGAAAG
Found at i:1677505 original size:3 final size:3
Alignment explanation
Indices: 1677485--1677550 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
1677475 TTATGTAAAT
* * * * *
1677485 TAA TAA -AA AAA TAA -AA TAA TAA TGA TAA TGA TAA CAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1677531 TAA TAC TAA TAA TAAA TAA T
1 TAA TAA TAA TAA T-AA TAA T
1677551 CTAGAGTTTG
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1683968 original size:9 final size:9
Alignment explanation
Indices: 1683954--1683990 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1683944 TATAGTTTGA
1683954 TATTCGAAT
1 TATTCGAAT
1683963 TATTCGAAT
1 TATTCGAAT
*
1683972 TATTCGAGT
1 TATTCGAAT
1683981 TATTCGAAT
1 TATTCGAAT
1683990 T
1 T
1683991 CGAAAGCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1684712 original size:106 final size:106
Alignment explanation
Indices: 1684527--1684727 Score: 366
Period size: 106 Copynumber: 1.9 Consensus size: 106
1684517 AAGCTTTAAG
*
1684527 AGGATATTTGGCTATTTAGTAGAACGAGAAATCAAAACCCAGCACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTAGTAGAACGAGAAATCAAAACCCAGCACGTTAGAGCACGTTTTCTCGA
1684592 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
66 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
* * *
1684633 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGAGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTAGTAGAACGAGAAATCAAAACCCAGCACGTTAGAGCACGTTTTCTCGA
1684698 TTTTCCAAACGCGAAATATTGCCTTATTTA
66 TTTTCCAAACGCGAAATATTGCCTTATTTA
1684728 GAAAAATTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 91 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (106 bp):
AGGATATTTGGCTATTTAGTAGAACGAGAAATCAAAACCCAGCACGTTAGAGCACGTTTTCTCGA
TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
Found at i:1685245 original size:38 final size:38
Alignment explanation
Indices: 1685186--1685291 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
1685176 TATTTTTAAG
*
1685186 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
1685223 AATATGTATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
1685261 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
1685292 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:1685634 original size:22 final size:23
Alignment explanation
Indices: 1685578--1685634 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
1685568 AGTTTAAAAT
1685578 AAAATATATAAAAGAAAGTCTTA
1 AAAATATATAAAAGAAAGTCTTA
*
1685601 AATAATA-A-AAAAGACAGT-TTA
1 AA-AATATATAAAAGAAAGTCTTA
1685622 AAAATATATAAAA
1 AAAATATATAAAA
1685635 ATAGTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 13 0.43
23 3 0.10
24 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAATATATAAAAGAAAGTCTTA
Found at i:1686372 original size:13 final size:13
Alignment explanation
Indices: 1686354--1686378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1686344 AAATGCGTAG
1686354 ATAAATAAATGAA
1 ATAAATAAATGAA
1686367 ATAAATAAATGA
1 ATAAATAAATGA
1686379 TAGATGATAA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
ATAAATAAATGAA
Found at i:1691357 original size:18 final size:19
Alignment explanation
Indices: 1691336--1691415 Score: 60
Period size: 21 Copynumber: 4.2 Consensus size: 19
1691326 GAAAAACCTT
1691336 AAAAATA-ATTAAAAATAA
1 AAAAATACATTAAAAATAA
* * *
1691354 AAAATTACA--AAGAATTA
1 AAAAATACATTAAAAATAA
*
1691371 AAAAATAACATTATAAAATTA
1 AAAAAT-ACATTA-AAAATAA
1691392 AAAAATA-ATATAAAATATAA
1 AAAAATACAT-TAAAA-ATAA
1691412 AAAA
1 AAAA
1691416 TTTACTAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
17 11 0.22
18 9 0.18
19 6 0.12
20 11 0.22
21 12 0.24
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (19 bp):
AAAAATACATTAAAAATAA
Found at i:1691424 original size:19 final size:18
Alignment explanation
Indices: 1691336--1691416 Score: 76
Period size: 18 Copynumber: 4.3 Consensus size: 18
1691326 GAAAAACCTT
*
1691336 AAAAATAAT-TAAAAATA
1 AAAAATAATATAAAATTA
* *
1691353 AAAAATTACA-AAGAATTA
1 AAAAATAATATAA-AATTA
1691371 AAAAATAACATTATAAAATTA
1 AAAAAT-A-A-TATAAAATTA
1691392 AAAAATAATATAAAATATA
1 AAAAATAATATAAAAT-TA
1691411 AAAAAT
1 AAAAAT
1691417 TTACTAAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
17 9 0.17
18 18 0.35
19 9 0.17
20 2 0.04
21 12 0.23
22 2 0.04
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.25
Consensus pattern (18 bp):
AAAAATAATATAAAATTA
Found at i:1691660 original size:26 final size:26
Alignment explanation
Indices: 1691626--1691677 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1691616 ATTATTTAAA
*
1691626 TAATGAAAATAATGTTATTTATTATT
1 TAATGAAAATAATATTATTTATTATT
* *
1691652 TAATTAAAATAATATTATTTTTTATT
1 TAATGAAAATAATATTATTTATTATT
1691678 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (26 bp):
TAATGAAAATAATATTATTTATTATT
Found at i:1692951 original size:9 final size:9
Alignment explanation
Indices: 1692920--1692944 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1692910 TTCCTGTTTC
1692920 TTTTTTTTA
1 TTTTTTTTA
1692929 TTTTTTTTA
1 TTTTTTTTA
1692938 TTTTTTT
1 TTTTTTT
1692945 CTCTTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1693388 original size:3 final size:3
Alignment explanation
Indices: 1693380--1693429 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1693370 GAATTAGTCC
1693380 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
1693428 TA
1 TA
1693430 CCTATTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1693918 original size:22 final size:23
Alignment explanation
Indices: 1693865--1693918 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
1693855 AAATATACTT
*
1693865 TATATATTTTGTTAATTCATGTA
1 TATATATATTGTTAATTCATGTA
* * * *
1693888 TACACATATT-TTAGTTCATGTC
1 TATATATATTGTTAATTCATGTA
1693910 TATATATAT
1 TATATATAT
1693919 CTTTTATACT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (23 bp):
TATATATATTGTTAATTCATGTA
Found at i:1701415 original size:19 final size:19
Alignment explanation
Indices: 1701391--1701427 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1701381 ATTATTTTAT
1701391 TTTATTAC-ACTTTAAAAAA
1 TTTATTACTAC-TTAAAAAA
1701410 TTTATTACTACTTAAAAA
1 TTTATTACTACTTAAAAA
1701428 GAAAATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTATTACTACTTAAAAAA
Found at i:1702870 original size:14 final size:16
Alignment explanation
Indices: 1702851--1702885 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1702841 AATAAAAGAA
1702851 ATAT-ATATAAACATAT
1 ATATAATATAAA-ATAT
1702867 ATATAATATAAAATAT
1 ATATAATATAAAATAT
1702883 ATA
1 ATA
1702886 AAAGTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATAATATAAAATAT
Found at i:1703407 original size:18 final size:18
Alignment explanation
Indices: 1703362--1703410 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1703352 GATAATAACC
1703362 ATAATAATAAATAATATA
1 ATAATAATAAATAATATA
*
1703380 ACAATAATAAATAATGAT-
1 ATAATAATAAATAAT-ATA
*
1703398 ATAATGATAAATA
1 ATAATAATAAATA
1703411 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (18 bp):
ATAATAATAAATAATATA
Found at i:1703407 original size:21 final size:21
Alignment explanation
Indices: 1703345--1703401 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1703335 ATGAATATAG
*
1703345 AAATAATGATAATAACCATAAT
1 AAATAATGAT-ATAACAATAAT
*
1703367 -AATAAATAATATAACAATAAT
1 AAAT-AATGATATAACAATAAT
1703388 AAATAATGATATAA
1 AAATAATGATATAA
1703402 TGATAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (21 bp):
AAATAATGATATAACAATAAT
Found at i:1705056 original size:89 final size:89
Alignment explanation
Indices: 1704939--1705523 Score: 967
Period size: 89 Copynumber: 6.6 Consensus size: 89
1704929 TTAGGGAGAT
* *
1704939 AAGATCT-GTAATCT-TCGATCTACTTCACGGCAGTACATGAAGACAAGATCTATTTTCTTCGAT
1 AAGATCTGGT-ATCTCT-GATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGAT
* *
1705002 CTGCTTTGCCACCAGTATGGGAAGAC
64 CTGCTTCGCCACCAGTATGGGAAGGC
* * *
1705028 AAGATCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTCGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
* *
1705093 ACTTTGCCACCAGTATGGGAAGGC
66 GCTTCGCCACCAGTATGGGAAGGC
* **
1705117 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGATAAGATCTGCTTTCTTTGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
1705182 GCTTCGCCACCAGTATGGGAAGGC
66 GCTTCGCCACCAGTATGGGAAGGC
*
1705206 AAGATCTGGTATCTCTGATCCACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
*
1705271 GCTTCGCCACCGGTATGGGAAGGC
66 GCTTCGCCACCAGTATGGGAAGGC
1705295 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
* *
1705360 GCTTCGCCACCGGTATGGGAATGC
66 GCTTCGCCACCAGTATGGGAAGGC
1705384 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
* *
1705449 ACTTCGCCACCGGTATGGGAAGGC
66 GCTTCGCCACCAGTATGGGAAGGC
*
1705473 AAGATCTGGTATCACTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
1 AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCT
1705524 GCTGCTTTTC
Statistics
Matches: 472, Mismatches: 22, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
89 470 1.00
90 2 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (89 bp):
AAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTCTTTGATCT
GCTTCGCCACCAGTATGGGAAGGC
Found at i:1708434 original size:16 final size:16
Alignment explanation
Indices: 1708413--1708544 Score: 92
Period size: 16 Copynumber: 8.4 Consensus size: 16
1708403 TTTGGTTGGC
*
1708413 TGTAATGAAATAGAGG
1 TGTAATGGAATAGAGG
*
1708429 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
1708445 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
* *****
1708461 CGTAATAGGTAATTCTTT
1 TGTAAT-GG-AATAGAGG
* * *
1708479 TGT-TTGG--TTGA-A
1 TGTAATGGAATAGAGG
*
1708491 TGGAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
1708507 TGTAATGGAATAGATG
1 TGTAATGGAATAGAGG
1708523 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
1708539 CGTAAT
1 TGTAAT
1708545 AGGTAATTCT
Statistics
Matches: 88, Mismatches: 22, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
12 2 0.02
13 5 0.06
15 3 0.03
16 70 0.80
17 3 0.03
18 5 0.06
ACGTcount: A:0.35, C:0.02, G:0.32, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:1708530 original size:78 final size:78
Alignment explanation
Indices: 1708401--1708591 Score: 328
Period size: 78 Copynumber: 2.4 Consensus size: 78
1708391 TTTAAGGGCA
** * *
1708401 TGTTTGGTTGGCTGTAATGAAATAGAGGTGTAATGGAATAGATGTGTAATGGAATAGAGGCGTAA
1 TGTTTGGTTGAATGGAATGGAATAGAGGTGTAATGGAATAGATGTGTAATGGAATAGAGGCGTAA
1708466 TAGGTAATTCTTT
66 TAGGTAATTCTTT
1708479 TGTTTGGTTGAATGGAATGGAATAGAGGTGTAATGGAATAGATGTGTAATGGAATAGAGGCGTAA
1 TGTTTGGTTGAATGGAATGGAATAGAGGTGTAATGGAATAGATGTGTAATGGAATAGAGGCGTAA
1708544 TAGGTAATTCTTT
66 TAGGTAATTCTTT
* *
1708557 TGTTTGGTTGAATGGAATGGAATAAAGGCGTAATG
1 TGTTTGGTTGAATGGAATGGAATAGAGGTGTAATG
1708592 ATATTATTGT
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 107 1.00
ACGTcount: A:0.31, C:0.03, G:0.32, T:0.34
Consensus pattern (78 bp):
TGTTTGGTTGAATGGAATGGAATAGAGGTGTAATGGAATAGATGTGTAATGGAATAGAGGCGTAA
TAGGTAATTCTTT
Found at i:1708799 original size:18 final size:17
Alignment explanation
Indices: 1708778--1708812 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1708768 TTATTATTAA
*
1708778 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
1708796 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
1708813 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:1708824 original size:15 final size:16
Alignment explanation
Indices: 1708804--1708833 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1708794 ATATATAATT
1708804 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
1708819 TAATAAATATTCTTA
1 TAATAAATATTCTTA
1708834 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:1713594 original size:16 final size:16
Alignment explanation
Indices: 1713573--1713625 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
1713563 TTGGTTCGCT
1713573 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
1713589 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
1713605 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
1713621 GTAAT
1 GTAAT
1713626 AGGTAATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.38, C:0.06, G:0.34, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:1713694 original size:44 final size:46
Alignment explanation
Indices: 1713607--1713699 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 46
1713597 ATAGATGCGT
*
1713607 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
1713653 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
1713697 AAT
1 AAT
1713700 AGAGGTGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 24 0.52
45 3 0.07
46 19 0.41
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:1713695 original size:39 final size:44
Alignment explanation
Indices: 1713607--1713712 Score: 141
Period size: 39 Copynumber: 2.5 Consensus size: 44
1713597 ATAGATGCGT
*
1713607 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
1713653 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
*
1713692 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
1713713 CATAAGTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
39 19 0.33
40 2 0.04
43 1 0.02
44 13 0.23
45 3 0.05
46 19 0.33
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:1713922 original size:59 final size:57
Alignment explanation
Indices: 1713858--1714039 Score: 151
Period size: 54 Copynumber: 3.1 Consensus size: 57
1713848 ATTATTATTA
*
1713858 AATATAATTTAATAAAATTCTTAGTATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATAATTTAATAAAATTCTTA-TA-TAATTATTCTTATATGAATTTACTAAAATCAT
* * * * *
1713917 AATATATAATACTATAAAATATAATT-TAAAATAATTATTATTAAATAT-AATTTAATAAAA--A
1 -A-ATATAAT--T-T--AATAAAATTCTTATATAATTATTCTT--ATATGAATTTACTAAAATCA
1713978 T
57 T
*
1713979 -ATATAATTTAATAAAATTC-AATATAATTATTCTTATATGAATTTACTAAAATCAT
1 AATATAATTTAATAAAATTCTTATATAATTATTCTTATATGAATTTACTAAAATCAT
*
1714034 ATTATA
1 AATATA
1714040 TAATCTATAA
Statistics
Matches: 98, Mismatches: 11, Indels: 30
0.71 0.08 0.22
Matches are distributed among these distances:
52 4 0.04
53 11 0.11
54 21 0.21
55 2 0.02
56 5 0.05
57 1 0.01
59 7 0.07
60 1 0.01
61 7 0.07
62 2 0.02
63 10 0.10
64 13 0.13
65 6 0.06
66 8 0.08
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (57 bp):
AATATAATTTAATAAAATTCTTATATAATTATTCTTATATGAATTTACTAAAATCAT
Found at i:1713996 original size:10 final size:10
Alignment explanation
Indices: 1713934--1714006 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
1713924 AATACTATAA
1713934 AATATAATTT
1 AATATAATTT
*
1713944 AAAATAA-TT
1 AATATAATTT
*
1713953 -AT-T-ATTA
1 AATATAATTT
1713960 AATATAATTT
1 AATATAATTT
**
1713970 AATA-AAAAT
1 AATATAATTT
1713979 -ATATAATTT
1 AATATAATTT
* *
1713988 AATAAAATTC
1 AATATAATTT
1713998 AATATAATT
1 AATATAATT
1714007 ATTCTTATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 6 0.13
9 9 0.20
10 28 0.61
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATAATTT
Found at i:1715761 original size:4 final size:4
Alignment explanation
Indices: 1715752--1715782 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1715742 GATGTTCATA
*
1715752 TATG TATG TATG TATG CATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
1715783 TTGGTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:1726048 original size:5 final size:6
Alignment explanation
Indices: 1726031--1726055 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1726021 ACTTTAAAAA
1726031 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
1726056 TTAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:1727853 original size:17 final size:18
Alignment explanation
Indices: 1727819--1727860 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1727809 AAATTTTAAA
*
1727819 ATTAAAAATATATGAATT
1 ATTAAAAATAAATGAATT
1727837 ATTAAAAATAAAT-AATT
1 ATTAAAAATAAATGAATT
1727854 ATTAAAA
1 ATTAAAA
1727861 TTATTTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTAAAAATAAATGAATT
Found at i:1727922 original size:17 final size:17
Alignment explanation
Indices: 1727900--1727933 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1727890 AAAAGAATAA
1727900 TTTAAAA-TAATTTAATT
1 TTTAAAATTAA-TTAATT
1727917 TTTAAAATTAATTAATT
1 TTTAAAATTAATTAATT
1727934 GCTAACGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAAATTAATTAATT
Found at i:1728928 original size:46 final size:46
Alignment explanation
Indices: 1728829--1728990 Score: 260
Period size: 46 Copynumber: 3.6 Consensus size: 46
1728819 TACGTATGAT
1728829 CACTTATCACTTGTC-C-C-TGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTT-TCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
1728872 CACTTATCACTTTGTCACTTAATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
1728918 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1728964 CACTTATCACTTTCTCACTTGATCAGA
1 CACTTATCACTTTCTCACTTGATCAGA
1728991 AGTACTCAAA
Statistics
Matches: 110, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
42 1 0.01
43 13 0.12
44 1 0.01
45 18 0.16
46 77 0.70
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:1734708 original size:3 final size:3
Alignment explanation
Indices: 1734700--1734728 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1734690 TTAAGGAATT
1734700 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1734729 TTCTTCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:1737328 original size:20 final size:20
Alignment explanation
Indices: 1737303--1737341 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1737293 AAAAATAAAG
**
1737303 AGAAAATAATGTAAAAGAAA
1 AGAAAATAAAATAAAAGAAA
1737323 AGAAAATAAAATAAAAGAA
1 AGAAAATAAAATAAAAGAA
1737342 TTAAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (20 bp):
AGAAAATAAAATAAAAGAAA
Found at i:1737332 original size:15 final size:15
Alignment explanation
Indices: 1737294--1737341 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1737284 GAAGAAAGAA
*
1737294 AAAATAAAGAGAAAAT
1 AAAATAAA-AGAAAAG
**
1737310 AATGTAAAAGAAAAG
1 AAAATAAAAGAAAAG
*
1737325 AAAATAAAATAAAAG
1 AAAATAAAAGAAAAG
1737340 AA
1 AA
1737342 TTAAAATATT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 20 0.77
16 6 0.23
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAATAAAAGAAAAG
Found at i:1740818 original size:44 final size:43
Alignment explanation
Indices: 1740722--1741062 Score: 118
Period size: 44 Copynumber: 7.8 Consensus size: 43
1740712 ATCTGATGTG
* * * *
1740722 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATTTCAGAGAGATAAGAT-CTTTATTTCA
* * *
1740766 ATCCGCTCCACTGTAATTTCAGGGAGATAGGAT-TATTATCTTCA
1 ATCTGCTCCACTGTAATTTCAGAGAGATAAGATCT-TTAT-TTCA
* * * *
1740810 ATCTGCTCCGCTGTAATCTT-AGAGAGATAATACCTGAATT-TCTTCG
1 ATCTGCTCCACTGTAAT-TTCAGAGAGATAAGATCT---TTAT-TTCA
* * ** * *** * *
1740856 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-CCAGA-TGCG
1 ATCTGCTCCACTGTAATTTCAGAGAGATAAGATCTTTATTTCA
* * ** ** *
1740897 ATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAAATTTTA
1 ATCTGCTCCACTGTAATTTCAGAGAGATAAGAT-CTTTATTTCA
* * * * * * * **
1740941 AGCCGCTCCACTGTAACTTCAGGGAGATAAGATAGTGT-CTTGG
1 ATCTGCTCCACTGTAATTTCAGAGAGATAAGAT-CTTTATTTCA
* * * * ***
1740984 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATATCTGGCTTCA
1 ATCTGCTCCACTGTAATTTCAGAGAGATAAGATCT-TTATTTCA
** *
1741028 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT
1 ATCTGCTCCACTGTAATTTCAGAGAGATAAGATCT
1741063 GAAATTCTTC
Statistics
Matches: 225, Mismatches: 59, Indels: 26
0.73 0.19 0.08
Matches are distributed among these distances:
41 32 0.14
42 2 0.01
43 37 0.16
44 118 0.52
45 5 0.02
46 28 0.12
47 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (43 bp):
ATCTGCTCCACTGTAATTTCAGAGAGATAAGATCTTTATTTCA
Found at i:1741006 original size:43 final size:43
Alignment explanation
Indices: 1740945--1741060 Score: 153
Period size: 44 Copynumber: 2.7 Consensus size: 43
1740935 ATTTTAAGCC
* * **
1740945 GCTCCACTGTAACTTCAGGGAGATAAGATA-GTGTCTTGGATCT
1 GCTCCACTGTAAC-TCAGGGAGATAAGATATCTGGCTTCAATCT
*
1740988 GCTCCGCTGTAATCTCAGGGAGATAAGATATCTGGCTTCAATCT
1 GCTCCACTGTAA-CTCAGGGAGATAAGATATCTGGCTTCAATCT
1741032 GCTCCACTGTAACCTCAGGGAGATAAGAT
1 GCTCCACTGTAA-CTCAGGGAGATAAGAT
1741061 CTGAAATTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
43 27 0.42
44 37 0.58
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (43 bp):
GCTCCACTGTAACTCAGGGAGATAAGATATCTGGCTTCAATCT
Found at i:1741011 original size:87 final size:87
Alignment explanation
Indices: 1740732--1741059 Score: 256
Period size: 87 Copynumber: 3.8 Consensus size: 87
1740722 ATCTACTCTA
** * ** *
1740732 CTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATTTCAGGGAGATAG
1 CTGTAATC-TCAGAGAGATAAGATCCTAAATTTTAAGCCGCTCCACTGTAACCTCAGGGAGATAA
* * * *
1740796 GATTATTATCTTCAATCTGCTCCG
65 GACTAGTGTCTT-GATCTGCTCCG
* * * ** **
1740820 CTGTAATCTTAGAGAGATAATA-CCTGAATTTCTTCGGTCTACTCCACTGTAACCTCAGGGAGAT
1 CTGTAATCTCAGAGAGATAAGATCCT-AAATT-TTAAG-CCGCTCCACTGTAACCTCAGGGAGAT
* * **
1740884 AAGACCAGATG-C--GATCTACTCTA
63 AAGACTAG-TGTCTTGATCTGCTCCG
* *
1740907 CTGTAACCTCAGAGAGATAAGATCCTAAATTTTAAGCCGCTCCACTGTAACTTCAGGGAGATAAG
1 CTGTAATCTCAGAGAGATAAGATCCTAAATTTTAAGCCGCTCCACTGTAACCTCAGGGAGATAAG
1740972 A-TAGTGTCTTGGATCTGCTCCG
66 ACTAGTGTCTT-GATCTGCTCCG
* * *** * * *
1740994 CTGTAATCTCAGGGAGATAAGATATCT-GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAA
1 CTGTAATCTCAGAGAGATAAGAT-CCTAAATTTTAAGCCGCTCCACTGTAACCTCAGGGAGATAA
1741058 GA
65 GA
1741060 TCTGAAATTC
Statistics
Matches: 185, Mismatches: 44, Indels: 23
0.73 0.17 0.09
Matches are distributed among these distances:
83 2 0.01
84 3 0.02
85 27 0.15
86 3 0.02
87 94 0.51
88 25 0.14
89 3 0.02
90 27 0.15
91 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (87 bp):
CTGTAATCTCAGAGAGATAAGATCCTAAATTTTAAGCCGCTCCACTGTAACCTCAGGGAGATAAG
ACTAGTGTCTTGATCTGCTCCG
Found at i:1753376 original size:22 final size:24
Alignment explanation
Indices: 1753338--1753386 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
1753328 GTGTATATGT
*
1753338 ATATGTATTTACTAAAA-TA-AAA
1 ATATGTATGTACTAAAAGTATAAA
1753360 ATATGTATGTA-TAAAAAGTATAAA
1 ATATGTATGTACT-AAAAGTATAAA
1753384 ATA
1 ATA
1753387 CAAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.61
23 2 0.09
24 6 0.26
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (24 bp):
ATATGTATGTACTAAAAGTATAAA
Found at i:1754519 original size:21 final size:20
Alignment explanation
Indices: 1754467--1754519 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
1754457 AAACAAGTAA
*
1754467 AAAATAAAAA-ATAAAAAGG
1 AAAAGAAAAAGATAAAAAGG
*
1754486 AAAATAAAGAAGATAAAAAGCG
1 AAAAGAAA-AAGATAAAAAG-G
*
1754508 AATAGAAAAAGA
1 AAAAGAAAAAGA
1754520 ATTGGAATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 8 0.28
20 2 0.07
21 12 0.41
22 7 0.24
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.09
Consensus pattern (20 bp):
AAAAGAAAAAGATAAAAAGG
Found at i:1756640 original size:12 final size:12
Alignment explanation
Indices: 1756623--1756648 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1756613 AAGGATGATA
1756623 CCATTAGAGTTC
1 CCATTAGAGTTC
1756635 CCATTAGAGTTC
1 CCATTAGAGTTC
1756647 CC
1 CC
1756649 GAGCTAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (12 bp):
CCATTAGAGTTC
Found at i:1759288 original size:31 final size:31
Alignment explanation
Indices: 1759250--1759319 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
1759240 GTTAGAAGCC
*
1759250 CTCAAATGTAATTTATATATTGCATCAAATG
1 CTCAAATGTAATCTATATATTGCATCAAATG
1759281 CTCAAATGTAATCTATATATTGCATCAAATG
1 CTCAAATGTAATCTATATATTGCATCAAATG
1759312 CTCAAATG
1 CTCAAATG
1759320 CATCCTTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.36
Consensus pattern (31 bp):
CTCAAATGTAATCTATATATTGCATCAAATG
Found at i:1761541 original size:37 final size:39
Alignment explanation
Indices: 1761483--1761585 Score: 101
Period size: 37 Copynumber: 2.7 Consensus size: 39
1761473 AAAAATAATT
* * *
1761483 TTATTTTAATAGTTTAATATTAAATTTGAT-TT-AA-TAC
1 TTATCTTAATAGTTTAATATT-AATTTAATATTAAAGTAA
*
1761520 TTATCTTAATAGTATT-TTATTAATTTAATATTAAAGTAA
1 TTATCTTAATAGT-TTAATATTAATTTAATATTAAAGTAA
*
1761559 TTATCTTAATA-TTAAAT-TTAATTTAAT
1 TTATCTTAATAGTTTAATATTAATTTAAT
1761586 GTTTATCTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
36 7 0.13
37 29 0.53
38 6 0.11
39 13 0.24
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (39 bp):
TTATCTTAATAGTTTAATATTAATTTAATATTAAAGTAA
Found at i:1761633 original size:62 final size:59
Alignment explanation
Indices: 1761564--1761680 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
1761554 AGTAATTATC
* * * *
1761564 TTAATATTAAATTTAATTTAATGTTTATCTTGTTGATAAATATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-TT-ATAAATATTATATTAATTTAATAAGAT
1761626 TTAATATTAAATTTAATCTAATATTTATCTTTATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTTATAAATATTATATTAATTTAATA
1761681 TTAAAATGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 21 0.41
60 2 0.04
61 1 0.02
62 27 0.53
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTTATAAATATTATATTAATTTAATAAGAT
Found at i:1763981 original size:20 final size:20
Alignment explanation
Indices: 1763950--1764003 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1763940 TTTTATAATG
1763950 AAATATTAAAAATATTTAAATT
1 AAATA-TAAAAATA-TTAAATT
*
1763972 AAA-ATAAAAATATTAATTT
1 AAATATAAAAATATTAAATT
*
1763991 AAATTTAAAAATA
1 AAATATAAAAATA
1764004 CCTTATTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.31
20 16 0.55
21 1 0.03
22 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATAAAAATATTAAATT
Found at i:1765584 original size:33 final size:33
Alignment explanation
Indices: 1765532--1765611 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1765522 TCATCACCCA
* *
1765532 GTAGAAGGTTTTTATACCCTTCTTCTTTCTCCC
1 GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
1765565 GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
1 GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
*
1765598 GAAGAAGGTGTTTA
1 GTAGAAGGTGTTTA
1765612 TTTATACCCT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (33 bp):
GTAGAAGGTGTTTAAACCCTTCTTCTTTCTCCC
Found at i:1770713 original size:24 final size:23
Alignment explanation
Indices: 1770655--1770743 Score: 90
Period size: 24 Copynumber: 3.7 Consensus size: 23
1770645 AATTTGTGTT
* *
1770655 TTATTATTTTAAGTTCATTATGTA
1 TTATTGTTTTAAATT-ATTATGTA
*
1770679 -TGTTGTTTTAAATCTATTATGTA
1 TTATTGTTTTAAAT-TATTATGTA
*
1770702 TTATTGTTTTAAAATTATTGTGTA
1 TTATTGTTTT-AAATTATTATGTA
*
1770726 TTATTATTTTAAAGTTAT
1 TTATTGTTTTAAA-TTAT
1770744 CTCATATTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
23 21 0.38
24 30 0.55
25 4 0.07
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.58
Consensus pattern (23 bp):
TTATTGTTTTAAATTATTATGTA
Found at i:1774507 original size:57 final size:56
Alignment explanation
Indices: 1774411--1774608 Score: 249
Period size: 50 Copynumber: 3.7 Consensus size: 56
1774401 TGAGTACTTC
*
1774411 TGATCAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACAAGTGACAAG
1 TGATAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGA-TAGTGACAAGTGACAAG
1774469 TGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTG--A-T--C-AGTGACAAG
1 TGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATAGTGACAAGTGACAAG
* *
1774519 TGACAAGTGATCAGTGGTAGCTTAGCTACACTTATCTG--A-T--C-AGTGACAAG
1 TGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATAGTGACAAGTGACAAG
* *
1774569 TAACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGAT
1 TGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGAT
1774609 CAGAGATAAT
Statistics
Matches: 133, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
50 93 0.70
51 1 0.01
53 1 0.01
54 1 0.01
57 17 0.13
58 20 0.15
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.30
Consensus pattern (56 bp):
TGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATAGTGACAAGTGACAAG
Found at i:1774520 original size:50 final size:50
Alignment explanation
Indices: 1774460--1774611 Score: 277
Period size: 50 Copynumber: 3.0 Consensus size: 50
1774450 ATTAGTGACA
*
1774460 AGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
1 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
*
1774510 AGTGACAAGTGACAAGTGATCAGTGGTAGCTTAGCTACACTTATCTGATC
1 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
*
1774560 AGTGACAAGTAACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
1 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
1774610 AG
1 AG
1774612 AGATAATAGA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 98 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (50 bp):
AGTGACAAGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
Found at i:1774630 original size:50 final size:51
Alignment explanation
Indices: 1774460--1774634 Score: 268
Period size: 50 Copynumber: 3.5 Consensus size: 51
1774450 ATTAGTGACA
*
1774460 AGTGACAAGT-GATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
1 AGTGACAAGTAGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
*
1774510 AGTGACAAGT-GACAAGTGATCAGTGGTAGCTTAGCTACACTTATCTGATC
1 AGTGACAAGTAGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
1774560 AGTGACAAGTA-ACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
1 AGTGACAAGTAGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
* * * *
1774610 AGAGATAA-TAGATAAATGATAAGTG
1 AGTGACAAGTAGACAAGTGATAAGTG
1774635 ATTCTGTGTA
Statistics
Matches: 116, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
49 2 0.02
50 114 0.98
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTAGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC
Found at i:1777268 original size:15 final size:15
Alignment explanation
Indices: 1777239--1777289 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1777229 ATAATAAACA
*
1777239 AAACATAAAATAAAAG
1 AAAC-TAAAAGAAAAG
*
1777255 AAAGTAAAAGAAAAG
1 AAACTAAAAGAAAAG
*
1777270 AAACAAAGAAGAAAAG
1 AAACTAA-AAGAAAAG
1777286 AAAC
1 AAAC
1777290 AGAGAAGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 15 0.50
16 15 0.50
ACGTcount: A:0.75, C:0.06, G:0.14, T:0.06
Consensus pattern (15 bp):
AAACTAAAAGAAAAG
Found at i:1777283 original size:16 final size:16
Alignment explanation
Indices: 1777262--1777307 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
1777252 AAGAAAGTAA
1777262 AAGAAAAGAAACAAAG
1 AAGAAAAGAAACAAAG
*
1777278 AAGAAAAGAAACAGAG
1 AAGAAAAGAAACAAAG
*
1777294 AAGCAAACGAAACA
1 AAG-AAAAGAAACA
1777308 TCGGAAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.70, C:0.11, G:0.20, T:0.00
Consensus pattern (16 bp):
AAGAAAAGAAACAAAG
Found at i:1777980 original size:3 final size:3
Alignment explanation
Indices: 1777972--1778007 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1777962 GTGAGGTAAG
1777972 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
1778008 GAGTGAGATT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1778316 original size:36 final size:37
Alignment explanation
Indices: 1778255--1778327 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
1778245 GAATATTGAC
* * *
1778255 TTGAAAATGGAAAAGTGAATTTTGAATCGAATTGTGA
1 TTGAAAATGAAAAAGTGAATATTGAATCGAAATGTGA
* *
1778292 TTGAAAGTGAAAAAGTGAA-ATTGAATTGAAATGTGA
1 TTGAAAATGAAAAAGTGAATATTGAATCGAAATGTGA
1778328 ATTTGGAGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
36 14 0.45
37 17 0.55
ACGTcount: A:0.44, C:0.01, G:0.25, T:0.30
Consensus pattern (37 bp):
TTGAAAATGAAAAAGTGAATATTGAATCGAAATGTGA
Found at i:1781042 original size:16 final size:17
Alignment explanation
Indices: 1781008--1781048 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
1780998 ATTATTTTAA
1781008 ATTTT-ATTAAATCATAT
1 ATTTTAATTAAA-CATAT
1781025 ATTTTAATTAAA-ATAT
1 ATTTTAATTAAACATAT
1781041 A-TTTAATT
1 ATTTTAATT
1781049 TTAATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 5 0.22
18 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTAATTAAACATAT
Found at i:1781119 original size:66 final size:65
Alignment explanation
Indices: 1781049--1781360 Score: 176
Period size: 61 Copynumber: 5.1 Consensus size: 65
1781039 ATATTTAATT
1781049 TTAATTATTTAAAATTATCTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
1 TTAATTATTTAAAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
1781114 A
65 A
* * * * **
1781115 TTAATTA-TTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TTAAT
1 TTAATTATTTAA-AATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAAT
1781168 A
65 A
* * *
1781169 ATAATTATGTT-AATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAA
1 TTAATTAT-TTAAAATTAT-TTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAA
1781233 TA
64 TA
* * * * * * * * **
1781235 TTGATTA-TTAAGAATT-TTATTA-A--ATTATATATTTTAATTAT-AATATATTTA-ATAATTA
1 TTAATTATTTAA-AATTATTTTTATAGTATAATATATTATGATT-TGAGTAAATTCATATAAGAA
*
1781293 TG
64 TA
*
1781295 TT-A--ATTT---A-TA-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TTAATTATTTAAAATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATA
*
1781352 TTGATTATT
1 TTAATTATT
1781361 AAGAATTTTA
Statistics
Matches: 181, Mismatches: 37, Indels: 62
0.65 0.13 0.22
Matches are distributed among these distances:
53 5 0.03
54 15 0.08
55 7 0.04
56 27 0.15
57 12 0.07
58 4 0.02
59 11 0.06
60 19 0.10
61 30 0.17
62 2 0.01
63 4 0.02
64 11 0.06
65 11 0.06
66 23 0.13
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (65 bp):
TTAATTATTTAAAATTATTTTTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATA
Found at i:1781131 original size:120 final size:120
Alignment explanation
Indices: 1781007--1781416 Score: 702
Period size: 120 Copynumber: 3.4 Consensus size: 120
1780997 AATTATTTTA
* * * *
1781007 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATTTTAATTAT-TTAAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTT-AATTTATATTT
* *
1781071 TATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
1781127 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTTAATTTATATTTT
1781192 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
1781247 AATTTTATTAAATTATATATTTTAATTATAATATATTT-A--ATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTTAATTTATATTTT
1781309 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
1781364 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTT
1781417 TAAATATGAT
Statistics
Matches: 277, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
117 115 0.42
118 1 0.00
119 1 0.00
120 158 0.57
121 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:1781167 original size:15 final size:15
Alignment explanation
Indices: 1781132--1781183 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1781122 TTAAGAATTT
*
1781132 TATTAAATTAT-ATA
1 TATTTAATTATAATA
1781146 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
1781160 TATTTAATAATAAT-
1 TATTTAATTATAATA
1781174 TATGTTAATT
1 TAT-TTAATT
1781184 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:1781393 original size:18 final size:18
Alignment explanation
Indices: 1781365--1781413 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
1781355 ATTATTAAGA
1781365 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
1781382 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
1781398 A-TTTAATTATAATTAT
1 ATTTTAATTA-AATTAT
1781414 GTTTAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 5 0.18
18 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:1781399 original size:16 final size:16
Alignment explanation
Indices: 1781365--1781419 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
1781355 ATTATTAAGA
1781365 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
1781382 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
1781398 A-TTTAATTATAAT-T
1 ATTTTAATTAAAATAT
1781412 ATGTTTAA
1 AT-TTTAA
1781420 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:1781629 original size:44 final size:45
Alignment explanation
Indices: 1781564--1781654 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1781554 ACCTCTATTC
* * *
1781564 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
1781608 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
1781653 CA
1 CA
1781655 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:1781669 original size:17 final size:16
Alignment explanation
Indices: 1781635--1781687 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
1781625 GATTAGCTAT
1781635 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1781651 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
1781668 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1781684 TACA
1 TACA
1781688 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1782820 original size:24 final size:24
Alignment explanation
Indices: 1782791--1782862 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
1782781 TTCAACTTCG
1782791 GCTTTTCATCTTCTACTCCATCGA
1 GCTTTTCATCTTCTACTCCATCGA
*
1782815 GCTTTTCATCTTCTAATCCATCGA
1 GCTTTTCATCTTCTACTCCATCGA
*
1782839 GCTTTTCATCTTCTACTTCATCGA
1 GCTTTTCATCTTCTACTCCATCGA
1782863 CAGCTCCTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.18, C:0.31, G:0.08, T:0.43
Consensus pattern (24 bp):
GCTTTTCATCTTCTACTCCATCGA
Found at i:1790382 original size:33 final size:33
Alignment explanation
Indices: 1790327--1790419 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1790317 CAATCATCAC
1790327 CCAGTAGAAGGTATTTATACCCTTCTTCTTTCT
1 CCAGTAGAAGGTATTTATACCCTTCTTCTTTCT
* * *
1790360 CCCGTAGAAGGTGTTTAAACCCTTCTTCTTTCT
1 CCAGTAGAAGGTATTTATACCCTTCTTCTTTCT
1790393 CCAGTAGAAGGTATTTATACCCTTCTT
1 CCAGTAGAAGGTATTTATACCCTTCTT
1790420 TCTAACTTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (33 bp):
CCAGTAGAAGGTATTTATACCCTTCTTCTTTCT
Found at i:1797433 original size:142 final size:142
Alignment explanation
Indices: 1797240--1797525 Score: 572
Period size: 142 Copynumber: 2.0 Consensus size: 142
1797230 CAAAGTCTTC
1797240 ATCGATAACGTGAACCGTCATAAATATTCTTGTCGCATCAAAGACGTCTCCTTGTGTTTCGTAAT
1 ATCGATAACGTGAACCGTCATAAATATTCTTGTCGCATCAAAGACGTCTCCTTGTGTTTCGTAAT
1797305 GATGACTAAATAACAAGTTTCACATATCACGGAACCCACACTTATAAATACTTCTAAGAATGATG
66 GATGACTAAATAACAAGTTTCACATATCACGGAACCCACACTTATAAATACTTCTAAGAATGATG
1797370 AAGAAGAGGTTG
131 AAGAAGAGGTTG
1797382 ATCGATAACGTGAACCGTCATAAATATTCTTGTCGCATCAAAGACGTCTCCTTGTGTTTCGTAAT
1 ATCGATAACGTGAACCGTCATAAATATTCTTGTCGCATCAAAGACGTCTCCTTGTGTTTCGTAAT
1797447 GATGACTAAATAACAAGTTTCACATATCACGGAACCCACACTTATAAATACTTCTAAGAATGATG
66 GATGACTAAATAACAAGTTTCACATATCACGGAACCCACACTTATAAATACTTCTAAGAATGATG
1797512 AAGAAGAGGTTG
131 AAGAAGAGGTTG
1797524 AT
1 AT
1797526 TTTCCAAGAT
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 144 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (142 bp):
ATCGATAACGTGAACCGTCATAAATATTCTTGTCGCATCAAAGACGTCTCCTTGTGTTTCGTAAT
GATGACTAAATAACAAGTTTCACATATCACGGAACCCACACTTATAAATACTTCTAAGAATGATG
AAGAAGAGGTTG
Found at i:1802389 original size:35 final size:35
Alignment explanation
Indices: 1802340--1802438 Score: 139
Period size: 35 Copynumber: 2.9 Consensus size: 35
1802330 AATTTAGAAG
*
1802340 TTATTAAAATTTTAACATTTTTATATATTTTTAAA
1 TTATTAAAAATTTAACATTTTTATATATTTTTAAA
1802375 TTATTAAAAATTTAACATTTTTATATATTTTTAAA
1 TTATTAAAAATTTAACATTTTTATATATTTTTAAA
* * * *
1802410 TTCTTTATAA-TT-ATATTTTTATATATTTT
1 TTATTAAAAATTTAACATTTTTATATATTTT
1802439 CTAATAATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 16 0.27
34 2 0.03
35 41 0.69
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (35 bp):
TTATTAAAAATTTAACATTTTTATATATTTTTAAA
Found at i:1804647 original size:24 final size:23
Alignment explanation
Indices: 1804619--1804667 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
1804609 ATGGAACAAT
*
1804619 ATTTTATGCACCGTCGGTGTAATA
1 ATTTTATGCACCATCGGTG-AATA
*
1804643 ATTTTATGCACCATCTGTGAATA
1 ATTTTATGCACCATCGGTGAATA
1804666 AT
1 AT
1804668 AACATGACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (23 bp):
ATTTTATGCACCATCGGTGAATA
Found at i:1807213 original size:21 final size:21
Alignment explanation
Indices: 1807187--1807279 Score: 143
Period size: 21 Copynumber: 4.4 Consensus size: 21
1807177 AACCAGGCCT
1807187 TGGAGGTGGAGCAGCATACTG
1 TGGAGGTGGAGCAGCATACTG
*
1807208 TGGAGGTGCAGCAGC-TAACTG
1 TGGAGGTGGAGCAGCAT-ACTG
1807229 TGGAGGTGGAGCAGCATACTG
1 TGGAGGTGGAGCAGCATACTG
*
1807250 TGGAGGTGCAGCAGCATACTG
1 TGGAGGTGGAGCAGCATACTG
*
1807271 TTGAGGTGG
1 TGGAGGTGG
1807280 CGCCATCACT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
20 1 0.02
21 63 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.20
Consensus pattern (21 bp):
TGGAGGTGGAGCAGCATACTG
Found at i:1807246 original size:42 final size:42
Alignment explanation
Indices: 1807187--1807279 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
1807177 AACCAGGCCT
1807187 TGGAGGTGGAGCAGCATACTGTGGAGGTGCAGCAGC-TAACTG
1 TGGAGGTGGAGCAGCATACTGTGGAGGTGCAGCAGCAT-ACTG
1807229 TGGAGGTGGAGCAGCATACTGTGGAGGTGCAGCAGCATACTG
1 TGGAGGTGGAGCAGCATACTGTGGAGGTGCAGCAGCATACTG
*
1807271 TTGAGGTGG
1 TGGAGGTGG
1807280 CGCCATCACT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 48 0.98
43 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.20
Consensus pattern (42 bp):
TGGAGGTGGAGCAGCATACTGTGGAGGTGCAGCAGCATACTG
Found at i:1825900 original size:17 final size:18
Alignment explanation
Indices: 1825867--1825901 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1825857 CGTATGGCTG
1825867 GGCCGTGTAACAAACTAA
1 GGCCGTGTAACAAACTAA
*
1825885 GGCCGTGTGA-AAACTAA
1 GGCCGTGTAACAAACTAA
1825902 ATGAACGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (18 bp):
GGCCGTGTAACAAACTAA
Found at i:1828225 original size:18 final size:17
Alignment explanation
Indices: 1828202--1828264 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 17
1828192 TGATCCGATT
1828202 AAAACACGATAATTTTTG
1 AAAACACGA-AATTTTTG
*
1828220 AAAACATGAAACTTTTTG
1 AAAACACGAAA-TTTTTG
*
1828238 -AAACACGGGAA-TTTTG
1 AAAACAC-GAAATTTTTG
1828254 AAAACACGAAA
1 AAAACACGAAA
1828265 AATTTTCCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 8 0.21
17 13 0.34
18 17 0.45
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (17 bp):
AAAACACGAAATTTTTG
Found at i:1828795 original size:10 final size:10
Alignment explanation
Indices: 1828780--1828830 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 10
1828770 CCCCTTTTTC
1828780 TTTTTTCTTT
1 TTTTTTCTTT
1828790 TTTTTTCTCTT
1 TTTTTTCT-TT
* *
1828801 TTTTCCTCTTC
1 TTTT-TTCTTT
1828812 TTTTTTCTTT
1 TTTTTTCTTT
1828822 TCTTTTTCT
1 T-TTTTTCT
1828831 GGCATGCTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 13 0.38
11 18 0.53
12 3 0.09
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:1828795 original size:12 final size:12
Alignment explanation
Indices: 1828782--1828828 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
1828772 CCTTTTTCTT
1828782 TTTTCTTTTTT-
1 TTTTCTTTTTTC
1828793 TTTCTCTTTTTTCC
1 TTT-TCTTTTTT-C
*
1828807 TCTTCTTTTTTC
1 TTTTCTTTTTTC
1828819 TTTTCTTTTT
1 TTTTCTTTTT
1828829 CTGGCATGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 3 0.10
12 18 0.58
13 8 0.26
14 2 0.06
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:1829004 original size:19 final size:22
Alignment explanation
Indices: 1828966--1829010 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 22
1828956 GTTGGGCTTG
1828966 GGGTGCTGGTGGGCTGCTGTT-
1 GGGTGCTGGTGGGCTGCTGTTC
*
1828987 GGGTGCT-G-GGGTTGCTGTTC
1 GGGTGCTGGTGGGCTGCTGTTC
1829007 GGGT
1 GGGT
1829011 TGGATCGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 5 0.23
21 7 0.32
ACGTcount: A:0.00, C:0.13, G:0.53, T:0.33
Consensus pattern (22 bp):
GGGTGCTGGTGGGCTGCTGTTC
Found at i:1829029 original size:21 final size:23
Alignment explanation
Indices: 1829005--1829057 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 23
1828995 GGGTTGCTGT
1829005 TCGGGTTGGATCG-TCGGT-GGG
1 TCGGGTTGGATCGATCGGTCGGG
*
1829026 TCGGGTCGGATCGATTCGGTCGGG
1 TCGGGTTGGATCGA-TCGGTCGGG
1829050 TCGGGTTG
1 TCGGGTTG
1829058 ACCCGACTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
23 5 0.19
24 10 0.37
ACGTcount: A:0.06, C:0.17, G:0.49, T:0.28
Consensus pattern (23 bp):
TCGGGTTGGATCGATCGGTCGGG
Found at i:1829118 original size:8 final size:8
Alignment explanation
Indices: 1829075--1829124 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
1829065 TGTTATAATA
*
1829075 TTTTTTAT
1 TTTTTTCT
1829083 TTTTATT-T
1 TTTT-TTCT
*
1829091 TTTTATTAT
1 TTTT-TTCT
1829100 TTTTTTC-
1 TTTTTTCT
1829107 TTTTTTCT
1 TTTTTTCT
1829115 TTTTTTCT
1 TTTTTTCT
1829123 TT
1 TT
1829125 CTTCTTCTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1829119 original size:15 final size:15
Alignment explanation
Indices: 1829075--1829124 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
1829065 TGTTATAATA
*
1829075 TTTTTTATTTTTATTT
1 TTTTTTATTTTT-TTC
1829091 TTTTATTATTTTTTTC
1 TTTT-TTATTTTTTTC
*
1829107 TTTTTTCTTTTTTTC
1 TTTTTTATTTTTTTC
1829122 TTT
1 TTT
1829125 CTTCTTCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
15 13 0.42
16 10 0.32
17 8 0.26
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTATTTTTTTC
Found at i:1829129 original size:3 final size:3
Alignment explanation
Indices: 1829123--1829152 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1829113 CTTTTTTTCT
*
1829123 TTC TTC TTC TTC TAC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1829153 AAAACCCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:1829129 original size:15 final size:15
Alignment explanation
Indices: 1829099--1829130 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1829089 TTTTTTATTA
*
1829099 TTTTTTTCTTTTTTC
1 TTTTTTTCTTTCTTC
1829114 TTTTTTTCTTTCTTC
1 TTTTTTTCTTTCTTC
1829129 TT
1 TT
1829131 CTTCTACTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTTCTTC
Found at i:1829549 original size:30 final size:29
Alignment explanation
Indices: 1829515--1829585 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
1829505 GGCTAAAACA
1829515 TAATTTTGAGGAAGTTTATGGGTCAAAATG
1 TAATTTT-AGGAAGTTTATGGGTCAAAATG
* **
1829545 TAATTTCAAAAAGTTTATGGGTCAAAATG
1 TAATTTTAGGAAGTTTATGGGTCAAAATG
1829574 TAATTTTAGGAA
1 TAATTTTAGGAA
1829586 AATTTAGGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 29 0.83
30 6 0.17
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (29 bp):
TAATTTTAGGAAGTTTATGGGTCAAAATG
Found at i:1829561 original size:29 final size:29
Alignment explanation
Indices: 1829526--1829639 Score: 124
Period size: 29 Copynumber: 3.9 Consensus size: 29
1829516 AATTTTGAGG
*
1829526 AAGTTTATGGGTCAAAATGTAATTTCAAA
1 AAGTTTATGGGTCAAAATATAATTTCAAA
* *
1829555 AAGTTTATGGGTCAAAATGTAATTTTAGGAA
1 AAGTTTATGGGTCAAAATATAATTTCA--AA
* *
1829586 AA-TTTA-GGGTTTAAAATACAATTTCAAA
1 AAGTTTATGGG-TCAAAATATAATTTCAAA
*
1829614 AAGTTTAGGGGGTCAAAATATAATTT
1 AAGTTTA-TGGGTCAAAATATAATTT
1829640 TTTATTTTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
28 4 0.06
29 33 0.46
30 28 0.39
31 7 0.10
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.35
Consensus pattern (29 bp):
AAGTTTATGGGTCAAAATATAATTTCAAA
Found at i:1829578 original size:59 final size:60
Alignment explanation
Indices: 1829494--1829640 Score: 167
Period size: 59 Copynumber: 2.5 Consensus size: 60
1829484 TAAATGCAGC
* * * * **
1829494 AAAAGTTTTGGGGCT-AAAACATAATTTTGAGG-AAGTTTATGGG-TCAAAATGTAATTTCA
1 AAAAGTTTAGGGGGTCAAAATATAATTTT-AGGAAAATTTA-GGGTTCAAAATACAATTTCA
* * *
1829553 AAAAGTTTA-TGGGTCAAAATGTAATTTTAGGAAAATTTAGGGTTTAAAATACAATTTCA
1 AAAAGTTTAGGGGGTCAAAATATAATTTTAGGAAAATTTAGGGTTCAAAATACAATTTCA
1829612 AAAAGTTTAGGGGGTCAAAATATAATTTT
1 AAAAGTTTAGGGGGTCAAAATATAATTTT
1829641 TTATTTTTTG
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
58 9 0.12
59 47 0.64
60 17 0.23
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (60 bp):
AAAAGTTTAGGGGGTCAAAATATAATTTTAGGAAAATTTAGGGTTCAAAATACAATTTCA
Found at i:1829632 original size:30 final size:29
Alignment explanation
Indices: 1829526--1829639 Score: 122
Period size: 30 Copynumber: 3.9 Consensus size: 29
1829516 AATTTTGAGG
* *
1829526 AAGTTTATGGGTCAAAATGTAATTTCAAA
1 AAGTTTAGGGGTCAAAATATAATTTCAAA
* * *
1829555 AAGTTTATGGGTCAAAATGTAATTTTAGGAA
1 AAGTTTAGGGGTCAAAATATAATTTCA--AA
* * *
1829586 AA-TTTAGGGTTTAAAATACAATTTCAAA
1 AAGTTTAGGGGTCAAAATATAATTTCAAA
1829614 AAGTTTAGGGGGTCAAAATATAATTT
1 AAGTTTA-GGGGTCAAAATATAATTT
1829640 TTTATTTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.06
29 30 0.42
30 33 0.46
31 4 0.06
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.35
Consensus pattern (29 bp):
AAGTTTAGGGGTCAAAATATAATTTCAAA
Found at i:1830116 original size:76 final size:78
Alignment explanation
Indices: 1829851--1830998 Score: 1309
Period size: 76 Copynumber: 14.7 Consensus size: 78
1829841 CGTGTGGCCT
* *
1829851 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTTAAAAGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTAAAAAACAGAAA-TTAAAAG-AAA
* * * *
1829916 TACCTCGGCATGTGACTC
61 TACCTCAGCGTGCGACCC
* ** *
1829934 GAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTTAAAACAGAAATTTAAACGAAATA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTAAAAAACAGAAA-TTAAAAGAAATA
* * * *
1829999 CCTCGGCATGTG-TCC
63 CCTCAGCGTGCGACCC
* *
1830014 GAGGTTCAACTCACCTCTCGCAATATGAGTTGA-TTTAAAAAAACAGAAATATAAAAGAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAAT-TAAAAGAAATACC
* * **
1830078 TCGGCATG-G-TTC
65 TCAGCGTGCGACCC
1830090 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAAACAGAAATTTAAAAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT--AAAAAACAGAAA-TTAAAAGAAAT
1830155 ACCTCAGCGT--GACCC
62 ACCTCAGCGTGCGACCC
* ** * * * *
1830170 GAGGCTCAACTAACCTCT-ATAATATGAGTTAATTTTTTTTTTGAAAAATAAAAATTTAAAAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTAAAAAACAGAAA-TTAAAAGAA
1830234 ATACCTCAGCGTGCGACCC
60 ATACCTCAGCGTGCGACCC
* * *
1830253 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAAAAACAGAGATTTAAAAGAAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTAAAAAACAGA-AATTAAAAGAAAT
1830318 ACCTCAGCGT--GACCC
62 ACCTCAGCGTGCGACCC
*
1830333 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAAACAGAAATT--TA-AAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTT-AAAAAACAGAAATTAAAAGAAAT
1830395 ACCTCAGCGTGCGACCC
62 ACCTCAGCGTGCGACCC
* *
1830412 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAACAGAAATT--TA-AAATACCT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTAAAAGAAATACCT
1830473 CAGCGTGCGACCC
66 CAGCGTGCGACCC
* * * *
1830486 GAGGCTCAACTCACATCTCACAATATGAGTTGATTTTTGAAAAAATAGAAATT--TA-AAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAAAACAGAAATTAAAAGAAATACC
1830548 TCAGCGTGCGACCC
65 TCAGCGTGCGACCC
* * *
1830562 GAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAA-TTAAAAGAAATACC
1830627 TCAGCGT--GACCC
65 TCAGCGTGCGACCC
*
1830639 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATT--TA-AAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAAAACAGAAATTAAAAGAAATACC
1830701 TCAGCGTGCGACCC
65 TCAGCGTGCGACCC
* * *
1830715 GAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTTAAAGAAATACCT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTAAAAGAAATACCT
1830780 CAGCGT--GACCC
66 CAGCGTGCGACCC
*
1830791 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATT--TA-AAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAAAACAGAAATTAAAAGAAATACC
1830853 TCAGCGTGCGACCC
65 TCAGCGTGCGACCC
* *
1830867 GAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATT--TA-AAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAAAACAGAAATTAAAAGAAATACC
1830929 TCAGCGTGCGACCC
65 TCAGCGTGCGACCC
* * * *
1830943 AAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAATAGAAATTGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATT-AAAA
1830999 ATATTTCTTG
Statistics
Matches: 961, Mismatches: 68, Indels: 78
0.87 0.06 0.07
Matches are distributed among these distances:
74 110 0.11
75 25 0.03
76 311 0.32
77 105 0.11
78 30 0.03
79 64 0.07
80 128 0.13
81 58 0.06
82 60 0.06
83 59 0.06
84 11 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (78 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAGAAATTAAAAGAAATACCT
CAGCGTGCGACCC
Found at i:1830711 original size:153 final size:153
Alignment explanation
Indices: 1829851--1830985 Score: 1471
Period size: 152 Copynumber: 7.3 Consensus size: 153
1829841 CGTGTGGCCT
*
1829851 GAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTG-AAAAACAGAAATTTAAAAGAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAAACAGAAATTT-----AAA
* * * * * **
1829915 ATACCTCGGCATGTGACTCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTTAAAA
58 ATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAA
* * *
1829980 CAGAAATTTAAACGAAATACCTCGGCATGTG-TCC
121 CAGAAATTTAAAAGAAATACCTCAGC--GTGACCC
* * *
1830014 GAGGTTCAACTCACCTCTCGCAATATGAGTTGA--TTTAAAAAAACAGAAATATAAAAGAAATAC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAAT-T--TA-AAATAC
* * **
1830077 CTCGGCATG-G-TTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAAACAG
62 CTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG--AAAAACAG
1830140 AAATTTAAAAGAAATACCTCAGCGTGACCC
124 AAATTTAAAAGAAATACCTCAGCGTGACCC
* ** *
1830170 GAGGCTCAACTAACCTCT-ATAATATGAGTTAATTTTTTTTTTGAAAAATA-A-AAATTTAAAAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTGAAAAA-ACAGAAATTT---A-
* *
1830232 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTTTAA
56 AAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAA
*
1830297 AAACAGAGATTTAAAAGAAATACCTCAGCGTGACCC
118 AAACAGAAATTTAAAAGAAATACCTCAGCGTGACCC
1830333 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAAACAGAAATTTAAAATACC
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAAACAGAAATTTAAAATACC
1830398 TCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAAT
63 TCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAAT
1830462 TT---A-AAATACCTCAGCGTGCGACCC
128 TTAAAAGAAATACCTCAGCGT--GACCC
* * *
1830486 GAGGCTCAACTCACATCTCACAATATGAGTTGATTTTTGAAAAAATAGAAATTTAAAATACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTTAAAATACCTCA
* *
1830551 GCGTGCGACCCGAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTTA
66 GCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTA
1830616 AAAGAAATACCTCAGCGTGACCC
131 AAAGAAATACCTCAGCGTGACCC
1830639 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTTAAAATACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTTAAAATACCTCA
*
1830704 GCGTGCGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTGAAAAACAGAAATTT-
66 GCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTA
1830768 AAAGAAATACCTCAGCGTGACCC
131 AAAGAAATACCTCAGCGTGACCC
1830791 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTTAAAATACCTCA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTTAAAATACCTCA
*
1830856 GCGTGCGACCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTT
66 GCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTT
1830921 ---A-AAATACCTCAGCGTGCGACCC
130 AAAAGAAATACCTCAGCGT--GACCC
* *
1830943 AAGACTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
1830986 TAGAAATTGA
Statistics
Matches: 891, Mismatches: 45, Indels: 83
0.87 0.04 0.08
Matches are distributed among these distances:
150 93 0.10
151 28 0.03
152 183 0.21
153 180 0.20
154 1 0.00
155 46 0.05
156 57 0.06
157 30 0.03
158 18 0.02
159 65 0.07
160 3 0.00
161 20 0.02
162 25 0.03
163 125 0.14
164 11 0.01
165 6 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (153 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAAATTTAAAATACCTCA
GCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTA
AAAGAAATACCTCAGCGTGACCC
Found at i:1831861 original size:1 final size:1
Alignment explanation
Indices: 1831850--1831951 Score: 51
Period size: 1 Copynumber: 102.0 Consensus size: 1
1831840 TTCATCTTGA
* * * ** * * *** *
1831850 TTTTTTCTTTTTTCTTTTTTTTTTGTTTTTTCCTTTTTTTTGTTTTTTGTTTTGACTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * ** *
1831915 TGTTTTTTCTATTTTTTTTCCTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1831952 AAGCATAATA
Statistics
Matches: 73, Mismatches: 28, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 73 1.00
ACGTcount: A:0.02, C:0.08, G:0.07, T:0.83
Consensus pattern (1 bp):
T
Found at i:1831871 original size:18 final size:18
Alignment explanation
Indices: 1831850--1831951 Score: 80
Period size: 18 Copynumber: 5.3 Consensus size: 18
1831840 TTCATCTTGA
1831850 TTTTTTCTTTTTTCTTTT
1 TTTTTTCTTTTTTCTTTT
*
1831868 TTTTTTGTTTTTTCCTTTTT
1 TTTTTTCTTTTTT-C-TTTT
* *
1831888 TTTGTTTTTTGTTTTGACTGTT
1 TTT-TTTCTT-TTTT--CTTTT
*
1831910 TTTTTTGTTTTTTCTATTT
1 TTTTTTCTTTTTTCT-TTT
*
1831929 TTTTTCCTTTTTT-TTTGT
1 TTTTTTCTTTTTTCTTT-T
1831947 TTTTT
1 TTTTT
1831952 AAGCATAATA
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
17 2 0.03
18 21 0.30
19 14 0.20
20 11 0.16
21 10 0.14
22 10 0.14
23 1 0.01
ACGTcount: A:0.02, C:0.08, G:0.07, T:0.83
Consensus pattern (18 bp):
TTTTTTCTTTTTTCTTTT
Found at i:1831896 original size:42 final size:43
Alignment explanation
Indices: 1831850--1831933 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
1831840 TTCATCTTGA
** * *
1831850 TTTTTTCTTTTTTCTTTTTTTTTTGTTTTTTC-CTTTTTTTTG
1 TTTTTTCTTTTGACTGTTTTTTTTGTTTTTTCTATTTTTTTTG
*
1831892 TTTTTTGTTTTGACTGTTTTTTTTGTTTTTTCTATTTTTTTT
1 TTTTTTCTTTTGACTGTTTTTTTTGTTTTTTCTATTTTTTTT
1831934 CCTTTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 28 0.78
43 8 0.22
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.83
Consensus pattern (43 bp):
TTTTTTCTTTTGACTGTTTTTTTTGTTTTTTCTATTTTTTTTG
Found at i:1831945 original size:42 final size:42
Alignment explanation
Indices: 1831866--1831945 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
1831856 CTTTTTTCTT
* **
1831866 TTTTTTTTGTTTTTTCCTTTTTTTTGTTTTTTGTTTTGACTG
1 TTTTTTTTGTTTTTTCATTTTTTTTCCTTTTTGTTTTGACTG
1831908 TTTTTTTTGTTTTTTCTATTTTTTTTCCTTTTT-TTTTG
1 TTTTTTTTGTTTTTTC-ATTTTTTTTCCTTTTTGTTTTG
1831946 TTTTTTAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
42 21 0.62
43 13 0.38
ACGTcount: A:0.03, C:0.07, G:0.09, T:0.81
Consensus pattern (42 bp):
TTTTTTTTGTTTTTTCATTTTTTTTCCTTTTTGTTTTGACTG
Found at i:1842995 original size:17 final size:17
Alignment explanation
Indices: 1842945--1843007 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 17
1842935 TGATCTGATT
1842945 AAAACACGATAATTTTTG
1 AAAACACGA-AATTTTTG
*
1842963 AAAACATGAAACTTTTTG
1 AAAACACGAAA-TTTTTG
1842981 -AAACACGAGAA-TTTTG
1 AAAACACGA-AATTTTTG
1842997 AAAACACGAAA
1 AAAACACGAAA
1843008 AAATTTTCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
16 7 0.17
17 17 0.43
18 16 0.40
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (17 bp):
AAAACACGAAATTTTTG
Found at i:1843155 original size:20 final size:21
Alignment explanation
Indices: 1843117--1843159 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1843107 CATTACCTTA
1843117 TTTTTGAAAACACGAGAAAATT
1 TTTTTGAAAACAC-AGAAAATT
*
1843139 TTTTTGAAGACAC-GAAAATT
1 TTTTTGAAAACACAGAAAATT
1843159 T
1 T
1843160 CAAAACCCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (21 bp):
TTTTTGAAAACACAGAAAATT
Found at i:1843538 original size:12 final size:12
Alignment explanation
Indices: 1843525--1843571 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1843515 CCTTTTTATT
1843525 TTTTCTTTTTT-
1 TTTTCTTTTTTC
*
1843536 TTTCTCTTTCTTCC
1 TTT-TCTTT-TTTC
*
1843550 TCTTCTTTTTTC
1 TTTTCTTTTTTC
1843562 TTTTCTTTTT
1 TTTTCTTTTT
1843572 CTGGCCTGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 3 0.10
12 17 0.59
13 7 0.24
14 2 0.07
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:1843553 original size:22 final size:21
Alignment explanation
Indices: 1843528--1843568 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1843518 TTTTATTTTT
*
1843528 TCTTTTTTTTTCTCTTTCTTCC
1 TCTTCTTTTTTCT-TTTCTTCC
1843550 TCTTCTTTTTTCTTTTCTT
1 TCTTCTTTTTTCTTTTCTT
1843569 TTTCTGGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TCTTCTTTTTTCTTTTCTTCC
Done.