Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 6 of 199
Found at i:1842922 original size:18 final size:18
Alignment explanation
Indices: 1842899--1842935 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1842889 CTAACTTCTG
*
1842899 ACCGAACTAAATCGATTA
1 ACCGAACTAAATCAATTA
*
1842917 ACCGAATTAAATCAATTA
1 ACCGAACTAAATCAATTA
1842935 A
1 A
1842936 ATTTAGAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (18 bp):
ACCGAACTAAATCAATTA
Found at i:1846489 original size:20 final size:21
Alignment explanation
Indices: 1846444--1846493 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 21
1846434 CCATACAAAG
* *
1846444 TTTAATAATTTGAAAATTTCA
1 TTTAATTATTTGAAAATTACA
*
1846465 -ATAATTATTT-AAAATTACA
1 TTTAATTATTTGAAAATTACA
1846484 TTTAA-TATTT
1 TTTAATTATTT
1846494 TTCTCCAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTAATTATTTGAAAATTACA
Found at i:1846693 original size:96 final size:96
Alignment explanation
Indices: 1846521--1846701 Score: 337
Period size: 96 Copynumber: 1.9 Consensus size: 96
1846511 TCAAGGAGAG
1846521 TGGTTTTGAAAAATAATGCTTAAAATTAAATGTTTAAATTGAGCACAAGATTTTGAACACTTCCT
1 TGGTTTTGAAAAATAATGCTTAAAATTAAATGTTTAAATTGAGCACAAGATTTTGAACACTTCCT
1846586 CACTTTTACACTTTCAACCAATCCACATTAA
66 CACTTTTACACTTTCAACCAATCCACATTAA
1846617 TGGTTTTGAAAAATAATGCTTAAAATTAAATGTTTAAATTGAGCACAAGATTTTGAACACTTCCT
1 TGGTTTTGAAAAATAATGCTTAAAATTAAATGTTTAAATTGAGCACAAGATTTTGAACACTTCCT
*
1846682 TA-TTTTCACACTTTCAACCA
66 CACTTTT-ACACTTTCAACCA
1846702 CAATGATTTT
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
95 4 0.05
96 79 0.95
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (96 bp):
TGGTTTTGAAAAATAATGCTTAAAATTAAATGTTTAAATTGAGCACAAGATTTTGAACACTTCCT
CACTTTTACACTTTCAACCAATCCACATTAA
Found at i:1846950 original size:18 final size:18
Alignment explanation
Indices: 1846927--1846961 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1846917 GGATGAAAAT
*
1846927 AAGTTTTTAATTAATTAA
1 AAGTTTTCAATTAATTAA
1846945 AAGTTTTCAATTAATTA
1 AAGTTTTCAATTAATTA
1846962 CACCTTGAAC
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:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (18 bp):
AAGTTTTCAATTAATTAA
Found at i:1848687 original size:23 final size:22
Alignment explanation
Indices: 1848655--1848716 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
1848645 CCGGCCCGTT
* *
1848655 TTTTTAATTAAAATTAAGATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
1848679 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
1848701 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
1848717 TTGTTATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 16 0.46
23 14 0.40
24 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:1848711 original size:16 final size:16
Alignment explanation
Indices: 1848690--1848746 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
1848680 TTTTATTAAA
*
1848690 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
1848706 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
* *
1848722 ATCAAAATTAATTATT
1 ATTAAAATTAATTGTT
1848738 ATTAAAATT
1 ATTAAAATT
1848747 GTATCAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:1848840 original size:28 final size:27
Alignment explanation
Indices: 1848800--1848856 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
1848790 ATCTAACATT
* * *
1848800 TTGTTAGTAAAATTATTAATTGTATTAA
1 TTGTTACTAAAATTATCAAAT-TATTAA
1848828 TTGTTACTAAAATTATCAAATTATTAA
1 TTGTTACTAAAATTATCAAATTATTAA
1848855 TT
1 TT
1848857 ATTAATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (27 bp):
TTGTTACTAAAATTATCAAATTATTAA
Found at i:1848872 original size:76 final size:80
Alignment explanation
Indices: 1848792--1848948 Score: 241
Period size: 83 Copynumber: 2.0 Consensus size: 80
1848782 TTTGTAAAAT
1848792 CTAACATTTTGTTAGT-AAA-ATT-A-TTAATTGTATTAATTGTTACTAAAATTATCAAATTATT
1 CTAACATTTTGTTAGTAAAATATTAATTTAATTGTATTAATTGTTACTAAAATTATCAAATTATT
1848853 AATTATTAATTGTTA
66 AATTATTAATTGTTA
*
1848868 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAA-TATTAA-T-TTAATTGTATTAATTGTTACTAAAATTATCAAATT
*
1848933 ATTAATTGTTAATTGT
63 ATTAATTATTAATTGT
1848949 ATTAATTGTT
Statistics
Matches: 72, Mismatches: 2, Indels: 7
0.89 0.02 0.09
Matches are distributed among these distances:
76 16 0.22
77 3 0.04
79 3 0.04
80 1 0.01
83 49 0.68
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.49
Consensus pattern (80 bp):
CTAACATTTTGTTAGTAAAATATTAATTTAATTGTATTAATTGTTACTAAAATTATCAAATTATT
AATTATTAATTGTTA
Found at i:1848900 original size:19 final size:19
Alignment explanation
Indices: 1848876--1848926 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 19
1848866 TACTAACATT
1848876 TTGTTAGTAAAATTATTAA
1 TTGTTAGTAAAATTATTAA
*
1848895 TTG-T--T-AATTGTATTAA
1 TTGTTAGTAAAAT-TATTAA
1848911 TTGTTAGTAAAATTAT
1 TTGTTAGTAAAATTAT
1848927 CAAATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
15 3 0.12
16 10 0.40
17 1 0.04
18 1 0.04
19 7 0.28
20 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (19 bp):
TTGTTAGTAAAATTATTAA
Found at i:1848910 original size:16 final size:16
Alignment explanation
Indices: 1848889--1848958 Score: 69
Period size: 16 Copynumber: 4.7 Consensus size: 16
1848879 TTAGTAAAAT
1848889 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
1848905 TATTAATTGTT-A--G
1 TATTAATTGTTAATTG
* * * *
1848918 TA-AAATTATCAAAT-
1 TATTAATTGTTAATTG
1848932 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
1848948 TATTAATTGTT
1 TATTAATTGTT
1848959 GTAACAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
12 5 0.12
13 4 0.10
14 2 0.05
15 9 0.21
16 22 0.52
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.53
Consensus pattern (16 bp):
TATTAATTGTTAATTG
Found at i:1848922 original size:35 final size:34
Alignment explanation
Indices: 1848876--1848948 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 34
1848866 TACTAACATT
* *
1848876 TTGTTAGTAAAATTAT-TAATTGTTAATTGTATTAA
1 TTGTTAGTAAAATTATCAAATTATTAATTG--TTAA
1848911 TTGTTAGTAAAATTATCAAATTATTAATTGTTAA
1 TTGTTAGTAAAATTATCAAATTATTAATTGTTAA
1848945 TTGT
1 TTGT
1848949 ATTAATTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 8 0.23
35 16 0.46
36 11 0.31
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (34 bp):
TTGTTAGTAAAATTATCAAATTATTAATTGTTAA
Found at i:1852182 original size:17 final size:17
Alignment explanation
Indices: 1852160--1852192 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1852150 CACACGATAC
*
1852160 TAATATAATATAATGAT
1 TAATATAATAAAATGAT
1852177 TAATATAATAAAATGA
1 TAATATAATAAAATGA
1852193 ATTTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
TAATATAATAAAATGAT
Found at i:1852466 original size:2 final size:2
Alignment explanation
Indices: 1852459--1852487 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1852449 GCATCCAAAG
1852459 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1852488 TTTCACCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1858914 original size:18 final size:18
Alignment explanation
Indices: 1858891--1858935 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1858881 AAGAGGGTTC
*
1858891 AATGGCAATGGCAAAATT
1 AATGGCAAGGGCAAAATT
1858909 AATGGCAAGGGCAAAATT
1 AATGGCAAGGGCAAAATT
1858927 AATGGCAAG
1 AATGGCAAG
1858936 AGTTATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.11, G:0.27, T:0.18
Consensus pattern (18 bp):
AATGGCAAGGGCAAAATT
Found at i:1864114 original size:3 final size:3
Alignment explanation
Indices: 1864106--1864154 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1864096 TCTAGGAACC
1864106 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1864154 T
1 T
1864155 CAGCAGTAGG
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1875052 original size:44 final size:44
Alignment explanation
Indices: 1875004--1875306 Score: 225
Period size: 44 Copynumber: 6.9 Consensus size: 44
1874994 CAATACAGAA
1875004 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
* * * * * *
1875048 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCACTGTCA-ATACAG-GA-
1 AGGCAAGATCTTTTGTCTTCAACCAGC-TC-C-ATCACA-ACCGAGAG
*
1875092 AGGCAAGATCTTTTGTCTTCAACCAACTCCATCACAACCGAGAG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
* * * * * *
1875136 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCGCTGTCA-ATA-C-AGAA
1 AGGCAAGATCTTTTGTCTTCAACCAGC-TC-C-ATCACA-ACCGAGAG
*
1875180 AGGCAAGATCTATTGTCTTCAACCAGCTCCATCACAACCGAGAG
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
* * * * * *
1875224 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCGCTGTCA-ATA-C-AGAA
1 AGGCAAGATCTTTTGTCTTCAACCAGC-TC-C-ATCACA-ACCGAGAG
*
1875268 AGGCAAGATCTTTTTTCTTCAACCAGCTCCATCACAACC
1 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACC
1875307 TGTAATAGCC
Statistics
Matches: 196, Mismatches: 40, Indels: 47
0.69 0.14 0.17
Matches are distributed among these distances:
42 14 0.07
43 50 0.26
44 69 0.35
45 49 0.25
46 14 0.07
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (44 bp):
AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
Found at i:1875103 original size:88 final size:88
Alignment explanation
Indices: 1874949--1875306 Score: 644
Period size: 88 Copynumber: 4.1 Consensus size: 88
1874939 TGTATATTAT
* *
1874949 ACAATCGAGAAAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATACAGAAAGGCAAGATC
1 ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATACAGAAAGGCAAGATC
1875014 TTTTGTCTTCAACCAGCTCCATC
66 TTTTGTCTTCAACCAGCTCCATC
*
1875037 ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATACAGGAAGGCAAGATC
1 ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATACAGAAAGGCAAGATC
*
1875102 TTTTGTCTTCAACCAACTCCATC
66 TTTTGTCTTCAACCAGCTCCATC
*
1875125 ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGCAAGATC
1 ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATACAGAAAGGCAAGATC
*
1875190 TATTGTCTTCAACCAGCTCCATC
66 TTTTGTCTTCAACCAGCTCCATC
*
1875213 ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAAAGGCAAGATC
1 ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATACAGAAAGGCAAGATC
*
1875278 TTTTTTCTTCAACCAGCTCCATC
66 TTTTGTCTTCAACCAGCTCCATC
1875301 ACAACC
1 ACAACC
1875307 TGTAATAGCC
Statistics
Matches: 260, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 260 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (88 bp):
ACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATACAGAAAGGCAAGATC
TTTTGTCTTCAACCAGCTCCATC
Found at i:1877382 original size:37 final size:37
Alignment explanation
Indices: 1877342--1877526 Score: 343
Period size: 37 Copynumber: 5.0 Consensus size: 37
1877332 TAGTTTTAGC
** *
1877342 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGGC
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1877379 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1877416 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1877453 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1877490 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1 TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
1877527 AGCCTAGCTA
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 145 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (37 bp):
TACACTTATCTGATCAAGAAACAAAGTGATAAGTGGT
Found at i:1878320 original size:88 final size:88
Alignment explanation
Indices: 1878166--1878594 Score: 664
Period size: 88 Copynumber: 4.9 Consensus size: 88
1878156 AGGGGTGTTA
* * *
1878166 CACAACCGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGAAAGGCAAGAT
1 CACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT
*
1878231 CTTTTATCTTCAACCAGCTCCAT
66 CTTTTGTCTTCAACCAGCTCCAT
* * *
1878254 CACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTATCAATGCAGGAAGACAGGAT
1 CACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT
1878319 CTTTTGTCTTCAACCAGCTCCAT
66 CTTTTGTCTTCAACCAGCTCCAT
* *
1878342 CACAATCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACA-GAAGGGCAAGA
1 CACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAA-GGCAAGA
*
1878406 TCTTTTTTCTTCAACCAGCTCCAT
65 TCTTTTGTCTTCAACCAGCTCCAT
*
1878430 CACAATCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT
1 CACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT
* *
1878495 CTGTTGTCTTCAACCAGCTTCAT
66 CTTTTGTCTTCAACCAGCTCCAT
* * *
1878518 CACAACCGAGAGAGGCAAGGTTTG-GTGCTTCAACCTGCTTCACTGTCAATGCAGAAAGGCAAGA
1 CACAACCGAGAGAGGCAAGGTTTGTGT-CTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGA
* *
1878582 TCTGTTGTTTTCA
65 TCTTTTGTCTTCA
1878595 CTGATCTGTT
Statistics
Matches: 316, Mismatches: 22, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
87 5 0.02
88 308 0.97
89 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (88 bp):
CACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT
CTTTTGTCTTCAACCAGCTCCAT
Found at i:1878578 original size:44 final size:44
Alignment explanation
Indices: 1878178--1878580 Score: 232
Period size: 44 Copynumber: 9.2 Consensus size: 44
1878168 CAACCGAGAG
* * * *
1878178 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGAA
1 AGGCAAGGTTTGTGTCTTCAACCTGCTTCACTGTCAATGCAGAA
* * * * * ** * *
1878222 AGGCAAGATCTTTTATCTTCAACCAGCTCCA-TCACAA-CCGAGAG
1 AGGCAAGGT-TTGTGTCTTCAACCTGCTTCACTGTCAATGC-AGAA
* * * *
1878266 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTATCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCAACCTGCTTCACTGTCAATGCAGAA
* * * * ** *
1878310 AGAC-AGGATCTTTTGTCTTCAACCAGCTCCA-TCACAAT-CGAGAG
1 AGGCAAGG-T-TTGTGTCTTCAACCTGCTTCACTGTCAATGC-AGAA
* * *
1878354 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGAA
1 AGGCAAGGTTTGTGTCTTCAACCTGCTTCACTGTCAATGCAGAA
* * * * * * ** *
1878398 GGGCAAGATCTTTTTTCTTCAACCAGCTCCA-TCACAAT-CGAGAG
1 AGGCAAGGT-TTGTGTCTTCAACCTGCTTCACTGTCAATGC-AGAA
* * *
1878442 AGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCAACCTGCTTCACTGTCAATGCAGAA
* * * ** * *
1878486 AGGCAAGATCTGTTGTCTTCAACCAGCTTCA-TCACAA-CCGAGAG
1 AGGCAAGGTTTG-TGTCTTCAACCTGCTTCACTGTCAATGC-AGAA
1878530 AGGCAAGGTTTG-GTGCTTCAACCTGCTTCACTGTCAATGCAGAA
1 AGGCAAGGTTTGTGT-CTTCAACCTGCTTCACTGTCAATGCAGAA
1878574 AGGCAAG
1 AGGCAAG
1878581 ATCTGTTGTT
Statistics
Matches: 256, Mismatches: 84, Indels: 38
0.68 0.22 0.10
Matches are distributed among these distances:
42 2 0.01
43 66 0.26
44 121 0.47
45 67 0.26
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCAACCTGCTTCACTGTCAATGCAGAA
Found at i:1879690 original size:21 final size:21
Alignment explanation
Indices: 1879664--1879710 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1879654 GGTATAGCAA
1879664 GATCACCACATGCCCCGA-TCT
1 GATCACCACATGCCCC-ATTCT
**
1879685 GATCACTTCATGCCCCATTCT
1 GATCACCACATGCCCCATTCT
1879706 GATCA
1 GATCA
1879711 ATATTTGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (21 bp):
GATCACCACATGCCCCATTCT
Found at i:1880718 original size:8 final size:8
Alignment explanation
Indices: 1880669--1880738 Score: 86
Period size: 8 Copynumber: 8.4 Consensus size: 8
1880659 CTATTTTGAC
1880669 TTTGATTT
1 TTTGATTT
*
1880677 TTTAATTT
1 TTTGATTT
*
1880685 TTTAATTT
1 TTTGATTT
*
1880693 TTTAATTT
1 TTTGATTT
1880701 TTTGATTTT
1 TTTGA-TTT
1880710 TTTGATTTT
1 TTTGA-TTT
1880719 TTTGATTTT
1 TTTGA-TTT
1880728 TTTGATTT
1 TTTGATTT
1880736 TTT
1 TTT
1880739 TTGAGTCTGA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
8 33 0.56
9 26 0.44
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (8 bp):
TTTGATTT
Found at i:1880742 original size:10 final size:9
Alignment explanation
Indices: 1880669--1880739 Score: 87
Period size: 9 Copynumber: 8.3 Consensus size: 9
1880659 CTATTTTGAC
1880669 TTTGA-TTT
1 TTTGATTTT
*
1880677 TTT-AATTT
1 TTTGATTTT
*
1880685 TTT-AATTT
1 TTTGATTTT
*
1880693 TTT-AATTT
1 TTTGATTTT
1880701 TTTGATTTT
1 TTTGATTTT
1880710 TTTGATTTT
1 TTTGATTTT
1880719 TTTGATTTT
1 TTTGATTTT
1880728 TTTGATTTT
1 TTTGATTTT
1880737 TTT
1 TTT
1880740 TGAGTCTGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
7 1 0.02
8 25 0.42
9 34 0.57
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.77
Consensus pattern (9 bp):
TTTGATTTT
Found at i:1883350 original size:19 final size:20
Alignment explanation
Indices: 1883321--1883372 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
1883311 CACTTCGTGA
* *
1883321 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAAATGCATG
*
1883340 CAATGTAATGCAAATGCATG
1 AAATGTAATGCAAATGCATG
1883360 AAATG-AATGCAAA
1 AAATGTAATGCAAA
1883373 AAGAGACGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (20 bp):
AAATGTAATGCAAATGCATG
Found at i:1885152 original size:107 final size:108
Alignment explanation
Indices: 1884780--1885184 Score: 679
Period size: 108 Copynumber: 3.8 Consensus size: 108
1884770 AATTTGACTA
* * *
1884780 AACGTGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAATGCAAAATATTGAC
1 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
*
1884845 TTATTTAGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCG
66 TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCG
* *
1884888 AACGAGAAATCGAAACTCAATACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
1 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
* *
1884953 TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCAATTGGTGG
66 TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCG
1884996 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
1 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
*
1885061 TTATTTTGAAAATTTTTG-AAAGGATATTTAG-CTATTTGGTCG
66 TTATTTTGAAAATTTTTGAAAAGGATATTAAGTC-ATTTGGTCG
*
1885103 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCTAAATATTGCC
1 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
*
1885168 TTAATTTGAAATATTTT
66 TTATTTTGAAA-ATTTT
1885185 CCTTTTTGAA
Statistics
Matches: 280, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
106 1 0.00
107 93 0.33
108 186 0.66
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (108 bp):
AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
TTATTTTGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCG
Found at i:1885178 original size:215 final size:217
Alignment explanation
Indices: 1884780--1885184 Score: 699
Period size: 215 Copynumber: 1.9 Consensus size: 217
1884770 AATTTGACTA
* *
1884780 AACGTGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAATGCAAAATATTGAC
1 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGAC
*
1884845 TTATTTAGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCGAACGAGAAATCGAAACTCAATA
66 TTATTTAGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCGAACGAGAAATCGAAACCCAATA
*
1884910 CCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTATTTTGAAA-ATTTTTGAAA
131 CCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTAATTTGAAATATTTTTGAAA
1884974 AGGATATTAAGTCAATTGGTGG
196 AGGATATTAAGTCAATTGGTGG
*
1884996 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCC
1 AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGAC
* * *
1885061 TTATTTTGAAAATTTTTG-AAAGGATATTTAG-CTATTTGGTCGAACGAGAAATCGAAACCCAGT
66 TTATTTAGAAAATTTTTGAAAAGGATATTAAGTC-ATTTGGTCGAACGAGAAATCGAAACCCAAT
*
1885124 ACCTTAGGGCACGTTCCTCGAATTTCCAAACGCTAAATATTGCCTTAATTTGAAATATTTT
130 ACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTAATTTGAAATATTTT
1885185 CCTTTTTGAA
Statistics
Matches: 178, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
214 1 0.01
215 93 0.52
216 84 0.47
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (217 bp):
AACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGAC
TTATTTAGAAAATTTTTGAAAAGGATATTAAGTCATTTGGTCGAACGAGAAATCGAAACCCAATA
CCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTAATTTGAAATATTTTTGAAA
AGGATATTAAGTCAATTGGTGG
Found at i:1885647 original size:8 final size:8
Alignment explanation
Indices: 1885636--1885713 Score: 59
Period size: 8 Copynumber: 9.2 Consensus size: 8
1885626 ATAAAATAAA
1885636 ATATACAT
1 ATATACAT
1885644 ATATACAT
1 ATATACAT
*
1885652 ATATATAT
1 ATATACAT
1885660 ATATACAT
1 ATATACAT
*
1885668 ACTTTA-AT
1 A-TATACAT
*
1885676 ATATAAAATT
1 ATAT-ACA-T
*
1885686 ATATATAT
1 ATATACAT
*
1885694 ATGAATAAAT
1 AT--ATACAT
1885704 ATATACAT
1 ATATACAT
1885712 AT
1 AT
1885714 TCGTGAAAGA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
7 2 0.04
8 37 0.65
9 6 0.11
10 12 0.21
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.41
Consensus pattern (8 bp):
ATATACAT
Found at i:1885843 original size:3 final size:3
Alignment explanation
Indices: 1885835--1885921 Score: 81
Period size: 3 Copynumber: 29.3 Consensus size: 3
1885825 AGGCTACTAT
* * *
1885835 ATA ATA ATA AT- ATG ATA AGTA ACA ATA AT- ATAA ATA ATA ATA AAA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA AT-A ATA ATA ATA ATA
* * *
1885880 ATG ATA AAA ATA ATA ATA ACA A-A ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1885922 AATTACAGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
2 6 0.09
3 58 0.84
4 5 0.07
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:1890092 original size:24 final size:25
Alignment explanation
Indices: 1890063--1890110 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1890053 ACCCAAACAG
*
1890063 ACCCAAAACTA-CCCAAGCCCAAAT
1 ACCCAAAACTAGCCCAAACCCAAAT
*
1890087 ACCCAAACCTAGCCCAAACCCAAA
1 ACCCAAAACTAGCCCAAACCCAAA
1890111 AACAAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.46, C:0.44, G:0.04, T:0.06
Consensus pattern (25 bp):
ACCCAAAACTAGCCCAAACCCAAAT
Found at i:1891055 original size:3 final size:3
Alignment explanation
Indices: 1891043--1891105 Score: 101
Period size: 3 Copynumber: 21.3 Consensus size: 3
1891033 TTTAGTTAAC
* *
1891043 TAT T-T TAT TAT TAT TGT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1891090 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
1891106 GCTTTTATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1891195 original size:34 final size:34
Alignment explanation
Indices: 1891125--1891224 Score: 103
Period size: 34 Copynumber: 2.9 Consensus size: 34
1891115 TAGATGTATA
*
1891125 TTAT-ATATATATATATATACTTACATACATACTTT
1 TTATAATATATATATATATAC--ATATACATACTTT
* * *
1891160 TTGTAATATATATATATATACATATACCTATTTT
1 TTATAATATATATATATATACATATACATACTTT
* * * *
1891194 TTATAATTTATTTATACATGCATATACATAC
1 TTATAATATATATATATATACATATACATAC
1891225 CTACATTCTT
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
34 34 0.64
35 3 0.06
36 16 0.30
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (34 bp):
TTATAATATATATATATATACATATACATACTTT
Found at i:1891351 original size:13 final size:13
Alignment explanation
Indices: 1891333--1891358 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1891323 TCTTTTTAAA
1891333 ATATGTATTTTAT
1 ATATGTATTTTAT
1891346 ATATGTATTTTAT
1 ATATGTATTTTAT
1891359 GTTTTATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
ATATGTATTTTAT
Found at i:1891614 original size:16 final size:16
Alignment explanation
Indices: 1891593--1891631 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1891583 AAAGTATACA
1891593 TATATATACATACTTT
1 TATATATACATACTTT
*
1891609 TATATATACATGCTTT
1 TATATATACATACTTT
*
1891625 CATATAT
1 TATATAT
1891632 CTCCATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.03, T:0.49
Consensus pattern (16 bp):
TATATATACATACTTT
Found at i:1897166 original size:22 final size:22
Alignment explanation
Indices: 1897138--1897180 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1897128 GGTTAGCTAA
1897138 TGAAAGTTTA-ATAGTCATTTAG
1 TGAAAGTTTATA-AGTCATTTAG
1897160 TGAAAGTTTATAAGTCATTTA
1 TGAAAGTTTATAAGTCATTTA
1897181 ATTGTAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (22 bp):
TGAAAGTTTATAAGTCATTTAG
Found at i:1897681 original size:31 final size:31
Alignment explanation
Indices: 1897646--1897773 Score: 77
Period size: 31 Copynumber: 4.2 Consensus size: 31
1897636 TTATGTTAGC
*
1897646 TATTTATATTTTATATATCATTATATTAAAT
1 TATTTATATTTAATATATCATTATATTAAAT
* * * *
1897677 TATTTGA-ATATAATTTATTATTATATTAGAT
1 TATTT-ATATTTAATATATCATTATATTAAAT
* * * * *
1897708 TATTAAAATATTT-TTATA-AATTTTA-CAAAT
1 TATT--TATATTTAATATATCATTATATTAAAT
* * *
1897738 AATTTATATTTAATGTATCATAATATT-AAT
1 TATTTATATTTAATATATCATTATATTAAAT
1897768 TATTTA
1 TATTTA
1897774 AATATCATAT
Statistics
Matches: 68, Mismatches: 22, Indels: 15
0.65 0.21 0.14
Matches are distributed among these distances:
28 6 0.09
29 3 0.04
30 18 0.26
31 33 0.49
32 5 0.07
33 3 0.04
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (31 bp):
TATTTATATTTAATATATCATTATATTAAAT
Found at i:1899856 original size:23 final size:22
Alignment explanation
Indices: 1899809--1899852 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1899799 ATAAAATTAT
* *
1899809 TAAATATTAAAATAATATAATA
1 TAAATATTAAAAAAATATAAAA
1899831 TAAATATTTAAAAAAAT-TAAAA
1 TAAATA-TTAAAAAAATATAAAA
1899853 ATAATATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATATTAAAAAAATATAAAA
Found at i:1900159 original size:15 final size:16
Alignment explanation
Indices: 1900141--1900173 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1900131 TATTTATTAA
*
1900141 ATTTATAAT-TATTTT
1 ATTTAAAATGTATTTT
1900156 ATTTAAAATGTATTTT
1 ATTTAAAATGTATTTT
1900172 AT
1 AT
1900174 GTCACTCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTTAAAATGTATTTT
Found at i:1902473 original size:17 final size:17
Alignment explanation
Indices: 1902451--1902484 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1902441 AATAATACAT
1902451 TTGGGATGGGAAAGTAG
1 TTGGGATGGGAAAGTAG
1902468 TTGGGATGGGAAAGTAG
1 TTGGGATGGGAAAGTAG
1902485 AGGTAGCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (17 bp):
TTGGGATGGGAAAGTAG
Found at i:1905079 original size:14 final size:15
Alignment explanation
Indices: 1905060--1905088 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1905050 TAATATATTC
1905060 AATATAT-TTTTTAA
1 AATATATATTTTTAA
1905074 AATATATATTTTTAA
1 AATATATATTTTTAA
1905089 TAGGTAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATATATTTTTAA
Found at i:1905234 original size:26 final size:26
Alignment explanation
Indices: 1905179--1905234 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
1905169 ATAACCAATT
* * **
1905179 TTAAAATTTTAATATATTCAAATGTA
1 TTAAAATTTTAACATATTAAAAAATA
*
1905205 TTAAAATTTTAACATATTAAAAAATG
1 TTAAAATTTTAACATATTAAAAAATA
1905231 TTAA
1 TTAA
1905235 GTATAACCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (26 bp):
TTAAAATTTTAACATATTAAAAAATA
Found at i:1905236 original size:68 final size:68
Alignment explanation
Indices: 1905136--1905263 Score: 215
Period size: 68 Copynumber: 1.9 Consensus size: 68
1905126 TTAAAAAATT
*
1905136 TTAAAATTTTAAATATATTAAAAAAGATTAAGTATAACCAATTTTAAAATTTTAATATATTCAAA
1 TTAAAATTTTAAACATATTAAAAAAGATTAAGTATAACCAATTTTAAAA-TTTAATATATTCAAA
1905201 TGTA
65 TGTA
1905205 TTAAAATTTT-AACATATTAAAAAATG-TTAAGTATAACCAATTTTAAAATTTAATATATT
1 TTAAAATTTTAAACATATTAAAAAA-GATTAAGTATAACCAATTTTAAAATTTAATATATT
1905264 TTTAATAGGT
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
67 11 0.19
68 35 0.61
69 11 0.19
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (68 bp):
TTAAAATTTTAAACATATTAAAAAAGATTAAGTATAACCAATTTTAAAATTTAATATATTCAAAT
GTA
Found at i:1905247 original size:34 final size:34
Alignment explanation
Indices: 1905140--1905257 Score: 111
Period size: 34 Copynumber: 3.5 Consensus size: 34
1905130 AAAATTTTAA
1905140 AATTTTAAATATATTAAAAAA-GATTAAGTATAACC
1 AATTTTAAA-ATATTAAAAAATG-TTAAGTATAACC
* * * *
1905175 AATTTTAAAATTTTAATATAT-TCAAATGTATTAA--
1 AATTTTAAAATATTAAAAAATGT-TAA-GTA-TAACC
*
1905209 AATTTTAACATATTAAAAAATGTTAAGTATAACC
1 AATTTTAAAATATTAAAAAATGTTAAGTATAACC
1905243 AATTTTAAAAT-TTAA
1 AATTTTAAAATATTAA
1905258 TATATTTTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
32 3 0.05
33 8 0.12
34 39 0.59
35 13 0.20
36 3 0.05
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (34 bp):
AATTTTAAAATATTAAAAAATGTTAAGTATAACC
Found at i:1905810 original size:20 final size:20
Alignment explanation
Indices: 1905759--1905801 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1905749 ATTTGATTAC
1905759 TTTTATAAT-TTTATAAATT
1 TTTTATAATATTTATAAATT
*
1905778 TTTTATAATATTTATAAGTT
1 TTTTATAATATTTATAAATT
1905798 TTTT
1 TTTT
1905802 TTATGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTATAATATTTATAAATT
Found at i:1905881 original size:21 final size:21
Alignment explanation
Indices: 1905843--1905910 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
1905833 ATTAATTTCA
* *
1905843 ATTTTTTTA-AACTGTTAATG
1 ATTTTTTTATAATTTTTAATG
* *
1905863 ATTTTTTTCTTATTTTTAATG
1 ATTTTTTTATAATTTTTAATG
*
1905884 ATCTTTTTATAATTTTTAA-G
1 ATTTTTTTATAATTTTTAATG
*
1905904 AATTTTT
1 ATTTTTT
1905911 ATATGTTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 14 0.37
21 24 0.63
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.63
Consensus pattern (21 bp):
ATTTTTTTATAATTTTTAATG
Found at i:1905901 original size:9 final size:9
Alignment explanation
Indices: 1905887--1906118 Score: 89
Period size: 9 Copynumber: 24.8 Consensus size: 9
1905877 TTTAATGATC
1905887 TTTTTATAA
1 TTTTTATAA
*
1905896 TTTTTAAGAA
1 TTTTT-ATAA
*
1905906 TTTTTATATG
1 TTTTTATA-A
1905916 TTTTTATAAA
1 TTTTTAT-AA
* *
1905926 ATTTTAAATA
1 TTTTTATA-A
*
1905936 TGTTTTATTCA
1 T-TTTTA-TAA
1905947 TTTTTATAA
1 TTTTTATAA
1905956 TTTTTTATAA
1 -TTTTTATAA
* *
1905966 TTTATTAGAT
1 TTT-TTATAA
1905976 TTTTTA-AA
1 TTTTTATAA
1905984 TATTATTATAA
1 T-TT-TTATAA
*
1905995 -TATT-TAA
1 TTTTTATAA
*
1906002 TTTTTATAC
1 TTTTTATAA
* *
1906011 TATTTATACG
1 TTTTTATA-A
* *
1906021 TTTCTATCA
1 TTTTTATAA
*
1906030 GTTTTA-ATA
1 TTTTTATA-A
*
1906039 TTTTTATTA
1 TTTTTATAA
*
1906048 -TTTAATAA
1 TTTTTATAA
1906056 -TTTTATAA
1 TTTTTATAA
*
1906064 ATTTTATAA
1 TTTTTATAA
* * *
1906073 ATTTAATGA
1 TTTTTATAA
1906082 TTTTTAATAA
1 TTTTT-ATAA
*
1906092 TTTTTTATGA
1 -TTTTTATAA
*
1906102 TTTTTAATAG
1 TTTTT-ATAA
1906112 TTTTTAT
1 TTTTTAT
1906119 GAGAAAATAT
Statistics
Matches: 165, Mismatches: 38, Indels: 40
0.68 0.16 0.16
Matches are distributed among these distances:
7 3 0.02
8 20 0.12
9 64 0.39
10 63 0.38
11 15 0.09
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1905960 original size:10 final size:10
Alignment explanation
Indices: 1905887--1905995 Score: 59
Period size: 10 Copynumber: 11.0 Consensus size: 10
1905877 TTTAATGATC
1905887 TTTTTATAAT
1 TTTTTATAAT
* *
1905897 TTTTAAGAA-
1 TTTTTATAAT
1905906 TTTTTAT-AT
1 TTTTTATAAT
*
1905915 GTTTTTATAAA
1 -TTTTTATAAT
*
1905926 ATTTTA-AAT
1 TTTTTATAAT
*
1905935 ATGTTTTATTCA-
1 -T-TTTTA-TAAT
1905947 TTTTTATAAT
1 TTTTTATAAT
1905957 TTTTTATAAT
1 TTTTTATAAT
* *
1905967 TTATTA-GAT
1 TTTTTATAAT
1905976 TTTTTA-AAT
1 TTTTTATAAT
*
1905985 ATTATTATAAT
1 -TTTTTATAAT
1905996 ATTTAATTTT
Statistics
Matches: 74, Mismatches: 15, Indels: 19
0.69 0.14 0.18
Matches are distributed among these distances:
8 1 0.01
9 18 0.24
10 44 0.59
11 10 0.14
13 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:1905962 original size:31 final size:29
Alignment explanation
Indices: 1905887--1905960 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
1905877 TTTAATGATC
*
1905887 TTTTTATAATTTTTAAGAATTTTTATATG
1 TTTTTATAATTTTTAAGAATTTTTATATA
*
1905916 TTTTTATAAAATTTTAA-ATATGTTTTAT-TCA
1 TTTTTAT-AATTTTTAAGA-AT-TTTTATAT-A
1905947 TTTTTATAATTTTT
1 TTTTTATAATTTTT
1905961 TATAATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 8 0.21
30 17 0.45
31 13 0.34
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (29 bp):
TTTTTATAATTTTTAAGAATTTTTATATA
Found at i:1905968 original size:19 final size:19
Alignment explanation
Indices: 1905887--1906118 Score: 76
Period size: 19 Copynumber: 12.4 Consensus size: 19
1905877 TTTAATGATC
* *
1905887 TTTTTATAATTTTTAAGAA
1 TTTTTATAATTTTTTATAA
1905906 TTTTTAT-ATGTTTTTATAAA
1 TTTTTATAAT-TTTTTAT-AA
* *
1905926 ATTTTA-AATATGTTTTATTCA
1 TTTTTATAAT-T-TTTTA-TAA
1905947 TTTTTATAATTTTTTATAA
1 TTTTTATAATTTTTTATAA
*
1905966 TTTATTA-GATTTTTTA-AA
1 TTT-TTATAATTTTTTATAA
*
1905984 TATTATTATAA--TATT-TAA
1 T-TT-TTATAATTTTTTATAA
* * *
1906002 TTTTTAT-ACTATTTATACG
1 TTTTTATAATTTTTTATA-A
* * * *
1906021 TTTCTATCAGTTTTAAT-A
1 TTTTTATAATTTTTTATAA
* *
1906039 TTTTTAT--TATTTAATAA
1 TTTTTATAATTTTTTATAA
*
1906056 -TTTTATAA-ATTTTATAA
1 TTTTTATAATTTTTTATAA
* * * *
1906073 ATTTAATGATTTTTAATAA
1 TTTTTATAATTTTTTATAA
* * *
1906092 TTTTTTATGATTTTTAATAG
1 -TTTTTATAATTTTTTATAA
1906112 TTTTTAT
1 TTTTTAT
1906119 GAGAAAATAT
Statistics
Matches: 163, Mismatches: 29, Indels: 42
0.70 0.12 0.18
Matches are distributed among these distances:
15 1 0.01
16 16 0.10
17 13 0.08
18 25 0.15
19 51 0.31
20 41 0.25
21 12 0.07
22 4 0.02
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTTATAATTTTTTATAA
Found at i:1906089 original size:10 final size:10
Alignment explanation
Indices: 1906074--1906109 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1906064 ATTTTATAAA
1906074 TTTAATGATT
1 TTTAATGATT
*
1906084 TTTAATAATT
1 TTTAATGATT
*
1906094 TTTTATGATT
1 TTTAATGATT
1906104 TTTAAT
1 TTTAAT
1906110 AGTTTTTATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (10 bp):
TTTAATGATT
Found at i:1906119 original size:19 final size:20
Alignment explanation
Indices: 1906078--1906120 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1906068 TATAAATTTA
*
1906078 ATGATTTTTAATAATTTTTT
1 ATGATTTTTAATAAGTTTTT
1906098 ATGATTTTTAAT-AGTTTTT
1 ATGATTTTTAATAAGTTTTT
1906117 ATGA
1 ATGA
1906121 GAAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.60
Consensus pattern (20 bp):
ATGATTTTTAATAAGTTTTT
Found at i:1907230 original size:19 final size:19
Alignment explanation
Indices: 1907175--1907236 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
1907165 TAAAAATATA
*
1907175 AAAAAATAATTAAAT-TGAT
1 AAAAAATAA-TAAATATTAT
* * * *
1907194 AGAAAGTTATAAAAATTAT
1 AAAAAATAATAAATATTAT
1907213 AAAAAATAATAAATATTAT
1 AAAAAATAATAAATATTAT
1907232 AAAAA
1 AAAAA
1907237 TCAAATTAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
18 4 0.12
19 29 0.88
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAAAATAATAAATATTAT
Found at i:1907321 original size:22 final size:22
Alignment explanation
Indices: 1907296--1907349 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1907286 ATATTTGAAA
*
1907296 TCTTATAAAAACGTATAAAAAT
1 TCTTAAAAAAACGTATAAAAAT
*
1907318 TCTTAAAAAAACTTATAAAAAGT
1 TCTTAAAAAAACGTATAAAAA-T
1907341 TCATTAAAA
1 TC-TTAAAA
1907350 TAAATTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 19 0.68
23 3 0.11
24 6 0.21
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (22 bp):
TCTTAAAAAAACGTATAAAAAT
Found at i:1908403 original size:9 final size:9
Alignment explanation
Indices: 1908199--1908408 Score: 79
Period size: 10 Copynumber: 21.9 Consensus size: 9
1908189 TTTTTAATGC
*
1908199 TTTTATGAT
1 TTTTATAAT
1908208 TTTTATAAACT
1 TTTTAT-AA-T
1908219 TTTTAGTAAT
1 TTTTA-TAAT
**
1908229 TTGGATAAT
1 TTTTATAAT
*
1908238 ATCTTATAAT
1 -TTTTATAAT
*
1908248 GTTTTAGAAT
1 -TTTTATAAT
1908258 TTATTAT-AT
1 TT-TTATAAT
*
1908267 TATTTA-ATGT
1 T-TTTATA-AT
*
1908277 TTTTATGAAA
1 TTTTAT-AAT
1908287 TTTTATAAGT
1 TTTTATAA-T
*
1908297 TTTTATACAA
1 TTTTATA-AT
1908307 TTTTA-AAT
1 TTTTATAAT
*
1908315 ATATTTTTAA-
1 -T-TTTATAAT
*
1908325 TTGTATAAT
1 TTTTATAAT
*
1908334 TTTAATAAT
1 TTTTATAAT
*
1908343 TTATTA-GAT
1 TT-TTATAAT
1908352 TTTTATAACT
1 TTTTATAA-T
*
1908362 TTTTACAAT
1 TTTTATAAT
**
1908371 ACTTATAAGT
1 TTTTATAA-T
*
1908381 TTTTATGATTT
1 TTTTAT-A-AT
1908392 TTTTATAAT
1 TTTTATAAT
1908401 TTTTATAA
1 TTTTATAA
1908409 ATTTGTATCG
Statistics
Matches: 147, Mismatches: 32, Indels: 44
0.66 0.14 0.20
Matches are distributed among these distances:
8 9 0.06
9 56 0.38
10 61 0.41
11 20 0.14
12 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1908449 original size:18 final size:18
Alignment explanation
Indices: 1908426--1908464 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1908416 TCGATTCCAA
* *
1908426 TAATTTTTTAATATTTTT
1 TAATTTTTCAATAGTTTT
1908444 TAA-TTTTCAATAGTTTT
1 TAATTTTTCAATAGTTTT
1908461 TAAT
1 TAAT
1908465 GATTTCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TAATTTTTCAATAGTTTT
Found at i:1908567 original size:30 final size:31
Alignment explanation
Indices: 1908533--1908619 Score: 101
Period size: 30 Copynumber: 2.9 Consensus size: 31
1908523 TTTAAATGTG
1908533 TTTTTATTAATTTTATAAATTTATTAGA-TA
1 TTTTTATTAATTTTATAAATTTATTAGATTA
* *
1908563 TTTTTA-TATTTTTATAATATTTATGAGATTA
1 TTTTTATTAATTTTATAA-ATTTATTAGATTA
*
1908594 TTTTT-TATAATTTTA-ATATTTATTAG
1 TTTTTAT-TAATTTTATAAATTTATTAG
1908620 TTTGTTTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
29 10 0.21
30 23 0.48
31 8 0.17
32 7 0.15
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (31 bp):
TTTTTATTAATTTTATAAATTTATTAGATTA
Found at i:1908686 original size:19 final size:19
Alignment explanation
Indices: 1908645--1908688 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1908635 TTTTTCTGTT
*
1908645 TTTTTATAAGTTTCAATGT
1 TTTTTATAAGTTTCAATGA
* **
1908664 TTTTTATAATTTTTTATGA
1 TTTTTATAAGTTTCAATGA
1908683 TTTTTA
1 TTTTTA
1908689 GTGTAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (19 bp):
TTTTTATAAGTTTCAATGA
Found at i:1909385 original size:21 final size:20
Alignment explanation
Indices: 1909361--1909424 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
1909351 AAAAACTTAT
1909361 AAAAATCATAAAAATATAAAA
1 AAAAAT-ATAAAAATATAAAA
* *
1909382 AAAATATTTAAAATTATTAAAA
1 AAAA-ATATAAAAATA-TAAAA
** *
1909404 ATCAATATAAACATATAAAA
1 AAAAATATAAAAATATAAAA
1909424 A
1 A
1909425 TTATAAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 6 0.18
21 19 0.56
22 9 0.26
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAAATATAAAAATATAAAA
Found at i:1911096 original size:8 final size:7
Alignment explanation
Indices: 1911072--1911104 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1911062 AAACTTTCAA
1911072 AAAATAT
1 AAAATAT
1911079 AAAATAT
1 AAAATAT
1911086 AAAATAT
1 AAAATAT
*
1911093 TAAA-AT
1 AAAATAT
1911099 AAAATA
1 AAAATA
1911105 AAATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATAT
Found at i:1911112 original size:22 final size:23
Alignment explanation
Indices: 1911087--1911130 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1911077 ATAAAATATA
1911087 AAATA-TTAAAATAAAA-TAAAAT
1 AAATATTTAAAA-AAAAGTAAAAT
1911109 AAATATTTAAAAAAAAGTAAAA
1 AAATATTTAAAAAAAAGTAAAA
1911131 AATAGTATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (23 bp):
AAATATTTAAAAAAAAGTAAAAT
Found at i:1924003 original size:20 final size:20
Alignment explanation
Indices: 1923978--1924019 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1923968 AAACAATATC
1923978 AATTATGGAAAATGA-GAAGA
1 AATTATGGAAAAT-ATGAAGA
*
1923998 AATTATTGAAAATATGAAGA
1 AATTATGGAAAATATGAAGA
1924018 AA
1 AA
1924020 ATGTAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24
Consensus pattern (20 bp):
AATTATGGAAAATATGAAGA
Found at i:1927383 original size:14 final size:14
Alignment explanation
Indices: 1927364--1927391 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1927354 CTTCTAAATA
1927364 TTAGACTTCATTAT
1 TTAGACTTCATTAT
1927378 TTAGACTTCATTAT
1 TTAGACTTCATTAT
1927392 CCTATCTCCG
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:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
TTAGACTTCATTAT
Found at i:1934023 original size:23 final size:23
Alignment explanation
Indices: 1933997--1934118 Score: 199
Period size: 23 Copynumber: 5.3 Consensus size: 23
1933987 ATAAGTGCAA
1933997 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1934020 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1934043 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1934066 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
1934089 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1934112 CACTGAT
1 CACTGAT
1934119 CAATAACACT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 90 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1934064 original size:46 final size:46
Alignment explanation
Indices: 1933997--1934116 Score: 222
Period size: 46 Copynumber: 2.6 Consensus size: 46
1933987 ATAAGTGCAA
*
1933997 CACTGATATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
1934043 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
*
1934089 CACTGAAACGTAGCCGAAGCTACCACTG
1 CACTGAAATGTAGCCGAAGCTACCACTG
1934117 ATCAATAACA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTAC
Found at i:1944850 original size:36 final size:36
Alignment explanation
Indices: 1944809--1945117 Score: 357
Period size: 36 Copynumber: 8.0 Consensus size: 36
1944799 CTAAGGCTAA
1944809 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
1944845 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
1944881 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* *
1944923 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
1944963 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
1944999 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* *
1945041 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
1945081 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1945117 C
1 C
1945118 TAAAGCTACC
Statistics
Matches: 242, Mismatches: 11, Indels: 40
0.83 0.04 0.14
Matches are distributed among these distances:
36 164 0.68
38 6 0.02
40 6 0.02
42 6 0.02
44 4 0.02
46 56 0.23
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:1944971 original size:118 final size:118
Alignment explanation
Indices: 1944763--1945117 Score: 647
Period size: 118 Copynumber: 3.0 Consensus size: 118
1944753 CTAAGGCTAC
* * * *
1944763 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
*
1944828 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
66 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1944881 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1944946 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
66 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1944999 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
* *
1945064 TGATCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
66 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1945117 C
1 C
1945118 TAAAGCTACC
Statistics
Matches: 230, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 230 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (118 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:1945049 original size:82 final size:82
Alignment explanation
Indices: 1944963--1945153 Score: 337
Period size: 82 Copynumber: 2.3 Consensus size: 82
1944953 ATAAGTGTAG
* * *
1944963 CACTTATCACTTTTTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAGCACTTATCACTTTGTCACTTGATCAGATA
1945028 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
* *
1945045 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCACTTATCACTTTGTCACTTGATCAGATA
1 CACTTATCACTTTATCTCTTGATCAGATAAGTATAGCACTTATCACTTTGTCACTTGATCAGATA
1945110 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
1945127 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTATCTCTTGATCAGA
1945154 AGTACTCAAA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 104 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (82 bp):
CACTTATCACTTTATCTCTTGATCAGATAAGTATAGCACTTATCACTTTGTCACTTGATCAGATA
AGTGTAGCTAAAGCTAC
Found at i:1948914 original size:51 final size:51
Alignment explanation
Indices: 1948780--1948903 Score: 187
Period size: 51 Copynumber: 2.4 Consensus size: 51
1948770 TATTTTAAAA
* * *
1948780 AAGGAAATTGAGAGCAAATTGAAATTAAATATGGGTTTGAGAGATTTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
* *
1948831 AATGAAATTGAGAGGAAATTGAAATTAAATATGGATTT-ATGAGAATTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGA-GAGAATTTTGG
1948882 AAGGAAATTGAGAGAAAATTGA
1 AAGGAAATTGAGAGAAAATTGA
1948904 GAGGAAATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 1 0.02
51 65 0.98
ACGTcount: A:0.44, C:0.01, G:0.26, T:0.30
Consensus pattern (51 bp):
AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
Found at i:1948916 original size:12 final size:11
Alignment explanation
Indices: 1948883--1948918 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1948873 GAATTTTGGA
1948883 AGGAAATTGAG
1 AGGAAATTGAG
*
1948894 AGAAAATTGAG
1 AGGAAATTGAG
1948905 AGGAAATATGAG
1 AGGAAAT-TGAG
1948917 AG
1 AG
1948919 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:1949168 original size:43 final size:43
Alignment explanation
Indices: 1949107--1949192 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
1949097 CGACTTCGGG
1949107 GAAAATGGATCAATCCGGTAAATAATTAAATAGTTGGCCCATT
1 GAAAATGGATCAATCCGGTAAATAATTAAATAGTTGGCCCATT
1949150 GAAAATGGATCAATCCGGTAAATAATTAAATAGTTGGCCCATT
1 GAAAATGGATCAATCCGGTAAATAATTAAATAGTTGGCCCATT
1949193 TCGGTAATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (43 bp):
GAAAATGGATCAATCCGGTAAATAATTAAATAGTTGGCCCATT
Found at i:1950278 original size:18 final size:18
Alignment explanation
Indices: 1950255--1950289 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1950245 GTGCCTAAAA
1950255 ATCTTAATTTTTAAGATC
1 ATCTTAATTTTTAAGATC
1950273 ATCTTAATTTTTAAGAT
1 ATCTTAATTTTTAAGAT
1950290 TATAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (18 bp):
ATCTTAATTTTTAAGATC
Found at i:1950301 original size:19 final size:18
Alignment explanation
Indices: 1950259--1950303 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1950249 CTAAAAATCT
**
1950259 TAATTTTTAAGATCATCT
1 TAATTTTTAAGATCATAA
*
1950277 TAATTTTTAAGATTATAA
1 TAATTTTTAAGATCATAA
1950295 TATATTTTT
1 TA-ATTTTT
1950304 TTGCAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (18 bp):
TAATTTTTAAGATCATAA
Found at i:1950439 original size:19 final size:19
Alignment explanation
Indices: 1950415--1950451 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1950405 ATTTTCAAAA
*
1950415 AAATATTTTAAAAAATTAT
1 AAATATTTGAAAAAATTAT
*
1950434 AAATATTTGAAAGAATTA
1 AAATATTTGAAAAAATTA
1950452 CAAGTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AAATATTTGAAAAAATTAT
Found at i:1962989 original size:4 final size:4
Alignment explanation
Indices: 1962976--1963004 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1962966 TAGTTTTTCG
1962976 AATT -ATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AATT AA
1963005 AGTAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:1963534 original size:19 final size:19
Alignment explanation
Indices: 1963488--1963534 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1963478 TTTAATGATG
*
1963488 AATGAAAAGAAAATAATAA
1 AATGAAAATAAAATAATAA
1963507 AATCG-AAATAATAATAA-AA
1 AAT-GAAAATAA-AATAATAA
1963526 AATGAAAAT
1 AATGAAAAT
1963535 CTAAATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 17 0.71
20 6 0.25
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (19 bp):
AATGAAAATAAAATAATAA
Found at i:1963629 original size:20 final size:20
Alignment explanation
Indices: 1963604--1963643 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1963594 TATTTAACTT
1963604 TAACTTAAATTAAATAATAA
1 TAACTTAAATTAAATAATAA
1963624 TAACTTAAATTAAATAATAA
1 TAACTTAAATTAAATAATAA
1963644 AAAATTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
TAACTTAAATTAAATAATAA
Found at i:1963703 original size:3 final size:3
Alignment explanation
Indices: 1963667--1963764 Score: 71
Period size: 3 Copynumber: 32.3 Consensus size: 3
1963657 TACTAATATA
* * *
1963667 AAT AAT AACT AAAT AAA AAT AAA AAT ATAT AAT AAT -AT TAT AAT AAT
1 AAT AAT AA-T -AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
*
1963714 -AT AAT AAT AAT AGAT AAT -AT AAT AAT AGAT -AG AAT AAT AA- AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
1963757 AAAT AAT A
1 -AAT AAT A
1963765 TAGAAATATA
Statistics
Matches: 77, Mismatches: 7, Indels: 22
0.73 0.07 0.21
Matches are distributed among these distances:
2 9 0.12
3 53 0.69
4 13 0.17
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1963709 original size:8 final size:8
Alignment explanation
Indices: 1963653--1963766 Score: 66
Period size: 8 Copynumber: 14.8 Consensus size: 8
1963643 AAAAATTCTA
*
1963653 AATATACT
1 AATATAAT
1963661 AATATAAAT
1 AATAT-AAT
*
1963670 AATA-ACT
1 AATATAAT
1963677 AA-ATAA-
1 AATATAAT
*
1963683 AA-ATAAA
1 AATATAAT
1963690 AATAT-AT
1 AATATAAT
1963697 -A-ATAAT
1 AATATAAT
*
1963703 ATTATAAT
1 AATATAAT
1963711 AATATAAT
1 AATATAAT
1963719 AATAATAGAT
1 AAT-ATA-AT
1963729 AATATAAT
1 AATATAAT
*
1963737 AATA-GAT
1 AATATAAT
1963744 AGA-ATAAT
1 A-ATATAAT
*
1963752 AAAATAAAT
1 AATAT-AAT
1963761 AATATA
1 AATATA
1963767 GAAATATAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 26
0.71 0.08 0.22
Matches are distributed among these distances:
5 2 0.02
6 10 0.12
7 13 0.15
8 35 0.42
9 19 0.23
10 5 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (8 bp):
AATATAAT
Found at i:1963710 original size:11 final size:11
Alignment explanation
Indices: 1963685--1963725 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
1963675 CTAAATAAAA
*
1963685 ATAAAAATA-T
1 ATAATAATATT
1963695 ATAATAATATT
1 ATAATAATATT
*
1963706 ATAATAATATA
1 ATAATAATATT
1963717 ATAATAATA
1 ATAATAATA
1963726 GATAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATAATAATATT
Found at i:1963717 original size:29 final size:29
Alignment explanation
Indices: 1963678--1963764 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
1963668 ATAATAACTA
1963678 AATAA-AA-ATAAAAATATATA-ATAATAT
1 AATAATAATATAAAAATA-ATAGATAATAT
* *
1963705 TATAATAATATAATAATAATAGATAATAT
1 AATAATAATATAAAAATAATAGATAATAT
* *
1963734 AATAATAGATAGAATAATAA-A-ATAA-AT
1 AATAATA-ATATAAAAATAATAGATAATAT
1963761 AATA
1 AATA
1963765 TAGAAATATA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
27 10 0.19
28 9 0.17
29 22 0.42
30 11 0.21
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (29 bp):
AATAATAATATAAAAATAATAGATAATAT
Found at i:1963731 original size:32 final size:31
Alignment explanation
Indices: 1963684--1963766 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 31
1963674 ACTAAATAAA
* *
1963684 AATAAAAATATATAATAATATTATAATA-ATAT
1 AATAATAATA-ATAATAATAT-ATAATAGATAG
1963716 AATAATAATAGATAAT-ATA-ATAATAGATAG
1 AATAATAATA-ATAATAATATATAATAGATAG
1963746 AATAATAA-AATAAATAATATA
1 AATAATAATAAT-AATAATATA
1963767 GAAATATAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
28 2 0.05
29 10 0.23
30 14 0.32
31 4 0.09
32 14 0.32
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (31 bp):
AATAATAATAATAATAATATATAATAGATAG
Found at i:1963737 original size:15 final size:15
Alignment explanation
Indices: 1963698--1963774 Score: 71
Period size: 15 Copynumber: 5.5 Consensus size: 15
1963688 AAAATATATA
*
1963698 ATAATATTATAATA-
1 ATAATATAATAATAG
1963712 AT-ATAATAATAATAG
1 ATAAT-ATAATAATAG
1963727 ATAATATAATAATAG
1 ATAATATAATAATAG
1963742 ATAGA-ATAATAA-A-
1 ATA-ATATAATAATAG
1963755 ATAA-ATAAT-ATAG
1 ATAATATAATAATAG
1963768 A-AATATA
1 ATAATATA
1963775 GATTTATAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
11 1 0.02
12 9 0.16
13 9 0.16
14 11 0.20
15 22 0.40
16 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
ATAATATAATAATAG
Found at i:1963751 original size:41 final size:39
Alignment explanation
Indices: 1963652--1963774 Score: 121
Period size: 38 Copynumber: 3.2 Consensus size: 39
1963642 AAAAAATTCT
* * *
1963652 AAATATACTAAT-ATA-AATAATAACTA-AATAAAAATAA
1 AAATATAATAATAATAGAATAATAA-TATAATAATAATAG
**
1963689 AAATAT-ATAATAATATTATAATAATATAATAATAATAG
1 AAATATAATAATAATAGAATAATAATATAATAATAATAG
*
1963727 ATAATATAATAATAGATAGAATAATAAAATAAATAAT-ATAG
1 A-AATATAATAATA-ATAGAATAATAATAT-AATAATAATAG
1963768 AAATATA
1 AAATATA
1963775 GATTTATAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
36 4 0.06
37 11 0.15
38 17 0.24
39 5 0.07
40 12 0.17
41 17 0.24
42 6 0.08
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (39 bp):
AAATATAATAATAATAGAATAATAATATAATAATAATAG
Found at i:1963807 original size:14 final size:14
Alignment explanation
Indices: 1963788--1963816 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1963778 TTATAAATCG
1963788 AAATATATTAATAT
1 AAATATATTAATAT
1963802 AAATATATTAATAT
1 AAATATATTAATAT
1963816 A
1 A
1963817 CATGAGATGA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATATTAATAT
Found at i:1965778 original size:29 final size:29
Alignment explanation
Indices: 1965745--1965802 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1965735 GGGTTATTTG
1965745 TATGATATGGTTAATGTTCATGGAATTGA
1 TATGATATGGTTAATGTTCATGGAATTGA
*
1965774 TATGATATGGTTAATGTTTATGGAATTGA
1 TATGATATGGTTAATGTTCATGGAATTGA
1965803 CGTTATAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.43
Consensus pattern (29 bp):
TATGATATGGTTAATGTTCATGGAATTGA
Found at i:1966320 original size:20 final size:19
Alignment explanation
Indices: 1966275--1966326 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
1966265 TTTTGTATAG
* *
1966275 GTTAGAAATATTGGTAAAT
1 GTTAGAATTTTTGGTAAAT
*
1966294 TTCTAGAATTTTTGGTAAAT
1 GT-TAGAATTTTTGGTAAAT
1966314 CGTTAGATATTTT
1 -GTTAGA-ATTTT
1966327 GGCATAGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 19 0.73
21 6 0.23
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (19 bp):
GTTAGAATTTTTGGTAAAT
Found at i:1966679 original size:2 final size:2
Alignment explanation
Indices: 1966672--1966702 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1966662 TGGCATGACC
1966672 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 T
1966703 TCTAAACACC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1969850 original size:33 final size:33
Alignment explanation
Indices: 1969808--1969874 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1969798 AACTAACAAG
*
1969808 TTATTAATTTATTTTTCTATTTTATTCTTCTTT
1 TTATTAATTTATTTTTCTAATTTATTCTTCTTT
*
1969841 TTATTAATTTATTTTTCTAATTTCTTCTTCTTT
1 TTATTAATTTATTTTTCTAATTTATTCTTCTTT
1969874 T
1 T
1969875 CTTTCTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (33 bp):
TTATTAATTTATTTTTCTAATTTATTCTTCTTT
Found at i:1976881 original size:34 final size:33
Alignment explanation
Indices: 1976834--1976904 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
1976824 AAATGAGTAC
* *
1976834 ATTTGTATTATTTA-TATATAGTTAGTAAAAAGAT
1 ATTTTTATTATTTATTAT-TAATTAGT-AAAAGAT
1976868 ATTTTTATTATTTATTATTAATTAGTAAAAGAT
1 ATTTTTATTATTTATTATTAATTAGTAAAAGAT
1976901 -TTTT
1 ATTTT
1976905 ATATGATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 4 0.12
33 7 0.21
34 20 0.59
35 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (33 bp):
ATTTTTATTATTTATTATTAATTAGTAAAAGAT
Found at i:1977015 original size:18 final size:19
Alignment explanation
Indices: 1976992--1977039 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1976982 TGTAATATTT
*
1976992 ATATTTGTTATTA-AATAG
1 ATATTTATTATTATAATAG
1977010 ATATTTATTATTATAATA-
1 ATATTTATTATTATAATAG
*
1977028 ATAATTATTATT
1 ATATTTATTATT
1977040 TTTATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (19 bp):
ATATTTATTATTATAATAG
Found at i:1977407 original size:21 final size:20
Alignment explanation
Indices: 1977383--1977423 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1977373 GGAGTCCTAG
1977383 AGTTGAATATTATTG-AATTTA
1 AGTTGAA-ATT-TTGAAATTTA
1977404 AGTTGAAATTTTGAAATTTA
1 AGTTGAAATTTTGAAATTTA
1977424 GTAGATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 9 0.47
21 7 0.37
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.46
Consensus pattern (20 bp):
AGTTGAAATTTTGAAATTTA
Found at i:1978056 original size:17 final size:17
Alignment explanation
Indices: 1978007--1978060 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
1977997 AGTGAATGAA
*
1978007 AAAGTGAATTTGATATTG
1 AAAGTGAATTTGA-AATG
*
1978025 AAAGTAAATTTTGAAATG
1 AAAGTGAA-TTTGAAATG
1978043 AAAGTGAATTTGAAATG
1 AAAGTGAATTTGAAATG
1978060 A
1 A
1978061 GAATTGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.31
18 17 0.53
19 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.33
Consensus pattern (17 bp):
AAAGTGAATTTGAAATG
Found at i:1978244 original size:37 final size:39
Alignment explanation
Indices: 1978153--1978251 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 39
1978143 GACCTCGAGT
* **
1978153 CGATGAGACACTGGGTGTCACTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTATCA--ATTTTACTTCGGATAGAGC
* *
1978194 CGATGAGATACTGGGTATCAA-TTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTATCAATTTTACTTCGGATAGAGC
1978231 CGATGAGACACTGGGTATCAA
1 CGATGAGACACTGGGTATCAA
1978252 CTTTGCTCCG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
37 20 0.38
38 13 0.25
39 1 0.02
41 18 0.35
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (39 bp):
CGATGAGACACTGGGTATCAATTTTACTTCGGATAGAGC
Found at i:1979458 original size:26 final size:26
Alignment explanation
Indices: 1979417--1979642 Score: 244
Period size: 26 Copynumber: 8.8 Consensus size: 26
1979407 AGTATATTGT
* *
1979417 TTATTTAGCAGACCTTGAGCCGGTGA
1 TTATTTAGTAGGCCTTGAGCCGGTGA
* * *
1979443 TTATTTGGTAGGCCTTAAGCCAGTGA
1 TTATTTAGTAGGCCTTGAGCCGGTGA
1979469 TTATTTAGTAGGCCTTGAGCCGGTGA
1 TTATTTAGTAGGCCTTGAGCCGGTGA
* *
1979495 TCATTTAGTAAGCCTTGAGCCGGTGA
1 TTATTTAGTAGGCCTTGAGCCGGTGA
* *
1979521 TTATTTAGCAGGCCTTGAGCCGGTGT
1 TTATTTAGTAGGCCTTGAGCCGGTGA
* ** *
1979547 TTATTTAGCAGGCCTTGAGCTAGCGA
1 TTATTTAGTAGGCCTTGAGCCGGTGA
*
1979573 TTATTTAGTAGGCTTTGAGCC----A
1 TTATTTAGTAGGCCTTGAGCCGGTGA
* *
1979595 TTATTTAGTAAGCTTTGAGCCGGTGA
1 TTATTTAGTAGGCCTTGAGCCGGTGA
* * * *
1979621 TTGTTTGGCAGGCTTTGAGCCG
1 TTATTTAGTAGGCCTTGAGCCG
1979643 ATGTTTGTTT
Statistics
Matches: 170, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
22 21 0.12
26 149 0.88
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (26 bp):
TTATTTAGTAGGCCTTGAGCCGGTGA
Found at i:1979600 original size:22 final size:22
Alignment explanation
Indices: 1979572--1979615 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1979562 TGAGCTAGCG
*
1979572 ATTATTTAGTAGGCTTTGAGCC
1 ATTATTTAGTAAGCTTTGAGCC
1979594 ATTATTTAGTAAGCTTTGAGCC
1 ATTATTTAGTAAGCTTTGAGCC
1979616 GGTGATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (22 bp):
ATTATTTAGTAAGCTTTGAGCC
Found at i:1979654 original size:100 final size:101
Alignment explanation
Indices: 1979417--1979658 Score: 306
Period size: 104 Copynumber: 2.4 Consensus size: 101
1979407 AGTATATTGT
* * * * * *
1979417 TTATTTAGCAGACCTTGAGCCGGTGATTATTTGGTAGGCCTTAAGCCAGTGATTATTTAGTAGGC
1 TTATTTAGCAGGCCTTGAGCCGATGTTTATTTAGCAGGCCTTAAGCCAGCGATTATTTAGTAGGC
1979482 CTTGAGCCGGTGATCATTTAGTAAGCCTTGAGCCGGTGA
66 CTTGAGCC---GATCATTTAGTAAGCCTTGAGCCGGTGA
* * *
1979521 TTATTTAGCAGGCCTTGAGCCGGTGTTTATTTAGCAGGCCTTGAGCTAGCGATTATTTAGTAGGC
1 TTATTTAGCAGGCCTTGAGCCGATGTTTATTTAGCAGGCCTTAAGCCAGCGATTATTTAGTAGGC
* * *
1979586 TTTGAGCC-ATTATTTAGTAAGCTTTGAGCCGGTGA
66 CTTGAGCCGATCATTTAGTAAGCCTTGAGCCGGTGA
* * * *
1979621 TTGTTTGGCAGGCTTTGAGCCGATGTTTGTTTAGCAGG
1 TTATTTAGCAGGCCTTGAGCCGATGTTTATTTAGCAGG
1979659 TATTACGTAT
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
100 58 0.47
104 65 0.53
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (101 bp):
TTATTTAGCAGGCCTTGAGCCGATGTTTATTTAGCAGGCCTTAAGCCAGCGATTATTTAGTAGGC
CTTGAGCCGATCATTTAGTAAGCCTTGAGCCGGTGA
Found at i:1983009 original size:4 final size:4
Alignment explanation
Indices: 1983000--1983025 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1982990 AAATTGAATA
1983000 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1983026 CTATAATCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1986922 original size:26 final size:26
Alignment explanation
Indices: 1986887--1986936 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1986877 TCCTTGTGCT
1986887 TTTTTTTACTGTTCTCTTCATTTACC
1 TTTTTTTACTGTTCTCTTCATTTACC
1986913 TTTTTTTACTGTTCTCTTCATTTA
1 TTTTTTTACTGTTCTCTTCATTTA
1986937 TTTGACAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.20, G:0.04, T:0.64
Consensus pattern (26 bp):
TTTTTTTACTGTTCTCTTCATTTACC
Found at i:1997824 original size:31 final size:31
Alignment explanation
Indices: 1997784--1997863 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
1997774 TTTAAAAAAT
1997784 TTGTT-ATTTTAGTCACTCCTAATAGATAAA
1 TTGTTAATTTTAGTCACTCCTAATAGATAAA
** *
1997814 TTGTTAATTTTAGTCACTCCTGGTAGATAAG
1 TTGTTAATTTTAGTCACTCCTAATAGATAAA
* *
1997845 TTGTCAATTTTAGTTACTC
1 TTGTTAATTTTAGTCACTC
1997864 TACCGTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 5 0.11
31 39 0.89
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (31 bp):
TTGTTAATTTTAGTCACTCCTAATAGATAAA
Found at i:1999166 original size:17 final size:17
Alignment explanation
Indices: 1999144--1999176 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1999134 ATATTTAATA
1999144 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
1999161 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
1999177 TAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:2013323 original size:11 final size:11
Alignment explanation
Indices: 2013309--2013372 Score: 94
Period size: 11 Copynumber: 5.7 Consensus size: 11
2013299 TTATTTTTAA
2013309 TTTTAAAATAT
1 TTTTAAAATAT
2013320 TTTTAAAATAT
1 TTTTAAAATAT
2013331 TTTTAAAATAT
1 TTTTAAAATAT
2013342 TTTTAAAATAAT
1 TTTTAAAAT-AT
*
2013354 TTTT-TAATAT
1 TTTTAAAATAT
2013364 TTATTAAAA
1 TT-TTAAAA
2013373 ATGAGCAGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
10 4 0.08
11 36 0.75
12 8 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:2014280 original size:17 final size:19
Alignment explanation
Indices: 2014247--2014281 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2014237 ATTGTTTGGA
2014247 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
2014266 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
2014282 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:2015397 original size:278 final size:277
Alignment explanation
Indices: 2014858--2015406 Score: 638
Period size: 278 Copynumber: 2.0 Consensus size: 277
2014848 GACCATGTTT
* **
2014858 GTGTAACTCATGTGCTTTGATATAGTGAAAATATGCGCTGATGATAGTGGATTGGAAGTTGGTAT
1 GTGTAACTCATGTGCTTTGATATAGTGAAAATATGCGCTAATGATAGTGGACCGGAAGTTGGTAT
* * * * * *
2014923 GTTAGGTACATTACTTATGCATGATATAGAGTCACTCACAATAGTGGAATCATGGCTTGTTAAAT
66 GTTAGGTACATGACTTATACATGATATAGAGTCACTCACAATAGTGGAATCATAGCTCGATAAAA
* * * * * *
2014988 GAGTAAATAATATCCTCTCACTAGTATTGTATGAATTATGAAAATAGAACCTGGCCATAGGTCAT
131 GAGTAAATAATATACTCTCACTAGCATTGTATGAATTATAAAAATAGAACCTAGCCACAGGTAAT
* ** * * *
2015053 TTGTTTAGGACACCTAATTTCTTCATTAATAAATTGTGTAATGATCATTTTTATTGTGAAAGATA
196 TTGTCTAGGACAAATAATTTCATCATTAATAAATTGAGTAATGACCATTTTTATTGTGAAAGATA
2015118 CAATGGTGACCTTATGG
261 CAATGGTGACCTTATGG
* * * *
2015135 GTGTAACT-ATGTGCTTTGATATATTGAAAACATTTGCTCTAATGATAGTGGACCGGAATTTGGT
1 GTGTAACTCATGTGCTTTGATATAGTG-AAA-ATATGCGCTAATGATAGTGGACCGGAAGTTGGT
* * ** **
2015199 ATGTTGGGTACATGACTTATACATGATATGGCTTCACTCACCGTAGTGGAATCATAGCTCGATAA
64 ATGTTAGGTACATGACTTATACATGATATAGAGTCACTCACAATAGTGGAATCATAGCTCGATAA
** * * * ** *
2015264 AAGAGTAAATGGTATAGTCTTACT-GACATTGTATGGATTATAAAAATAGAACCTAGTTACGGGT
129 AAGAGTAAATAATATACTCTCACTAG-CATTGTATGAATTATAAAAATAGAACCTAGCCACAGGT
* * * *
2015328 AATTTGTCTGGGACAAATGATTTCATCATTACTAATTTGAGTAATGACCATTTTCT-TTGT-AAC
193 AATTTGTCTAGGACAAATAATTTCATCATTAATAAATTGAGTAATGACCATTTT-TATTGTGAA-
2015391 AGATACAATGGTGACC
256 AGATACAATGGTGACC
2015407 ATGAGATAAT
Statistics
Matches: 224, Mismatches: 43, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
276 17 0.08
277 14 0.06
278 192 0.86
279 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Consensus pattern (277 bp):
GTGTAACTCATGTGCTTTGATATAGTGAAAATATGCGCTAATGATAGTGGACCGGAAGTTGGTAT
GTTAGGTACATGACTTATACATGATATAGAGTCACTCACAATAGTGGAATCATAGCTCGATAAAA
GAGTAAATAATATACTCTCACTAGCATTGTATGAATTATAAAAATAGAACCTAGCCACAGGTAAT
TTGTCTAGGACAAATAATTTCATCATTAATAAATTGAGTAATGACCATTTTTATTGTGAAAGATA
CAATGGTGACCTTATGG
Found at i:2023792 original size:223 final size:223
Alignment explanation
Indices: 2023404--2023850 Score: 876
Period size: 223 Copynumber: 2.0 Consensus size: 223
2023394 GGTGCGATAC
2023404 TTGTGGCTCAATAGTCAAATTTTGAAGAAAAGAACTAGACCTCAAAGGCTAAGGTATTGATACCT
1 TTGTGGCTCAATAGTCAAATTTTGAAGAAAAGAACTAGACCTCAAAGGCTAAGGTATTGATACCT
2023469 CTAGCTTTGCAAGTGCATTTAATGCCCATATTAATGACTCCAACAGCTCAATCCATTCTCTATCA
66 CTAGCTTTGCAAGTGCATTTAATGCCCATATTAATGACTCCAACAGCTCAATCCATTCTCTATCA
*
2023534 ACATCAAACTTACAAAAGTCAAGAGCAAAAATCTAATCATTTCTCTTTGTTATTCTTATTTTCAC
131 ACACCAAACTTACAAAAGTCAAGAGCAAAAATCTAATCATTTCTCTTTGTTATTCTTATTTTCAC
2023599 TTGTACACACTTGTGGGTTTATTTGTGA
196 TTGTACACACTTGTGGGTTTATTTGTGA
2023627 TTGTGGCTCAATAGTCAAATTTTGAAGAAAAGAACTAGACCTCAAAGGCTAAGGTATTGATACCT
1 TTGTGGCTCAATAGTCAAATTTTGAAGAAAAGAACTAGACCTCAAAGGCTAAGGTATTGATACCT
*
2023692 CTAGCTTTGCAAGTGCATTTAATGCCCATATTAATGACTCCAATAGCTCAATCCATTCTCTATCA
66 CTAGCTTTGCAAGTGCATTTAATGCCCATATTAATGACTCCAACAGCTCAATCCATTCTCTATCA
2023757 ACACCAAACTTACAAAAGTCAAGAGCAAAAATCTAATCATTTCTCTTTGTTATTCTTATTTTCAC
131 ACACCAAACTTACAAAAGTCAAGAGCAAAAATCTAATCATTTCTCTTTGTTATTCTTATTTTCAC
2023822 TTGTACACACTTGTGGGTTTATTTGTGA
196 TTGTACACACTTGTGGGTTTATTTGTGA
2023850 T
1 T
2023851 CCATTCTTCC
Statistics
Matches: 222, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
223 222 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (223 bp):
TTGTGGCTCAATAGTCAAATTTTGAAGAAAAGAACTAGACCTCAAAGGCTAAGGTATTGATACCT
CTAGCTTTGCAAGTGCATTTAATGCCCATATTAATGACTCCAACAGCTCAATCCATTCTCTATCA
ACACCAAACTTACAAAAGTCAAGAGCAAAAATCTAATCATTTCTCTTTGTTATTCTTATTTTCAC
TTGTACACACTTGTGGGTTTATTTGTGA
Found at i:2024967 original size:3 final size:3
Alignment explanation
Indices: 2024959--2024984 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2024949 TGAGAAGATA
2024959 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
2024985 AAGGTACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2051292 original size:12 final size:12
Alignment explanation
Indices: 2051275--2051299 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2051265 CTTGAAATGC
2051275 CTTCTCTTCACT
1 CTTCTCTTCACT
2051287 CTTCTCTTCACT
1 CTTCTCTTCACT
2051299 C
1 C
2051300 CTTTCTGCTA
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:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCTCTTCACT
Found at i:2056206 original size:76 final size:76
Alignment explanation
Indices: 2056080--2056232 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
2056070 TTGAAAAAGA
2056080 CAAGTAGATATTATTCCTCCTAGAAATTCAGTGAAATTCAGTGGTCATGGTATAACTGTACAACA
1 CAAGTAGATATTATTCCTCCTAGAAATTCAGTGAAATTCAGTGGTCATGGTATAACTGTACAACA
2056145 TAGCAGACTAC
66 TAGCAGACTAC
2056156 CAAGTAGATATTATTCCTCCTAGAAATTCAGTGAAATTCAGTGGTCATGGTATAACTGTACAACA
1 CAAGTAGATATTATTCCTCCTAGAAATTCAGTGAAATTCAGTGGTCATGGTATAACTGTACAACA
2056221 TAGCAGACTAC
66 TAGCAGACTAC
2056232 C
1 C
2056233 TTAGTAAAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (76 bp):
CAAGTAGATATTATTCCTCCTAGAAATTCAGTGAAATTCAGTGGTCATGGTATAACTGTACAACA
TAGCAGACTAC
Found at i:2056729 original size:21 final size:21
Alignment explanation
Indices: 2056690--2056730 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2056680 ATTTTCCTGT
*
2056690 AAAAGATTGAAGGAAATAAAG
1 AAAAGATTGAAAGAAATAAAG
* *
2056711 AAAAGATTTAAAGATATAAA
1 AAAAGATTGAAAGAAATAAA
2056731 AAGTCAGATT
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:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AAAAGATTGAAAGAAATAAAG
Found at i:2058917 original size:2 final size:2
Alignment explanation
Indices: 2058912--2058943 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2058902 ACACCAAGTG
2058912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2058944 GTACACACAC
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):
AT
Found at i:2059888 original size:27 final size:27
Alignment explanation
Indices: 2059866--2059922 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
2059856 TCATATTATT
2059866 AATATATATA-TACAAATTTATATAATA
1 AATATATATATTA-AAATTTATATAATA
*
2059893 AATATATTTATTAAAATTTATATAA-A
1 AATATATATATTAAAATTTATATAATA
2059919 AATA
1 AATA
2059923 AAAAATCGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 5 0.18
27 21 0.75
28 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
AATATATATATTAAAATTTATATAATA
Found at i:2063231 original size:23 final size:23
Alignment explanation
Indices: 2063201--2063251 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
2063191 TTTTACTTAC
2063201 AAAA-AGAAGAAAAAAAACTCCT
1 AAAACAGAAGAAAAAAAACTCCT
2063223 AAAACAGAAGAAAAAAAACTCCT
1 AAAACAGAAGAAAAAAAACTCCT
2063246 AAAACA
1 AAAACA
2063252 AGTCTAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.69, C:0.16, G:0.08, T:0.08
Consensus pattern (23 bp):
AAAACAGAAGAAAAAAAACTCCT
Found at i:2065540 original size:28 final size:29
Alignment explanation
Indices: 2065517--2065581 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
2065507 TTTAAATTTT
2065517 ATTAAAAATAGGAAAAAT-TATAAAAATC
1 ATTAAAAATAGGAAAAATATATAAAAATC
* *
2065545 ATTAAAAATA-TATAAAATATATAGAAAT-
1 ATTAAAAATAGGA-AAAATATATAAAAATC
*
2065573 ATAAAAAAT
1 ATTAAAAAT
2065582 TTATAAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.03
28 23 0.72
29 8 0.25
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (29 bp):
ATTAAAAATAGGAAAAATATATAAAAATC
Found at i:2065562 original size:19 final size:19
Alignment explanation
Indices: 2065529--2065588 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
2065519 TAAAAATAGG
2065529 AAAAAT-TATAAAA-ATCATT
1 AAAAATATATAAAATAT-A-T
2065548 AAAAATATATAAAATATAT
1 AAAAATATATAAAATATAT
* * *
2065567 AGAAATATAAAAAATTTAT
1 AAAAATATATAAAATATAT
2065586 AAA
1 AAA
2065589 CTTTTATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 25 0.71
20 8 0.23
21 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATATATAAAATATAT
Found at i:2065566 original size:11 final size:10
Alignment explanation
Indices: 2065529--2065588 Score: 65
Period size: 9 Copynumber: 6.3 Consensus size: 10
2065519 TAAAAATAGG
2065529 AAAAAT-TAT
1 AAAAATATAT
2065538 AAAAATCAT-T
1 AAAAAT-ATAT
2065548 AAAAATATAT
1 AAAAATATAT
2065558 -AAAATATAT
1 AAAAATATAT
*
2065567 AGAAATATA-
1 AAAAATATAT
*
2065576 AAAAATTTAT
1 AAAAATATAT
2065586 AAA
1 AAA
2065589 CTTTTATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
9 24 0.56
10 18 0.42
11 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAAATATAT
Found at i:2065686 original size:11 final size:11
Alignment explanation
Indices: 2065670--2065702 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2065660 AAAAGTATTT
2065670 TATAATTTTTA
1 TATAATTTTTA
2065681 TATAATTTTTA
1 TATAATTTTTA
*
2065692 T-TGATTTTTA
1 TATAATTTTTA
2065702 T
1 T
2065703 TTTTTATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
TATAATTTTTA
Found at i:2072233 original size:29 final size:29
Alignment explanation
Indices: 2072176--2072234 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
2072166 TTTATTTGAT
*
2072176 TTTATTTAATAGTAAAGAGATTAAATTAA
1 TTTATTTAATAGTAAAGAGAATAAATTAA
*
2072205 TTTATTTAATAGTACAAGA-AATAATTTAA
1 TTTATTTAATAGTA-AAGAGAATAAATTAA
2072234 T
1 T
2072235 CAGATACCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.42
Consensus pattern (29 bp):
TTTATTTAATAGTAAAGAGAATAAATTAA
Found at i:2074189 original size:121 final size:121
Alignment explanation
Indices: 2073984--2074226 Score: 432
Period size: 121 Copynumber: 2.0 Consensus size: 121
2073974 TACAATTCAT
* * *
2073984 TTCTGATTTCAACGAGTTAGGGGAGAGACCAACTAAACATATGTAATTAGGGTTCAAATATTTTA
1 TTCTGATTTCAACGAGTTAAGGAAGAGACCAACTAAACATATGTAATTAGGGCTCAAATATTTTA
*
2074049 TAATTAAGTTTTAAGTTTTCTCATATCAATTATAAACTTATTTAGTCACAATACTA
66 TAATTAAGTTCTAAGTTTTCTCATATCAATTATAAACTTATTTAGTCACAATACTA
*
2074105 TTCTGATTTCAACGAGTTAAGGAAGAGACCGACTAAACATATGTAATTAGGGCTCAAATATTTTA
1 TTCTGATTTCAACGAGTTAAGGAAGAGACCAACTAAACATATGTAATTAGGGCTCAAATATTTTA
*
2074170 TAATTAAGTTCTAAGTTTTCTCATATCAATTATAAACTTATTTAGTCACGATACTA
66 TAATTAAGTTCTAAGTTTTCTCATATCAATTATAAACTTATTTAGTCACAATACTA
2074226 T
1 T
2074227 AGTATCGTGA
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 116 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (121 bp):
TTCTGATTTCAACGAGTTAAGGAAGAGACCAACTAAACATATGTAATTAGGGCTCAAATATTTTA
TAATTAAGTTCTAAGTTTTCTCATATCAATTATAAACTTATTTAGTCACAATACTA
Found at i:2075558 original size:146 final size:147
Alignment explanation
Indices: 2075190--2075624 Score: 728
Period size: 147 Copynumber: 3.0 Consensus size: 147
2075180 AGCCATGAAA
* * * *
2075190 ACCTCTCCATGATAAGCTTGACTTTTACATCTTGGCCTCAAACATCATGATATTTTAAACCTTCA
1 ACCTCTCCATGATAAGCTTGACTTTTACATCTTGGCCTCAAACATCATGATGTTTTTAAGCTCCA
* *
2075255 CTCTTCAAATTAAATACTAATCTGGAGCGGATCGATTCAGAATATATCGAGTAGTTCAAAAATCG
66 CTCTTCAAATTAAATACTAATTTGGAGCGGATCGATTCAGAATATATCGAGTAGTTAAAAAATCG
2075320 AAACTATAATTTCACTG
131 AAACTATAATTTCACTG
*
2075337 ACCTCTCCATGATAAGCTTGACTTTTACATCTTGGCCTCCAACATCATGATGTTTTTAAGCTCCA
1 ACCTCTCCATGATAAGCTTGACTTTTACATCTTGGCCTCAAACATCATGATGTTTTTAAGCTCCA
* * * *
2075402 TTCTTCAAATTAAGTACTAATTTGGAGCGGATCGATTTAGAATATATTGAGTAGTTAAAAAATCG
66 CTCTTCAAATTAAATACTAATTTGGAGCGGATCGATTCAGAATATATCGAGTAGTTAAAAAATCG
* *
2075467 AAACAATAATTTCGCTG
131 AAACTATAATTTCACTG
*
2075484 A-CTCTCCATGTTAAGCTTGACTTTTACATCTTGGCCTCAAACATCATGATGTTTTTAAGCTCCA
1 ACCTCTCCATGATAAGCTTGACTTTTACATCTTGGCCTCAAACATCATGATGTTTTTAAGCTCCA
*
2075548 CTCTTCAAATTAAATACTAATTTGGAGCGGATCGATTCAGAATATATCGAGTAATTAAAAAATCG
66 CTCTTCAAATTAAATACTAATTTGGAGCGGATCGATTCAGAATATATCGAGTAGTTAAAAAATCG
2075613 AAACTATAATTT
131 AAACTATAATTT
2075625 TACCATTACA
Statistics
Matches: 267, Mismatches: 21, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
146 132 0.49
147 135 0.51
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.34
Consensus pattern (147 bp):
ACCTCTCCATGATAAGCTTGACTTTTACATCTTGGCCTCAAACATCATGATGTTTTTAAGCTCCA
CTCTTCAAATTAAATACTAATTTGGAGCGGATCGATTCAGAATATATCGAGTAGTTAAAAAATCG
AAACTATAATTTCACTG
Found at i:2084611 original size:63 final size:64
Alignment explanation
Indices: 2084518--2084637 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 64
2084508 TATTTATTTT
*
2084518 AATACAAAAATTATGTTAATAACTTGTAATG-GTTATTATTTAAAATAAATATGATTTTTTTCTA
1 AATACAAAAATTATGTTAATAACTTGTAATGAG-TATTATTTAAAATAAATATAATTTTTTTCTA
* * * * *
2084582 AATATAAATATTAT-TTAATAAGTTTTAATGAGTATTATTTAACATAAATATAATTT
1 AATACAAAAATTATGTTAATAACTTGTAATGAGTATTATTTAAAATAAATATAATTT
2084638 CGATATATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
63 36 0.73
64 13 0.27
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (64 bp):
AATACAAAAATTATGTTAATAACTTGTAATGAGTATTATTTAAAATAAATATAATTTTTTTCTA
Found at i:2085802 original size:23 final size:24
Alignment explanation
Indices: 2085776--2085825 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
2085766 AAACAATTAC
*
2085776 AAATCCTAACATTATGAA-TTCTA
1 AAATCCTAACATTATAAACTTCTA
* * *
2085799 AAATGCTAGCATTTTAAACTTCTA
1 AAATCCTAACATTATAAACTTCTA
2085823 AAA
1 AAA
2085826 AATTTAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (24 bp):
AAATCCTAACATTATAAACTTCTA
Found at i:2092607 original size:18 final size:18
Alignment explanation
Indices: 2092580--2092614 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2092570 AACTACAGTT
2092580 ACATTCTAAATAAACCCA
1 ACATTCTAAATAAACCCA
* *
2092598 ACATTGTAAATTAACCC
1 ACATTCTAAATAAACCC
2092615 CTTTGTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.26, G:0.03, T:0.26
Consensus pattern (18 bp):
ACATTCTAAATAAACCCA
Done.