Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 5 of 97
Found at i:2043122 original size:4 final size:4
Alignment explanation
Indices: 2043113--2043183 Score: 79
Period size: 4 Copynumber: 17.8 Consensus size: 4
2043103 GATAACAACA
* * * ** *
2043113 ACAT ACAT ACAT ACGT ACAT ACAC ACAC ACAT ACAT ATGT ACAT ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
2043161 ACAC ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACA
2043184 CAATCATCTG
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.48, C:0.30, G:0.03, T:0.20
Consensus pattern (4 bp):
ACAT
Found at i:2043149 original size:24 final size:24
Alignment explanation
Indices: 2043117--2043185 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
2043107 ACAACAACAT
2043117 ACATACATACGTACATACACACAC
1 ACATACATACGTACATACACACAC
*
2043141 ACATACATATGTACATACACACAC
1 ACATACATACGTACATACACACAC
*
2043165 ACATACATACATACATACACA
1 ACATACATACGTACATACACA
2043186 ATCATCTGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.48, C:0.30, G:0.03, T:0.19
Consensus pattern (24 bp):
ACATACATACGTACATACACACAC
Found at i:2044384 original size:31 final size:30
Alignment explanation
Indices: 2044324--2044393 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
2044314 CTCACAGTAC
* *
2044324 ATTTTTTAAAGACTTAAAAATAAATAT-AA
1 ATTTTTTAAAGAATTAAAAATAAAAATAAA
*
2044353 ATTTTTTAAATAATTAATTAAATAAAAATAAA
1 ATTTTTTAAAGAATTAA--AAATAAAAATAAA
2044385 ATATTTTTA
1 AT-TTTTTA
2044394 CTTTTCTCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.44
31 9 0.26
32 4 0.12
33 6 0.18
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (30 bp):
ATTTTTTAAAGAATTAAAAATAAAAATAAA
Found at i:2044980 original size:14 final size:14
Alignment explanation
Indices: 2044953--2045017 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
2044943 TTTTATTTAA
*
2044953 TTAATTATTAATTTT
1 TTAA-TATTTATTTT
2044968 TTAATATTTATTTT
1 TTAATATTTATTTT
*
2044982 TAAAT-TCTTATAATTT
1 TTAATAT-TTAT--TTT
*
2044998 TTATTATTTATTTT
1 TTAATATTTATTTT
2045012 ATTAAT
1 -TTAAT
2045018 GAGGTGGCAG
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
13 1 0.03
14 20 0.50
15 8 0.20
16 10 0.25
17 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (14 bp):
TTAATATTTATTTT
Found at i:2044980 original size:30 final size:30
Alignment explanation
Indices: 2044944--2045017 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
2044934 ATATTTTATT
*
2044944 TTTATTTAATTAATTATTA-ATTTTTTAATA
1 TTTATTT-ATTAATTATTATAATTTTTAATA
* *
2044974 TTTATTT-TTAAATTCTTATAATTTTTATTA
1 TTTATTTATT-AATTATTATAATTTTTAATA
2045004 TTTATTTTATTAAT
1 TTTA-TTTATTAAT
2045018 GAGGTGGCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 2 0.05
29 7 0.19
30 20 0.54
31 6 0.16
32 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTATTTATTAATTATTATAATTTTTAATA
Found at i:2045322 original size:2 final size:2
Alignment explanation
Indices: 2045282--2045310 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2045272 CGTTTCATTT
2045282 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2045311 TTGCTTTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2072809 original size:14 final size:14
Alignment explanation
Indices: 2072778--2072827 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
2072768 AAAGTACACG
* *
2072778 CCATGGACCATGGA
1 CCATGGACCAGGGT
2072792 CCATGGACCAGGGT
1 CCATGGACCAGGGT
*
2072806 CCATAGGTCCATGGGT
1 CCAT-GGACCA-GGGT
2072822 CCATGG
1 CCATGG
2072828 GTCAAGGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 16 0.52
15 7 0.23
16 8 0.26
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.18
Consensus pattern (14 bp):
CCATGGACCAGGGT
Found at i:2090433 original size:23 final size:23
Alignment explanation
Indices: 2090407--2090452 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2090397 TGTACAGTGC
*
2090407 GTATAGAGATAATATTAAACATT
1 GTATAGAGACAATATTAAACATT
* *
2090430 GTATAGAGACATTATTATACATT
1 GTATAGAGACAATATTAAACATT
2090453 TACCTAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (23 bp):
GTATAGAGACAATATTAAACATT
Found at i:2092084 original size:29 final size:27
Alignment explanation
Indices: 2091981--2092086 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 27
2091971 CTCTCAATAA
* *
2091981 TTTTTAAATTTTTATAATATATTTGTAT
1 TTTTTAAAATTTTATAAT-TATTTTTAT
*
2092009 TTTTTAAAAATTTTATAATTCGTTTCTTCAAT
1 TTTTT-AAAATTTTATAATT-ATTT-TT--AT
*
2092041 AATTTTTAAATTTTTATAACTTATTTTTAT
1 --TTTTTAAAATTTTATAA-TTATTTTTAT
2092071 TTTTTAGAAATTTTAT
1 TTTTTA-AAATTTTAT
2092087 CATTTCAGCC
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
28 12 0.19
29 23 0.37
30 3 0.05
32 4 0.06
33 14 0.22
34 7 0.11
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (27 bp):
TTTTTAAAATTTTATAATTATTTTTAT
Found at i:2092225 original size:63 final size:63
Alignment explanation
Indices: 2091971--2092232 Score: 230
Period size: 62 Copynumber: 4.2 Consensus size: 63
2091961 GGGCCACGCC
* *
2091971 CTCT-CAATAATTTT-TAAATTTTTATAATATATTTGTATTTTTTAAAAATTTTATAATTCGTT-
1 CTCTACAATAATTTTAT-AATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATT--TTA
2092033 T
63 T
* * * * *
2092034 CT-T-CAATAATTTT-TAAATTTTTATAACTTATTTTTATTTTTTAGAAATTTTATCATTTCAG
1 CTCTACAATAATTTTAT-AATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATTTTAT
* *
2092095 C-CTTACAA-AACTTTTAAAATTTTT-TCTACATA-TTTTA-TTTTT-AAAA-TTTATAA-TTTA
1 CTC-TACAATAA-TTTTATAATTTTTAT-AACATATTTTTATTTTTTAAAAATTTTATAATTTTA
2092152 TT
63 -T
* *
2092154 CTCTACAATATATTTTATNATTTTTCTAACATATTTTTA-TTTTTAAAAATTTTATAATTTTAT
1 CTCTACAATA-ATTTTATAATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATTTTAT
2092217 CTCTACAATATATTTT
1 CTCTACAATA-ATTTT
2092233 TATATAGTGA
Statistics
Matches: 166, Mismatches: 17, Indels: 32
0.77 0.08 0.15
Matches are distributed among these distances:
58 3 0.02
59 12 0.07
60 22 0.13
61 18 0.11
62 63 0.38
63 44 0.27
64 4 0.02
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (63 bp):
CTCTACAATAATTTTATAATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATTTTAT
Found at i:2097518 original size:2 final size:2
Alignment explanation
Indices: 2097511--2097558 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2097501 CAGCTGATAC
2097511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2097553 AT -T AT A
1 AT AT AT A
2097559 CACACACACA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2113973 original size:2 final size:2
Alignment explanation
Indices: 2113964--2114010 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2113954 GAAATAAAAA
2113964 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2114005 AT -T AT A
1 AT AT AT A
2114011 ACTCAAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2127579 original size:14 final size:14
Alignment explanation
Indices: 2127562--2127592 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2127552 TCTCTCTCTA
2127562 TATATATATATATG
1 TATATATATATATG
*
2127576 TATATATATGTATG
1 TATATATATATATG
2127590 TAT
1 TAT
2127593 GTATTCTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (14 bp):
TATATATATATATG
Found at i:2146238 original size:28 final size:28
Alignment explanation
Indices: 2146203--2146257 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2146193 ATTCTTGAAT
** *
2146203 TATATCTAATTAAATTCCTATTTTTTAA
1 TATATCTAAACAAATTCCTATATTTTAA
*
2146231 TATATCTAAACAAATTCTTATATTTTA
1 TATATCTAAACAAATTCCTATATTTTA
2146258 CCTTACACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (28 bp):
TATATCTAAACAAATTCCTATATTTTAA
Found at i:2147527 original size:19 final size:19
Alignment explanation
Indices: 2147503--2147558 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
2147493 TGAGATTCAT
*
2147503 AAAATTTATAGGTGTATGG
1 AAAATTTATAAGTGTATGG
2147522 AAAATTTATAAGTGTATGG
1 AAAATTTATAAGTGTATGG
2147541 AAAATTTATAAGTGTATG
1 AAAATTTATAAGTGTATG
2147559 CAACGCCTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (19 bp):
AAAATTTATAAGTGTATGG
Found at i:2161595 original size:15 final size:15
Alignment explanation
Indices: 2161575--2161604 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2161565 TTATCTATGA
2161575 AAGAAAACTCTCCTT
1 AAGAAAACTCTCCTT
2161590 AAGAAAACTCTCCTT
1 AAGAAAACTCTCCTT
2161605 TTCTCATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (15 bp):
AAGAAAACTCTCCTT
Found at i:2165381 original size:28 final size:29
Alignment explanation
Indices: 2165350--2165424 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 29
2165340 TTTAAAAAAT
2165350 TTTAAATAAATTTTTATTTTTTATTAT-A
1 TTTAAATAAATTTTTATTTTTTATTATGA
* * *
2165378 TTTAATTAAATTTTTACATTTTTATTTTGA
1 TTTAAATAAATTTTTA-TTTTTTATTATGA
*
2165408 TTTAAGTAAATTTTTAT
1 TTTAAATAAATTTTTAT
2165425 AATTAATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 15 0.38
29 9 0.22
30 16 0.40
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (29 bp):
TTTAAATAAATTTTTATTTTTTATTATGA
Found at i:2181290 original size:21 final size:21
Alignment explanation
Indices: 2181264--2181309 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2181254 AGTAAAAATA
*
2181264 TCATATAATCATGTTATCATG
1 TCATATAATCATGTCATCATG
*
2181285 TCATATAATCATGTCATTATG
1 TCATATAATCATGTCATCATG
2181306 TCAT
1 TCAT
2181310 GTTAACGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (21 bp):
TCATATAATCATGTCATCATG
Found at i:2181732 original size:41 final size:41
Alignment explanation
Indices: 2181675--2181757 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
2181665 AATATATATA
*
2181675 TATATATATTTTACTTGACAATAACATGCAAAATTTAATTT
1 TATATATATATTACTTGACAATAACATGCAAAATTTAATTT
*
2181716 TATATATATATTACTTGACAATAACATGCAAATTTTAATTT
1 TATATATATATTACTTGACAATAACATGCAAAATTTAATTT
2181757 T
1 T
2181758 GTTTTAAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.45
Consensus pattern (41 bp):
TATATATATATTACTTGACAATAACATGCAAAATTTAATTT
Found at i:2201475 original size:31 final size:30
Alignment explanation
Indices: 2201416--2201475 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
2201406 CAATCAAACT
*
2201416 CTTATACTTTTATTTTGAGCTAAATAAATA
1 CTTATACTTTTATTTTAAGCTAAATAAATA
*
2201446 CTTATATTTTTATTTTTAAG-TCAAATAAAT
1 CTTATACTTTTA-TTTTAAGCT-AAATAAAT
2201476 TTTTATAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (30 bp):
CTTATACTTTTATTTTAAGCTAAATAAATA
Found at i:2203043 original size:22 final size:23
Alignment explanation
Indices: 2203015--2203061 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2203005 ATTTCTACGC
*
2203015 ATTATTATGAAAACTAAGCT-AA
1 ATTATTATCAAAACTAAGCTCAA
*
2203037 ATTATTATCAAAATTAAGCTCAA
1 ATTATTATCAAAACTAAGCTCAA
2203060 AT
1 AT
2203062 AACTCTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (23 bp):
ATTATTATCAAAACTAAGCTCAA
Found at i:2205028 original size:13 final size:14
Alignment explanation
Indices: 2205010--2205044 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2205000 TGCCACTTTT
2205010 TTTTTTTTTTG-AA
1 TTTTTTTTTTGTAA
*
2205023 TTTTTTTTTTGTTA
1 TTTTTTTTTTGTAA
2205037 TTTTTTTT
1 TTTTTTTT
2205045 AAAAATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTTGTAA
Found at i:2205148 original size:65 final size:63
Alignment explanation
Indices: 2205063--2205186 Score: 230
Period size: 65 Copynumber: 1.9 Consensus size: 63
2205053 AAAAAAATTT
2205063 ATGAACTTGCACAAAATAAAAAAAAGTGTTAATAAATTAATAATTAAATAAATAAAGATNTTTA
1 ATGAACTTGCACAAAATAAAAAAAAGTGTTAATAAATTAATAATTAAATAAATAAAGAT-TTTA
2205127 ATGAACTTGCAACAAAATAAAAAAAAGTGTTAATAAATTAATAATTAAATAAATAAAGAT
1 ATGAACTTGC-ACAAAATAAAAAAAAGTGTTAATAAATTAATAATTAAATAAATAAAGAT
2205187 AAAAAATAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 10 0.17
65 49 0.83
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.28
Consensus pattern (63 bp):
ATGAACTTGCACAAAATAAAAAAAAGTGTTAATAAATTAATAATTAAATAAATAAAGATTTTA
Found at i:2232872 original size:22 final size:20
Alignment explanation
Indices: 2232825--2232875 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2232815 AGGGGTAGCA
2232825 TCTTTTTTCTAAGAATTGAC
1 TCTTTTTTCTAAGAATTGAC
* *
2232845 TCTTTTTTCTAAGAGTTGTC
1 TCTTTTTTCTAAGAATTGAC
*
2232865 TCTGTTTTCTA
1 TCTTTTTTCTA
2232876 GTCGTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.16, G:0.12, T:0.55
Consensus pattern (20 bp):
TCTTTTTTCTAAGAATTGAC
Found at i:2242780 original size:79 final size:80
Alignment explanation
Indices: 2242581--2242926 Score: 330
Period size: 82 Copynumber: 4.3 Consensus size: 80
2242571 ATATTACAGG
* * * ** *
2242581 TCATGTTG-AAAAAATATTATTGTTGCACGCTATATATAAAAATATATTACACATTATGGTTAAA
1 TCATGTTGAAAAAAATATTATTGTTGCACGCCATATATAAAAACATGTTACACACCATAGTTAAA
2242645 AAAAGTTGTT--ATA
66 AAAAGTTGTTACATA
** * * *
2242658 TGCTATGTTGAAAAAAAATATTATTGTTATATGTCATGTATAAAAACATGTTACACACCATAGTT
1 T-C-ATGTTG-AAAAAAATATTATTGTTGCACGCCATATATAAAAACATGTTACACACCATAGTT
*
2242723 -AAAAAAGTTGTTATATA
63 AAAAAAAGTTGTTACATA
* * * **
2242740 TCATATTGAAAAAAATATTATTGTTGCACGCCATATATAAAAACACGTTACACGCCATAAATAAA
1 TCATGTTGAAAAAAATATTATTGTTGCACGCCATATATAAAAACATGTTACACACCATAGTTAAA
* *
2242805 AAAAGTTATTACACA
66 AAAAGTTGTTACATA
* * **
2242820 -CTATGTTAGAAAAAAAATATTATTGTTAG-ACGTCATGTATAAAAACATGTTACACGTCAT-GA
1 TC-ATGTT-G-AAAAAAATATTATTGTT-GCACGCCATATATAAAAACATGTTACACACCATAG-
*
2242882 TTAAAAAAAGTTGTTACAAA
61 TTAAAAAAAGTTGTTACATA
*
2242902 TCATATTGAAAAAAA-ATATATTGTT
1 TCATGTTGAAAAAAATAT-TATTGTT
2242927 ATTACATATT
Statistics
Matches: 221, Mismatches: 34, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
77 1 0.00
78 1 0.00
79 54 0.24
80 49 0.22
81 45 0.20
82 69 0.31
83 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (80 bp):
TCATGTTGAAAAAAATATTATTGTTGCACGCCATATATAAAAACATGTTACACACCATAGTTAAA
AAAAGTTGTTACATA
Found at i:2242896 original size:26 final size:25
Alignment explanation
Indices: 2242841--2242916 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 25
2242831 AAAAAATATT
* *
2242841 ATTGTTAGACGTCATG-TATAAAAAC
1 ATTGTTACACGTCATGAT-TAAAAAA
2242866 A-TGTTACACGTCATGATTAAAAAA
1 ATTGTTACACGTCATGATTAAAAAA
**
2242890 AGTTGTTACAAATCAT-ATTGAAAAAA
1 A-TTGTTACACGTCATGATT-AAAAAA
2242916 A
1 A
2242917 ATATATTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
24 20 0.47
25 5 0.12
26 18 0.42
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (25 bp):
ATTGTTACACGTCATGATTAAAAAA
Found at i:2242913 original size:25 final size:26
Alignment explanation
Indices: 2242867--2242916 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2242857 TATAAAAACA
**
2242867 TGTTACACGTCATGATTAAAAAAAGT
1 TGTTACAAATCATGATTAAAAAAAGT
2242893 TGTTACAAATCAT-ATTGAAAAAAA
1 TGTTACAAATCATGATT-AAAAAAA
2242917 ATATATTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (26 bp):
TGTTACAAATCATGATTAAAAAAAGT
Found at i:2243126 original size:27 final size:27
Alignment explanation
Indices: 2243035--2243146 Score: 82
Period size: 27 Copynumber: 4.1 Consensus size: 27
2243025 CGCTATATAT
* *
2243035 AAAAATA-TGTTACATGTTATGTTCAA
1 AAAAATATTGTTACATGTTATATTTAA
* * * * * * * *
2243061 AAATATTTTTTTATACGTCATGTTAAA
1 AAAAATATTGTTACATGTTATATTTAA
2243088 AAAATATTATTGTTACATGTTATATTTAA
1 AAAA-A-TATTGTTACATGTTATATTTAA
* *
2243117 AAAAATATTGTTACATTTTAATACTTAA
1 AAAAATATTGTTACATGTT-ATATTTAA
2243145 AA
1 AA
2243147 TGTTGTTGTT
Statistics
Matches: 65, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
26 5 0.08
27 30 0.46
28 11 0.17
29 19 0.29
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (27 bp):
AAAAATATTGTTACATGTTATATTTAA
Found at i:2243679 original size:11 final size:11
Alignment explanation
Indices: 2243663--2243700 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
2243653 AAGTAATTTT
2243663 ATTAAATAATA
1 ATTAAATAATA
*
2243674 ATTAAAT-ATG
1 ATTAAATAATA
2243684 ATTAAA-AATA
1 ATTAAATAATA
2243694 ATTAAAT
1 ATTAAAT
2243701 TTATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
ATTAAATAATA
Found at i:2246485 original size:2 final size:2
Alignment explanation
Indices: 2246478--2246503 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2246468 TGCCTCACTA
2246478 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
2246504 TATGAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2247322 original size:2 final size:2
Alignment explanation
Indices: 2247317--2247376 Score: 52
Period size: 2 Copynumber: 30.5 Consensus size: 2
2247307 ACCACACATA
* * **
2247317 CT CT CT CC CT CC CT CT CT CT CT CT CT CT NA CT ACT CT CT C- CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT CT CT CT
*
2247359 CC CT C- CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
2247377 CCTCCCTCCC
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
1 2 0.04
2 41 0.91
3 2 0.04
ACGTcount: A:0.03, C:0.55, G:0.00, T:0.40
Consensus pattern (2 bp):
CT
Found at i:2247381 original size:4 final size:4
Alignment explanation
Indices: 2247356--2247419 Score: 101
Period size: 4 Copynumber: 15.8 Consensus size: 4
2247346 ACTACTCTCT
* *
2247356 CCTC CCTC CTCTC TCTC TCTC CCTC CCTC CCTC CCTC CCTC CCTC CCTC
1 CCTC CCTC C-CTC CCTC CCTC CCTC CCTC CCTC CCTC CCTC CCTC CCTC
2247405 CCTC CCTC CCTC CCT
1 CCTC CCTC CCTC CCT
2247420 AGTTATAGTG
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
4 54 0.95
5 3 0.05
ACGTcount: A:0.00, C:0.70, G:0.00, T:0.30
Consensus pattern (4 bp):
CCTC
Found at i:2248565 original size:2 final size:2
Alignment explanation
Indices: 2248558--2248589 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2248548 GCTTTAAAGC
2248558 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2248590 AAGGGAGCAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2253900 original size:11 final size:11
Alignment explanation
Indices: 2253856--2253903 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
2253846 AACAATATTT
2253856 TTAATAAATTA
1 TTAATAAATTA
2253867 TT-ATAAA-TA
1 TTAATAAATTA
*
2253876 AT-ATAAATTTA
1 TTAATAAA-TTA
2253887 TTAATAAATTA
1 TTAATAAATTA
2253898 TTAATA
1 TTAATA
2253904 TTTAATTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 8 0.25
10 5 0.16
11 14 0.44
12 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTAATAAATTA
Found at i:2253906 original size:21 final size:19
Alignment explanation
Indices: 2253860--2253923 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 19
2253850 ATATTTTTAA
*
2253860 TAAA-TTATTATAAATAAT
1 TAAATTTATTATAAATTAT
2253878 ATAAATTTATTAATAAATTAT
1 -TAAATTTATT-ATAAATTAT
*
2253899 TAATATTTAATTGTAAATTAT
1 TAA-ATTT-ATTATAAATTAT
2253920 TAAA
1 TAAA
2253924 ATATTAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.10
20 9 0.23
21 23 0.59
22 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TAAATTTATTATAAATTAT
Found at i:2253928 original size:29 final size:30
Alignment explanation
Indices: 2253886--2253951 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
2253876 ATATAAATTT
* * *
2253886 ATTAATAAATTATTAATA-TTTAATTGTAA
1 ATTATTAAAATATTAATATTTTAATTATAA
2253915 ATTATTAAAATATTAATATTTTAATTATAA
1 ATTATTAAAATATTAATATTTTAATTATAA
2253945 ATTATTA
1 ATTATTA
2253952 TTATGTTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
ATTATTAAAATATTAATATTTTAATTATAA
Found at i:2254125 original size:21 final size:22
Alignment explanation
Indices: 2254085--2254125 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2254075 TTAAATATTT
* *
2254085 TAAAAGTAAAATAGAGAAAACA
1 TAAAAGTAAAATAAAAAAAACA
2254107 TAAAA-TAAAATAAAAAAAA
1 TAAAAGTAAAATAAAAAAAA
2254126 GTAATCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (22 bp):
TAAAAGTAAAATAAAAAAAACA
Found at i:2255157 original size:2 final size:2
Alignment explanation
Indices: 2255150--2255184 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2255140 AGGATACGTG
2255150 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2255185 TAAATTAAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2256503 original size:18 final size:18
Alignment explanation
Indices: 2256461--2256503 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2256451 TATGCTTAAT
2256461 AAGAGAAAAAAAAAAGGG
1 AAGAGAAAAAAAAAAGGG
* * *
2256479 AAAAGAAAATATAAAGGG
1 AAGAGAAAAAAAAAAGGG
*
2256497 GAGAGAA
1 AAGAGAA
2256504 GGAAATTAGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (18 bp):
AAGAGAAAAAAAAAAGGG
Found at i:2256894 original size:2 final size:2
Alignment explanation
Indices: 2256887--2256924 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2256877 TTATAGCAAG
* *
2256887 TA TA TA TA TT TA TA TA TT TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2256925 GGTTAATATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2279235 original size:22 final size:22
Alignment explanation
Indices: 2279200--2279241 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2279190 AATGATGACG
*
2279200 TGACATATTAATGTGATATTGA
1 TGACATAATAATGTGATATTGA
* *
2279222 TGACATAATCATGTGGTATT
1 TGACATAATAATGTGATATT
2279242 TTTACCATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.40
Consensus pattern (22 bp):
TGACATAATAATGTGATATTGA
Found at i:2284496 original size:14 final size:13
Alignment explanation
Indices: 2284456--2284502 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
2284446 ATGATTTTAA
*
2284456 AATTTAATTTATT
1 AATTTAATTCATT
*
2284469 -ATTTAA-TAATT
1 AATTTAATTCATT
2284480 AATTTTAATTCATT
1 AA-TTTAATTCATT
2284494 AATTTAATT
1 AATTTAATT
2284503 TGCATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 4 0.14
12 7 0.24
13 12 0.41
14 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTTAATTCATT
Found at i:2284500 original size:19 final size:20
Alignment explanation
Indices: 2284456--2284503 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2284446 ATGATTTTAA
* *
2284456 AATTTAATTTATTATTTAAT
1 AATTTAATTTATAATTCAAT
*
2284476 AA-TTAATTT-TAATTCATT
1 AATTTAATTTATAATTCAAT
2284494 AATTTAATTT
1 AATTTAATTT
2284504 GCATAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.33
19 14 0.58
20 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTAATTTATAATTCAAT
Found at i:2296106 original size:16 final size:17
Alignment explanation
Indices: 2296086--2296122 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2296076 GGTTAAATTG
2296086 ATTTTT-TTAAAAATA-
1 ATTTTTATTAAAAATAT
*
2296101 ATTTTTATTATAAATAT
1 ATTTTTATTAAAAATAT
2296118 ATTTT
1 ATTTT
2296123 CTCTCTCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 8 0.42
17 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTTATTAAAAATAT
Found at i:2316357 original size:2 final size:2
Alignment explanation
Indices: 2316350--2316390 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
2316340 GTCTTGACAA
2316350 AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT -T AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2316388 AT A
1 AT A
2316391 AGCAAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.11
2 31 0.89
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:2316361 original size:8 final size:8
Alignment explanation
Indices: 2316350--2316390 Score: 54
Period size: 7 Copynumber: 5.6 Consensus size: 8
2316340 GTCTTGACAA
2316350 ATATATAT
1 ATATATAT
2316358 ATATATAT
1 ATATATAT
2316366 ATAT-TAT
1 ATATATAT
2316373 AT-TAT-T
1 ATATATAT
2316379 ATATATAT
1 ATATATAT
2316387 -TATA
1 ATATA
2316391 AGCAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
6 4 0.13
7 13 0.43
8 13 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
ATATATAT
Found at i:2316381 original size:17 final size:19
Alignment explanation
Indices: 2316351--2316390 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
2316341 TCTTGACAAA
2316351 TATATATATATATATATAT
1 TATATATATATATATATAT
2316370 TATAT-TAT-TATATATAT
1 TATATATATATATATATAT
2316387 TATA
1 TATA
2316391 AGCAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.62
18 3 0.14
19 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATATATATATATATAT
Found at i:2339608 original size:24 final size:25
Alignment explanation
Indices: 2339575--2339622 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
2339565 TACTAGGCCA
2339575 AAAGCAGCAAGAGA-AAGCAACACT
1 AAAGCAGCAAGAGACAAGCAACACT
*
2339599 AAAGCGGCAAGAGAGCAAGCAACA
1 AAAGCAGCAAGAGA-CAAGCAACA
2339623 AAAAACCGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
26 8 0.38
ACGTcount: A:0.52, C:0.21, G:0.25, T:0.02
Consensus pattern (25 bp):
AAAGCAGCAAGAGACAAGCAACACT
Found at i:2343029 original size:13 final size:13
Alignment explanation
Indices: 2343011--2343044 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2343001 TCATTTTATT
2343011 TATTTTTTACTAA
1 TATTTTTTACTAA
*
2343024 TATTTTTTATTAA
1 TATTTTTTACTAA
2343037 T-TTTTTTA
1 TATTTTTTA
2343045 AAAAAGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTTTTACTAA
Found at i:2355703 original size:28 final size:27
Alignment explanation
Indices: 2355677--2355737 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
2355667 ATCCTAAATT
2355677 AAAATCACAAAGTAAAAATTATTAAATAA
1 AAAATCA-AAAGTAAAAA-TATTAAATAA
* *
2355706 AAAATTAAAATTAAAAATATTAAA-AA
1 AAAATCAAAAGTAAAAATATTAAATAA
2355732 TAAAAT
1 -AAAAT
2355738 AAGTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 2 0.07
27 12 0.41
28 9 0.31
29 6 0.21
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (27 bp):
AAAATCAAAAGTAAAAATATTAAATAA
Found at i:2355706 original size:14 final size:14
Alignment explanation
Indices: 2355689--2355729 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2355679 AATCACAAAG
2355689 TAAAAATTATTAAA-
1 TAAAAA-TATTAAAT
2355703 TAAAAA-ATTAAAAT
1 TAAAAATATT-AAAT
2355717 TAAAAATATTAAA
1 TAAAAATATTAAA
2355730 AATAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.12
13 3 0.12
14 15 0.62
15 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAAAATATTAAAT
Found at i:2355710 original size:15 final size:15
Alignment explanation
Indices: 2355690--2355747 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
2355680 ATCACAAAGT
2355690 AAAAATTATTAAATA
1 AAAAATTATTAAATA
*
2355705 AAAAATTA--AAATT
1 AAAAATTATTAAATA
2355718 AAAAA-TATTAAA-A
1 AAAAATTATTAAATA
* *
2355731 ATAAAATAAGTAAATA
1 A-AAAATTATTAAATA
2355747 A
1 A
2355748 GCCAAACTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
12 2 0.06
13 10 0.29
14 7 0.21
15 13 0.38
16 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (15 bp):
AAAAATTATTAAATA
Found at i:2364332 original size:2 final size:2
Alignment explanation
Indices: 2364325--2364355 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2364315 GTGTCAAATC
2364325 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2364356 ATAATTATTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2374500 original size:100 final size:100
Alignment explanation
Indices: 2374321--2374613 Score: 387
Period size: 98 Copynumber: 3.0 Consensus size: 100
2374311 GAAAGATCGG
* * * * *
2374321 AGTAAAAGGAACGTTACAAAATATTTTGAAAGACTTGATAAAAATATTAAGTCTAATTCAATAAA
1 AGTAAAATGAACGTTACAAAATATTTTGAAAGACTTGGTAAAAAGATTGAGTCTAATTCAATCAA
*
2374386 AAATTAGTTCTTTTTTTACCAGGATAAAAATTTCA
66 AAATTAATTCTTTTTTTACCAGGATAAAAATTTCA
* *
2374421 AGTAAAATGAACGTTACAGAATATTTTGAAAGAGTTGGTAAAAAGATTGAGTCTAATTCAATCAA
1 AGTAAAATGAACGTTACAAAATATTTTGAAAGACTTGGTAAAAAGATTGAGTCTAATTCAATCAA
* * *
2374486 AAATTAA-T-TTTTTTTAGCATGAGAAAAATTTCA
66 AAATTAATTCTTTTTTTACCAGGATAAAAATTTCA
** * *
2374519 AGTAAAATGAACGTTACAAAATATACTAAAAGACCTGGTAAAAAGATTGAGT-TAGATTCAATCA
1 AGTAAAATGAACGTTACAAAATATTTTGAAAGACTTGGTAAAAAGATTGAGTCTA-ATTCAATCA
* *
2374583 AAAACTAATTCTTTCTTTACCATGG-TAAAAA
65 AAAATTAATTCTTTTTTTACCA-GGATAAAAA
2374614 GACTAAGTCA
Statistics
Matches: 167, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
97 2 0.01
98 84 0.50
99 2 0.01
100 78 0.47
101 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (100 bp):
AGTAAAATGAACGTTACAAAATATTTTGAAAGACTTGGTAAAAAGATTGAGTCTAATTCAATCAA
AAATTAATTCTTTTTTTACCAGGATAAAAATTTCA
Found at i:2382109 original size:2 final size:2
Alignment explanation
Indices: 2382104--2382153 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2382094 TATTTGTGTG
2382104 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2382146 TA T- TA TA T
1 TA TA TA TA T
2382154 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2382179 original size:2 final size:2
Alignment explanation
Indices: 2382172--2382226 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
2382162 NNNNNNGTTA
*
2382172 AT AT AT AT AT AT -T AT AT AT AT GT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2382212 AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2382227 TATCTGTTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2382189 original size:11 final size:11
Alignment explanation
Indices: 2382173--2382229 Score: 89
Period size: 11 Copynumber: 5.3 Consensus size: 11
2382163 NNNNNGTTAA
2382173 TATATATATAT
1 TATATATATAT
*
2382184 TATATATATGT
1 TATATATATAT
*
2382195 AATATATATA-
1 TATATATATAT
2382205 TATATATATAT
1 TATATATATAT
2382216 TATATATATAT
1 TATATATATAT
2382227 TAT
1 TAT
2382230 CTGTTACATT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.22
11 32 0.78
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
TATATATATAT
Found at i:2389842 original size:123 final size:121
Alignment explanation
Indices: 2389705--2389951 Score: 440
Period size: 123 Copynumber: 2.0 Consensus size: 121
2389695 CACACAGTAG
*
2389705 CAGCTAAAACCGAAACAGTTATCAGCAATTGGACAAACTGGAGAATACCCAGATAAACAAATGCG
1 CAGCTAAAACCGAAACAGTTATCAGCAATTGGACAAACTGGAGAATACCCAGATAAACAAATGCC
*
2389770 ACTTAAAAGAGAAAAGAAAGAGTTTTTTTTACCTCAGCTTTTGTAAATCCAGAGAAGA
66 ACTTAAAAGAG-AAAGAAAGAG-TTTTTTTACCTCAGCTTTCGTAAATCCAGAGAAGA
* *
2389828 CAGCTAAAACCGAAACAGTTATCAGCAATTGGACAAACTGGTGAATGCCCAGATAAACAAATGCC
1 CAGCTAAAACCGAAACAGTTATCAGCAATTGGACAAACTGGAGAATACCCAGATAAACAAATGCC
2389893 ACTTAAAAGAGAAAGAAAGAGTTTTTTTACCTCAGCTTTCGTAAATCCAGAGAAGA
66 ACTTAAAAGAGAAAGAAAGAGTTTTTTTACCTCAGCTTTCGTAAATCCAGAGAAGA
2389949 CAG
1 CAG
2389952 GTCTCTGTCT
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
121 37 0.31
122 10 0.08
123 73 0.61
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (121 bp):
CAGCTAAAACCGAAACAGTTATCAGCAATTGGACAAACTGGAGAATACCCAGATAAACAAATGCC
ACTTAAAAGAGAAAGAAAGAGTTTTTTTACCTCAGCTTTCGTAAATCCAGAGAAGA
Found at i:2390589 original size:20 final size:21
Alignment explanation
Indices: 2390545--2390592 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
2390535 GTTAATAAAA
*
2390545 TATAAA-ATAAATTTTCAGTT
1 TATAAATAAAAATTTTCAGTT
2390565 TATAAATAAAAATTTT-A-TT
1 TATAAATAAAAATTTTCAGTT
2390584 TAATAAATA
1 T-ATAAATA
2390593 TATATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 14 0.56
21 8 0.32
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TATAAATAAAAATTTTCAGTT
Found at i:2414558 original size:437 final size:436
Alignment explanation
Indices: 2413744--2414621 Score: 1722
Period size: 437 Copynumber: 2.0 Consensus size: 436
2413734 TTTTCTTTTG
2413744 TTACATGGCTTCGCTAATTAGAAGAACCTTTTTATACTAAAACAAACTAAAGCCAAATGTTATTA
1 TTACATGGCTTCGCTAATTAGAAGAACCTTTTTATACTAAAACAAACTAAAGCCAAATGTTATTA
2413809 TGAAATTGTGGTTTTGGTAATGCAATTTCTTTGACATAGTTGCCTGTACTTCTATCAATTGTTGA
66 TGAAATTGTGGTTTTGGTAATGCAATTTCTTTGACATAGTTGCCTGTACTTCTATCAATTGTTGA
2413874 CTATATCTAATCTAGTGGCAGCCATATGCTAATTTCATTTTGTTTAAGACATTCCAATTCTAGGC
131 CTATATCTAATCTAGTGGCAGCCATATGCTAATTTCATTTTGTTTAAGACATTCCAATTCTAGGC
2413939 TAGCCAATTAGCATGTGTCTGTACCTTTTGTAAACATGTTGCTAGTTGCATATGGTTTCTACATC
196 TAGCCAATTAGCATGTGTCTGTACCTTTTGTAAACATGTTGCTAGTTGCATATGGTTTCTACATC
2414004 GGGATCCATTGATCTTTCTAGAGCATGATCTGTTTGACTGTACATTTTGCTTGCTCCAGATTCCA
261 GGGATCCATTGATCTTTCTAGAGCATGATCTGTTTGACTGTACATTTTGCTTGCTCCAGATTCCA
2414069 CTCCTATGGAATTTTATCTGCATATGGTGCCCTGATCTGAAAAGTTGAATGCAAA-TTTTTTTTT
326 CTCCTATGGAATTTTATCTGCATATGGTGCCCTGATCTGAAAAGTTGAATGCAAATTTTTTTTTT
2414133 TCTAGTAATTGACTCGTGACAATGATTAGTTGCTTTATTCTTTGTCTT
391 TCTAGTAATTGACTCGTGACAATGATTAGTTGCTTTATTC--TGTCTT
2414181 TTACATGGCTTCGCTAATTAGAAGAACCTTTTTATACTAAAACAAACTAAAGCCAAATGTTATTA
1 TTACATGGCTTCGCTAATTAGAAGAACCTTTTTATACTAAAACAAACTAAAGCCAAATGTTATTA
2414246 TGAAATTGTGGTTTTGGTAATGCAATTTCTTTGACATAGTTGCCTGTACTTCTATCAATTGTTGA
66 TGAAATTGTGGTTTTGGTAATGCAATTTCTTTGACATAGTTGCCTGTACTTCTATCAATTGTTGA
2414311 CTATATCTAATCTAGTGGCAGCCATATGCTAATTTCATTTTGTTTAAGACATTCCAATTCTAGGC
131 CTATATCTAATCTAGTGGCAGCCATATGCTAATTTCATTTTGTTTAAGACATTCCAATTCTAGGC
2414376 TAGCCAATTAGCATGTGTCTGTACCTTTTGTAAACATGTTGCTAGTTGCATATGGTTTCTACATC
196 TAGCCAATTAGCATGTGTCTGTACCTTTTGTAAACATGTTGCTAGTTGCATATGGTTTCTACATC
2414441 GGGATCCATTGATCTTTCTAGAGCATGATCTGTTTGACTGTACATTTTGCTTGCTCCAGATTCCA
261 GGGATCCATTGATCTTTCTAGAGCATGATCTGTTTGACTGTACATTTTGCTTGCTCCAGATTCCA
*
2414506 CTCCTATGGAATTTTGTCTGCATATGGTGCCCTGATCTGAAAAGTTGAATGCAAATTTTTTTTTT
326 CTCCTATGGAATTTTATCTGCATATGGTGCCCTGATCTGAAAAGTTGAATGCAAATTTTTTTTTT
2414571 TCTAGTAATTGACTCGTGACAATGATTAGTTGCTTTATTCTGTCTT
391 TCTAGTAATTGACTCGTGACAATGATTAGTTGCTTTATTCTGTCTT
2414617 TTACA
1 TTACA
2414622 ATTCTTAAAT
Statistics
Matches: 439, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
436 11 0.03
437 379 0.86
438 49 0.11
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (436 bp):
TTACATGGCTTCGCTAATTAGAAGAACCTTTTTATACTAAAACAAACTAAAGCCAAATGTTATTA
TGAAATTGTGGTTTTGGTAATGCAATTTCTTTGACATAGTTGCCTGTACTTCTATCAATTGTTGA
CTATATCTAATCTAGTGGCAGCCATATGCTAATTTCATTTTGTTTAAGACATTCCAATTCTAGGC
TAGCCAATTAGCATGTGTCTGTACCTTTTGTAAACATGTTGCTAGTTGCATATGGTTTCTACATC
GGGATCCATTGATCTTTCTAGAGCATGATCTGTTTGACTGTACATTTTGCTTGCTCCAGATTCCA
CTCCTATGGAATTTTATCTGCATATGGTGCCCTGATCTGAAAAGTTGAATGCAAATTTTTTTTTT
TCTAGTAATTGACTCGTGACAATGATTAGTTGCTTTATTCTGTCTT
Found at i:2415967 original size:4 final size:4
Alignment explanation
Indices: 2415952--2415984 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
2415942 AAATGATATT
2415952 TTAA TTAA -TAA TTAA TTAA TTAA TT-A TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
2415985 TAAAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:2415972 original size:15 final size:15
Alignment explanation
Indices: 2415952--2415984 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2415942 AAATGATATT
2415952 TTAATTAATAATTAA
1 TTAATTAATAATTAA
*
2415967 TTAATTAATTATTAA
1 TTAATTAATAATTAA
2415982 TTA
1 TTA
2415985 TAAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAATTAATAATTAA
Found at i:2415983 original size:11 final size:12
Alignment explanation
Indices: 2415952--2415984 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2415942 AAATGATATT
2415952 TTAATTAA-TAA
1 TTAATTAATTAA
2415963 TTAATTAATTAA
1 TTAATTAATTAA
2415975 TT-ATTAATTA
1 TTAATTAATTA
2415985 TAAAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTAATTAA
Found at i:2416019 original size:30 final size:27
Alignment explanation
Indices: 2415983--2416053 Score: 99
Period size: 30 Copynumber: 2.5 Consensus size: 27
2415973 AATTATTAAT
2415983 TATAAAAATTTATTAAATTTAAAATAAAAA
1 TATAAAAATTTATT-AATTT--AATAAAAA
2416013 TATAAAAATTTAATTAATTTAATAAAAA
1 TATAAAAATTT-ATTAATTTAATAAAAA
2416041 -ATAAAAATTTATT
1 TATAAAAATTTATT
2416054 TAAAATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
26 3 0.08
27 10 0.25
28 8 0.20
30 16 0.40
31 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TATAAAAATTTATTAATTTAATAAAAA
Found at i:2420825 original size:15 final size:15
Alignment explanation
Indices: 2420798--2420842 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
2420788 TCAACTAAAC
2420798 TTATTTTCTAAGAAT
1 TTATTTTCTAAGAAT
*
2420813 TT-TTTTTTGAAG-AT
1 TTATTTTCT-AAGAAT
2420827 TTATTTTCTAAGAAT
1 TTATTTTCTAAGAAT
2420842 T
1 T
2420843 AAAATATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (15 bp):
TTATTTTCTAAGAAT
Found at i:2420839 original size:14 final size:14
Alignment explanation
Indices: 2420798--2420839 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2420788 TCAACTAAAC
2420798 TTATTTTCTAAGAAT
1 TTATTTTCTAAG-AT
*
2420813 TT-TTTTTTGAAGAT
1 TTATTTTCT-AAGAT
2420827 TTATTTTCTAAGA
1 TTATTTTCTAAGA
2420840 ATTAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.57
Consensus pattern (14 bp):
TTATTTTCTAAGAT
Found at i:2423677 original size:20 final size:19
Alignment explanation
Indices: 2423648--2423685 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2423638 AAAAATTTTA
*
2423648 TTTAAAATTTTTTGAAATG
1 TTTAAAATTTTTTAAAATG
2423667 TTTATAAATTTTTTAAAAT
1 TTTA-AAATTTTTTAAAAT
2423686 ATTATACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTAAAATTTTTTAAAATG
Found at i:2423690 original size:19 final size:20
Alignment explanation
Indices: 2423652--2423691 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2423642 ATTTTATTTA
* *
2423652 AAATTTTTTGAAATGTTTAT
1 AAATTTTTTAAAATGATTAT
2423672 AAATTTTTTAAAAT-ATTAT
1 AAATTTTTTAAAATGATTAT
2423691 A
1 A
2423692 CTAAAATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
AAATTTTTTAAAATGATTAT
Found at i:2425160 original size:18 final size:18
Alignment explanation
Indices: 2425137--2425172 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2425127 GAGGCAGGGC
2425137 TCACCGTCATCAACATCA
1 TCACCGTCATCAACATCA
*
2425155 TCACCGTCATCATCATCA
1 TCACCGTCATCAACATCA
2425173 GCTTCCTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.39, G:0.06, T:0.25
Consensus pattern (18 bp):
TCACCGTCATCAACATCA
Found at i:2428702 original size:20 final size:20
Alignment explanation
Indices: 2428674--2428723 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2428664 ATAATATTGT
* *
2428674 AATTATTTTTAACAAATGA-A
1 AATTTTTTTTAACAAA-AATA
*
2428694 AATTTTTTTAAACAAAAATA
1 AATTTTTTTTAACAAAAATA
2428714 AATTTTTTTT
1 AATTTTTTTT
2428724 TTGTATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (20 bp):
AATTTTTTTTAACAAAAATA
Found at i:2429565 original size:3 final size:3
Alignment explanation
Indices: 2429557--2429590 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2429547 ATTACAAACT
*
2429557 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2429591 ATTTCAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2436404 original size:2 final size:2
Alignment explanation
Indices: 2436381--2436429 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
2436371 GAAGTGTAAA
* *
2436381 AG AG TG AG AG ATG -G AG AC AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
2436423 AA AG AG A
1 AG AG AG A
2436430 TGATTTAACT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.45, T:0.04
Consensus pattern (2 bp):
AG
Found at i:2452354 original size:169 final size:169
Alignment explanation
Indices: 2452068--2452406 Score: 660
Period size: 169 Copynumber: 2.0 Consensus size: 169
2452058 CAATAAAGAT
2452068 AGCCATATTATGATGTGACAATCGTACTATACTCAATCATAATAAGAGTCATTCCCATATCCCTT
1 AGCCATATTATGATGTGACAATCGTACTATACTCAATCATAATAAGAGTCATTCCCATATCCCTT
*
2452133 ATATTTCTATGTTATCACAAGATGGCCATTAATATGATGCTATATAGAAATCATGGATGCACAAG
66 ATATTTCTATGTTATCACAAGATGGCCATTAATATGATGCTATATAGAAATCATGGATACACAAG
2452198 TTAGGACTCATGAGAATCTATGGCTAAGACTAATAAATC
131 TTAGGACTCATGAGAATCTATGGCTAAGACTAATAAATC
*
2452237 AGCCATTTTATGATGTGACAATCGTACTATACTCAATCATAATAAGAGTCATTCCCATATCCCTT
1 AGCCATATTATGATGTGACAATCGTACTATACTCAATCATAATAAGAGTCATTCCCATATCCCTT
2452302 ATATTTCTATGTTATCACAAGATGGCCATTAATATGATGCTATATAGAAATCATGGATACACAAG
66 ATATTTCTATGTTATCACAAGATGGCCATTAATATGATGCTATATAGAAATCATGGATACACAAG
2452367 TTAGGACTCATGAGAATCTATGGCTAAGACTAATAAATC
131 TTAGGACTCATGAGAATCTATGGCTAAGACTAATAAATC
2452406 A
1 A
2452407 TACAGTACAG
Statistics
Matches: 168, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 168 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (169 bp):
AGCCATATTATGATGTGACAATCGTACTATACTCAATCATAATAAGAGTCATTCCCATATCCCTT
ATATTTCTATGTTATCACAAGATGGCCATTAATATGATGCTATATAGAAATCATGGATACACAAG
TTAGGACTCATGAGAATCTATGGCTAAGACTAATAAATC
Found at i:2461323 original size:17 final size:18
Alignment explanation
Indices: 2461301--2461336 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2461291 AGAGAGAAAA
*
2461301 AAAAGAAAGAAAA-TAAT
1 AAAAGAAACAAAAGTAAT
2461318 AAAAGAAACAAAAGTAAT
1 AAAAGAAACAAAAGTAAT
2461336 A
1 A
2461337 TATAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.75, C:0.03, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAAGAAACAAAAGTAAT
Found at i:2461485 original size:31 final size:33
Alignment explanation
Indices: 2461438--2461504 Score: 102
Period size: 31 Copynumber: 2.1 Consensus size: 33
2461428 TTTTGAAATA
2461438 AAAATATTAAAAAAATTAAATTAAAATAATTTT
1 AAAATATTAAAAAAATTAAATTAAAATAATTTT
**
2461471 AAAAT-TT-AAAAAATTAAATTATTATAATTTT
1 AAAATATTAAAAAAATTAAATTAAAATAATTTT
2461502 AAA
1 AAA
2461505 CAAAAAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 25 0.78
32 2 0.06
33 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
AAAATATTAAAAAAATTAAATTAAAATAATTTT
Found at i:2461703 original size:17 final size:19
Alignment explanation
Indices: 2461681--2461716 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2461671 TAAAATTTTG
2461681 ATAAAATA-AT-ATAATAT
1 ATAAAATATATGATAATAT
2461698 ATAAAATATATGATAATAT
1 ATAAAATATATGATAATAT
2461717 TTATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
ATAAAATATATGATAATAT
Found at i:2469944 original size:7 final size:7
Alignment explanation
Indices: 2469932--2469960 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2469922 GAGAAGGAAA
2469932 GGGAGAG
1 GGGAGAG
2469939 GGGAGAG
1 GGGAGAG
2469946 GGGAGAG
1 GGGAGAG
2469953 GGGAGAG
1 GGGAGAG
2469960 G
1 G
2469961 CCAAGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.72, T:0.00
Consensus pattern (7 bp):
GGGAGAG
Found at i:2471876 original size:19 final size:19
Alignment explanation
Indices: 2471852--2471888 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2471842 AACAGAACAT
*
2471852 TTTTACTCTTTGATTGAAA
1 TTTTACTCTTTAATTGAAA
*
2471871 TTTTACTTTTTAATTGAA
1 TTTTACTCTTTAATTGAA
2471889 TCACTAATTT
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:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (19 bp):
TTTTACTCTTTAATTGAAA
Found at i:2472864 original size:30 final size:30
Alignment explanation
Indices: 2472830--2472897 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
2472820 TGTGTATATC
* *
2472830 TAACTCTAACTAGCTAACAGTATTATATTA
1 TAACTCTAACTAGCTAACAATATTACATTA
*
2472860 TAACTCTAACTAGCTAACAATATTGCATTA
1 TAACTCTAACTAGCTAACAATATTACATTA
*
2472890 TAATTCTA
1 TAACTCTA
2472898 CTTAGATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.40, C:0.18, G:0.06, T:0.37
Consensus pattern (30 bp):
TAACTCTAACTAGCTAACAATATTACATTA
Found at i:2479142 original size:2 final size:2
Alignment explanation
Indices: 2479137--2479178 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2479127 CGCGCGCGCG
* *
2479137 CA CA CA CA CA CA CA CA CA CC CA CA CA CA CA CA CA CA TA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2479179 TGCATCATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.50, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:2487033 original size:336 final size:336
Alignment explanation
Indices: 2486420--2487096 Score: 1336
Period size: 336 Copynumber: 2.0 Consensus size: 336
2486410 TCCAAGCTAC
2486420 AAGGAGCCATATATCAAAGTTCCTAAAGTATTGAACAAGGAGTAAGACTGTTTGGGTACCACATT
1 AAGGAGCCATATATCAAAGTTCCTAAAGTATTGAACAAGGAGTAAGACTGTTTGGGTACCACATT
2486485 ATTCTCTCTTTAGTACCCAAAGAATTTCATGTACGTAAGTGGCCTCAAATTCTCATTTATAAGCT
66 ATTCTCTCTTTAGTACCCAAAGAATTTCATGTACGTAAGTGGCCTCAAATTCTCATTTATAAGCT
2486550 TTGGAGGAGATGAATTCCCCACTGATATCCCTCTTTGTATTGTTTGTCAATGAACTGATACGCAT
131 TTGGAGGAGATGAATTCCCCACTGATATCCCTCTTTGTATTGTTTGTCAATGAACTGATACGCAT
2486615 TCCCTACACACTTTTCTCTGAAAGATTATGCTTTTTGTTCACTTTGATCAGTTAAATTCTGAGTA
196 TCCCTACACACTTTTCTCTGAAAGATTATGCTTTTTGTTCACTTTGATCAGTTAAATTCTGAGTA
*
2486680 TGTATAGGCAGAACTTAGTGGAACCATTCATGCATATAGAAATCTCGATTATAAGGGAAGAGTGG
261 TGTATAGGCAGAACTTAGTGGAACCATTCATGCACATAGAAATCTCGATTATAAGGGAAGAGTGG
2486745 CTGCCATGACG
326 CTGCCATGACG
2486756 AAGGAGCCATATATCAAAGTTCCTAAAGTATTGAACAAGGAGTAAGACTGTTTGGGTACCACATT
1 AAGGAGCCATATATCAAAGTTCCTAAAGTATTGAACAAGGAGTAAGACTGTTTGGGTACCACATT
*
2486821 ATTCTCTCTTTAGTACCCAAAGAATTTCATGTACGTAGGTGGCCTCAAATTCTCATTTATAAGCT
66 ATTCTCTCTTTAGTACCCAAAGAATTTCATGTACGTAAGTGGCCTCAAATTCTCATTTATAAGCT
2486886 TTGGAGGAGATGAATTCCCCACTGATATCCCTCTTTGTATTGTTTGTCAATGAACTGATACGCAT
131 TTGGAGGAGATGAATTCCCCACTGATATCCCTCTTTGTATTGTTTGTCAATGAACTGATACGCAT
2486951 TCCCTACACACTTTTCTCTGAAAGATTATGCTTTTTGTTCACTTTGATCAGTTAAATTCTGAGTA
196 TCCCTACACACTTTTCTCTGAAAGATTATGCTTTTTGTTCACTTTGATCAGTTAAATTCTGAGTA
2487016 TGTATAGGCAGAACTTAGTGGAACCATTCATGCACATAGAAATCTCGATTATAAGGGAAGAGTGG
261 TGTATAGGCAGAACTTAGTGGAACCATTCATGCACATAGAAATCTCGATTATAAGGGAAGAGTGG
2487081 CTGCCATGACG
326 CTGCCATGACG
2487092 AAGGA
1 AAGGA
2487097 AACTTGCTCG
Statistics
Matches: 339, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
336 339 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (336 bp):
AAGGAGCCATATATCAAAGTTCCTAAAGTATTGAACAAGGAGTAAGACTGTTTGGGTACCACATT
ATTCTCTCTTTAGTACCCAAAGAATTTCATGTACGTAAGTGGCCTCAAATTCTCATTTATAAGCT
TTGGAGGAGATGAATTCCCCACTGATATCCCTCTTTGTATTGTTTGTCAATGAACTGATACGCAT
TCCCTACACACTTTTCTCTGAAAGATTATGCTTTTTGTTCACTTTGATCAGTTAAATTCTGAGTA
TGTATAGGCAGAACTTAGTGGAACCATTCATGCACATAGAAATCTCGATTATAAGGGAAGAGTGG
CTGCCATGACG
Found at i:2499033 original size:83 final size:84
Alignment explanation
Indices: 2498892--2499065 Score: 287
Period size: 83 Copynumber: 2.1 Consensus size: 84
2498882 AGGGTTTGTT
*
2498892 TCATCAATATTCTTCACTCTAGTTAGTATGCATGCTAGGAGCAATATTAGAGCTTTAAGAGGCTT
1 TCATCAATATCCTTCACTC-AGTTAGTATGCATGCTAGGAGCAATATTAGAGCTTTAAGAGGCTT
* *
2498957 CACCAAATAATTTGAATTCA
65 CACCAAAGAATTTAAATTCA
2498977 TCATCAATATCCTTCACTC-GTTAGTATGCATGCTAGGAGCAATATTAGAGCTTTAAGAGGCTTC
1 TCATCAATATCCTTCACTCAGTTAGTATGCATGCTAGGAGCAATATTAGAGCTTTAAGAGGCTTC
* *
2499041 ATCAAAGGATTTAAATTCA
66 ACCAAAGAATTTAAATTCA
2499060 TCATCA
1 TCATCA
2499066 CAACAGCCAA
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
83 66 0.79
85 18 0.21
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (84 bp):
TCATCAATATCCTTCACTCAGTTAGTATGCATGCTAGGAGCAATATTAGAGCTTTAAGAGGCTTC
ACCAAAGAATTTAAATTCA
Found at i:2518350 original size:22 final size:24
Alignment explanation
Indices: 2518319--2518363 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2518309 TGATGTTGGG
*
2518319 TTTTTATGAATCCA-TTTAAGGGA
1 TTTTTATGAATCAAGTTTAAGGGA
2518342 TTTTT-TGAATCAAGTTTAAGGG
1 TTTTTATGAATCAAGTTTAAGGG
2518364 TTGCTGAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (24 bp):
TTTTTATGAATCAAGTTTAAGGGA
Found at i:2522126 original size:2 final size:2
Alignment explanation
Indices: 2522119--2522150 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2522109 CTTTCGTCAA
*
2522119 AG AG AG AG AG AG AG AG AG AG AG CG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2522151 GTATACATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2537258 original size:29 final size:28
Alignment explanation
Indices: 2537226--2537296 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
2537216 AGAATAAAAT
*
2537226 TTTAAATAAATTTTTATTCTTGTATTACA
1 TTTAAATAAATTTTTATTCTTATATTA-A
* * * * *
2537255 TTTAATTAAATATATATTTTTATTTTAA
1 TTTAAATAAATTTTTATTCTTATATTAA
*
2537283 GTTAAATAAATTTT
1 TTTAAATAAATTTT
2537297 AATTATTAAT
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (28 bp):
TTTAAATAAATTTTTATTCTTATATTAA
Found at i:2546089 original size:62 final size:62
Alignment explanation
Indices: 2546013--2546137 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
2546003 ATATTATGGT
2546013 AATATTTTTACACATCTGTTGGGGTTTGGTGAGGGGTTTTATTTCCTTATGAAGATCAACTC
1 AATATTTTTACACATCTGTTGGGGTTTGGTGAGGGGTTTTATTTCCTTATGAAGATCAACTC
2546075 AATATTTTTACACATCTGTTGGGGTTTGGTGAGGGGTTTTATTTCCTTATGAAGATCAACTC
1 AATATTTTTACACATCTGTTGGGGTTTGGTGAGGGGTTTTATTTCCTTATGAAGATCAACTC
2546137 A
1 A
2546138 TTACTTAGTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (62 bp):
AATATTTTTACACATCTGTTGGGGTTTGGTGAGGGGTTTTATTTCCTTATGAAGATCAACTC
Found at i:2547138 original size:37 final size:37
Alignment explanation
Indices: 2547088--2547162 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2547078 CATTGTCAAG
2547088 TAAGTTTTCATTGTTAGTTACAATGTCTTGGAATTAT
1 TAAGTTTTCATTGTTAGTTACAATGTCTTGGAATTAT
2547125 TAAGTTTTCATTGTTAGTTACAATGTCTTGGAATTAT
1 TAAGTTTTCATTGTTAGTTACAATGTCTTGGAATTAT
2547162 T
1 T
2547163 TCACTTTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (37 bp):
TAAGTTTTCATTGTTAGTTACAATGTCTTGGAATTAT
Found at i:2565769 original size:24 final size:24
Alignment explanation
Indices: 2565742--2565808 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
2565732 TATTATAGTG
*
2565742 TAATTTTAATAAAATATTGTA-ATT
1 TAATTTTAATAAAATATTGTATA-A
2565766 TAA--TTAGATAATAATATTGTATAA
1 TAATTTTA-ATAA-AATATTGTATAA
2565790 TAATTTTAATATAAATATT
1 TAATTTTAATA-AAATATT
2565809 TTATGTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
22 3 0.08
23 4 0.11
24 15 0.42
25 10 0.28
26 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
TAATTTTAATAAAATATTGTATAA
Found at i:2575151 original size:414 final size:408
Alignment explanation
Indices: 2574440--2575193 Score: 980
Period size: 414 Copynumber: 1.8 Consensus size: 408
2574430 TTATTTATTC
* *
2574440 AATGACGACTATGTACTATGTATATTAAGAAATGAATAAACCTTTTTAATTTTTTTATTTTGTTC
1 AATGACGACTATGTACTATGTATATTAAGAAATGAATAAACCTTCTTAACTTTTTTATTTTGTTC
* * * * * *
2574505 AATGAATTTGATAAATGTTTATTAGAATTTAAACATTCATATACAAAAAATGTCTATATACTATA
66 AATGAATTGGATAAATATTTATTAAAAATTAAACATTAATATACAAAAAATATCTATATACTATA
* * * * * * *
2574570 AATTTAGGTTGATGCAGAATAAGAAAATATAGATAAAAAATAATATTAAATTGTAATTGATAAAT
131 AATTCAAGTTCATGCAGAATAAGAAAATATAAACAAAAAATAATATTAAATTATAATTGATAAAC
2574635 ATTAAATGAATCTATCTTATAAACATTAAAAGTTGAAAATTATTATTTTTAAATATTTTTTACTA
196 ATTAAATGAATCTATCTTATAAACATT-AAA--TGAAAATTATTATTTTTAAATATTTTTTACTA
*
2574700 AAATAAATAAAAGTAAAAAAAAAACCCTTCAAATGTCAAAAAC-A-TTGTAGTTTTAACATAAGG
258 AAATAAATAAAAGTAAAAAAAAAACCCTTCAAATGTCAAAAACAACTTCT--TTTTAACATAAGG
2574763 TGTAAAAAAAATTAATTTAATTATGAATGACAAATGTCAATTAATTGATCCAATCAATTATCCTA
321 TGTAAAAAAAATTAATTTAATTATGAATGACAAATGTCAATTAATTGATCCAATCAATTATCCTA
2574828 CTTTTATATAATAAATTGGATGA
386 CTTTTATATAATAAATTGGATGA
* * * *
2574851 NAATGATGACTATGTGCTATTTATATTAAGAAATGAATAAACCTTCTTGACTTTTTTATTTTGTT
1 -AATGACGACTATGTACTATGTATATTAAGAAATGAATAAACCTTCTTAACTTTTTTATTTTGTT
* * * * *
2574916 TAATGAATTGGATGAATATTTATTAAAAATTAAACATTTAAGTGTA-AAAGATATATTTATATAC
65 CAATGAATTGGATAAATATTTATTAAAAATTAAACA-TTAA-TATACAAA-AAATATCTATATAC
* * ** * *
2574980 TATAGATTCAAGTTCATGTAGAATAAGAGGATATAAACATAAAATAATATTAAATTATAATTTAT
127 TATAAATTCAAGTTCATGCAGAATAAGAAAATATAAACAAAAAATAATATTAAATTATAATTGAT
* * * * * *
2575045 AAACATTAAATGAATCTGTCTTCTAAGCATT-AA-G-AAATTATTATTTTTTAAGTTTTTTTTAT
192 AAACATTAAATGAATCTATCTTATAAACATTAAATGAAAATTATTA-TTTTTAAATATTTTTTAC
* *
2575107 TAAAATAAATAAAAGTAAAAAAGAAAAAAAATCCTTCAAATGTCAAAAACAACTTCTTTTTGACA
256 TAAAATAAATAAAAGT----AA-AAAAAAAACCCTTCAAATGTCAAAAACAACTTCTTTTTAACA
2575172 TAAGGTGTAAAAAAAATTAATT
316 TAAGGTGTAAAAAAAATTAATT
2575194 CAATAGAAAA
Statistics
Matches: 292, Mismatches: 39, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
408 9 0.03
409 32 0.11
412 90 0.31
413 8 0.03
414 149 0.51
415 1 0.00
416 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (408 bp):
AATGACGACTATGTACTATGTATATTAAGAAATGAATAAACCTTCTTAACTTTTTTATTTTGTTC
AATGAATTGGATAAATATTTATTAAAAATTAAACATTAATATACAAAAAATATCTATATACTATA
AATTCAAGTTCATGCAGAATAAGAAAATATAAACAAAAAATAATATTAAATTATAATTGATAAAC
ATTAAATGAATCTATCTTATAAACATTAAATGAAAATTATTATTTTTAAATATTTTTTACTAAAA
TAAATAAAAGTAAAAAAAAAACCCTTCAAATGTCAAAAACAACTTCTTTTTAACATAAGGTGTAA
AAAAAATTAATTTAATTATGAATGACAAATGTCAATTAATTGATCCAATCAATTATCCTACTTTT
ATATAATAAATTGGATGA
Found at i:2576796 original size:22 final size:22
Alignment explanation
Indices: 2576771--2576827 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
2576761 TAATTATCGT
*
2576771 GTGACTAGTTTTTAGTCATTAC
1 GTGACTAGTTTTTAGGCATTAC
* *
2576793 GTGATTA-ATTTTAGGCATTAC
1 GTGACTAGTTTTTAGGCATTAC
2576814 GTGACTAGTTTTTA
1 GTGACTAGTTTTTA
2576828 TACATTGCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.46
Consensus pattern (22 bp):
GTGACTAGTTTTTAGGCATTAC
Found at i:2576894 original size:23 final size:23
Alignment explanation
Indices: 2576868--2577079 Score: 175
Period size: 22 Copynumber: 9.2 Consensus size: 23
2576858 ATAAGTCATA
*
2576868 CAATGCCTTACGAACTAGTCACG
1 CAATGCCTTACTAACTAGTCACG
**
2576891 CAATGCCTTACTAAAAAGTCACG
1 CAATGCCTTACTAACTAGTCACG
* * *
2576914 CAATACTTTACTAACAAGTCACG
1 CAATGCCTTACTAACTAGTCACG
*
2576937 TAATGCC-TACTAACTAGTCACG
1 CAATGCCTTACTAACTAGTCACG
2576959 CAATGCC-TACTAACTAGTCACG
1 CAATGCCTTACTAACTAGTCACG
* *
2576981 CAATGCCTTATCAGAAACTAGTCATG
1 CAATGCCTTA-C--TAACTAGTCACG
* * *
2577007 GAATGCCTTATCAAAAACTAGTCATG
1 CAATGCCTTA-C--TAACTAGTCACG
* *
2577033 CAATGCC---CAAAGTCAGTCACG
1 CAATGCCTTACTAACT-AGTCACG
* *
2577054 CAATGTC-TATTAACTAGTCACG
1 CAATGCCTTACTAACTAGTCACG
2577076 CAAT
1 CAAT
2577080 AACTTATCAG
Statistics
Matches: 160, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
20 4 0.03
21 12 0.08
22 54 0.34
23 49 0.31
24 1 0.01
26 40 0.25
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (23 bp):
CAATGCCTTACTAACTAGTCACG
Found at i:2576999 original size:26 final size:25
Alignment explanation
Indices: 2576868--2577133 Score: 142
Period size: 26 Copynumber: 11.2 Consensus size: 25
2576858 ATAAGTCATA
*
2576868 CAATGCCTTA-C-GAACTAGTCACG
1 CAATGCCTTATCAAAACTAGTCACG
2576891 CAATGCCTTA-CTAAAA--AGTCACG
1 CAATGCCTTATC-AAAACTAGTCACG
* * * *
2576914 CAATACTTTA-C-TAACAAGTCACG
1 CAATGCCTTATCAAAACTAGTCACG
* *
2576937 TAATGCC-TA-C-TAACTAGTCACG
1 CAATGCCTTATCAAAACTAGTCACG
*
2576959 CAATGCC-TA-C-TAACTAGTCACG
1 CAATGCCTTATCAAAACTAGTCACG
*
2576981 CAATGCCTTATCAGAAACTAGTCATG
1 CAATGCCTTATCA-AAACTAGTCACG
* *
2577007 GAATGCCTTATCAAAAACTAGTCATG
1 CAATGCCTTATC-AAAACTAGTCACG
*
2577033 CAATGCC----C-AAAGTCAGTCACG
1 CAATGCCTTATCAAAACT-AGTCACG
* *
2577054 CAATGTC-TAT--TAACTAGTCACG
1 CAATGCCTTATCAAAACTAGTCACG
** * *
2577076 CAATAACTTATCAGAAACTAGTTATG
1 CAATGCCTTATCA-AAACTAGTCACG
* *
2577102 CAATGTCTTATCAAAAATCAGTCACG
1 CAATGCCTTATCAAAACT-AGTCACG
*
2577128 TAATGC
1 CAATGC
2577134 TCAAAGTCAG
Statistics
Matches: 195, Mismatches: 30, Indels: 33
0.76 0.12 0.13
Matches are distributed among these distances:
20 4 0.02
21 14 0.07
22 55 0.28
23 46 0.24
24 1 0.01
25 6 0.03
26 68 0.35
27 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.26
Consensus pattern (25 bp):
CAATGCCTTATCAAAACTAGTCACG
Found at i:2577072 original size:95 final size:95
Alignment explanation
Indices: 2576952--2577152 Score: 296
Period size: 95 Copynumber: 2.1 Consensus size: 95
2576942 CCTACTAACT
** *
2576952 AGTCACGCAATGCCTACTAACTAGTCACGCAATGCCTTATCAGAAACTAGTCATGGAATGCCTTA
1 AGTCACGCAATGCCTACTAACTAGTCACGCAATAACTTATCAGAAACTAGTCATGCAATGCCTTA
*
2577017 TCAAAAA-CTAGTCATGCAATGCCCAAAGTC
66 TCAAAAATC-AGTCACGCAATGCCCAAAGTC
* * * *
2577047 AGTCACGCAATGTCTATTAACTAGTCACGCAATAACTTATCAGAAACTAGTTATGCAATGTCTTA
1 AGTCACGCAATGCCTACTAACTAGTCACGCAATAACTTATCAGAAACTAGTCATGCAATGCCTTA
* *
2577112 TCAAAAATCAGTCACGTAATGCTCAAAGTC
66 TCAAAAATCAGTCACGCAATGCCCAAAGTC
2577142 AGTCACGCAAT
1 AGTCACGCAAT
2577153 ACTTAAAAAC
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 94 0.99
96 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (95 bp):
AGTCACGCAATGCCTACTAACTAGTCACGCAATAACTTATCAGAAACTAGTCATGCAATGCCTTA
TCAAAAATCAGTCACGCAATGCCCAAAGTC
Found at i:2577164 original size:95 final size:94
Alignment explanation
Indices: 2576930--2577169 Score: 277
Period size: 95 Copynumber: 2.5 Consensus size: 94
2576920 TTTACTAACA
* * * * **
2576930 AGTCACGTAATGCCTACTAACT-AGTCACGCAATGCCTACTAACTAGTCACGCAATGCCTTATCA
1 AGTCACGTAATG-CT-CAAAGTCAGTCACGCAAT-CTTAATAACTAGTCACGCAATAACTTATCA
*
2576994 GAAACTAGTCATGGAATGCCTTATCAAAAACT
63 GAAACTAGTCATGCAATGCCTTATCAAAAACT
* * * * *
2577026 AGTCATGCAATGCCCAAAGTCAGTCACGCAATGTCTATTAACTAGTCACGCAATAACTTATCAGA
1 AGTCACGTAATGCTCAAAGTCAGTCACGCAATCT-TAATAACTAGTCACGCAATAACTTATCAGA
* *
2577091 AACTAGTTATGCAATGTCTTATCAAAAA-T
65 AACTAGTCATGCAATGCCTTATCAAAAACT
*
2577120 CAGTCACGTAATGCTCAAAGTCAGTCACGCAATACTTAAAAACTAGTCAC
1 -AGTCACGTAATGCTCAAAGTCAGTCACGCAAT-CTTAATAACTAGTCAC
2577170 ATAATTCATA
Statistics
Matches: 121, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
94 5 0.04
95 105 0.87
96 11 0.09
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (94 bp):
AGTCACGTAATGCTCAAAGTCAGTCACGCAATCTTAATAACTAGTCACGCAATAACTTATCAGAA
ACTAGTCATGCAATGCCTTATCAAAAACT
Found at i:2581471 original size:15 final size:17
Alignment explanation
Indices: 2581441--2581472 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2581431 TATAGATATT
2581441 TAGAATATATAAATAAA
1 TAGAATATATAAATAAA
2581458 TAGAATA-A-AAATAAA
1 TAGAATATATAAATAAA
2581473 CTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (17 bp):
TAGAATATATAAATAAA
Found at i:2586240 original size:16 final size:16
Alignment explanation
Indices: 2586219--2586271 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
2586209 TGATATTAAT
2586219 ATATAAAAATGTTATC
1 ATATAAAAATGTTATC
2586235 ATAT-AAAAT-TATATC
1 ATATAAAAATGT-TATC
***
2586250 ATATAGTTATGTTATC
1 ATATAAAAATGTTATC
2586266 ATATAA
1 ATATAA
2586272 TATTATCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 13 0.43
16 15 0.50
17 1 0.03
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (16 bp):
ATATAAAAATGTTATC
Found at i:2586254 original size:31 final size:31
Alignment explanation
Indices: 2586219--2586277 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2586209 TGATATTAAT
2586219 ATATAAAAATGTTATCATATAAAATTATATC
1 ATATAAAAATGTTATCATATAAAATTATATC
*** *
2586250 ATATAGTTATGTTATCATATAATATTAT
1 ATATAAAAATGTTATCATATAAAATTAT
2586278 CATATCACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (31 bp):
ATATAAAAATGTTATCATATAAAATTATATC
Found at i:2586277 original size:13 final size:15
Alignment explanation
Indices: 2586261--2586292 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
2586251 TATAGTTATG
2586261 TTATCATAT-A-ATA
1 TTATCATATCACATA
2586274 TTATCATATCACATA
1 TTATCATATCACATA
2586289 TTAT
1 TTAT
2586293 TTATTATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 1 0.06
15 7 0.41
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATCATATCACATA
Found at i:2587926 original size:21 final size:21
Alignment explanation
Indices: 2587897--2587951 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2587887 CTCAATTATA
* * *
2587897 AATTATTTTAATTTTTTAAAT
1 AATTTTTTTAAATTTATAAAT
2587918 AATTTTTTTAAAATTTATAAAT
1 AATTTTTTT-AAATTTATAAAT
2587940 -ATTTATTTTAAA
1 AATTT-TTTTAAA
2587952 AAAGTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTTTTTTAAATTTATAAAT
Found at i:2607979 original size:94 final size:94
Alignment explanation
Indices: 2607810--2607980 Score: 236
Period size: 94 Copynumber: 1.8 Consensus size: 94
2607800 CACTTCCAAA
* * * * *
2607810 TTTTCATAACTTTATGAATATATTCAAATTTGATCCCTAAAACCTGTGTTGGATTTCACCTTGTT
1 TTTTCACAACTTTATGAATACATTCAAATTCGATCCCTAAAACCTGTGTTGAATTTCACCATGTT
*
2607875 CTGATGTTCTCAATTTCTCTCCAAGTACT
66 CTAATGTTCTCAATTTCTCTCCAAGTACT
* * **
2607904 TTTTCACAACTTTATGGATACATTCAAATTCGATCCCTAAAACCTTTGTTGAATTTCATGATGTT
1 TTTTCACAACTTTATGAATACATTCAAATTCGATCCCTAAAACCTGTGTTGAATTTCACCATGTT
2607969 CTCAAT-TTCTCA
66 CT-AATGTTCTCA
2607981 TTATTACTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
94 64 0.97
95 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (94 bp):
TTTTCACAACTTTATGAATACATTCAAATTCGATCCCTAAAACCTGTGTTGAATTTCACCATGTT
CTAATGTTCTCAATTTCTCTCCAAGTACT
Found at i:2609460 original size:28 final size:28
Alignment explanation
Indices: 2609395--2609461 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 28
2609385 GAATATATCT
* *
2609395 AAGATAAAATATTAAAATTTTATTTTATA
1 AAGAGAAAA-ATTAAAATTTAATTTTATA
* *
2609424 AA-AGGAAAATTCAAATTTAATTTTTATA
1 AAGAGAAAAATTAAAATTTAA-TTTTATA
*
2609452 AAGAAAAAAA
1 AAGAGAAAAA
2609462 ATAATTATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
27 10 0.33
28 13 0.43
29 7 0.23
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (28 bp):
AAGAGAAAAATTAAAATTTAATTTTATA
Found at i:2617641 original size:3 final size:3
Alignment explanation
Indices: 2617628--2617658 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
2617618 TACGAGACAC
2617628 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
2617659 TGACAACTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2618026 original size:8 final size:8
Alignment explanation
Indices: 2618000--2618034 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
2617990 TTGTTCAACC
*
2618000 TTTTCTCT
1 TTTTCTTT
2618008 TTTTCTTT
1 TTTTCTTT
2618016 TTTTCTTT
1 TTTTCTTT
2618024 TTTT-TTT
1 TTTTCTTT
2618031 TTTT
1 TTTT
2618035 GTGCTAGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTCTTT
Found at i:2618034 original size:16 final size:16
Alignment explanation
Indices: 2618000--2618033 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
2617990 TTGTTCAACC
2618000 TTTTCTCTTTTTCTTT
1 TTTTCTCTTTTTCTTT
2618016 TTTTCT-TTTTT-TTT
1 TTTTCTCTTTTTCTTT
2618030 TTTT
1 TTTT
2618034 TGTGCTAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 5 0.28
16 6 0.33
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTCTCTTTTTCTTT
Found at i:2618444 original size:2 final size:2
Alignment explanation
Indices: 2618423--2618473 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
2618413 TTCTTCAGGA
* * *
2618423 AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2618465 AT AT AT AT A
1 AT AT AT AT A
2618474 ACTTGAACAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2621524 original size:67 final size:67
Alignment explanation
Indices: 2621416--2621556 Score: 248
Period size: 67 Copynumber: 2.1 Consensus size: 67
2621406 CTACAATAGT
* *
2621416 TCCCAATGACAATATCAGTCTCATCATTTACAATTAATAAGCACA-TTCGGTGGCTAAACATGCC
1 TCCCAACGACAATATCAGTCTCATCATTTACAATTAATAAGCACAGTT-GGTAGCTAAACATGCC
2621480 TAA
65 TAA
2621483 TCCCAACGACAATATCAGTCTCATCATTTACAATTAATAAGCACAGTTGGTAGCTAAACATGCCT
1 TCCCAACGACAATATCAGTCTCATCATTTACAATTAATAAGCACAGTTGGTAGCTAAACATGCCT
2621548 AA
66 AA
2621550 TCCCAAC
1 TCCCAAC
2621557 AAGTCACTTA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
67 69 0.97
68 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.27
Consensus pattern (67 bp):
TCCCAACGACAATATCAGTCTCATCATTTACAATTAATAAGCACAGTTGGTAGCTAAACATGCCT
AA
Found at i:2627156 original size:21 final size:21
Alignment explanation
Indices: 2627130--2627194 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
2627120 TAGTATAAAA
2627130 TAAAACCCTAAGAAATGAGAT
1 TAAAACCCTAAGAAATGAGAT
* * * *
2627151 TAAAA-CAT-AG-TAT-AAAA
1 TAAAACCCTAAGAAATGAGAT
2627168 TAAAACCCTAAGAAATGAGAT
1 TAAAACCCTAAGAAATGAGAT
2627189 TAAAAC
1 TAAAAC
2627195 ATACTTGCGG
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
17 7 0.22
18 4 0.12
19 4 0.12
20 4 0.12
21 13 0.41
ACGTcount: A:0.57, C:0.12, G:0.11, T:0.20
Consensus pattern (21 bp):
TAAAACCCTAAGAAATGAGAT
Found at i:2627162 original size:38 final size:38
Alignment explanation
Indices: 2627120--2627197 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
2627110 AGTATTAAAT
2627120 TAGTATAAAATAAAACCCTAAGAAATGAGATTAAAACA
1 TAGTATAAAATAAAACCCTAAGAAATGAGATTAAAACA
2627158 TAGTATAAAATAAAACCCTAAGAAATGAGATTAAAACA
1 TAGTATAAAATAAAACCCTAAGAAATGAGATTAAAACA
2627196 TA
1 TA
2627198 CTTGCGGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.22
Consensus pattern (38 bp):
TAGTATAAAATAAAACCCTAAGAAATGAGATTAAAACA
Found at i:2634258 original size:2 final size:2
Alignment explanation
Indices: 2634253--2634322 Score: 124
Period size: 2 Copynumber: 35.0 Consensus size: 2
2634243 CTTCTATTCC
2634253 CT CT CT CT CT CT CT NCT CT CT CT CT C- CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2634295 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2634323 TCTTCTTTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 63 0.95
3 2 0.03
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2634694 original size:30 final size:31
Alignment explanation
Indices: 2634642--2634699 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
2634632 AATCTTATGC
* **
2634642 TTTTGAAAGTGGTTTTTTTTTTATTTTAGTT
1 TTTTGAAAGAGGTTTTAATTTTATTTTAGTT
2634673 TTTTGAAA-AGGTTTTAATTTTATTTTA
1 TTTTGAAAGAGGTTTTAATTTTATTTTA
2634700 TATACTGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.64
Consensus pattern (31 bp):
TTTTGAAAGAGGTTTTAATTTTATTTTAGTT
Found at i:2636657 original size:18 final size:18
Alignment explanation
Indices: 2636636--2636682 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
2636626 TGAAAAACTC
*
2636636 TTAAAAAAAAT-AATTTT
1 TTAAAAAAAATAAAATTT
*
2636653 TTTAAAAAAATAAAATTT
1 TTAAAAAAAATAAAATTT
*
2636671 TGAAAAAAAATA
1 TTAAAAAAAATA
2636683 GTGTCAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
TTAAAAAAAATAAAATTT
Found at i:2636661 original size:17 final size:17
Alignment explanation
Indices: 2636639--2636679 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2636629 AAAACTCTTA
** *
2636639 AAAAAAATAATTTTTTT
1 AAAAAAATAAAATTTTG
2636656 AAAAAAATAAAATTTTG
1 AAAAAAATAAAATTTTG
2636673 AAAAAAA
1 AAAAAAA
2636680 ATAGTGTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAAAAATAAAATTTTG
Found at i:2652740 original size:132 final size:132
Alignment explanation
Indices: 2652557--2652806 Score: 353
Period size: 132 Copynumber: 1.9 Consensus size: 132
2652547 TTGATGGCCC
2652557 AAACGTATATATCATGAGAAAAAAATAAGATAGCAAATTTGTTTTACTGAAA-TCAATAAGCTTT
1 AAACGTATATATCATGAGAAAAAAATAAGATAGCAAATTTGTTTTACTGAAACT-AATAAGCTTT
* *
2652621 AA-TCTAGTGCAAACAAGTGCATTGAACTAGAGT-TGTGGTGCTTTATGAATGGCAGCAAAACAA
65 AATTC-AGTGCAAACAAGTGCATTGAACTAGAGTATGTGGCGCCTTATGAATGGCAGCAAAACAA
2652684 GATA
129 GATA
* ** ** * *
2652688 AAACGTATATATCATGAGAAAACAACTTGGATAGCAAATTTGTTTTGTTGAAACTAATAGGTTTT
1 AAACGTATATATCATGAGAAAA-AAATAAGATAGCAAATTTGTTTTACTGAAACTAATAAGCTTT
*
2652753 AATTCAGTGCAAACAAGTGCATTTAACTAGAGTCATGTGGCGCCTTATGAATGG
65 AATTCAGTGCAAACAAGTGCATTGAACTAGAGT-ATGTGGCGCCTTATGAATGG
2652807 TAAGAAAATA
Statistics
Matches: 104, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
131 22 0.21
132 62 0.60
133 3 0.03
134 17 0.16
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (132 bp):
AAACGTATATATCATGAGAAAAAAATAAGATAGCAAATTTGTTTTACTGAAACTAATAAGCTTTA
ATTCAGTGCAAACAAGTGCATTGAACTAGAGTATGTGGCGCCTTATGAATGGCAGCAAAACAAGA
TA
Found at i:2654294 original size:27 final size:29
Alignment explanation
Indices: 2654264--2654361 Score: 83
Period size: 33 Copynumber: 3.3 Consensus size: 29
2654254 AGATATTAAA
*
2654264 GTGTAACAA-AAT-GTTTTTGAATATGAC
1 GTGTAACAATAATAGTTTTTCAATATGAC
* * *
2654291 GTGTAATAATAATATTTTTTCAATATGAT
1 GTGTAACAATAATAGTTTTTCAATATGAC
** *
2654320 GTGTAACAACAATATATTTTTTTTTAATATGAC
1 GTGT---AACAATA-ATAGTTTTTCAATATGAC
2654353 GTGTAACAA
1 GTGTAACAA
2654362 CCTAACCATG
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
27 8 0.14
28 3 0.05
29 16 0.28
30 5 0.09
32 6 0.11
33 19 0.33
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (29 bp):
GTGTAACAATAATAGTTTTTCAATATGAC
Found at i:2654316 original size:29 final size:30
Alignment explanation
Indices: 2654277--2654361 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 30
2654267 TAACAAAATG
* *
2654277 TTTTTGAATATGACGTGTAATAATA-ATAT
1 TTTTTCAATATGACGTGTAACAATATATAT
* *
2654306 TTTTTCAATATGATGTGTAACAACAATATATTT
1 TTTTTCAATATGACGTGT---AACAATATATAT
*
2654339 TTTTTTAATATGACGTGTAACAA
1 TTTTTCAATATGACGTGTAACAA
2654362 CCTAACCATG
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 16 0.35
30 5 0.11
32 6 0.13
33 19 0.41
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (30 bp):
TTTTTCAATATGACGTGTAACAATATATAT
Found at i:2654407 original size:45 final size:45
Alignment explanation
Indices: 2654348--2654675 Score: 413
Period size: 45 Copynumber: 7.3 Consensus size: 45
2654338 TTTTTTTAAT
* *
2654348 ATGACGTGTAACAACCTAACCATGACGTGTCATATGTTTTTGTAC
1 ATGACGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTAC
* * *
2654393 ATGACGTGTGACAACCTAACCATGGAGTGTCACATGTTTTTGTAT
1 ATGACGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTAC
* * *
2654438 ATGGCGTGTAACAATCTAATCATGGCGTGTCACATGTTTTTGTAC
1 ATGACGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTAC
* * ** *
2654483 ATGACATGTAATAACCTAACCATGGCGTGAAACATATTTTTGTAC
1 ATGACGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTAC
* ***
2654528 ATGGCGTGTAACAACCTAACCATATTGTGTCACATGTTTTTGTAC
1 ATGACGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTAC
* *
2654573 ATGACGTGTAACAACCTAACTATGGCATGTCACATGTTTTTGTAC
1 ATGACGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTAC
* * * * * * *
2654618 ATGGCATGAAACAATCTAATCATGGCGTGTAACATATTTTTGTAC
1 ATGACGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTAC
*
2654663 TTGACGTGTAACA
1 ATGACGTGTAACA
2654676 TCATGATGTG
Statistics
Matches: 236, Mismatches: 47, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 236 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (45 bp):
ATGACGTGTAACAACCTAACCATGGCGTGTCACATGTTTTTGTAC
Found at i:2660295 original size:17 final size:18
Alignment explanation
Indices: 2660265--2660300 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
2660255 ACACAGAATA
2660265 GAGAAAAGAAAGAAAATG
1 GAGAAAAGAAAGAAAATG
2660283 GAGAAAA-AAAGAAAATG
1 GAGAAAAGAAAGAAAATG
2660300 G
1 G
2660301 CGATTTGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.06
Consensus pattern (18 bp):
GAGAAAAGAAAGAAAATG
Found at i:2678778 original size:2 final size:2
Alignment explanation
Indices: 2678766--2678802 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2678756 GGTTAACATT
*
2678766 AC AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2678803 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.49, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2683953 original size:29 final size:30
Alignment explanation
Indices: 2683905--2683963 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
2683895 TTATTCTACC
* *
2683905 TTTATTTTGAATTAAGT-AAATTTTATATT
1 TTTATTTTGAATTAAATAAAATTTAATATT
2683934 TTTATTTTGAGA-TAAATAAAATTTAATATT
1 TTTATTTTGA-ATTAAATAAAATTTAATATT
2683964 AATGATTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (30 bp):
TTTATTTTGAATTAAATAAAATTTAATATT
Found at i:2700275 original size:23 final size:22
Alignment explanation
Indices: 2700249--2700297 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2700239 AGTCATTCAG
*
2700249 TTTTTGAATCTTTAAATTAAAAT
1 TTTTTAAAT-TTTAAATTAAAAT
**
2700272 TTTTTAAATTTTTTATTAAAAT
1 TTTTTAAATTTTAAATTAAAAT
2700294 TTTT
1 TTTT
2700298 AAAAGAAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTTAAATTTTAAATTAAAAT
Done.