Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold53
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: 4419549
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 41486 characters in sequence are not A, C, G, or T
File 8 of 28
Found at i:1247617 original size:33 final size:35
Alignment explanation
Indices: 1247550--1247623 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
1247540 TTTCCAAAGT
* * *
1247550 CCACAACTCTGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCTATAGCACTCTTTTTCCTTTGTAAGC
*
1247585 TCACAACTCTATAGCACT-TTTTTCCTTT-TAAGC
1 CCACAACTCTATAGCACTCTTTTTCCTTTGTAAGC
1247618 CCACAA
1 CCACAA
1247624 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 10 0.29
34 9 0.26
35 15 0.44
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.38
Consensus pattern (35 bp):
CCACAACTCTATAGCACTCTTTTTCCTTTGTAAGC
Found at i:1247679 original size:33 final size:33
Alignment explanation
Indices: 1247619--1247802 Score: 264
Period size: 33 Copynumber: 5.6 Consensus size: 33
1247609 CTTTTAAGCC
** *
1247619 CACAAGTTAGTGGC-ACCCTTTTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCTTTTTCTAAAGCCCA
1247651 CACAAGTCGGTGGCAACCTTTTTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCTTTTTCTAAAGCCCA
*
1247684 CACAAGTCGGTGGCAACCGTTTTC-AAAGCCCA
1 CACAAGTCGGTGGCAACCTTTTTCTAAAGCCCA
* *
1247716 CATAAGTCGGTGGCAACCTTCTTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCTTTTTCTAAAGCCCA
* * * *
1247749 CATAAGTTGGTGGCAACCATTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCTTTTTCTAAAGCCCA
1247782 CACAAGTCGGTGGCAACCTTT
1 CACAAGTCGGTGGCAACCTTT
1247803 CTAAGCCCAA
Statistics
Matches: 136, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
32 41 0.30
33 95 0.70
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (33 bp):
CACAAGTCGGTGGCAACCTTTTTCTAAAGCCCA
Found at i:1247697 original size:65 final size:66
Alignment explanation
Indices: 1247619--1247802 Score: 282
Period size: 65 Copynumber: 2.8 Consensus size: 66
1247609 CTTTTAAGCC
* *
1247619 CACAAGTTAGTGGC-ACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCC
1 CACAAGTTGGTGGCAACCATTTTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCC
1247683 A
66 A
* * * *
1247684 CACAAGTCGGTGGCAACCGTTTTC-AAAGCCCACATAAGTCGGTGGCAACCTTCTTCTAAAGCCC
1 CACAAGTTGGTGGCAACCATTTTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCC
1247748 A
66 A
* *
1247749 CATAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTT
1 CACAAGTTGGTGGCAACCATTTTCTAAAGCCCACACAAGTCGGTGGCAACCTTT
1247803 CTAAGCCCAA
Statistics
Matches: 106, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
65 71 0.67
66 35 0.33
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (66 bp):
CACAAGTTGGTGGCAACCATTTTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCC
A
Found at i:1247745 original size:98 final size:95
Alignment explanation
Indices: 1247628--1247811 Score: 287
Period size: 98 Copynumber: 1.9 Consensus size: 95
1247618 CCACAAGTTA
* * *
1247628 GTGGCACCCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCCACACAAGTCG
1 GTGGCAACCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCG
1247693 GTGGCAACCGTTTTCAAAGCCCACATAAGTCG
66 GTGGCAACC--TTTCAAAGCCCACATAAGTCG
* *
1247725 GTGGCAACCTTCTTCTAAAGCCCACATAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTC
1 GTGGCAACCTT-TTCTAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTC
*
1247790 GGTGGCAACCTTTCTAAGCCCA
65 GGTGGCAACCTTTCAAAGCCCA
1247812 ATATAGCTGG
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
96 11 0.14
97 10 0.12
98 59 0.74
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (95 bp):
GTGGCAACCTTTTCTAAAGCCCACACAAGTCGGTGGCAACCATTCTCTAAAGCCCACACAAGTCG
GTGGCAACCTTTCAAAGCCCACATAAGTCG
Found at i:1247862 original size:49 final size:49
Alignment explanation
Indices: 1247804--1248371 Score: 582
Period size: 49 Copynumber: 12.1 Consensus size: 49
1247794 GCAACCTTTC
*
1247804 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
1247853 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--C-T-TC
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
1247898 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* **
1247947 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACGTTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1247990 TAAGTCTAAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTC-CAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
1248040 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-A----CACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1248083 TAAGTCCAATATCA-TTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATAT-AGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
1248132 TAAGTCCAATGTAGCTAGCCTTGAATCAGCATATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
1248175 TAAGTCTAATATCGCTGCCCTTGAATCAGCATATTGGAACCCTCATCTTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TT
* * * *
1248225 TAAGCCCAATGTAGCTAGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
1248268 TAAGTCCAATATCGTTGGCCTTGGATCAGCATATTGGCGTCTTTGTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC-AC-CT-TCATCTT
* *
1248320 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1248369 TAA
1 TAA
1248372 CATTCCTAAG
Statistics
Matches: 428, Mismatches: 56, Indels: 70
0.77 0.10 0.13
Matches are distributed among these distances:
43 113 0.26
44 31 0.07
45 42 0.10
46 2 0.00
47 4 0.01
48 4 0.01
49 149 0.35
50 44 0.10
51 1 0.00
52 38 0.09
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:1248064 original size:93 final size:92
Alignment explanation
Indices: 1247804--1248362 Score: 839
Period size: 93 Copynumber: 6.0 Consensus size: 92
1247794 GCAACCTTTC
* *
1247804 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1247869 GGCCTTGAATCAGCACATTGGCACCCTT
66 GGCCTTGAATCAGCACATTGGCA-CCTT
* *
1247897 CTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGC
1 -TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGC
*
1247962 TGGCCTTGAATCAGCACGTTGGCACCTT
65 TGGCCTTGAATCAGCACATTGGCACCTT
*
1247990 TAAGTCTAAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGC
1 TAAGTC-CAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGC
*
1248055 TGGCCTTGAATCAGCACATTGACACCTT
65 TGGCCTTGAATCAGCACATTGGCACCTT
** *
1248083 TAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* *
1248148 AGCCTTGAATCAGCATATTGGCACCTT
66 GGCCTTGAATCAGCACATTGGCACCTT
* * * * *
1248175 TAAGTCTAATATCGCTGCCCTTGAATCAGCATATTGGAACCCTCATCTTTTAAGCCCAATGTAGC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTCCAATGTAGC
*
1248240 TAGCCTTGAATCAGCACATTGGCACCTT
65 TGGCCTTGAATCAGCACATTGGCACCTT
* * * * * *
1248268 TAAGTCCAATATCGTTGGCCTTGGATCAGCATATTGGCGTCTTTGTCATCTTTAAGTCCAATATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC-CT-TCATCTTTAAGTCCAATGTA
1248333 GCTGGCCTTGAATCAGCACATTGGCACCTT
63 GCTGGCCTTGAATCAGCACATTGGCACCTT
1248363 CATCTTTAAC
Statistics
Matches: 426, Mismatches: 34, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
92 124 0.29
93 168 0.39
94 88 0.21
95 41 0.10
96 5 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (92 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
GGCCTTGAATCAGCACATTGGCACCTT
Found at i:1248171 original size:185 final size:184
Alignment explanation
Indices: 1247811--1248362 Score: 863
Period size: 185 Copynumber: 3.0 Consensus size: 184
1247801 TTCTAAGCCC
*
1247811 AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
* * *
1247876 AATCAGCACATTGGCACCCTTCTAAGCCCAATAT-AGCTGGCCTTGAATCAGCATATTGGCACCT
66 AATCAGCACATTGGCA-CCTT-TAAGTCCAATATCA-TTGGCCTTGAATCAGCATATTGGCATCT
*
1247940 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACGTTGGCACCTTTAAGTCT
128 TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCT
1247997 AAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTT
1 -AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTT
*
1248062 GAATCAGCACATTGACACCTTTAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCATCTTC
65 GAATCAGCACATTGGCACCTTTAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCATCTTC
* *
1248127 ATCTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCATATTGGCACCTTTAAGTCT
130 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCT
* * * * *
1248182 AATATCGCTGCCCTTGAATCAGCATATTGGAACCCTCATCTTTTAAGCCCAATGTAGCTAGCCTT
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTCCAATGTAGCTGGCCTT
* * *
1248247 GAATCAGCACATTGGCACCTTTAAGTCCAATATCGTTGGCCTTGGATCAGCATATTGGCGTCTTT
65 GAATCAGCACATTGGCACCTTTAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCATC--T
* *
1248312 GTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
128 -TCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
1248363 CATCTTTAAC
Statistics
Matches: 339, Mismatches: 21, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
184 37 0.11
185 171 0.50
186 5 0.01
187 80 0.24
188 46 0.14
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (184 bp):
AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
AATCAGCACATTGGCACCTTTAAGTCCAATATCATTGGCCTTGAATCAGCATATTGGCATCTTCA
TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCT
Found at i:1249160 original size:13 final size:13
Alignment explanation
Indices: 1249142--1249166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1249132 CATAAAGTGT
1249142 TGTATCGATACAA
1 TGTATCGATACAA
1249155 TGTATCGATACA
1 TGTATCGATACA
1249167 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1249164 original size:33 final size:33
Alignment explanation
Indices: 1249122--1249188 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1249112 TTCAACGATT
1249122 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1249155 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1249188 T
1 T
1249189 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1249299 original size:52 final size:50
Alignment explanation
Indices: 1249242--1249390 Score: 199
Period size: 52 Copynumber: 2.9 Consensus size: 50
1249232 ATTGATACAT
* * *
1249242 TGTATCGATACACTGATCTTTGTATCAATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACA-TTAT-TATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
1249294 TGTATCGGTACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAGA
1249346 TGTATCGATACATTATTAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATTATT--ATGTATCGATACATGCAGGCAAATTT
1249391 TCATATTTCG
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
51 3 0.03
52 83 0.97
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (50 bp):
TGTATCGATACATTATTATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1254272 original size:9 final size:8
Alignment explanation
Indices: 1254260--1254364 Score: 97
Period size: 8 Copynumber: 12.5 Consensus size: 8
1254250 TTTATTATTA
1254260 TTTTGAATT
1 TTTTG-ATT
1254269 TTTT-ATTT
1 TTTTGA-TT
*
1254277 TTTTTATT
1 TTTTGATT
1254285 TTTTGATTT
1 TTTTGA-TT
1254294 TTTTGATT
1 TTTTGATT
1254302 TTTTGATTT
1 TTTTGA-TT
1254311 TTTTGATT
1 TTTTGATT
1254319 TCTTTGATT
1 T-TTTGATT
*
1254328 TCTTGAATTT
1 TTTTG-A-TT
*
1254338 TTTTAATT
1 TTTTGATT
*
1254346 CTTTGA-T
1 TTTTGATT
1254353 TTTTGATT
1 TTTTGATT
1254361 TTTT
1 TTTT
1254365 TATTATTATA
Statistics
Matches: 81, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
7 7 0.09
8 38 0.47
9 31 0.38
10 5 0.06
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (8 bp):
TTTTGATT
Found at i:1254280 original size:17 final size:16
Alignment explanation
Indices: 1254254--1254365 Score: 100
Period size: 17 Copynumber: 6.6 Consensus size: 16
1254244 ATTAACTTTA
*
1254254 TTATTATTTTGAATTTT
1 TTATTTTTTTG-ATTTT
*
1254271 TTATTTTTTTTATTTT
1 TTATTTTTTTGATTTT
1254287 TTGATTTTTTTGATTTT
1 TT-ATTTTTTTGATTTT
1254304 TTGATTTTTTTGATTTCT
1 TT-ATTTTTTTGATTT-T
*
1254322 TTGA-TTTCTTGAATTTTT
1 TT-ATTTTTTTG-A-TTTT
* *
1254340 TTAATTCTTTGATTTT
1 TTATTTTTTTGATTTT
*
1254356 TGATTTTTTT
1 TTATTTTTTT
1254366 ATTATTATAT
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
16 18 0.22
17 46 0.57
18 14 0.17
19 3 0.04
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (16 bp):
TTATTTTTTTGATTTT
Found at i:1254312 original size:26 final size:26
Alignment explanation
Indices: 1254287--1254364 Score: 56
Period size: 26 Copynumber: 3.1 Consensus size: 26
1254277 TTTTTATTTT
*
1254287 TTGATTTTTTTG-ATTTTTTGATTTTT
1 TTGATTTTTTTGAATTCTTTGA-TTTT
* *
1254313 TTGATTTCTTTGATTTC-TTGAATTTT
1 TTGATTTTTTTGAATTCTTTG-ATTTT
* * *
1254339 TTTAATTCTTTG-ATT-TTTGATTTT
1 TTGATTTTTTTGAATTCTTTGATTTT
1254363 TT
1 TT
1254365 TATTATTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
24 7 0.16
25 5 0.12
26 28 0.65
27 3 0.07
ACGTcount: A:0.14, C:0.04, G:0.10, T:0.72
Consensus pattern (26 bp):
TTGATTTTTTTGAATTCTTTGATTTT
Found at i:1254365 original size:26 final size:25
Alignment explanation
Indices: 1254303--1254365 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 25
1254293 TTTTTGATTT
*
1254303 TTTGATTTTTTTGATTTCTTTGATT
1 TTTGATTTTTTTGAATTCTTTGATT
1254328 TCTTGAATTTTTTT-AATTCTTTGATT
1 T-TTG-ATTTTTTTGAATTCTTTGATT
1254354 TTTGATTTTTTT
1 TTTGATTTTTTT
1254366 ATTATTATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 8 0.23
25 4 0.11
26 15 0.43
27 8 0.23
ACGTcount: A:0.14, C:0.05, G:0.10, T:0.71
Consensus pattern (25 bp):
TTTGATTTTTTTGAATTCTTTGATT
Found at i:1254370 original size:3 final size:3
Alignment explanation
Indices: 1254364--1254404 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
1254354 TTTGATTTTT
* *
1254364 TTA TTA TTA -TA TTA TTA TTT TTA TTA TTT TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1254405 GATTTTACCA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:1254389 original size:9 final size:9
Alignment explanation
Indices: 1254351--1254402 Score: 70
Period size: 9 Copynumber: 5.6 Consensus size: 9
1254341 TAATTCTTTG
1254351 ATTTTTGATT
1 ATTTTT-ATT
1254361 -TTTTTATT
1 ATTTTTATT
1254369 ATTATATTATT
1 ATT-T-TTATT
1254380 ATTTTTATT
1 ATTTTTATT
1254389 ATTTTTATT
1 ATTTTTATT
1254398 ATTTT
1 ATTTT
1254403 ATGATTTTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 3 0.08
9 26 0.67
10 2 0.05
11 8 0.21
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (9 bp):
ATTTTTATT
Found at i:1259134 original size:13 final size:13
Alignment explanation
Indices: 1259116--1259141 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1259106 AATATTTTTG
1259116 TGTATCGATACAT
1 TGTATCGATACAT
1259129 TGTATCGATACAT
1 TGTATCGATACAT
1259142 ACTTGGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1259156 original size:32 final size:34
Alignment explanation
Indices: 1259095--1259159 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
1259085 TACAAGCCAA
* *
1259095 TGTATCGATACAATATTTTTGTGTATCGATACAT
1 TGTATCGATACAATATCTTGGTGTATCGATACAT
1259129 TGTATCGATAC-ATA-CTTGGTGTATCGATACA
1 TGTATCGATACAATATCTTGGTGTATCGATACA
1259160 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 15 0.52
33 3 0.10
34 11 0.38
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (34 bp):
TGTATCGATACAATATCTTGGTGTATCGATACAT
Found at i:1260838 original size:13 final size:13
Alignment explanation
Indices: 1260820--1260857 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1260810 ATAATCCCCC
*
1260820 TGTATCAATACAG
1 TGTATCGATACAG
*
1260833 TGTATCGATACAT
1 TGTATCGATACAG
1260846 TGTATCGATACA
1 TGTATCGATACA
1260858 AAGAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1262931 original size:15 final size:15
Alignment explanation
Indices: 1262911--1262941 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1262901 ATTTCGTTTG
*
1262911 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1262926 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1262941 G
1 G
1262942 GATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1264772 original size:21 final size:21
Alignment explanation
Indices: 1264743--1264787 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1264733 AAGTTTTTAT
*
1264743 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1264763 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1264785 TTT
1 TTT
1264788 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1267024 original size:13 final size:13
Alignment explanation
Indices: 1267006--1267031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1266996 ATATTTTTTG
1267006 TGTATCGATACAT
1 TGTATCGATACAT
1267019 TGTATCGATACAT
1 TGTATCGATACAT
1267032 ATTTTGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1267042 original size:32 final size:33
Alignment explanation
Indices: 1266985--1267049 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1266975 TACAAGCCAA
1266985 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
1267019 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
1267050 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:1267043 original size:19 final size:19
Alignment explanation
Indices: 1266985--1267049 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
1266975 TACAAGCCAA
1266985 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
1267006 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
1267019 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
1267038 TGTATCGATACA
1 TGTATCGATACA
1267050 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:1273521 original size:2 final size:2
Alignment explanation
Indices: 1273514--1273545 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1273504 ACATACATGC
1273514 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
1273546 CCCTTAAGTT
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:1273632 original size:2 final size:2
Alignment explanation
Indices: 1273603--1273648 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
1273593 ATTATCACTC
* * *
1273603 TA TA -A TA TC TA TA TC TA TA -A TT 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
1273643 TA TA TA
1 TA TA TA
1273649 AAAGTACCAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1274402 original size:34 final size:34
Alignment explanation
Indices: 1274359--1274423 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
1274349 TACGCTCGAG
*
1274359 GGGCGAACACAATCGCCATGCTTGGCAACCAGAA
1 GGGCGAACACAATCGCCACGCTTGGCAACCAGAA
* * *
1274393 GGGCGAACACAGTTGCCACGCTTGGCGACCA
1 GGGCGAACACAATCGCCACGCTTGGCAACCA
1274424 AACATGGGCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.28, C:0.31, G:0.29, T:0.12
Consensus pattern (34 bp):
GGGCGAACACAATCGCCACGCTTGGCAACCAGAA
Found at i:1278399 original size:59 final size:59
Alignment explanation
Indices: 1278335--1278634 Score: 186
Period size: 58 Copynumber: 5.1 Consensus size: 59
1278325 CCGAGTCTGA
1278335 GTGACTTGGTGTCA--T-GTGATGTGTAGATCTAGGTCACCTTGATGGCGATCTAAGTTTGG
1 GTGACTTGGTGTCACTTAGTG-TG-GTA-ATCTAGGTCACCTTGATGGCGATCTAAGTTTGG
* ** *
1278394 GTGACTTGGTGTCACTTAGTGTGGTAATCTGGGTTGCCTTGGTGGCGATCTAAGTTTGG
1 GTGACTTGGTGTCACTTAGTGTGGTAATCTAGGTCACCTTGATGGCGATCTAAGTTTGG
** * * * * * * * ** * * *
1278453 GTGACTTGGCCTCACCTAGTATGTTAGTC-GGGTTACCCTGGCGACAATCTAAGTTCGG
1 GTGACTTGGTGTCACTTAGTGTGGTAATCTAGGTCACCTTGATGGCGATCTAAGTTTGG
* * * * * * *
1278511 GTTACTTGGTGTCACTTAGTGT-ATGAATC-GGGTCGCCTTGGA-GGTGATCTAAGTTCGA
1 GTGACTTGGTGTCACTTAGTGTGGT-AATCTAGGTCACCTT-GATGGCGATCTAAGTTTGG
** * * * * * *
1278569 GTGACTTGGCATCACTTAGTGTGAG-AATCGA-GTCTCCCTGGTGGCTATCTAAGTTCGG
1 GTGACTTGGTGTCACTTAGTGTG-GTAATCTAGGTCACCTTGATGGCGATCTAAGTTTGG
1278627 GTGACTTG
1 GTGACTTG
1278635 ACATCACCCA
Statistics
Matches: 190, Mismatches: 42, Indels: 19
0.76 0.17 0.08
Matches are distributed among these distances:
57 2 0.01
58 112 0.59
59 67 0.35
60 3 0.02
61 3 0.02
62 3 0.02
ACGTcount: A:0.18, C:0.17, G:0.31, T:0.34
Consensus pattern (59 bp):
GTGACTTGGTGTCACTTAGTGTGGTAATCTAGGTCACCTTGATGGCGATCTAAGTTTGG
Found at i:1278542 original size:58 final size:58
Alignment explanation
Indices: 1278377--1278634 Score: 234
Period size: 58 Copynumber: 4.4 Consensus size: 58
1278367 GTCACCTTGA
* * * *
1278377 TGGCGATCTAAGTTTGGGTGACTTGGTGTCACTTAGTGT-GGTAATCTGGGTTGCCTTGG
1 TGGCGATCTAAGTTCGGGTGACTTGGCGTCACTTAGTGTATG-AATC-GGGTTGCCCTGG
* * * * * * * *
1278436 TGGCGATCTAAGTTTGGGTGACTTGGCCTCACCTAGTATGTTAGTCGGGTTACCCTGG
1 TGGCGATCTAAGTTCGGGTGACTTGGCGTCACTTAGTGTATGAATCGGGTTGCCCTGG
* * * * * * *
1278494 CGACAATCTAAGTTCGGGTTACTTGGTGTCACTTAGTGTATGAATCGGGTCGCCTTGG
1 TGGCGATCTAAGTTCGGGTGACTTGGCGTCACTTAGTGTATGAATCGGGTTGCCCTGG
* * * * *
1278552 AGGTGATCTAAGTTCGAGTGACTTGGCATCACTTAGTGTGA-GAATCGAGTCT-CCCTGG
1 TGGCGATCTAAGTTCGGGTGACTTGGCGTCACTTAGTGT-ATGAATCGGGT-TGCCCTGG
*
1278610 TGGCTATCTAAGTTCGGGTGACTTG
1 TGGCGATCTAAGTTCGGGTGACTTG
1278635 ACATCACCCA
Statistics
Matches: 157, Mismatches: 39, Indels: 7
0.77 0.19 0.03
Matches are distributed among these distances:
58 118 0.75
59 39 0.25
ACGTcount: A:0.17, C:0.18, G:0.31, T:0.33
Consensus pattern (58 bp):
TGGCGATCTAAGTTCGGGTGACTTGGCGTCACTTAGTGTATGAATCGGGTTGCCCTGG
Found at i:1278608 original size:116 final size:117
Alignment explanation
Indices: 1278382--1278634 Score: 305
Period size: 116 Copynumber: 2.2 Consensus size: 117
1278372 CTTGATGGCG
* * *
1278382 ATCTAAGTTTGGGTGACTTGGTGTCACTTAGTGTGGTAATCTGGGTTGCCTTGGTGGCGATCTAA
1 ATCTAAGTTCGGGTGACTTGGTGTCACTTAGTGTGGTAATCTGGGTCGCCTTGGAGGCGATCTAA
* * * ** * *
1278447 GTTTGGGTGACTTGGCCTCACCTAGTATGTTAGTCGGGTTACCCTGGCGACA
66 GTTCGAGTGACTTGGCATCACCTAGTATGAGAATCGAGTTACCCTGGCGACA
* * *
1278499 ATCTAAGTTCGGGTTACTTGGTGTCACTTAGTGT-ATGAATC-GGGTCGCCTTGGAGGTGATCTA
1 ATCTAAGTTCGGGTGACTTGGTGTCACTTAGTGTGGT-AATCTGGGTCGCCTTGGAGGCGATCTA
* * * * *
1278562 AGTTCGAGTGACTTGGCATCACTTAGTGTGAGAATCGAGTCT-CCCTGGTGGCT
65 AGTTCGAGTGACTTGGCATCACCTAGTATGAGAATCGAGT-TACCCTGGCGACA
1278615 ATCTAAGTTCGGGTGACTTG
1 ATCTAAGTTCGGGTGACTTG
1278635 ACATCACCCA
Statistics
Matches: 115, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
116 78 0.68
117 37 0.32
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.34
Consensus pattern (117 bp):
ATCTAAGTTCGGGTGACTTGGTGTCACTTAGTGTGGTAATCTGGGTCGCCTTGGAGGCGATCTAA
GTTCGAGTGACTTGGCATCACCTAGTATGAGAATCGAGTTACCCTGGCGACA
Found at i:1284938 original size:34 final size:34
Alignment explanation
Indices: 1284895--1284961 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
1284885 TACGCTTAAG
* *
1284895 GGGCGAACACGATCGCCATGCTTGGCGACCAGAA
1 GGGCAAACACGATCGCCACGCTTGGCGACCAGAA
* *
1284929 GGGCAAACACGGTCGCCACGCTTGGTGACCAGA
1 GGGCAAACACGATCGCCACGCTTGGCGACCAGA
1284962 CATGGGCGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.25, C:0.30, G:0.33, T:0.12
Consensus pattern (34 bp):
GGGCAAACACGATCGCCACGCTTGGCGACCAGAA
Found at i:1286064 original size:144 final size:137
Alignment explanation
Indices: 1285906--1286176 Score: 325
Period size: 138 Copynumber: 1.9 Consensus size: 137
1285896 CTTGTTAATC
* *
1285906 TTGAATTCCTTATTAATGTATATTTTTTCTTAAATGATA-TAT-AGTTTTATTAATATTAACTAA
1 TTGAATTCCTTATTAATGTA-A-CTTTT-TTAAATGATATTATAATTTTTA-TAATATTAACTAA
* * *
1285969 TTTTTTAACTACTTTTTCTTACTAATGAATTTTTATTAAATTAAAACT-TTGACTAATCTTTATT
62 -TTTTTAA-T-CATTTT-TTACTAAT-AATTTTTATTAAATTAAAA-TATTAACTAATATTTATT
1286033 TATTATTTTCATTTACT
121 TATTATTTTCATTTACT
* *
1286050 TTGAAGTT-CTTATTAATGTAACTTTTTTAATTGATATTTATAATTTTTATATTATTAACTAATT
1 TTGAA-TTCCTTATTAATGTAACTTTTTTAAATGATA-TTATAATTTTTATAATATTAACTAATT
* *
1286114 TTTAATCATTTTTTATTAATAATTTTTCTTAAATTAAAATATTAACTAATATTTATTTATTAT
64 TTTAATCATTTTTTACTAATAATTTTTATTAAATTAAAATATTAACTAATATTTATTTATTAT
1286177 ATTCCTACTT
Statistics
Matches: 113, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
137 1 0.01
138 38 0.34
139 7 0.06
140 5 0.04
141 10 0.09
142 11 0.10
143 16 0.14
144 23 0.20
145 2 0.02
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.56
Consensus pattern (137 bp):
TTGAATTCCTTATTAATGTAACTTTTTTAAATGATATTATAATTTTTATAATATTAACTAATTTT
TAATCATTTTTTACTAATAATTTTTATTAAATTAAAATATTAACTAATATTTATTTATTATTTTC
ATTTACT
Found at i:1287195 original size:21 final size:20
Alignment explanation
Indices: 1287169--1287225 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1287159 CAACCCTGTG
*
1287169 ATTGTATCGATACATGTTTAA
1 ATTGTATCGATACAT-TATAA
*
1287190 ATTGTATCGATACATTATGA
1 ATTGTATCGATACATTATAA
*
1287210 ATTATATCGATACATT
1 ATTGTATCGATACATT
1287226 TGGGCCAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (20 bp):
ATTGTATCGATACATTATAA
Found at i:1287885 original size:61 final size:61
Alignment explanation
Indices: 1287785--1287906 Score: 181
Period size: 61 Copynumber: 2.0 Consensus size: 61
1287775 TATAGGTGTC
* * * *
1287785 GAGTCAAGGACTGAACCTCTATAGATTCTCGTATTAGCTTTTTCTTATCATTACTCTTTTT
1 GAGTCAAGGACTGAACCACTATAAATTCTCATATTAGCTTTTTCTTATCATTACTCCTTTT
* * *
1287846 GAGTTAAGGACTGAACCACTATAAATTCTCATGTTAGCTTTTTCTTATCCTTACTCCTTTT
1 GAGTCAAGGACTGAACCACTATAAATTCTCATATTAGCTTTTTCTTATCATTACTCCTTTT
1287907 ATCTTTCAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.43
Consensus pattern (61 bp):
GAGTCAAGGACTGAACCACTATAAATTCTCATATTAGCTTTTTCTTATCATTACTCCTTTT
Found at i:1291523 original size:13 final size:13
Alignment explanation
Indices: 1291505--1291530 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1291495 TACACAAAGT
1291505 ATGTATCGATACA
1 ATGTATCGATACA
1291518 ATGTATCGATACA
1 ATGTATCGATACA
1291531 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1291528 original size:32 final size:33
Alignment explanation
Indices: 1291487--1291550 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1291477 TAGCCAAACT
**
1291487 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1291519 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1291551 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1292152 original size:20 final size:20
Alignment explanation
Indices: 1292129--1292201 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1292119 ACAATTCAAA
1292129 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1292149 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1292170 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1292190 GTATCGATACAT
1 GTATCGATACAT
1292202 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1292173 original size:21 final size:21
Alignment explanation
Indices: 1292147--1292222 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1292137 ACATGTTGCA
1292147 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1292168 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1292188 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1292209 ATGTATCGATACAT
1 ATGTATCGATACAT
1292223 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1292180 original size:41 final size:41
Alignment explanation
Indices: 1292129--1292222 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1292119 ACAATTCAAA
*
1292129 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1292170 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1292211 GTATCGATACAT
1 GTATCGATACAT
1292223 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1292279 original size:13 final size:13
Alignment explanation
Indices: 1292261--1292286 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1292251 TATAGCAAGT
1292261 ATGTATCGATACA
1 ATGTATCGATACA
1292274 ATGTATCGATACA
1 ATGTATCGATACA
1292287 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1296361 original size:15 final size:15
Alignment explanation
Indices: 1296341--1296371 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1296331 TAAAAATGTC
*
1296341 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1296356 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1296371 C
1 C
1296372 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1298466 original size:20 final size:21
Alignment explanation
Indices: 1298387--1298465 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
1298377 AATGTCCAAA
*
1298387 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
1298407 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
1298432 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
1298452 TTGTATCGATACAT
1 ATGTATCGATACAT
1298466 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:1298470 original size:13 final size:13
Alignment explanation
Indices: 1298452--1298490 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1298442 ACATTTTTCT
1298452 TTGTATCGATACA
1 TTGTATCGATACA
1298465 TTGTATCGATACA
1 TTGTATCGATACA
*
1298478 CTGTATCGATACA
1 TTGTATCGATACA
1298491 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1300952 original size:20 final size:20
Alignment explanation
Indices: 1300929--1301001 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1300919 ACAATTCAAA
1300929 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1300949 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1300970 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1300990 GTATCGATACAT
1 GTATCGATACAT
1301002 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1300973 original size:21 final size:21
Alignment explanation
Indices: 1300947--1301022 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1300937 ACATGTTGCA
1300947 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1300968 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1300988 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
1301009 ATGTATCGATACAT
1 ATGTATCGATACAT
1301023 TTCTTGGTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1300980 original size:41 final size:41
Alignment explanation
Indices: 1300929--1301022 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1300919 ACAATTCAAA
*
1300929 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1300970 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1301011 GTATCGATACAT
1 GTATCGATACAT
1301023 TTCTTGGTAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1301079 original size:13 final size:13
Alignment explanation
Indices: 1301061--1301086 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1301051 TACAGCAAGT
1301061 ATGTATCGATACA
1 ATGTATCGATACA
1301074 ATGTATCGATACA
1 ATGTATCGATACA
1301087 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1307047 original size:13 final size:13
Alignment explanation
Indices: 1307029--1307066 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1307019 TATTTTTCTT
1307029 TGTATCGATACAA
1 TGTATCGATACAA
*
1307042 TGTATCGATACAC
1 TGTATCGATACAA
1307055 TGTATCGATACA
1 TGTATCGATACA
1307067 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1308992 original size:47 final size:47
Alignment explanation
Indices: 1308922--1309017 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
1308912 GGGAGAATGC
1308922 GTAAATTTGCTAAAATTACCTTATTAAGGGGGAGAATGTACAAACTT
1 GTAAATTTGCTAAAATTACCTTATTAAGGGGGAGAATGTACAAACTT
*
1308969 GTAAATTTGCTAAAATTATCTTATTAAGGGGGAGAATGTACAAACTT
1 GTAAATTTGCTAAAATTACCTTATTAAGGGGGAGAATGTACAAACTT
1309016 GT
1 GT
1309018 TAAAATTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (47 bp):
GTAAATTTGCTAAAATTACCTTATTAAGGGGGAGAATGTACAAACTT
Found at i:1309688 original size:13 final size:13
Alignment explanation
Indices: 1309670--1309695 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1309660 TACACAAAGT
1309670 ATGTATCGATACA
1 ATGTATCGATACA
1309683 ATGTATCGATACA
1 ATGTATCGATACA
1309696 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1309693 original size:32 final size:33
Alignment explanation
Indices: 1309652--1309715 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1309642 TAGCCAAACT
**
1309652 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1309684 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1309716 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1310588 original size:13 final size:13
Alignment explanation
Indices: 1310570--1310598 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1310560 AAATAGTACC
1310570 CAATGTATCGATA
1 CAATGTATCGATA
1310583 CAATGTATCGATA
1 CAATGTATCGATA
1310596 CAA
1 CAA
1310599 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1312863 original size:33 final size:33
Alignment explanation
Indices: 1312821--1312885 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1312811 GTTACAAGCT
1312821 ATGTATCGATACATT-T-CTTCATGTATCGATACG
1 ATGTATCGATACATTGTAC--CATGTATCGATACG
1312854 ATGTATCGATACATTGTACCATGTATCGATAC
1 ATGTATCGATACATTGTACCATGTATCGATAC
1312886 AAATAGTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACG
Found at i:1312871 original size:13 final size:13
Alignment explanation
Indices: 1312841--1312865 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1312831 ACATTTCTTC
1312841 ATGTATCGATACG
1 ATGTATCGATACG
1312854 ATGTATCGATAC
1 ATGTATCGATAC
1312866 ATTGTACCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACG
Found at i:1313569 original size:18 final size:19
Alignment explanation
Indices: 1313546--1313584 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1313536 CTTAAACGAT
1313546 TATCTTCT-CCCCTTTTTA
1 TATCTTCTCCCCCTTTTTA
*
1313564 TATCTTTTCCCCCTTTTTA
1 TATCTTCTCCCCCTTTTTA
1313583 TA
1 TA
1313585 ATAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.13, C:0.31, G:0.00, T:0.56
Consensus pattern (19 bp):
TATCTTCTCCCCCTTTTTA
Found at i:1314572 original size:27 final size:25
Alignment explanation
Indices: 1314534--1314613 Score: 74
Period size: 27 Copynumber: 3.1 Consensus size: 25
1314524 TATTTTTATA
*
1314534 TTTAAAAAATTATATATTTATATAATT
1 TTTAAAATATTATATATTTATAT--TT
1314561 TTTAAAATATTA-ATAATTT-TATTT
1 TTTAAAATATTATAT-ATTTATATTT
* *
1314585 TATTTAAATTTTAATATATTTATATTT
1 T-TTAAAATATT-ATATATTTATATTT
1314612 TT
1 TT
1314614 AATTTATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.07
25 8 0.18
26 11 0.24
27 23 0.51
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTAAAATATTATATATTTATATTT
Found at i:1314596 original size:16 final size:17
Alignment explanation
Indices: 1314554--1314622 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
1314544 TATATATTTA
**
1314554 TATAATTTTTAAAATATT
1 TATAA-TTTTAATTTATT
* *
1314572 AATAATTTTATTTTATT
1 TATAATTTTAATTTATT
*
1314589 TA-AATTTTAATATATT
1 TATAATTTTAATTTATT
*
1314605 TATATTTTTAATTTATT
1 TATAATTTTAATTTATT
1314622 T
1 T
1314623 TTATATTATA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
16 14 0.34
17 23 0.56
18 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATAATTTTAATTTATT
Found at i:1314614 original size:28 final size:29
Alignment explanation
Indices: 1314545--1314657 Score: 93
Period size: 25 Copynumber: 4.1 Consensus size: 29
1314535 TTAAAAAATT
* * *
1314545 ATATATTTATATAATTT-TTAAAATATTA
1 ATATATTTATATATTTTATTTAAATTTTA
1314573 ATA-A-TT-T-TATTTTATTTAAATTTTA
1 ATATATTTATATATTTTATTTAAATTTTA
1314598 ATATATTTATAT-TTTTAATTT--ATTTT-
1 ATATATTTATATATTTT-ATTTAAATTTTA
*
1314624 -TATATTATATATTATTTTAATTAAATTTTA
1 ATATATT-TATA-TATTTTATTTAAATTTTA
1314654 ATAT
1 ATAT
1314658 TATATTATGT
Statistics
Matches: 68, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
24 5 0.07
25 19 0.28
26 7 0.10
27 12 0.18
28 12 0.18
29 10 0.15
31 3 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
ATATATTTATATATTTTATTTAAATTTTA
Found at i:1314621 original size:33 final size:33
Alignment explanation
Indices: 1314549--1314622 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
1314539 AAAATTATAT
* *
1314549 ATTTATATAATTTTTAAAATATTAATAATTTTA
1 ATTTATTTAAATTTTAAAATATTAATAATTTTA
* * * *
1314582 TTTTATTTAAATTTTAATATATTTATATTTTTA
1 ATTTATTTAAATTTTAAAATATTAATAATTTTA
1314615 ATTTATTT
1 ATTTATTT
1314623 TTATATTATA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
ATTTATTTAAATTTTAAAATATTAATAATTTTA
Found at i:1314639 original size:29 final size:29
Alignment explanation
Indices: 1314579--1314662 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 29
1314569 ATTAATAATT
* *
1314579 TTATTTTATTTAAATTTTAATA-TATTTA
1 TTATTTTAATTAAATTTTAATATTATATA
* *
1314607 -TATTTTTAATT-TATTTTTATATTATATA
1 TTA-TTTTAATTAAATTTTAATATTATATA
1314635 TTATTTTAATTAAATTTTAATATTATAT
1 TTATTTTAATTAAATTTTAATATTATAT
1314663 TATGTGAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 10 0.22
28 20 0.43
29 16 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
TTATTTTAATTAAATTTTAATATTATATA
Found at i:1314864 original size:17 final size:17
Alignment explanation
Indices: 1314812--1314866 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 17
1314802 TAGAAAAATA
*
1314812 TAATAAAAAGTTATTATTT
1 TAATAAAAA-TT-TAATTT
*
1314831 TTA-AAAAATTTAA--T
1 TAATAAAAATTTAATTT
1314845 TAATAAAAATTTAATTT
1 TAATAAAAATTTAATTT
1314862 TAATA
1 TAATA
1314867 TTTAATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
16 2 0.07
17 8 0.27
18 5 0.17
19 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
TAATAAAAATTTAATTT
Found at i:1314969 original size:14 final size:14
Alignment explanation
Indices: 1314950--1314976 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1314940 ATTTATTTAA
1314950 TTTAAAATTTATAT
1 TTTAAAATTTATAT
1314964 TTTAAAATTTATA
1 TTTAAAATTTATA
1314977 ATTAGTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAAAATTTATAT
Found at i:1315185 original size:27 final size:26
Alignment explanation
Indices: 1315149--1315205 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
1315139 AGAAAATTTA
* * *
1315149 ATTAATTTAAATATTATTTTAATTAAT
1 ATTAAATTAAATATTAATTAAATT-AT
*
1315176 ATTAAATTAAATTTTAATTAAATTAT
1 ATTAAATTAAATATTAATTAAATTAT
1315202 ATTA
1 ATTA
1315206 TAGTTTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTAAATTAAATATTAATTAAATTAT
Found at i:1318350 original size:13 final size:13
Alignment explanation
Indices: 1318332--1318362 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1318322 ACCTTGCTTC
1318332 ATGTATCGATACA
1 ATGTATCGATACA
1318345 ATGTATCGATACA
1 ATGTATCGATACA
*
1318358 TTGTA
1 ATGTA
1318363 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1318350 original size:33 final size:33
Alignment explanation
Indices: 1318312--1318378 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
1318302 ATTACAAGCT
* *
1318312 ATGTATCGATACCTTGCT-TCATGTATCGATACA
1 ATGTATCGATACATTG-TACCATGTATCGATACA
1318345 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
1318378 A
1 A
1318379 ATAGTGCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:1318451 original size:19 final size:19
Alignment explanation
Indices: 1318407--1318479 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
1318397 CTGCCAGTTT
* **
1318407 CATGTATCGATGCAATTGTC
1 CATGTATCGATACAA-TGAA
1318427 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1318446 CATGTATCGATACAAGGCAA
1 CATGTATCGATACAATG-AA
*
1318466 GATGTATCGATACA
1 CATGTATCGATACA
1318480 TCTGGGTGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 18 0.38
20 29 0.62
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1319543 original size:19 final size:19
Alignment explanation
Indices: 1319519--1319586 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1319509 AATTCAACAG
1319519 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1319538 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1319553 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1319570 GTTGTATCGATACATAA
1 TTTGTATCGATACATAA
1319587 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1319557 original size:32 final size:32
Alignment explanation
Indices: 1319521--1319583 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1319511 TTCAACAGTT
*
1319521 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1319553 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
1319584 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1319558 original size:13 final size:13
Alignment explanation
Indices: 1319540--1319564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1319530 ACATAAGTTT
1319540 TGTATCGATACAA
1 TGTATCGATACAA
1319553 TGTATCGATACA
1 TGTATCGATACA
1319565 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1322096 original size:51 final size:52
Alignment explanation
Indices: 1322015--1322402 Score: 204
Period size: 52 Copynumber: 7.4 Consensus size: 52
1322005 AATTCTCCGC
* * * * *
1322015 AATCAGGGATATTCCATCTCCGATTTTATTTTC-AAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAATTTTCTAT
* * *
1322066 AATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAAAACACAAATTTT-TCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTC--AAAAACACCAATTTTCT-AT
* * ** ** * * ***
1322120 AATCGGGGATACTTCAACCCCG--TTAATCATCGGGGATACTCCAA-CCCCGTTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTC--AAAAACACCAATTTTC--TAT
** * * ***
1322173 TTTCGAGGGGATACTCCAACCCCTG-CTTTATTCTT--AAAATATTGA-TTTCTCAT
1 AATC--GGGGATACTCCAACCCC-GATTTTATT-TTCAAAAACACCAATTTTCT-AT
* * * *
1322226 AATCGGGGATACTCCAACCCCGATTTTA-TTGCAAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAA-TTTTCTAT
* * *
1322278 AATCGAGGATACTCCAACCCCGATTTTATTTT-TAAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAATTTT-CTAT
* * * * *
1322330 AATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAAACACCAATTTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAAACACCAATTTTCT-AT
*
1322384 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
1322403 TCGTTTTTTC
Statistics
Matches: 250, Mismatches: 64, Indels: 43
0.70 0.18 0.12
Matches are distributed among these distances:
49 1 0.00
50 2 0.01
51 62 0.25
52 79 0.32
53 15 0.06
54 69 0.28
55 16 0.06
56 1 0.00
57 4 0.02
58 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (52 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACCAATTTTCTAT
Found at i:1322189 original size:28 final size:27
Alignment explanation
Indices: 1322121--1322195 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
1322111 ATTTTTCACA
*
1322121 ATCGGGGATACTTCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
1322148 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
1322174 TTCGAGGGGATACTCCAACCCC
1 ATC--GGGGATACTCCAACCCC
1322196 TGCTTTATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.09
27 22 0.51
28 17 0.40
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:1322304 original size:52 final size:52
Alignment explanation
Indices: 1322226--1322402 Score: 212
Period size: 52 Copynumber: 3.4 Consensus size: 52
1322216 GATTTCTCAT
* * *
1322226 AATCGGGGATACTCCAACCCCGATTTTATTGCAAAAACACTAATTTTTCCAC
1 AATCGAGGATACTCCAACCCCGATTTTATTCCAAAAACACCAATTTTTCCAC
*** **
1322278 AATCGAGGATACTCCAACCCCGATTTTATTTTTAAAACACCAA-TTTTCCTTT
1 AATCGAGGATACTCCAACCCCGATTTTATTCCAAAAACACCAATTTTTCC-AC
* * * *
1322330 AATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAAACACCAATTTTTTCAC
1 AATCGAGGATACTCCAACCCCGATTTTA-TTCC-AAAAACACCAATTTTTCCAC
1322384 AATCGAGGATACTCCAACC
1 AATCGAGGATACTCCAACC
1322403 TCGTTTTTTC
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
51 6 0.06
52 63 0.62
53 2 0.02
54 26 0.25
55 5 0.05
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.31
Consensus pattern (52 bp):
AATCGAGGATACTCCAACCCCGATTTTATTCCAAAAACACCAATTTTTCCAC
Found at i:1322505 original size:265 final size:263
Alignment explanation
Indices: 1322034--1322512 Score: 753
Period size: 265 Copynumber: 1.8 Consensus size: 263
1322024 TATTCCATCT
* *
1322034 CCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTTC
1 CCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCC
* *
1322099 AAAAAAACACAAATTTTTCACAATCGGGGATACTTCAACCCCGTTAATCATCGGGGATACTCCAA
66 AAAAAAACACAAATTTTTCACAATCGAGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAA
** * * * **
1322164 CCCCGTTATTTTCGAGGGGATACTCCAACCCCTGCTTTATTCTTAAAATATTGATTTCTCATAAT
131 CCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTGTATTCCCAAAATATTGATTTCTCATAAT
1322229 CGGGGATACTCCAACCCCGATTTTATTGCAAAAACACTAATTTTTCCACAATCGAGGATACTCCA
196 CGGGGATACTCCAACCCCGATTTTATTGCAAAAACACTAATTTTTCCACAATCGAGGATACTCCA
1322294 ACC
261 ACC
* * *
1322297 CCGATTTTATTTTTAAAACACCAATTTTCCTTTAATCGGGGATACTCCAGCTCCGATTTTATTTC
1 CCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACTCCAACTCCGATTTTATTTC
* * **
1322362 C-AAAAAACACCAATTTTTTCACAATCGAGGATACTCCAACCTCGTTTTTTCATCGGGGATACTC
65 CAAAAAAACA-CAAATTTTTCACAATCGAGGATACTCCAACCCCG-TTAATCATCGGGGATACTC
1322426 CAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTGTATTCCCAAAATATTGATTTCTCAT
128 CAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTGTATTCCCAAAATATTGATTTCTCAT
*
1322491 AATTGGGGATACTCCAACCCCG
193 AATCGGGGATACTCCAACCCCG
1322513 TTATTTTCGA
Statistics
Matches: 194, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
263 34 0.18
264 64 0.33
265 96 0.49
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (263 bp):
CCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCC
AAAAAAACACAAATTTTTCACAATCGAGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAA
CCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTGTATTCCCAAAATATTGATTTCTCATAAT
CGGGGATACTCCAACCCCGATTTTATTGCAAAAACACTAATTTTTCCACAATCGAGGATACTCCA
ACC
Found at i:1322564 original size:79 final size:79
Alignment explanation
Indices: 1322415--1322596 Score: 204
Period size: 79 Copynumber: 2.3 Consensus size: 79
1322405 GTTTTTTCAT
** *
1322415 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTGTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTGTATTCCCAAAATAT
* * *
1322480 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * * * ** *
1322494 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTGTATTCCCAAAAT-A
1322558 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
*
1322573 CGCGGATACTCCAACCCCGTTATT
1 CGGGGATACTCCAACCCCGTTATT
1322597 ATCTCCAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 3 0.04
79 82 0.96
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTGTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:1325234 original size:13 final size:13
Alignment explanation
Indices: 1325216--1325244 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1325206 AAATAGTACC
1325216 CAATGTATCGATA
1 CAATGTATCGATA
1325229 CAATGTATCGATA
1 CAATGTATCGATA
1325242 CAA
1 CAA
1325245 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1327516 original size:13 final size:13
Alignment explanation
Indices: 1327486--1327510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1327476 ACATTTCTTC
1327486 ATGTATCGATACG
1 ATGTATCGATACG
1327499 ATGTATCGATAC
1 ATGTATCGATAC
1327511 ATTGTACCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACG
Found at i:1327606 original size:19 final size:19
Alignment explanation
Indices: 1327561--1327617 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1327551 CTACCAGTTT
**
1327561 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
1327582 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1327601 CATGTATCTATACAATG
1 CATGTATCGATACAATG
1327618 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
21 15 0.45
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1327624 original size:32 final size:33
Alignment explanation
Indices: 1327583--1327647 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1327573 CAATTTGTCC
* *
1327583 ATGTATCGATACAATG-AACATGTATCTATACA
1 ATGTATCGATACAAAGCAACATGTATCGATACA
*
1327615 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAGCAACATGTATCGATACA
1327648 TCTGGGTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAACATGTATCGATACA
Found at i:1328227 original size:18 final size:19
Alignment explanation
Indices: 1328204--1328242 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1328194 CTTAAACGAT
1328204 TATCTTCT-CCCCTTTTTA
1 TATCTTCTCCCCCTTTTTA
*
1328222 TATCTTTTCCCCCTTTTTA
1 TATCTTCTCCCCCTTTTTA
1328241 TA
1 TA
1328243 ATAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.13, C:0.31, G:0.00, T:0.56
Consensus pattern (19 bp):
TATCTTCTCCCCCTTTTTA
Found at i:1330100 original size:13 final size:13
Alignment explanation
Indices: 1330082--1330110 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1330072 AAATAGTACC
1330082 CAATGTATCGATA
1 CAATGTATCGATA
1330095 CAATGTATCGATA
1 CAATGTATCGATA
1330108 CAA
1 CAA
1330111 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1333998 original size:21 final size:21
Alignment explanation
Indices: 1333972--1334011 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1333962 ACGCAAGTTT
* *
1333972 TTATTTTTCTTAGCTAATTCA
1 TTATTTTTATTAGCCAATTCA
1333993 TTATTTTTATTAGCCAATT
1 TTATTTTTATTAGCCAATT
1334012 TTTTCATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.57
Consensus pattern (21 bp):
TTATTTTTATTAGCCAATTCA
Found at i:1335613 original size:28 final size:28
Alignment explanation
Indices: 1335579--1335660 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1335569 TTTTGGAGAT
*
1335579 AATAACGAGGTTGGAGTGTTCCCTC-A-GA
1 AATAACGAGGTTGGAGT-ATCCC-CGATGA
* *
1335607 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCCCGATGA
*
1335635 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCCCGAT
1335661 TGTGAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 5 0.11
28 40 0.87
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCCCGATGA
Found at i:1335803 original size:51 final size:50
Alignment explanation
Indices: 1335643--1335813 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 50
1335633 GAAATAACGA
* * * *
1335643 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATGA-TA-TTTTGAAAATAAAATCGG
** * * * * * *
1335695 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGA-AAAATGATATTTTGAAAATAAAATCGG
*
1335748 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAAT-GATATTTTGAAAATAAAATCGG
1335799 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1335814 TCAGAAATAA
Statistics
Matches: 94, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
50 4 0.04
51 35 0.37
52 16 0.17
53 32 0.34
54 3 0.03
55 4 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATGATATTTTGAAAATAAAATCGG
Found at i:1335859 original size:27 final size:28
Alignment explanation
Indices: 1335796--1335871 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
1335786 AAAATAAAGT
*
1335796 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
1335824 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1335851 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1335872 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1338358 original size:13 final size:13
Alignment explanation
Indices: 1338340--1338365 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1338330 ACAAAGATCC
1338340 ATGTATCGATACA
1 ATGTATCGATACA
1338353 ATGTATCGATACA
1 ATGTATCGATACA
1338366 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1338361 original size:33 final size:33
Alignment explanation
Indices: 1338319--1338385 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1338309 AAAATTTCCA
***
1338319 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1338352 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1338385 A
1 A
1338386 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1338445 original size:13 final size:13
Alignment explanation
Indices: 1338427--1338452 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1338417 ACAATACTTA
1338427 TGTATCGATACAT
1 TGTATCGATACAT
1338440 TGTATCGATACAT
1 TGTATCGATACAT
1338453 AAGTACAAAT
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1338541 original size:21 final size:21
Alignment explanation
Indices: 1338517--1338573 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1338507 CATTTGTAGG
1338517 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1338538 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1338559 ATGTATCGATACATT
1 ATGTATCGATACATT
1338574 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1338584 original size:1 final size:1
Alignment explanation
Indices: 1338578--1338647 Score: 95
Period size: 1 Copynumber: 70.0 Consensus size: 1
1338568 TACATTTAAA
*** * *
1338578 TTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1338643 TTTTT
1 TTTTT
1338648 CAAACACTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.03, C:0.01, G:0.03, T:0.93
Consensus pattern (1 bp):
T
Found at i:1340473 original size:19 final size:20
Alignment explanation
Indices: 1340449--1340501 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1340439 TACAATTGTC
*
1340449 CATGTATCGATACAATG-AA
1 CATGTATCGATACAAAGTAA
*
1340468 CATGTATCGATGCAAAGTAA
1 CATGTATCGATACAAAGTAA
*
1340488 GATGTATCGATACA
1 CATGTATCGATACA
1340502 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (20 bp):
CATGTATCGATACAAAGTAA
Found at i:1344295 original size:19 final size:19
Alignment explanation
Indices: 1344260--1344310 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
1344250 AGTTTCATGT
1344260 ATCGATACAATTGAGTATGA
1 ATCGATACAA-TGAGTATGA
*
1344280 ATCGATACAATGAGTATGT
1 ATCGATACAATGAGTATGA
*
1344299 ATCGATATAATG
1 ATCGATACAATG
1344311 TATCAATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (19 bp):
ATCGATACAATGAGTATGA
Found at i:1344848 original size:32 final size:32
Alignment explanation
Indices: 1344807--1344869 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1344797 CAAGGAAATG
1344807 TATCGATACATT-ATTCAATGTATCGATACATT
1 TATCGATACATTGA-TCAATGTATCGATACATT
**
1344839 TATCGATACATTGATCTTTGTATCGATACAT
1 TATCGATACATTGATCAATGTATCGATACAT
1344870 CTGGGAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (32 bp):
TATCGATACATTGATCAATGTATCGATACATT
Found at i:1349457 original size:1 final size:1
Alignment explanation
Indices: 1349453--1349529 Score: 64
Period size: 1 Copynumber: 77.0 Consensus size: 1
1349443 ATTGTTGTTG
* * * * * * * * *
1349453 TTTTTTCTTTTCTTTTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTGTTTGTTTTTTTTCTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
1349518 TTTTCTTTTTTT
1 TTTTTTTTTTTT
1349530 GCGGAGGACG
Statistics
Matches: 56, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (1 bp):
T
Found at i:1349476 original size:28 final size:26
Alignment explanation
Indices: 1349438--1349521 Score: 93
Period size: 24 Copynumber: 3.3 Consensus size: 26
1349428 ATCCAGACCC
*
1349438 TTTTTATTGTTGTTGTTTTTTCTTTTCT
1 TTTTTTTTGTT-TTGTTTTTT-TTTTCT
*
1349466 TTTTTTTTGTTTT-TTTTGTTTTT-T
1 TTTTTTTTGTTTTGTTTTTTTTTTCT
* *
1349490 TTGTTTTTG-TTTGTTTTTTTTCTCT
1 TTTTTTTTGTTTTGTTTTTTTTTTCT
1349515 TTTTTTT
1 TTTTTTT
1349522 CTTTTTTTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
23 3 0.06
24 17 0.35
25 11 0.23
26 5 0.10
27 2 0.04
28 10 0.21
ACGTcount: A:0.01, C:0.05, G:0.10, T:0.85
Consensus pattern (26 bp):
TTTTTTTTGTTTTGTTTTTTTTTTCT
Found at i:1349478 original size:9 final size:9
Alignment explanation
Indices: 1349466--1349530 Score: 87
Period size: 9 Copynumber: 7.0 Consensus size: 9
1349456 TTTCTTTTCT
1349466 TTTTTTTTG
1 TTTTTTTTG
1349475 TTTTTTTTG
1 TTTTTTTTG
1349484 TTTTTTTTG
1 TTTTTTTTG
1349493 TTTTTGTTTG
1 TTTTT-TTTG
*
1349503 TTTTTTTTC
1 TTTTTTTTG
1349512 TCTTTTTTT-
1 T-TTTTTTTG
1349521 TCTTTTTTTG
1 T-TTTTTTTG
1349531 CGGAGGACGC
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
9 36 0.69
10 16 0.31
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1349530 original size:28 final size:27
Alignment explanation
Indices: 1349438--1349530 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 27
1349428 ATCCAGACCC
* * *
1349438 TTTTTATTGTTGTTGTTTTT-TC-TTT
1 TTTTTTTTTTTGTTTTTTTTCTCTTTT
* * *
1349463 TCTTTTTTTTTGTTTTTTTTGTTTTTT
1 TTTTTTTTTTTGTTTTTTTTCTCTTTT
*
1349490 TTGTTTTTGTTTGTTTTTTTTCTCTTTT
1 TT-TTTTTTTTTGTTTTTTTTCTCTTTT
1349518 TTTTCTTTTTTTG
1 TTTT-TTTTTTTG
1349531 CGGAGGACGC
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
25 16 0.30
26 1 0.02
27 6 0.11
28 31 0.57
ACGTcount: A:0.01, C:0.05, G:0.10, T:0.84
Consensus pattern (27 bp):
TTTTTTTTTTTGTTTTTTTTCTCTTTT
Found at i:1363490 original size:13 final size:13
Alignment explanation
Indices: 1363472--1363497 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1363462 CAAAAAATCC
1363472 ATGTATCGATACA
1 ATGTATCGATACA
1363485 ATGTATCGATACA
1 ATGTATCGATACA
1363498 TGGAATAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1365561 original size:42 final size:42
Alignment explanation
Indices: 1365499--1365598 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
1365489 GATACAGTTC
* *
1365499 TTCATGTATCGATACATTTCACTTAGAGTAGCTACTGTTAGT
1 TTCATGTATCGATACATTTCACTTAGAGTAGCTACTATCAGT
* * * *
1365541 TTTATGTATTGATACATTTCACTTAGGGTAGCTATTATCAGT
1 TTCATGTATCGATACATTTCACTTAGAGTAGCTACTATCAGT
1365583 TTCATGTATCGATACA
1 TTCATGTATCGATACA
1365599 ATTGAGTATG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (42 bp):
TTCATGTATCGATACATTTCACTTAGAGTAGCTACTATCAGT
Found at i:1365611 original size:20 final size:19
Alignment explanation
Indices: 1365585--1365657 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
1365575 TTATCAGTTT
1365585 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAG
* *
1365605 TATGTATCGATATAATGAG
1 CATGTATCGATACAATGAG
* *
1365624 CATGTATCGATACAAAGCAT
1 CATGTATCGATACAATG-AG
*
1365644 AATGTATCGATACA
1 CATGTATCGATACA
1365658 TCTGGATATG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 18 0.40
20 27 0.60
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:1365628 original size:19 final size:20
Alignment explanation
Indices: 1365585--1365638 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1365575 TTATCAGTTT
1365585 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
* *
1365605 TATGTATCGATATAA-TGAG
1 CATGTATCGATACAATTGAG
1365624 CATGTATCGATACAA
1 CATGTATCGATACAA
1365639 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:1368712 original size:20 final size:21
Alignment explanation
Indices: 1368669--1368721 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1368659 TAAGTAAATG
**
1368669 TATTGATACATTTATTGTTTA
1 TATTGATACATTTATTCATTA
1368690 TATTGATACATTT-TTCATTA
1 TATTGATACATTTATTCATTA
*
1368710 TATAGATACATT
1 TATTGATACATT
1368722 CTCAGTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.53
Consensus pattern (21 bp):
TATTGATACATTTATTCATTA
Found at i:1368770 original size:51 final size:51
Alignment explanation
Indices: 1368694--1368824 Score: 181
Period size: 51 Copynumber: 2.6 Consensus size: 51
1368684 TGTTTATATT
* *
1368694 GATACATTTTTCATTATATAGATACATTCTCAGTTTTAACCTAGATGTATC
1 GATACATTTCTCATTATATCGATACATTCTCAGTTTTAACCTAGATGTATC
* * ** *
1368745 GATACATTTCTCATTGTATCGATACATTTTGGGTTTTCACCTAGATGTATC
1 GATACATTTCTCATTATATCGATACATTCTCAGTTTTAACCTAGATGTATC
* *
1368796 GATACATTTCTCAATATATCGATATATTC
1 GATACATTTCTCATTATATCGATACATTC
1368825 AGGCATTTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (51 bp):
GATACATTTCTCATTATATCGATACATTCTCAGTTTTAACCTAGATGTATC
Found at i:1369725 original size:51 final size:51
Alignment explanation
Indices: 1369659--1369772 Score: 194
Period size: 51 Copynumber: 2.2 Consensus size: 51
1369649 TTACTGTTTG
1369659 TATCGATACATTATTCATTGTATCGATACATT-TCGAGTTTTTACCTAGATC
1 TATCGATACATTATTCATTGTATCGATACATTCT-GAGTTTTTACCTAGATC
* *
1369710 TATTGATACATTATTCATTGTATCGATACATTCTGGGTTTTTACCTAGATC
1 TATCGATACATTATTCATTGTATCGATACATTCTGAGTTTTTACCTAGATC
1369761 TATCGATACATT
1 TATCGATACATT
1369773 CTGGGTTTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 58 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (51 bp):
TATCGATACATTATTCATTGTATCGATACATTCTGAGTTTTTACCTAGATC
Found at i:1369789 original size:30 final size:31
Alignment explanation
Indices: 1369730--1369798 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
1369720 TTATTCATTG
1369730 TATCGATACATTCTGGGTTTTTACCTAGATC
1 TATCGATACATTCTGGGTTTTTACCTAGATC
*
1369761 TATCGATACATTCTGGGTTTTT-CCTAGATG
1 TATCGATACATTCTGGGTTTTTACCTAGATC
1369791 TATCGATA
1 TATCGATA
1369799 TATTATTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 15 0.41
31 22 0.59
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (31 bp):
TATCGATACATTCTGGGTTTTTACCTAGATC
Found at i:1371026 original size:13 final size:13
Alignment explanation
Indices: 1371008--1371054 Score: 94
Period size: 13 Copynumber: 3.6 Consensus size: 13
1370998 CCTTAAAATG
1371008 TTTGTGCCTTGGT
1 TTTGTGCCTTGGT
1371021 TTTGTGCCTTGGT
1 TTTGTGCCTTGGT
1371034 TTTGTGCCTTGGT
1 TTTGTGCCTTGGT
1371047 TTTGTGCC
1 TTTGTGCC
1371055 AAAACCATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.00, C:0.17, G:0.30, T:0.53
Consensus pattern (13 bp):
TTTGTGCCTTGGT
Found at i:1374484 original size:117 final size:117
Alignment explanation
Indices: 1374275--1374509 Score: 407
Period size: 117 Copynumber: 2.0 Consensus size: 117
1374265 CTAAATGAGT
1374275 TTGGGGTGATTTTTCAAAGTTCAATAAACCACTTTTCTCATATGCTTTGCTGATCACCATATACC
1 TTGGGGTGATTTTTCAAAGTTCAATAAACCACTTTTCTCATATGCTTTGCTGATCACCATATACC
*
1374340 TGAGTTCAAAGATTTATTCTGCGTAGAAAATGATTTTATGAGATTTTTGAAA
66 TGAGTTCAAAGATTTATTCTGCCTAGAAAATGATTTTATGAGATTTTTGAAA
* *
1374392 TTGGGGTGATTTTTCAAAGTTCAATAAACTATTTTTCTCATATGCTTTGCTGATCACCATATACC
1 TTGGGGTGATTTTTCAAAGTTCAATAAACCACTTTTCTCATATGCTTTGCTGATCACCATATACC
* * * *
1374457 TGTGTTCAAGGATTTATTCTGCCTAGAAAATGATTTTTTTAGATTTTTGAAA
66 TGAGTTCAAAGATTTATTCTGCCTAGAAAATGATTTTATGAGATTTTTGAAA
1374509 T
1 T
1374510 ATTTTTAGAT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 111 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (117 bp):
TTGGGGTGATTTTTCAAAGTTCAATAAACCACTTTTCTCATATGCTTTGCTGATCACCATATACC
TGAGTTCAAAGATTTATTCTGCCTAGAAAATGATTTTATGAGATTTTTGAAA
Found at i:1375047 original size:130 final size:130
Alignment explanation
Indices: 1374811--1375050 Score: 281
Period size: 130 Copynumber: 1.8 Consensus size: 130
1374801 TTTCATTGAT
* * * * *
1374811 GGTTTTATTTCTAAACTATTGATTTTCAACCATCGGGGATACTCTAACTCTGTTATTTTTGAAGA
1 GGTTTTATTTCTAAACTACTGATTTTCAACCATCAGGGATACTCTAACCCCGTTATTTTCGAAGA
* * * *
1374876 GATACTCTGACCCCGATTTCATTTCTAAAATACTAATTTTTCACCATCGAAGATACTCCAACTCC
66 GATACTCTAACCACGATTTCATTTCCAAAATACTAACTTTTCACCATCGAAGATACTCCAACTCC
* * * * *
1374941 GGTTTTATTTCTGCAAC-ACTGATTTTCCACCATTAGGGATACTTTAACCCCGTTATTTTCGATT
1 GGTTTTATTTCT-AAACTACTGATTTTCAACCATCAGGGATACTCTAACCCCGTTATTTTCGA-A
*
1375005 G-GATACTCTAACCACGATTTTC-TTTCCAAAATA-TCGACTTTTCACC
64 GAGATACTCTAACCACGA-TTTCATTTCCAAAATACT-AACTTTTCACC
1375051 TCGGGGATAC
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
129 1 0.01
130 82 0.90
131 8 0.09
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (130 bp):
GGTTTTATTTCTAAACTACTGATTTTCAACCATCAGGGATACTCTAACCCCGTTATTTTCGAAGA
GATACTCTAACCACGATTTCATTTCCAAAATACTAACTTTTCACCATCGAAGATACTCCAACTCC
Found at i:1381105 original size:20 final size:20
Alignment explanation
Indices: 1381076--1381133 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1381066 GCAGTAGCTT
1381076 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
1381095 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
1381115 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
1381134 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:1381404 original size:34 final size:34
Alignment explanation
Indices: 1381366--1381512 Score: 157
Period size: 34 Copynumber: 4.5 Consensus size: 34
1381356 TCTACAAAAG
*
1381366 GGAAAAAGAGTGCCACGGAGTTGTGGACATAGAA
1 GGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAA
* * * *
1381400 GGAAAACGAGTGCCATGAAGTTGTGGGCTT----
1 GGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAA
* *
1381430 ---AAAAGGGTTCCACGGAGTTGTGGACTTAGAA
1 GGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAA
*
1381461 GGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAA
1 GGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAA
1381495 GGAAAACA-AGTGCCACGG
1 GGAAAA-AGAGTGCCACGG
1381513 GGGCTTAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
27 21 0.23
34 69 0.76
35 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.34, T:0.18
Consensus pattern (34 bp):
GGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAA
Found at i:1381448 original size:61 final size:61
Alignment explanation
Indices: 1381369--1381496 Score: 193
Period size: 61 Copynumber: 2.1 Consensus size: 61
1381359 ACAAAAGGGA
* * * *
1381369 AAAAGAGTGCCACGGAGTTGTGGACATAGAAGGAAAACGAGTGCCATGAAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACATAGAAGGAAAAAGAGTGCCACGAAGTTGTGGACTT
* * *
1381430 AAAAGGGTTCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACATAGAAGGAAAAAGAGTGCCACGAAGTTGTGGACTT
1381491 AAAAGG
1 AAAAGG
1381497 AAAACAAGTG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACATAGAAGGAAAAAGAGTGCCACGAAGTTGTGGACTT
Found at i:1381552 original size:55 final size:60
Alignment explanation
Indices: 1381464--1381635 Score: 204
Period size: 55 Copynumber: 3.0 Consensus size: 60
1381454 CTTAGAAGGA
*
1381464 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAACA-AGTGCCAC-G-G-G-GG-CTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAA-AGAGTGCCACGGAGTGTGGACTT
*
1381519 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAG-TGTGGACTT
* *
1381580 AAAAGGGTGCCACGGAGTTGTGGGCTT-----TAAAAAGAGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAG-TGTGGACTT
1381636 TGAAAAGAAA
Statistics
Matches: 106, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
54 1 0.01
55 43 0.41
56 29 0.27
57 1 0.01
59 1 0.01
60 2 0.02
61 29 0.27
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.20
Consensus pattern (60 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTGTGGACTT
Found at i:1381557 original size:89 final size:92
Alignment explanation
Indices: 1381366--1381585 Score: 347
Period size: 89 Copynumber: 2.4 Consensus size: 92
1381356 TCTACAAAAG
* * *
1381366 GGAAAAAGAGTGCCACGGAGTTGTGGACATAGAAGGAAAACGAGTGCCATGAAGTTGTGGGCTTA
1 GGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAACAAGTGCCA--AAG-TGTGGGCTTA
*
1381431 AAAGGGTTCCACGGAGTTGTGGACTTAGAA
63 AAAGGGTGCCACGGAGTTGTGGACTTAGAA
*
1381461 GGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAACAAGTGCC-ACG-G-GGGCTTAAAA
1 GGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAACAAGTGCCAAAGTGTGGGCTTAAAA
1381523 GGGTGCCACGGAGTTGTGGACTTAGAA
66 GGGTGCCACGGAGTTGTGGACTTAGAA
1381550 GGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGG
1 GGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGG
1381586 GTGCCACGGA
Statistics
Matches: 120, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
89 72 0.60
90 1 0.01
92 2 0.02
95 45 0.38
ACGTcount: A:0.34, C:0.13, G:0.35, T:0.18
Consensus pattern (92 bp):
GGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAACAAGTGCCAAAGTGTGGGCTTAAAA
GGGTGCCACGGAGTTGTGGACTTAGAA
Found at i:1381563 original size:34 final size:32
Alignment explanation
Indices: 1381519--1381836 Score: 225
Period size: 34 Copynumber: 10.0 Consensus size: 32
1381509 ACGGGGGCTT
* *
1381519 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTTG-A-GA
1381553 AAAAGAGTGCCACGGAGTTGTGGAC-TT----
1 AAAAGAGTGCCACGGAGTTGTGGACTTTGAGA
* *
1381580 AAAAGGGTGCCACGGAGTTGTGGGCTTT---A
1 AAAAGAGTGCCACGGAGTTGTGGACTTTGAGA
1381609 AAAAGAGTGCCACGGAGTTGTGGACTTTGAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTTG---AGA
1381644 AAAAG-GATGCCACAGG-GTTGTGGACTTTGAGA
1 AAAAGAG-TGCCAC-GGAGTTGTGGACTTTGAGA
* * * *
1381676 CAAAAGA-TGCCACTGAGTCGTGGCCTTTGAAA
1 -AAAAGAGTGCCACGGAGTTGTGGACTTTGAGA
* *
1381708 AGAAAAATGTGCCACGGAGTTGTGGGCTTTGAGA
1 A-AAAGA-GTGCCACGGAGTTGTGGACTTTGAGA
* * * *
1381742 CAAA-A-TGCCACTGAGTCGTGGCCTTTGA-A
1 AAAAGAGTGCCACGGAGTTGTGGACTTTGAGA
* *
1381771 AAGAAAATGTGCCACGGAGTCGTGGACTTTGAG-
1 AA-AAGA-GTGCCACGGAGTTGTGGACTTTGAGA
* * * ** *
1381804 AAGAGATTGCCACTGAGTCATGGGCTTTGAGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTTGAGA
1381836 A
1 A
1381837 GAGATTTGAA
Statistics
Matches: 234, Mismatches: 28, Indels: 46
0.76 0.09 0.15
Matches are distributed among these distances:
27 23 0.10
28 2 0.01
29 28 0.12
30 22 0.09
31 24 0.10
32 30 0.13
33 32 0.14
34 46 0.20
35 25 0.11
36 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.22
Consensus pattern (32 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTTGAGA
Found at i:1381622 original size:29 final size:29
Alignment explanation
Indices: 1381519--1381643 Score: 146
Period size: 29 Copynumber: 4.2 Consensus size: 29
1381509 ACGGGGGCTT
* *
1381519 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTT-----TA
1381553 AAAAGAGTGCCACGGAGTTGTGGAC-TT-
1 AAAAGAGTGCCACGGAGTTGTGGACTTTA
* *
1381580 AAAAGGGTGCCACGGAGTTGTGGGCTTTA
1 AAAAGAGTGCCACGGAGTTGTGGACTTTA
*
1381609 AAAAGAGTGCCACGGAGTTGTGGACTTTG
1 AAAAGAGTGCCACGGAGTTGTGGACTTTA
1381638 AAAAGA
1 AAAAGA
1381644 AAAAGGATGC
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
27 23 0.28
28 2 0.02
29 32 0.39
33 1 0.01
34 24 0.29
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (29 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTTA
Found at i:1381771 original size:64 final size:64
Alignment explanation
Indices: 1381586--1381838 Score: 309
Period size: 64 Copynumber: 3.9 Consensus size: 64
1381576 ACTTAAAAGG
* * * * *
1381586 GTGCCACGGAGTTGTGGGCTTT-A-AAAAGAGTGCCACGGAGTTGTGGACTTTGAAAAGAAAAAG
1 GTGCCACGGAGTTGTGGACTTTGAGAAAAGA-TGCCACTGAGTCGTGGCCTTTGAAAAGAAAAAT
1381649 GATGCCACAGG-GTTGTGGACTTTGAGACAAAAGATGCCACTGAGTCGTGGCCTTTGAAAAGAAA
1 G-TGCCAC-GGAGTTGTGGACTTTGAG--AAAAGATGCCACTGAGTCGTGGCCTTTGAAAAGAAA
1381713 AAT
62 AAT
*
1381716 GTGCCACGGAGTTGTGGGCTTTGAGACAAA-ATGCCACTGAGTCGTGGCCTTTGAAAAG-AAAAT
1 GTGCCACGGAGTTGTGGACTTTGAGA-AAAGATGCCACTGAGTCGTGGCCTTTGAAAAGAAAAAT
* * * * *
1381779 GTGCCACGGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTCATGGGCTTTGAGAAGA
1 GTGCCACGGAGTTGTGGACTTTGAGAAAAGA-TGCCACTGAGTCGTGGCCTTTGAAAAGA
1381839 GATTTGAAGA
Statistics
Matches: 167, Mismatches: 12, Indels: 20
0.84 0.06 0.10
Matches are distributed among these distances:
62 2 0.01
63 31 0.19
64 70 0.42
65 8 0.05
66 20 0.12
67 30 0.18
68 6 0.04
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.23
Consensus pattern (64 bp):
GTGCCACGGAGTTGTGGACTTTGAGAAAAGATGCCACTGAGTCGTGGCCTTTGAAAAGAAAAAT
Found at i:1381785 original size:33 final size:33
Alignment explanation
Indices: 1381586--1381838 Score: 179
Period size: 33 Copynumber: 7.9 Consensus size: 33
1381576 ACTTAAAAGG
* * *
1381586 GTGCCACGGAGTTGTGGGCTTT--AAA-AAGA-
1 GTGCCACGGAGTCGTGGACTTTGAAAAGAAAAT
* *
1381615 GTGCCACGGAGTTGTGGACTTTGAAAAGAAAAAG
1 GTGCCACGGAGTCGTGGACTTTGAAAAG-AAAAT
* * *
1381649 GATGCCACAGG-GTTGTGGACTTTG-AGACAAAA-
1 G-TGCCAC-GGAGTCGTGGACTTTGAAAAGAAAAT
* *
1381681 GATGCCACTGAGTCGTGGCCTTTGAAAAGAAAAAT
1 G-TGCCACGGAGTCGTGGACTTTGAAAAG-AAAAT
* * * *
1381716 GTGCCACGGAGTTGTGGGCTTTG-AGACAAAA-
1 GTGCCACGGAGTCGTGGACTTTGAAAAGAAAAT
* *
1381747 -TGCCACTGAGTCGTGGCCTTTGAAAAGAAAAT
1 GTGCCACGGAGTCGTGGACTTTGAAAAGAAAAT
* *
1381779 GTGCCACGGAGTCGTGGACTTTGAGAAG-AGAT
1 GTGCCACGGAGTCGTGGACTTTGAAAAGAAAAT
* * * *
1381811 -TGCCACTGAGTCATGGGCTTTGAGAAGA
1 GTGCCACGGAGTCGTGGACTTTGAAAAGA
1381839 GATTTGAAGA
Statistics
Matches: 183, Mismatches: 26, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
29 21 0.11
30 19 0.10
31 34 0.19
32 26 0.14
33 35 0.19
34 26 0.14
35 20 0.11
36 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.23
Consensus pattern (33 bp):
GTGCCACGGAGTCGTGGACTTTGAAAAGAAAAT
Found at i:1381822 original size:31 final size:31
Alignment explanation
Indices: 1381663--1381842 Score: 141
Period size: 31 Copynumber: 5.6 Consensus size: 31
1381653 CCACAGGGTT
*
1381663 GTGGACTTTGAGACAAAAGA-TGCCACTGAGTC
1 GTGGACTTTGAG--AAGAGATTGCCACTGAGTC
* * * * *
1381695 GTGGCCTTTGAAAAGAAAAATGTGCCACGGAGTT
1 GTGGACTTTGAGAAG--AGAT-TGCCACTGAGTC
* *
1381729 GTGGGCTTTGAGACA-A-AATGCCACTGAGTC
1 GTGGACTTTGAGA-AGAGATTGCCACTGAGTC
* * * *
1381759 GTGGCCTTTGAAAAGAAAATGTGCCACGGAGTC
1 GTGGACTTTGAGAAG-AGAT-TGCCACTGAGTC
1381792 GTGGACTTTGAGAAGAGATTGCCACTGAGTC
1 GTGGACTTTGAGAAGAGATTGCCACTGAGTC
* *
1381823 ATGGGCTTTGAGAAGAGATT
1 GTGGACTTTGAGAAGAGATT
1381843 TGAAGAATTG
Statistics
Matches: 118, Mismatches: 21, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
29 1 0.01
30 23 0.19
31 31 0.26
32 17 0.14
33 24 0.20
34 21 0.18
35 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (31 bp):
GTGGACTTTGAGAAGAGATTGCCACTGAGTC
Found at i:1383132 original size:11 final size:11
Alignment explanation
Indices: 1383118--1383145 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1383108 ACCTTTTTTC
1383118 TTTTTTTTTGT
1 TTTTTTTTTGT
1383129 TTTTTTTTTGT
1 TTTTTTTTTGT
1383140 TTTTTT
1 TTTTTT
1383146 CCATCATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:1388871 original size:19 final size:20
Alignment explanation
Indices: 1388828--1388884 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1388818 TACAAGCCAA
*
1388828 TGTATCGATATAATTTGTGG
1 TGTATCGATACAATTTGTGG
1388848 TGTATCGATAC-ATATTGT-G
1 TGTATCGATACAAT-TTGTGG
1388867 TGTATCGATACAAATTTG
1 TGTATCGATAC-AATTTG
1388885 GCTACTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 14 0.42
20 17 0.52
21 2 0.06
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATTTGTGG
Found at i:1388969 original size:13 final size:13
Alignment explanation
Indices: 1388951--1388980 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1388941 ACATTTGGTC
*
1388951 ATGTATCGATATA
1 ATGTATCGATACA
1388964 ATGTATCGATACA
1 ATGTATCGATACA
1388977 ATGT
1 ATGT
1388981 GTTAGGATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Done.