Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008158.1 Hibiscus syriacus cultivar Beakdansim tig00110725_pilon, whole genome shotgun sequence
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: 344415
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:171609 original size:12 final size:12
Alignment explanation
Indices: 171592--171616 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
171582 ATATTTTCAG
171592 TAAAAAATTATT
1 TAAAAAATTATT
171604 TAAAAAATTATT
1 TAAAAAATTATT
171616 T
1 T
171617 TTTACTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAAATTATT
Found at i:173218 original size:2 final size:2
Alignment explanation
Indices: 173213--173253 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
173203 AAAAATCTTT
173213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
173254 TAAAACATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:173348 original size:2 final size:2
Alignment explanation
Indices: 173341--173402 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
173331 ACATTTATCT
173341 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
173383 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
173403 CTTGTTCATG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:175324 original size:17 final size:17
Alignment explanation
Indices: 175284--175328 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
175274 ATTATTTTTA
175284 TATATTTTATTTTATTT
1 TATATTTTATTTTATTT
175301 T-TCATTTTGA-TTTATTT
1 TAT-ATTTT-ATTTTATTT
175318 TATA-TTTATTT
1 TATATTTTATTT
175329 ATTATTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
15 1 0.04
16 6 0.25
17 15 0.62
18 2 0.08
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (17 bp):
TATATTTTATTTTATTT
Found at i:178357 original size:8 final size:7
Alignment explanation
Indices: 178344--178409 Score: 59
Period size: 7 Copynumber: 9.4 Consensus size: 7
178334 AATAAGAAGC
178344 AAAAAAGG
1 AAAAAA-G
178352 AAAAAAG
1 AAAAAAG
178359 --AAAAG
1 AAAAAAG
178364 -AAAAAG
1 AAAAAAG
*
178370 AAAAGAAAC
1 -AAA-AAAG
178379 AAAAAAG
1 AAAAAAG
178386 AAAAAA-
1 AAAAAAG
178392 AATAAAAG
1 AA-AAAAG
178400 AAAAAAG
1 AAAAAAG
178407 AAA
1 AAA
178410 GAACAAAGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
5 5 0.10
6 7 0.14
7 22 0.44
8 13 0.26
9 3 0.06
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:178364 original size:5 final size:5
Alignment explanation
Indices: 178354--178403 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
178344 AAAAAAGGAA
* *
178354 AAAAG AAAAG AAAAAG AAAAG AAACAA AAAAG AAAA- AAAAT AAAAG AAAA
1 AAAAG AAAAG -AAAAG AAAAG AAA-AG AAAAG AAAAG AAAAG AAAAG AAAA
178404 AAGAAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
4 4 0.10
5 26 0.67
6 9 0.23
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:178375 original size:16 final size:15
Alignment explanation
Indices: 178354--178403 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
178344 AAAAAAGGAA
178354 AAAAGAAAAGAAAAAG
1 AAAAGAAAA-AAAAAG
178370 AAAAGAAACAAAAAAG
1 AAAAGAAA-AAAAAAG
*
178386 AAAA-AAAATAAAAG
1 AAAAGAAAAAAAAAG
178400 AAAA
1 AAAA
178404 AAGAAAGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 10 0.31
15 3 0.09
16 18 0.56
17 1 0.03
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:178383 original size:35 final size:36
Alignment explanation
Indices: 178337--178416 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 36
178327 AAGATTCAAT
* *
178337 AAGAAGCAAAAAAG-GAAAAAAGAAAAG-AAAAAGAA
1 AAGAAACAAAAAAGAAAAAAAAGAAAAGAAAAAAG-A
*
178372 AAGAAACAAAAAAGAAAAAAAATAAAAGAAAAAAGA
1 AAGAAACAAAAAAGAAAAAAAAGAAAAGAAAAAAGA
178408 AAG-AACAAA
1 AAGAAACAAA
178417 GATCAAAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
35 19 0.47
36 15 0.38
37 6 0.15
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.01
Consensus pattern (36 bp):
AAGAAACAAAAAAGAAAAAAAAGAAAAGAAAAAAGA
Found at i:178393 original size:11 final size:11
Alignment explanation
Indices: 178344--178409 Score: 71
Period size: 11 Copynumber: 6.0 Consensus size: 11
178334 AATAAGAAGC
*
178344 AAAAAAGGAAA
1 AAAAAAAGAAA
178355 AAAGAAAAGAAA
1 AAA-AAAAGAAA
*
178367 AAGAAAAGAAA
1 AAAAAAAGAAA
*
178378 CAAAAAAGAAA
1 AAAAAAAGAAA
*
178389 AAAAATA-AAA
1 AAAAAAAGAAA
*
178399 GAAAAAAGAAA
1 AAAAAAAGAAA
178410 GAACAAAGAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.18
11 28 0.62
12 9 0.20
ACGTcount: A:0.83, C:0.02, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:178403 original size:21 final size:22
Alignment explanation
Indices: 178359--178409 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
178349 AGGAAAAAAG
178359 AAAAGAAAAAGAAAAGAAACAA
1 AAAAGAAAAAGAAAAGAAACAA
*
178381 AAAAGAAAAA-AAATA-AAAGAA
1 AAAAGAAAAAGAAA-AGAAACAA
178402 AAAAGAAA
1 AAAAGAAA
178410 GAACAAAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAGAAAAAGAAAAGAAACAA
Found at i:178405 original size:16 final size:16
Alignment explanation
Indices: 178344--178398 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
178334 AATAAGAAGC
*
178344 AAAAAAGGAAAAAAGAA
1 AAAAAAAGAAAAAA-AA
*
178361 AAGAAAAAGAAAAGAAA
1 AA-AAAAAGAAAAAAAA
*
178378 CAAAAAAGAAAAAAAA
1 AAAAAAAGAAAAAAAA
178394 TAAAA
1 -AAAA
178399 GAAAAAAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 13 0.42
17 8 0.26
18 10 0.32
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.02
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAA
Found at i:178417 original size:11 final size:11
Alignment explanation
Indices: 178344--178418 Score: 66
Period size: 11 Copynumber: 6.7 Consensus size: 11
178334 AATAAGAAGC
*
178344 AAAAAAGGAAAA
1 AAAAAA-GAAAG
178356 AAGAAAAGAAA-
1 AA-AAAAGAAAG
*
178367 AAGAAAAGAAAC
1 AA-AAAAGAAAG
178379 AAAAAAGAAA-
1 AAAAAAGAAAG
178389 AAAAATA-AAAG
1 AAAAA-AGAAAG
178400 AAAAAAGAAAG
1 AAAAAAGAAAG
*
178411 AACAAAGA
1 AAAAAAGA
178419 TCAAAAAGAA
Statistics
Matches: 57, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
10 9 0.16
11 36 0.63
12 8 0.14
13 4 0.07
ACGTcount: A:0.81, C:0.03, G:0.15, T:0.01
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:178425 original size:32 final size:32
Alignment explanation
Indices: 178354--178431 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
178344 AAAAAAGGAA
*
178354 AAAAGAAAAGAAAA-AGAAAAGAAACAAAAAAG
1 AAAA-AAAAGAAAAGAAAAAAGAAACAAAAAAG
* * *
178386 AAAAAAAATAAAAGAAAAAAGAAAGAACAAAG
1 AAAAAAAAGAAAAGAAAAAAGAAACAAAAAAG
**
178418 ATCAAAAAGAAAAG
1 AAAAAAAAGAAAAG
178432 GGGACAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 8 0.21
32 30 0.79
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.03
Consensus pattern (32 bp):
AAAAAAAAGAAAAGAAAAAAGAAACAAAAAAG
Found at i:180744 original size:106 final size:106
Alignment explanation
Indices: 180620--181392 Score: 1265
Period size: 106 Copynumber: 7.3 Consensus size: 106
180610 ATATCGTGCC
*
180620 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * * *
180685 AATTTCATATCTAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
180726 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
180791 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
180832 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
180897 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
*
180938 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
181003 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
181044 ACT-CATGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCC
1 ACTCCA-GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
* *
181108 CAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
65 CAATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
181150 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
181215 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
181256 ACTCCAGACAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGATTGTCAAC-AA-AATTT--C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
181317 -A-TTCAGAGT-TAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGA-TCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
181356 ACTCAAGACAACGCAAGTTCAACTTCACAACGAAGGG
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
181393 GCCACTCGTG
Statistics
Matches: 635, Mismatches: 29, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
100 67 0.11
101 1 0.00
102 1 0.00
104 4 0.01
105 4 0.01
106 556 0.88
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:185145 original size:20 final size:20
Alignment explanation
Indices: 185120--185170 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
185110 TTTGAAAGTA
185120 CATCGATGCATTAAGGGGTG
1 CATCGATGCATTAAGGGGTG
*
185140 CATCGATACATTAAGGGGTG
1 CATCGATGCATTAAGGGGTG
185160 CATCGATGCAT
1 CATCGATGCAT
185171 GGGAATTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (20 bp):
CATCGATGCATTAAGGGGTG
Found at i:185872 original size:23 final size:23
Alignment explanation
Indices: 185838--185946 Score: 121
Period size: 23 Copynumber: 4.7 Consensus size: 23
185828 ACATATTATA
*
185838 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
185861 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
185884 CGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * **
185907 CTGTC-CTTCAGAACAAATTCTACG
1 -TGGCACTTCGGTGC-AATTCTACG
185931 TGGCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
185947 ATTTATACGA
Statistics
Matches: 70, Mismatches: 13, Indels: 6
0.79 0.15 0.07
Matches are distributed among these distances:
23 54 0.77
24 16 0.23
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:190871 original size:41 final size:41
Alignment explanation
Indices: 190814--190909 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
190804 GTTCCTCATT
* * *
190814 TAATTCAATGCATTTAATCATATTGTTAAATGTAGCACGTC
1 TAATTCAATGCATTTAATCATAATGTTAAATGCAGCACATC
*
190855 TAATTTAATGCATTTAATCATAATGTTAAATGCAGCACATC
1 TAATTCAATGCATTTAATCATAATGTTAAATGCAGCACATC
190896 TAATTCAATGCATT
1 TAATTCAATGCATT
190910 ATCTTGCTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (41 bp):
TAATTCAATGCATTTAATCATAATGTTAAATGCAGCACATC
Found at i:190886 original size:22 final size:22
Alignment explanation
Indices: 190820--190888 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
190810 CATTTAATTC
*
190820 AATGCATTTAATCATATTGTTA
1 AATGCATTTAATCATAATGTTA
* ** *
190842 AATGTA-GCACGTC-TAAT-TT-
1 AATGCATTTA-ATCATAATGTTA
190861 AATGCATTTAATCATAATGTTA
1 AATGCATTTAATCATAATGTTA
190883 AATGCA
1 AATGCA
190889 GCACATCTAA
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 7 0.21
20 7 0.21
21 6 0.18
22 13 0.39
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (22 bp):
AATGCATTTAATCATAATGTTA
Found at i:191998 original size:51 final size:51
Alignment explanation
Indices: 191940--192054 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
191930 GTAACTACTG
* * ***
191940 AATAAAATAATAATAAGCT-AAATATAATGTTTTGGTTCTATCCTAATTCCT
1 AATAAAATAATAATAAACTGAAA-ATAATATTTTAACTCTATCCTAATTCCT
* * *
191991 AATAAAATAATAATAAATTGAAAATTATATTTTAACTCTATCTTAATTCCT
1 AATAAAATAATAATAAACTGAAAATAATATTTTAACTCTATCCTAATTCCT
192042 AATAAAATAATAA
1 AATAAAATAATAA
192055 ATCTAATTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 52 0.95
52 3 0.05
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (51 bp):
AATAAAATAATAATAAACTGAAAATAATATTTTAACTCTATCCTAATTCCT
Found at i:193367 original size:27 final size:27
Alignment explanation
Indices: 193314--193367 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
193304 TGCAAAAGCT
**
193314 CGACTTTGGTACCTCCTCTATTGTGCA
1 CGACTTTGGTACCTCCTCTATCATGCA
** *
193341 CGACTTTGGTATTTCCTCTGTCATGCA
1 CGACTTTGGTACCTCCTCTATCATGCA
193368 TAGGATTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.15, C:0.28, G:0.19, T:0.39
Consensus pattern (27 bp):
CGACTTTGGTACCTCCTCTATCATGCA
Found at i:197167 original size:235 final size:234
Alignment explanation
Indices: 196757--197229 Score: 919
Period size: 235 Copynumber: 2.0 Consensus size: 234
196747 TTTTAATATA
196757 TTGTCATTAAAAACTTAACGTGTTTACGACCCAAACTATCAATTTTAGTCTATTTTAGTATCGAA
1 TTGTCATTAAAAACTTAACGTGTTTACGACCCAAACTATCAATTTTAGTCTATTTTAGTATCGAA
196822 ATTTTAATTTTTTTCAAAACTTTTCGTTAAGTTTTTAACAAGATACTAAATGAAACAAAAGCTAA
66 ATTTTAATTTTTTTCAAAACTTTTCGTTAAGTTTTTAACAAGATACTAAATGAAACAAAAGCTAA
196887 ACGTTAGACATAATTTGAAAAGATTGAAAGTTTAGGTGCTAAAATGAATCAAAACTATTTAGGTA
131 ACGTTAGACATAATTTGAAAAGATTGAAAGTTTAGGTGCTAAAATGAATCAAAACTATTTAGGTA
*
196952 CTAAACATGTAATTTACCCTAAATATAATACTATTTGCC
196 CTAAACATATAATTTACCCTAAATATAATACTATTTGCC
*
196991 TTGTCATTAAAAACTTAACGTGTTTAGGACCCAAACTATCAATTTTAGTCTATTTTAGTATCGAA
1 TTGTCATTAAAAACTTAACGTGTTTACGACCCAAACTATCAATTTTAGTCTATTTTAGTATCGAA
197056 ATTTTAATTTTTTTTCAAAACTTTTCGTTAAGTTTTTAACAAGATACTAAATGAAACAAAAGCTA
66 ATTTTAA-TTTTTTTCAAAACTTTTCGTTAAGTTTTTAACAAGATACTAAATGAAACAAAAGCTA
197121 AACGTTAGACATAATTTGAAAAGATTGAAAGTTTAGGTGCTAAAATGAATCAAAACTATTTAGGT
130 AACGTTAGACATAATTTGAAAAGATTGAAAGTTTAGGTGCTAAAATGAATCAAAACTATTTAGGT
197186 ACTAAACATATAATTTACCCTAAATATAATACTATTTGCC
195 ACTAAACATATAATTTACCCTAAATATAATACTATTTGCC
197226 TTGT
1 TTGT
197230 TTTCGATCAA
Statistics
Matches: 236, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
234 71 0.30
235 165 0.70
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (234 bp):
TTGTCATTAAAAACTTAACGTGTTTACGACCCAAACTATCAATTTTAGTCTATTTTAGTATCGAA
ATTTTAATTTTTTTCAAAACTTTTCGTTAAGTTTTTAACAAGATACTAAATGAAACAAAAGCTAA
ACGTTAGACATAATTTGAAAAGATTGAAAGTTTAGGTGCTAAAATGAATCAAAACTATTTAGGTA
CTAAACATATAATTTACCCTAAATATAATACTATTTGCC
Found at i:197419 original size:31 final size:31
Alignment explanation
Indices: 197349--197433 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
197339 AGTACTAAAG
* * **
197349 TATTTTTTTTGTCAAAAT-GAGTATTTAAAGT
1 TATTTTTTTAGTCAAAATAGA-TATCTAAAAA
*
197380 TATATTTTTAGTCAAAATAGATATCTAAAAA
1 TATTTTTTTAGTCAAAATAGATATCTAAAAA
197411 TATTTTTTTTA-TCAAAATAGATA
1 TA-TTTTTTTAGTCAAAATAGATA
197434 CTTAAACTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 37 0.80
32 9 0.20
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (31 bp):
TATTTTTTTAGTCAAAATAGATATCTAAAAA
Found at i:198761 original size:77 final size:79
Alignment explanation
Indices: 198605--198753 Score: 221
Period size: 77 Copynumber: 1.9 Consensus size: 79
198595 GAATATAGTC
*
198605 AATAAACATTAAAAGAATGTAATTCTGATTACAACTCTTTTAATAGATATTTAATTCGAAATAAT
1 AATAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTTAATAGATATTTAATTCGAAATAAT
198670 TAAATAAGAGTTTA
66 TAAATAAGAGTTTA
* * * * * *
198684 AATAAACATT-AAAGATTGTAATTCAGATTATAAGTC-TTTAATGGATATTTAATTTGAATTAAT
1 AATAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTTAATAGATATTTAATTCGAAATAAT
198747 TAAATAA
66 TAAATAA
198754 TATTTTAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
77 31 0.49
78 22 0.35
79 10 0.16
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.38
Consensus pattern (79 bp):
AATAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTTAATAGATATTTAATTCGAAATAAT
TAAATAAGAGTTTA
Found at i:204190 original size:16 final size:15
Alignment explanation
Indices: 204164--204193 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
204154 TATGTGTTTA
204164 ACATAAACTGAAAGT
1 ACATAAACTGAAAGT
204179 ACATATAACTGAAAG
1 ACATA-AACTGAAAG
204194 ATAATAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.13, G:0.13, T:0.20
Consensus pattern (15 bp):
ACATAAACTGAAAGT
Found at i:205229 original size:77 final size:79
Alignment explanation
Indices: 205084--205242 Score: 198
Period size: 77 Copynumber: 2.0 Consensus size: 79
205074 CCAAATATAG
*
205084 TAAATAAACATTAAAAGAATGTAATTCTGATTACAACTCTTTTAATAGATATTTAATTCGAAATA
1 TAAATAAACATTAAAAGAATGTAATTCTGATTACAACTCTTTAAATAGATATTTAATTCGAAATA
205149 ATTAAATAAGAGTT
66 ATTAAATAAGAGTT
* * * * * * *
205163 TAAATAAGCATT-AAAGATTGTAATT-TGGATTATAAGTC-TTAAATGGATATTTAATTTGAATT
1 TAAATAAACATTAAAAGAATGTAATTCT-GATTACAACTCTTTAAATAGATATTTAATTCGAAAT
* *
205225 AATTAAGTAAGATTT
65 AATTAAATAAGAGTT
205240 TAA
1 TAA
205243 TTAATTCGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
77 37 0.54
78 21 0.30
79 11 0.16
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (79 bp):
TAAATAAACATTAAAAGAATGTAATTCTGATTACAACTCTTTAAATAGATATTTAATTCGAAATA
ATTAAATAAGAGTT
Found at i:206050 original size:134 final size:130
Alignment explanation
Indices: 205879--206121 Score: 314
Period size: 134 Copynumber: 1.8 Consensus size: 130
205869 CTATTAATTT
* **
205879 TATATATATAAATAAGATATTTATTTATTTAGTAATATCAGAAAA-GGACT-TCTAGGTGCTTTA
1 TATATATATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGA-TATC-AGGTGCTTTA
* * * *
205942 AGA-TAGCTCTTTTCTTAATAT-TAAAATATAAATAATTATTAATAAAACGTTTATTAAAAATAG
64 AGACT-GC-CCTTTCTTAATATGGAAAA-AGAAATAAATATTAATAAAACGTTTATTAAAAATAG
206005 ATTAA
126 ATTAA
*
206010 TATATATAATAAAAGTAAAATATTTATTTATTTAAAAATATCAGAAAATGGATATCAGTTGCTTT
1 TATATAT-AT-AAA-TAAAATATTTATTTATTTAAAAATATCAGAAAATGGATATCAGGTGCTTT
206075 AAGACTGCCCTTTCTTAATATGGAAAAAGAAATAAATATTAATAAAA
63 AAGACTGCCCTTTCTTAATATGGAAAAAGAAATAAATATTAATAAAA
206122 ATATAATAAT
Statistics
Matches: 97, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
131 7 0.07
132 2 0.02
133 33 0.34
134 49 0.51
135 6 0.06
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (130 bp):
TATATATATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGATATCAGGTGCTTTAAG
ACTGCCCTTTCTTAATATGGAAAAAGAAATAAATATTAATAAAACGTTTATTAAAAATAGATTAA
Found at i:207681 original size:3 final size:3
Alignment explanation
Indices: 207673--207732 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
207663 TTTATTTATT
* * *
207673 TAA TAA TAA TAA TAA TATA TAT TAA TAA TAA TAA TGA TAA AAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
207719 TAA TTAA AAA TAA T
1 TAA -TAA TAA TAA T
207733 TTTATTCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
3 41 0.87
4 6 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:207717 original size:28 final size:28
Alignment explanation
Indices: 207673--207732 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
207663 TTTATTTATT
* *
207673 TAATAATAATAATAAT-ATATATTAATAA
1 TAATAATAATAAAAATAATA-ATTAAAAA
*
207701 TAATAATGATAAAAATAATAATTAAAAA
1 TAATAATAATAAAAATAATAATTAAAAA
207729 TAAT
1 TAAT
207733 TTTATTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (28 bp):
TAATAATAATAAAAATAATAATTAAAAA
Found at i:207719 original size:15 final size:13
Alignment explanation
Indices: 207674--207732 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
207664 TTATTTATTT
*
207674 AATAATAA-TAAT
1 AATAATAATTAAA
*
207686 AAT-ATATATTAAT
1 AATAATA-ATTAAA
207699 AATAATAATGATAAA
1 AATAATAAT--TAAA
207714 AATAATAATTAAA
1 AATAATAATTAAA
207727 AATAAT
1 AATAAT
207733 TTTATTCAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 3 0.07
12 4 0.10
13 19 0.46
14 3 0.07
15 12 0.29
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
AATAATAATTAAA
Found at i:208048 original size:73 final size:73
Alignment explanation
Indices: 207891--208477 Score: 953
Period size: 73 Copynumber: 8.0 Consensus size: 73
207881 GGTCTTATGA
* * * *
207891 ATGACCCTGAGGTTTTAAGATCAAAAAGCTCCTGAAGGCTTTTTTAAAAACATCATGCACTGTAA
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGC-TTTTTGAAAACATCATGCACTGTAG
*
207956 GTCTTATAG
65 GTCTTACAG
*
207965 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGATTTTTGAAAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
208030 TCTTACAG
66 TCTTACAG
* *
208038 ATGATCCTGAGGCTTTAAGAT-AAAAAACTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
*
208102 TCTTACTG
66 TCTTACAG
* *
208110 ATGACCATGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAAG
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
208175 TCTTACAG
66 TCTTACAG
* *
208183 ATGACCCTGAGACTTTAAGATCAAAAAAACTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAG
1 ATGACCCTGAGGCTTTAAGATC-AAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAG
208248 GTCTTACAG
65 GTCTTACAG
* * *
208257 ATGACCCTGAGGCTTTAAGATCAAAAATCTTCCGAAGGCTTTTTAAAAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
*
208322 TCTTACAA
66 TCTTACAG
* *
208330 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGACTTTTTGAAAA-ATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
208394 TCTTACAG
66 TCTTACAG
* *
208402 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGTCTTTTTGAGAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
208467 TCTTACAG
66 TCTTACAG
208475 ATG
1 ATG
208478 TGGGAAATAA
Statistics
Matches: 477, Mismatches: 33, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
72 135 0.28
73 236 0.49
74 106 0.22
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (73 bp):
ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
TCTTACAG
Found at i:208125 original size:145 final size:146
Alignment explanation
Indices: 207891--208477 Score: 953
Period size: 145 Copynumber: 4.0 Consensus size: 146
207881 GGTCTTATGA
* * * * *
207891 ATGACCCTGAGGTTTTAAGATCAAAAAGCTCCTGAAGGCTTTTTTAAAAACATCATGCACTGTAA
1 ATGACCCTGAGGCTTTAAGATCAAAAAACTCCCGAAGGC-TTTTTGAAAACATCATGCACTGTAG
* *
207956 GTCTTATAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGATTTTTGAAAACATCATG
65 GTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATG
208021 CACTGTAGGTCTTACAG
130 CACTGTAGGTCTTACAG
*
208038 ATGATCCTGAGGCTTTAAGAT-AAAAAACTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAACTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
* *
208102 TCTTACTGATGACCATGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGC
66 TCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGC
*
208167 ACTGTAAGTCTTACAG
131 ACTGTAGGTCTTACAG
*
208183 ATGACCCTGAGACTTTAAGATCAAAAAAACTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAG
1 ATGACCCTGAGGCTTTAAGATC-AAAAAACTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAG
* * *
208248 GTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAATCTTCCGAAGGCTTTTTAAAAACATCATG
65 GTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATG
*
208313 CACTGTAGGTCTTACAA
130 CACTGTAGGTCTTACAG
* * *
208330 ATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGACTTTTTGAAAA-ATCATGCACTGTAGG
1 ATGACCCTGAGGCTTTAAGATCAAAAAACTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
* *
208394 TCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGTCTTTTTGAGAACATCATGC
66 TCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGC
208459 ACTGTAGGTCTTACAG
131 ACTGTAGGTCTTACAG
208475 ATG
1 ATG
208478 TGGGAAATAA
Statistics
Matches: 408, Mismatches: 30, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
145 212 0.52
146 39 0.10
147 157 0.38
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (146 bp):
ATGACCCTGAGGCTTTAAGATCAAAAAACTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGG
TCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGC
ACTGTAGGTCTTACAG
Found at i:209159 original size:22 final size:22
Alignment explanation
Indices: 209131--209204 Score: 103
Period size: 22 Copynumber: 3.4 Consensus size: 22
209121 AATAAAGCTT
* * *
209131 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGGAGAGAGAATCTA
*
209153 TCATCTTTGGAGTGAGAATCTA
1 TCATCTTTGGAGAGAGAATCTA
209175 TCATCTTTGGAGAGAGAATCTA
1 TCATCTTTGGAGAGAGAATCTA
*
209197 TTATCTTT
1 TCATCTTT
209205 AAAGAGTGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (22 bp):
TCATCTTTGGAGAGAGAATCTA
Found at i:216143 original size:21 final size:21
Alignment explanation
Indices: 216105--216144 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
216095 TTACAAAACC
*
216105 TTTTATGAATTATTTATATGT
1 TTTTATGAATTATGTATATGT
216126 TTTTAT-AATTAATGTATAT
1 TTTTATGAATT-ATGTATAT
216145 AACAATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTTATGAATTATGTATATGT
Found at i:219237 original size:4 final size:4
Alignment explanation
Indices: 219230--219268 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
219220 ATAAATAAGA
* *
219230 TATT TATT TATT TATT TATA TATGA TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TAT-T TATT TATT TATT TA
219269 GTAATATCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:219238 original size:25 final size:25
Alignment explanation
Indices: 219217--219268 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
219207 TTAATTTTTA
219217 TATATAAATAAGATATTTATTTATT
1 TATATAAATAAGATATTTATTTATT
* * *
219242 TATTTATATATGATATTTATTTATT
1 TATATAAATAAGATATTTATTTATT
219267 TA
1 TA
219269 GTAATATCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
TATATAAATAAGATATTTATTTATT
Found at i:219275 original size:25 final size:25
Alignment explanation
Indices: 219228--219275 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
219218 ATATAAATAA
* *
219228 GATATTTATTTATTTATTTATATAT
1 GATATTTATTTATTTAGTAATATAT
219253 GATATTTATTTATTTAGTAATAT
1 GATATTTATTTATTTAGTAATAT
219276 CAGAAAAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (25 bp):
GATATTTATTTATTTAGTAATATAT
Found at i:219631 original size:2 final size:2
Alignment explanation
Indices: 219624--219667 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
219614 ATAAATAAAC
219624 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
219666 AT
1 AT
219668 GACTAAGATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:221049 original size:3 final size:3
Alignment explanation
Indices: 221041--221100 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
221031 TTTATTTATT
* * *
221041 TAA TAA TAA TAA TAA TATA TAT TAA TAA TAA TAA TGA TAA AAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
221087 TAA TTAA AAA TAA T
1 TAA -TAA TAA TAA T
221101 TTTAAAGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
3 41 0.87
4 6 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:221085 original size:28 final size:28
Alignment explanation
Indices: 221041--221100 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
221031 TTTATTTATT
* *
221041 TAATAATAATAATAAT-ATATATTAATAA
1 TAATAATAATAAAAATAATA-ATTAAAAA
*
221069 TAATAATGATAAAAATAATAATTAAAAA
1 TAATAATAATAAAAATAATAATTAAAAA
221097 TAAT
1 TAAT
221101 TTTAAAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (28 bp):
TAATAATAATAAAAATAATAATTAAAAA
Found at i:221087 original size:15 final size:13
Alignment explanation
Indices: 221042--221100 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
221032 TTATTTATTT
*
221042 AATAATAA-TAAT
1 AATAATAATTAAA
*
221054 AAT-ATATATTAAT
1 AATAATA-ATTAAA
221067 AATAATAATGATAAA
1 AATAATAAT--TAAA
221082 AATAATAATTAAA
1 AATAATAATTAAA
221095 AATAAT
1 AATAAT
221101 TTTAAAGAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 3 0.07
12 4 0.10
13 19 0.46
14 3 0.07
15 12 0.29
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
AATAATAATTAAA
Found at i:229825 original size:20 final size:20
Alignment explanation
Indices: 229800--229854 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
229790 TTATGAGAAG
229800 TATGTGATATGTGATGTATA
1 TATGTGATATGTGATGTATA
*
229820 TATGTGTTATGTGATGTATA
1 TATGTGATATGTGATGTATA
* *
229840 TATGAGCTATGTGAT
1 TATGTGATATGTGAT
229855 CCTATGAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (20 bp):
TATGTGATATGTGATGTATA
Found at i:231473 original size:28 final size:29
Alignment explanation
Indices: 231433--231497 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
231423 GCGGCGAGAT
* * *
231433 TATTTATTTTGAC-CAAAATTACTTTAAG
1 TATTTATTTTGACAAAAAAATACTTTAAA
*
231461 TATTTATTTTGACAAAAAAATAGTTTAAA
1 TATTTATTTTGACAAAAAAATACTTTAAA
231490 TATTTATT
1 TATTTATT
231498 CATAATATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (29 bp):
TATTTATTTTGACAAAAAAATACTTTAAA
Found at i:232187 original size:76 final size:76
Alignment explanation
Indices: 232059--232210 Score: 277
Period size: 76 Copynumber: 2.0 Consensus size: 76
232049 CAGAAATGCA
* *
232059 AGTTCGAAATAAGTAAAGAAATCAAAGTGGTAGGATGTTCGTACCACGTAGAATAAACGCTAATT
1 AGTTCGAAATAAGTAAAGAAATCAAAATGGTAGGATGTTCGTACCACATAGAATAAACGCTAATT
232124 TATTATTTGTC
66 TATTATTTGTC
*
232135 AGTTCGAAATAAGTAAAGAAATCAAAATGGTTGGATGTTCGTACCACATAGAATAAACGCTAATT
1 AGTTCGAAATAAGTAAAGAAATCAAAATGGTAGGATGTTCGTACCACATAGAATAAACGCTAATT
232200 TATTATTTGTC
66 TATTATTTGTC
232211 CTTAATGATA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (76 bp):
AGTTCGAAATAAGTAAAGAAATCAAAATGGTAGGATGTTCGTACCACATAGAATAAACGCTAATT
TATTATTTGTC
Found at i:234837 original size:10 final size:10
Alignment explanation
Indices: 234822--234846 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
234812 TGGATGATTA
234822 AATTTATTTT
1 AATTTATTTT
234832 AATTTATTTT
1 AATTTATTTT
234842 AATTT
1 AATTT
234847 TATATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
AATTTATTTT
Found at i:242543 original size:15 final size:15
Alignment explanation
Indices: 242506--242544 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
242496 CCATTAGGCG
*
242506 CAAAGTAAAAACACT
1 CAAAGTATAAACACT
242521 CAAAGTATAAACACT
1 CAAAGTATAAACACT
242536 CAAAGTATA
1 CAAAGTATA
242545 TGGGGATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (15 bp):
CAAAGTATAAACACT
Found at i:243999 original size:11 final size:10
Alignment explanation
Indices: 243983--244034 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 10
243973 TGTCTGCATG
243983 AAAAAAAGAGA
1 AAAAAAAGA-A
243994 AAAAAAAGAGA
1 AAAAAAAGA-A
***
244005 AAAAGTTGAA
1 AAAAAAAGAA
244015 AAAAAAAG-A
1 AAAAAAAGAA
244024 AAAAAAAGAA
1 AAAAAAAGAA
244034 A
1 A
244035 CGATAAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 9 0.26
10 8 0.24
11 17 0.50
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:244009 original size:19 final size:19
Alignment explanation
Indices: 243985--244027 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
243975 TCTGCATGAA
243985 AAAAAG-AGAAAAAAAAGAG
1 AAAAAGTAGAAAAAAAA-AG
*
244004 AAAAAGTTGAAAAAAAAAG
1 AAAAAGTAGAAAAAAAAAG
244023 AAAAA
1 AAAAA
244028 AAAGAAACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAAAGTAGAAAAAAAAAG
Found at i:244026 original size:8 final size:9
Alignment explanation
Indices: 243982--244034 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
243972 ATGTCTGCAT
243982 GAAAAAAAGA
1 GAAAAAAA-A
243992 GAAAAAAAA
1 GAAAAAAAA
**
244001 GAGAAAAAGTT
1 GA-AAAAA-AA
244012 GAAAAAAAAA
1 G-AAAAAAAA
244022 GAAAAAAAA
1 GAAAAAAAA
244031 GAAA
1 GAAA
244035 CGATAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
9 15 0.42
10 14 0.39
11 6 0.17
12 1 0.03
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:247578 original size:2 final size:2
Alignment explanation
Indices: 247571--247617 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
247561 GTTGGTATTA
247571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
247612 AT AT AT
1 AT AT AT
247618 CTTAAGTAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:251564 original size:122 final size:123
Alignment explanation
Indices: 251377--251600 Score: 378
Period size: 122 Copynumber: 1.8 Consensus size: 123
251367 TGAGCCATTA
* *
251377 TCTATTTTCCTTTGTCTCGATCTCCCCCAATTTTGTCCCTATCACTAGGCATGGGTTTGGATGAT
1 TCTATTTTCCCTTGTCTCAATCTCCCCCAATTTTGTCCCTATCACTAGGCATGGGTTTGGATGAT
251442 TCGCTACCAGTTGACATGACTTCTACAAGTTCTAACTATGAGCTTTCTTCGTCATCTG
66 TCGCTACCAGTTGACATGACTTCTACAAGTTCTAACTATGAGCTTTCTTCGTCATCTG
* * * *
251500 TCTATTTTCCCTTGTCTTAATCT-CCCCACTTTTTTCCTTATCACTAGGCATGGGTTTGGATGAT
1 TCTATTTTCCCTTGTCTCAATCTCCCCCAATTTTGTCCCTATCACTAGGCATGGGTTTGGATGAT
*
251564 TCTCTACCAGTTGACATGACTTCTACAAGTTCTAACT
66 TCGCTACCAGTTGACATGACTTCTACAAGTTCTAACT
251601 CTGATTAGGC
Statistics
Matches: 94, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
122 74 0.79
123 20 0.21
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (123 bp):
TCTATTTTCCCTTGTCTCAATCTCCCCCAATTTTGTCCCTATCACTAGGCATGGGTTTGGATGAT
TCGCTACCAGTTGACATGACTTCTACAAGTTCTAACTATGAGCTTTCTTCGTCATCTG
Found at i:253590 original size:45 final size:44
Alignment explanation
Indices: 253450--253597 Score: 152
Period size: 45 Copynumber: 3.3 Consensus size: 44
253440 TGAGATGACA
* * * *
253450 CAATAATCAAAAAGAACTAATCTTTTGATTTTACTGTTGACAAAC
1 CAATAATC-AAAAGAACTAATCGTTTGATTTTACTTTTGGCAACC
* * * * *
253495 CAATGATTAAAAGAAACTAATCGTTTGATTATACTTTTGGTAACA
1 CAATAATCAAAAG-AACTAATCGTTTGATTTTACTTTTGGCAACC
* * *
253540 TAATAATCAAAATGAATTAATCGTTTGATTTTATTTTTGGCAACC
1 CAATAATCAAAA-GAACTAATCGTTTGATTTTACTTTTGGCAACC
*
253585 CAATAATTAAAAG
1 CAATAATCAAAAG
253598 TCTAGGATTA
Statistics
Matches: 82, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
44 6 0.07
45 75 0.91
46 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (44 bp):
CAATAATCAAAAGAACTAATCGTTTGATTTTACTTTTGGCAACC
Found at i:253861 original size:13 final size:14
Alignment explanation
Indices: 253836--253865 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
253826 GGGTGAAATC
253836 TTACCATAATAATA
1 TTACCATAATAATA
253850 TTACCA-AATAATA
1 TTACCATAATAATA
253863 TTA
1 TTA
253866 TAACATGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (14 bp):
TTACCATAATAATA
Found at i:255532 original size:17 final size:18
Alignment explanation
Indices: 255486--255537 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
255476 ATTATTTCTT
* *
255486 ATATAGTTTTTGTATAATAT
1 ATATA-TTTTTATATAA-AA
255506 ATATATTTTTATATAAAA
1 ATATATTTTTATATAAAA
255524 ATATATTTTGTATA
1 ATATATTTT-TATA
255538 AAATATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 10 0.34
19 14 0.48
20 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (18 bp):
ATATATTTTTATATAAAA
Found at i:255538 original size:17 final size:18
Alignment explanation
Indices: 255486--255540 Score: 67
Period size: 17 Copynumber: 3.0 Consensus size: 18
255476 ATTATTTCTT
*
255486 ATATAGTTTTTGTATAATAT
1 ATATA-TTTTTGTATAA-AA
*
255506 ATATATTTTTATATAAAA
1 ATATATTTTTGTATAAAA
255524 ATATA-TTTTGTATAAAA
1 ATATATTTTTGTATAAAA
255541 TATTTATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 11 0.34
18 6 0.19
19 10 0.31
20 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
ATATATTTTTGTATAAAA
Found at i:264853 original size:19 final size:19
Alignment explanation
Indices: 264831--264867 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
264821 ATAGTTCCAG
*
264831 TAAAAAAATTGAGTTTTTA
1 TAAAAAAATTAAGTTTTTA
*
264850 TAAATAAATTAAGTTTTT
1 TAAAAAAATTAAGTTTTT
264868 TTTTATTTTT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
TAAAAAAATTAAGTTTTTA
Found at i:264897 original size:21 final size:23
Alignment explanation
Indices: 264871--264917 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
264861 AGTTTTTTTT
264871 TATTTTTTA-AATT-AAAAATAA
1 TATTTTTTATAATTAAAAAATAA
*
264892 TA-TTTTTATTATTAAAAAATAA
1 TATTTTTTATAATTAAAAAATAA
264914 TATT
1 TATT
264918 AAAAGTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 6 0.27
21 5 0.23
22 10 0.45
23 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTTTATAATTAAAAAATAA
Found at i:273527 original size:22 final size:21
Alignment explanation
Indices: 273491--273541 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
273481 TCATCTCACA
* *
273491 CTTTTTTTAATCTTTTTTCTC
1 CTTTTTTTAAACTTTTTGCTC
273512 CTTTTTTTGAAACTTTTTGCTC
1 CTTTTTTT-AAACTTTTTGCTC
273534 CTTTTTTT
1 CTTTTTTT
273542 TGTTCGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.10, C:0.18, G:0.04, T:0.69
Consensus pattern (21 bp):
CTTTTTTTAAACTTTTTGCTC
Found at i:277212 original size:134 final size:133
Alignment explanation
Indices: 276875--277603 Score: 647
Period size: 134 Copynumber: 5.5 Consensus size: 133
276865 GTAATCAGAT
* * * * *
276875 CTCGA-AAAATTTTGATTCACTTTACTGCTCTTCAGTGAAG-TTGAACCGAACTAGATTTGCTTC
1 CTCGAGAAAACTTTGATCCACTTTACTGCTCTTCAGGGAAGATTGAATCGAACT-GATTTGCTTT
* * ** * * *
276938 ACTATTCTTCAAGAAGACCAAATCTGAAAGAAGGTGAGTCTACTCCACTACTCTTTAGGGGAGAT
65 ACTGTTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTATTCCACTACTCTTTAGGGGAGGT
277003 CAA-A
130 -AAGA
* * * * * * * * * *
277007 CAC--G-TAATTTTGATCCACTTTGCCGCTCTTCAGAGAATATTAAATTGGAA-TCAATTTGCTT
1 CTCGAGAAAACTTTGATCCACTTTACTGCTCTTCAGGGAAGATTGAA-TCGAACT-GATTTGCTT
** * * * *
277068 TGTTGTTCTTCAGGAAGACCAAATCTAAAAGAAAAAGAATCTGTTCCACTACTCTTTAGGGGAGA
64 TACTGTTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTATTCCACTACTCTTTAGGGGAGG
277133 TAAGA
129 TAAGA
* * * * *
277138 CTTGAGAGAACTTTGATCCACTTTGCTCCTCTTCAGGGAAGATTGAATCAAACGTGATTTGCTTT
1 CTCGAGAAAACTTTGATCCACTTTACTGCTCTTCAGGGAAGATTGAATCGAAC-TGATTTGCTTT
* * * * ***
277203 GCTGTTCTTCAGGAAGACCAAATCTGAAAGAATAAGAATATACTCTGGTACTCTTTAGGGGAGGT
65 ACTGTTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTATTCCACTACTCTTTAGGGGAGGT
277268 CAA-A
130 -AAGA
* * * *
277272 CTCGAGAAAACTTTGATCCACTTCACTACTCTTCAAGGAAGATTGAATCGAATTTGATTTG-TTT
1 CTCGAGAAAACTTTGATCCACTTTACTGCTCTTCAGGGAAGATTGAATCGAA-CTGATTTGCTTT
* * * *
277336 CACTGCTCTTCAGGAAGACCAAATCTAAAAGAAGAAGAATCT-TCTCCGCTACTCTTTAGAGGAG
65 -ACTGTTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTAT-TCCACTACTCTTTAGGGGAG
*
277400 GTCAGA
128 GTAAGA
* * * * * **
277406 CTCGAGGAAACTTTTATTCACTTTGCTGCTTTTCAGGGAAGATTGAATCGGATTGTGATTTG-TT
1 CTCGAGAAAACTTTGATCCACTTTACTGCTCTTCAGGGAAGATTGAATC-GA-ACTGATTTGCTT
* * *
277470 TCACTGCTCTTCAGGAAGACCAAATCTTGAAAGAAGAAGAATCTGCTT-CACTACTCTTTAAGGG
64 T-ACTGTTCTTCAGGAAGACCAAATC-TGAAAGAAGAAGAATCT-ATTCCACTACTCTTTAGGGG
*
277534 AGGTCAGA
126 AGGTAAGA
* * * *
277542 CTCTAGAAAACTTTGATCCACTTCACTGCTTTTCAGGGAAGGTTGAATCAGAA-TCGATTTGC
1 CTCGAGAAAACTTTGATCCACTTTACTGCTCTTCAGGGAAGATTGAATC-GAACT-GATTTGC
277604 GTCTCTTATC
Statistics
Matches: 489, Mismatches: 87, Indels: 38
0.80 0.14 0.06
Matches are distributed among these distances:
130 30 0.06
131 69 0.14
132 5 0.01
133 8 0.02
134 248 0.51
135 46 0.09
136 81 0.17
137 1 0.00
138 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (133 bp):
CTCGAGAAAACTTTGATCCACTTTACTGCTCTTCAGGGAAGATTGAATCGAACTGATTTGCTTTA
CTGTTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTATTCCACTACTCTTTAGGGGAGGTA
AGA
Found at i:277430 original size:268 final size:271
Alignment explanation
Indices: 277074--277595 Score: 716
Period size: 268 Copynumber: 1.9 Consensus size: 271
277064 GCTTTGTTGT
*
277074 TCTTCAGGAAGACCAAATCTAAAAGAAAAAGAATCTGTTCCACTACTCTTTAGGGGAGATAAGAC
1 TCTTCAGGAAGACCAAATCTAAAAGAAAAAGAATCTGTTCCACTACTCTTTAGAGGAGATAAGAC
*
277139 TTGAGAGAACTTTGATCCACTTTGCTCCTCTTCAGGGAAGATTGAATC-AAACGTGATTTGCTTT
66 TCGAGAGAACTTTGATCCACTTTGCTCCTCTTCAGGGAAGATTGAATCGAAACGTGATTTG-TTT
* * * ** *
277203 -GCTGTTCTTCAGGAAGACCAAATC-TGAAAGAATAAGAATATAC-TCTGGTACTCTTTAGGGGA
130 CACTGCTCTTCAGGAAGACCAAATCTTGAAAGAAGAAGAATATACTTC-ACTACTCTTTAAGGGA
277265 GGTCAAACTCGAGAAAACTTTGATCCACTTCACTACTCTTCAAGGAAGATTGAATC-GAATTTGA
194 GGTCAAACTCGAGAAAACTTTGATCCACTTCACTACTCTTCAAGGAAGATTGAATCAGAATTTGA
277329 TTTGTTTCACTGC
259 TTTGTTTCACTGC
* * * *
277342 TCTTCAGGAAGACCAAATCTAAAAGAAGAAGAATCT-TCTCCGCTACTCTTTAGAGGAGGTCAGA
1 TCTTCAGGAAGACCAAATCTAAAAGAAAAAGAATCTGT-TCCACTACTCTTTAGAGGAGATAAGA
* * * * * **
277406 CTCGAG-GAAACTTTTATTCACTTTGCTGCTTTTCAGGGAAGATTGAATCGGATTGTGATTTGTT
65 CTCGAGAG-AACTTTGATCCACTTTGCTCCTCTTCAGGGAAGATTGAATCGAAACGTGATTTGTT
* *
277470 TCACTGCTCTTCAGGAAGACCAAATCTTGAAAGAAGAAGAATCTGCTTCACTACTCTTTAAGGGA
129 TCACTGCTCTTCAGGAAGACCAAATCTTGAAAGAAGAAGAATATACTTCACTACTCTTTAAGGGA
* * * * * *
277535 GGTCAGACTCTAGAAAACTTTGATCCACTTCACTGCTTTTCAGGGAAGGTTGAATCAGAAT
194 GGTCAAACTCGAGAAAACTTTGATCCACTTCACTACTCTTCAAGGAAGATTGAATCAGAAT
277596 CGATTTGCGT
Statistics
Matches: 220, Mismatches: 27, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
267 2 0.01
268 102 0.46
269 31 0.14
270 79 0.36
271 6 0.03
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (271 bp):
TCTTCAGGAAGACCAAATCTAAAAGAAAAAGAATCTGTTCCACTACTCTTTAGAGGAGATAAGAC
TCGAGAGAACTTTGATCCACTTTGCTCCTCTTCAGGGAAGATTGAATCGAAACGTGATTTGTTTC
ACTGCTCTTCAGGAAGACCAAATCTTGAAAGAAGAAGAATATACTTCACTACTCTTTAAGGGAGG
TCAAACTCGAGAAAACTTTGATCCACTTCACTACTCTTCAAGGAAGATTGAATCAGAATTTGATT
TGTTTCACTGC
Found at i:279169 original size:42 final size:41
Alignment explanation
Indices: 279067--279173 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 41
279057 GGCTGAAGGT
* * * *
279067 CTTATAGATGGCTCGAAGGGCTTATCATCTTGCTCGAAAGA
1 CTTACAGATGGCTCGAAGGACTTATCATCATGCTCAAAAGA
* * * *
279108 CTTACAGATGACTCTAAGGATTTAATCATCATGCTCAAAAGG
1 CTTACAGATGGCTCGAAGGACTT-ATCATCATGCTCAAAAGA
* *
279150 CTTACTGATGGCCCGAAGGACTTA
1 CTTACAGATGGCTCGAAGGACTTA
279174 CCAATTTCGA
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 19 0.37
42 33 0.63
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
CTTACAGATGGCTCGAAGGACTTATCATCATGCTCAAAAGA
Found at i:279192 original size:259 final size:258
Alignment explanation
Indices: 278648--279284 Score: 848
Period size: 259 Copynumber: 2.5 Consensus size: 258
278638 ATCTTGCTTG
* *
278648 AAAGACTTA-CAGATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAAT-TGCTTTCTTACT
1 AAAGACTTACCA-ATTTCGAAAATAGTTTACTGGGTAAGAAACTTTGGAAATCT-CTTTCTTACT
*
278711 TTTCAAAAATTTCACTTTCCGAAAATACTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTT
64 TTTCAAAAATTTCACTTTCTGAAAATACTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTT
** * * * *
278776 TTAATTCATGTGAAAACATCCTACCTGAAGGTCTTATGGATGGCCCGAAGGATTTATCATCTTGC
129 GAAAATCACGTGAAAACATCCTACCTGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGC
* * * *
278841 TCGAAAGACTTACAGATTACCCAAAGGATTTAATTATCATACTCGAAAGACTTGCTAATAGCCCA
194 TCGAAAGACTTACAGATGACCCAAAGGATTTAATCATCATACTCAAAAGACTTACTAATAGCCCA
* * * * *
278906 AAAGACTTACCAATTTTGGAAATAGTTTACCGGGTAAGAAACTTTGGGAATCTTTTTCTTACTTT
1 AAAGACTTACCAATTTCGAAAATAGTTTACTGGGTAAGAAACTTTGGAAATCTCTTTCTTACTTT
* * *
278971 TCAAAAATTTCACTTTCTGAAAATACTAAATGAGACACTTTGGAAATCCCTTTCTCATATTTTTG
66 TCAAAAATTTCACTTTCTGAAAATACTAAATGAGAAACTTTGAAAATCACTTTCTCAT-TTTTTG
** * *
279036 AAAATCACGTGAAAACATCCTGGCTGAAGGTCTTATAGATGGCTCGAAGGGCTTATCATCTTGCT
130 AAAATCACGTGAAAACATCCTACCTGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCT
* * * * * * *
279101 CGAAAGACTTACAGATGACTCTAAGGATTTAATCATCATGCTCAAAAGGCTTACTGATGGCCCG
195 CGAAAGACTTACAGATGACCCAAAGGATTTAATCATCATACTCAAAAGACTTACTAATAGCCCA
* *
279165 AAGGACTTACCAATTTCGAAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTT
1 AAAGACTTACCAATTTCGAAAATAGTTTACTGGGTAAGAAACTTTGGAAATCTCTTTCTTACTTT
* * * * * * *
279230 T-AAAAATTTTCATTTTCTGAAAACAATATATGAAAAACTTTGATAATCGCTTTCT
66 TCAAAAA-TTTCACTTTCTGAAAATACTAAATGAGAAACTTTGAAAATCACTTTCT
279285 TACTTTTAAA
Statistics
Matches: 331, Mismatches: 44, Indels: 7
0.87 0.12 0.02
Matches are distributed among these distances:
258 116 0.35
259 215 0.65
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Consensus pattern (258 bp):
AAAGACTTACCAATTTCGAAAATAGTTTACTGGGTAAGAAACTTTGGAAATCTCTTTCTTACTTT
TCAAAAATTTCACTTTCTGAAAATACTAAATGAGAAACTTTGAAAATCACTTTCTCATTTTTTGA
AAATCACGTGAAAACATCCTACCTGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTC
GAAAGACTTACAGATGACCCAAAGGATTTAATCATCATACTCAAAAGACTTACTAATAGCCCA
Found at i:279280 original size:61 final size:61
Alignment explanation
Indices: 279203--279345 Score: 270
Period size: 61 Copynumber: 2.3 Consensus size: 61
279193 ACTGGGTAAG
279203 AAACTTTGGA-AATCGCTTTCTTACTTTTAAAAATTTTCATTTTCTGAAAACAATATATGAA
1 AAACTTT-GATAATCGCTTTCTTACTTTTAAAAATTTTCATTTTCTGAAAACAATATATGAA
279264 AAACTTTGATAATCGCTTTCTTACTTTTAAAAATTTTCATTTTCTGAAAACAATATATGAA
1 AAACTTTGATAATCGCTTTCTTACTTTTAAAAATTTTCATTTTCTGAAAACAATATATGAA
279325 AAACTTTGATAATCGCTTTCT
1 AAACTTTGATAATCGCTTTCT
279346 CATTTTTTGA
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
60 2 0.02
61 79 0.98
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (61 bp):
AAACTTTGATAATCGCTTTCTTACTTTTAAAAATTTTCATTTTCTGAAAACAATATATGAA
Found at i:279524 original size:319 final size:320
Alignment explanation
Indices: 278960--279603 Score: 949
Period size: 319 Copynumber: 2.0 Consensus size: 320
278950 TGGGAATCTT
* * * *
278960 TTTCTTACTTTTCAAAAATTTCACTTTCTGAAAATACTAAATGAGACACTTTGGAAATCCCTTTC
1 TTTCTTACTTTTCAAAAATTTCACTTTCTGAAAACAATAAATGAAAAACTTTGGAAATCCCTTTC
* *
279025 TCATATTTTTGAAAATCACGTGAAAACATCCTGGCTGAAGGTCTTATAGATGGCTCGAAGGGCTT
66 TCATATTTTTGAAAATCACGTGAAAACATCCTGGCCGAAGGTCTTATAGATGGCTCGAAGGACTT
* * * *
279090 ATCATCTTGCTCGAAAGACTTACAGATGACTCTAAGGATTTAATCATCATGCTCAAAAGGCTTAC
131 ATCATCTTGCTCGAAAGACTTACAAATGACCCGAAGGATTTAATCATCATGCTCAAAAGACTTAC
279155 TGATGGCCCGAAGGACTTACCAATTTCGAAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCT
196 TGATGGCCCGAAGGACTTACCAATTTCGAAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCT
* * *
279220 TTCTTACTTTT-AAAAATTTTCATTTTCTGAAAACAATATATGAAAAACTTTGATAATCGC
261 TTCTTACTTTTCAAAAA-TTTCACTTTCTGAAAACAATAAATGAAAAACTTTGAAAATCGC
* * *
279280 TTTCTTACTTTT-AAAAATTTTCATTTTCTGAAAACAATATATGAAAAACTTT-GATAATCGCTT
1 TTTCTTACTTTTCAAAAA-TTTCACTTTCTGAAAACAATAAATGAAAAACTTTGGA-AATCCCTT
279343 TCTCAT-TTTTTGAAAATCACGTGAAAACATCCT-GCACGAAGGTCTTATAGATGGC-CTGAAGG
64 TCTCATATTTTTGAAAATCACGTGAAAACATCCTGGC-CGAAGGTCTTATAGATGGCTC-GAAGG
* * *
279405 ACTTATCATCTTGTTTGAAAGACTTACAAATGACCCGAAGGATTTAATCATCATGCTCGAAAGAC
127 ACTTATCATCTTGCTCGAAAGACTTACAAATGACCCGAAGGATTTAATCATCATGCTCAAAAGAC
* * ** * *
279470 TTACTGATGGCCCGAATGATTTACTGATTTTGGAAATAGTTTACTGGGTAAGAAACTTTGGAAAT
192 TTACTGATGGCCCGAAGGACTTACCAATTTCGAAAATAGTTTACTGGGTAAGAAACTTTGGAAAT
* * *
279535 CGCTTTCTTACTTTTCAAAAATTTCACTTTCTGAAAATACTAAATGAGAAACTTTGAAAATCGC
257 CGCTTTCTTACTTTTCAAAAATTTCACTTTCTGAAAACAATAAATGAAAAACTTTGAAAATCGC
279599 TTTCT
1 TTTCT
279604 CATTTTTTTA
Statistics
Matches: 291, Mismatches: 28, Indels: 11
0.88 0.08 0.03
Matches are distributed among these distances:
318 3 0.01
319 230 0.79
320 58 0.20
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (320 bp):
TTTCTTACTTTTCAAAAATTTCACTTTCTGAAAACAATAAATGAAAAACTTTGGAAATCCCTTTC
TCATATTTTTGAAAATCACGTGAAAACATCCTGGCCGAAGGTCTTATAGATGGCTCGAAGGACTT
ATCATCTTGCTCGAAAGACTTACAAATGACCCGAAGGATTTAATCATCATGCTCAAAAGACTTAC
TGATGGCCCGAAGGACTTACCAATTTCGAAAATAGTTTACTGGGTAAGAAACTTTGGAAATCGCT
TTCTTACTTTTCAAAAATTTCACTTTCTGAAAACAATAAATGAAAAACTTTGAAAATCGC
Found at i:279719 original size:42 final size:41
Alignment explanation
Indices: 279658--279749 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 41
279648 AGATAGCGCG
* *
279658 AAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCA
1 AAGGATTTATCATCATGCTCGAAAGACTTACAGATGACCCA
* * *
279699 AAGGATTTAGTCATCATGCTCGAAAGACTTACTGATGGCCCG
1 AAGGATTTA-TCATCATGCTCGAAAGACTTACAGATGACCCA
279741 AAGGATTTA
1 AAGGATTTA
279750 CTAATTAAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 8 0.18
42 37 0.82
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (41 bp):
AAGGATTTATCATCATGCTCGAAAGACTTACAGATGACCCA
Found at i:279721 original size:257 final size:258
Alignment explanation
Indices: 279264--279751 Score: 743
Period size: 257 Copynumber: 1.9 Consensus size: 258
279254 AATATATGAA
* *
279264 AAACTTTGATAATCGCTTTCTTACTTTTAAAAATTTTCATTTTCTGAAAACAATATATGAAAAAC
1 AAACTTTGATAATCGCTTTCTTACTTTTAAAAATTTTCACTTTCTGAAAACAATAAATGAAAAAC
* * *
279329 TTTGATAATCGCTTTCTCATTTTTTGAAAATCACGTGAAAACATCCTGCACGAAGGTCTTATAGA
66 TTTGAAAATCGCTTTCTCATTTTTTGAAAATCACGTGAAAACATCATGCACGAAGGTATTATAGA
* * * *
279394 TGGCCTGAAGGACTTATCATCTTGTTTGAAAGACTTACAAATGACCCGAAGGATTTAATCATCAT
131 TAGCCTGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGACCCAAAGGATTTAATCATCAT
*
279459 GCTCGAAAGACTTACTGATGGCCCGAATGATTTACTGATTTTGGAAATAGTTTACTGGGTAAG
196 GCTCGAAAGACTTACTGATGGCCCGAAGGATTTACTGATTTTGGAAATAGTTTACTGGGTAAG
* * *
279522 AAACTTTGGA-AATCGCTTTCTTACTTTTCAAAAA-TTTCACTTTCTGAAAATACTAAATGAGAA
1 AAACTTT-GATAATCGCTTTCTTACTTTT-AAAAATTTTCACTTTCTGAAAACAATAAATGAAAA
* * *
279585 ACTTTGAAAATCGCTTTCTCATTTTTT-TAAATTATGTGAAAACATCATGC-CTGAAGGTATTAT
64 ACTTTGAAAATCGCTTTCTCATTTTTTGAAAATCACGTGAAAACATCATGCAC-GAAGGTATTAT
* *
279648 AGATAGCGC-GAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCAAAGGATTTAGTCA
128 AGATAGC-CTGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGACCCAAAGGATTTAATCA
279712 TCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTACT
192 TCATGCTCGAAAGACTTACTGATGGCCCGAAGGATTTACT
279752 AATTAAGAAA
Statistics
Matches: 208, Mismatches: 18, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
256 1 0.00
257 124 0.60
258 76 0.37
259 7 0.03
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (258 bp):
AAACTTTGATAATCGCTTTCTTACTTTTAAAAATTTTCACTTTCTGAAAACAATAAATGAAAAAC
TTTGAAAATCGCTTTCTCATTTTTTGAAAATCACGTGAAAACATCATGCACGAAGGTATTATAGA
TAGCCTGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGACCCAAAGGATTTAATCATCAT
GCTCGAAAGACTTACTGATGGCCCGAAGGATTTACTGATTTTGGAAATAGTTTACTGGGTAAG
Found at i:292449 original size:23 final size:22
Alignment explanation
Indices: 292434--292512 Score: 79
Period size: 24 Copynumber: 3.5 Consensus size: 22
292424 AAATCCTAAG
292434 AGATAATTCCTAAAAAATTACAA
1 AGATAATTCCT-AAAAATTACAA
*
292457 AGATAATTCCT-AAAATAACAAA
1 AGATAATTCCTAAAAATTAC-AA
* * *
292479 AGGTAATTCATAATAAATTGCAAA
1 AGATAATTCCTAA-AAATTAC-AA
292503 AGATAATTCC
1 AGATAATTCC
292513 CATAATTGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.15
22 11 0.24
23 12 0.26
24 16 0.35
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.27
Consensus pattern (22 bp):
AGATAATTCCTAAAAATTACAA
Found at i:295185 original size:22 final size:23
Alignment explanation
Indices: 295157--295218 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
295147 ATTGTTATGA
*
295157 CACTTTTTTATCAGTG-TGAATG
1 CACTTTTGTATCAGTGCTGAATG
*
295179 CACTTTTGTATCAGTGCTGAA-A
1 CACTTTTGTATCAGTGCTGAATG
* *
295201 CACTTTAGTATTAGTGCT
1 CACTTTTGTATCAGTGCT
295219 AAGACATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 31 0.89
23 4 0.11
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (23 bp):
CACTTTTGTATCAGTGCTGAATG
Found at i:296111 original size:58 final size:57
Alignment explanation
Indices: 296045--296245 Score: 187
Period size: 58 Copynumber: 3.5 Consensus size: 57
296035 ATAAACTTTG
* *
296045 AAAAGGAAATAAATCGTTGAATTTATGTTCCTATGAATCTTATATGATTTTGTTTGGT
1 AAAAGGAAATAAATCATTAAATTTAT-TTCCTATGAATCTTATATGATTTTGTTTGGT
* * * * ** *
296103 AAAAGGAAATAAAACGTTAAATTTAATTT-CTTTGAAATCTTGA-ACGATTTCATTTTGT
1 AAAAGGAAATAAATCATTAAATTT-ATTTCCTATG-AATCTT-ATATGATTTTGTTTGGT
* * * *
296161 AAAAGGAAATAAATTATTAAATTTATTTTC-ATAGAATCTTGTATGATTCTGTTTTGG-
1 AAAAGGAAATAAATCATTAAATTTATTTCCTAT-GAATCTTATATGATTTTG-TTTGGT
*
296218 AAAA-GAAATAAATCATTCAATTTATTTC
1 AAAAGGAAATAAATCATTAAATTTATTTC
296246 TTGAAAATTT
Statistics
Matches: 116, Mismatches: 20, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
56 21 0.18
57 24 0.21
58 68 0.59
59 3 0.03
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.41
Consensus pattern (57 bp):
AAAAGGAAATAAATCATTAAATTTATTTCCTATGAATCTTATATGATTTTGTTTGGT
Found at i:300035 original size:2 final size:2
Alignment explanation
Indices: 300028--300052 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
300018 TATTACAAAA
300028 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
300053 ACTGATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:300200 original size:19 final size:18
Alignment explanation
Indices: 300161--300196 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
300151 GAAGAAGAAG
*
300161 GTGGGTTTAAGGGGGTTA
1 GTGGGGTTAAGGGGGTTA
300179 GTGGGGTTAAGGGGGTTA
1 GTGGGGTTAAGGGGGTTA
300197 AGTGTCTAGT
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:0.17, C:0.00, G:0.53, T:0.31
Consensus pattern (18 bp):
GTGGGGTTAAGGGGGTTA
Found at i:302309 original size:64 final size:64
Alignment explanation
Indices: 302201--302407 Score: 276
Period size: 64 Copynumber: 3.2 Consensus size: 64
302191 TAATGAAGGT
* * ** * * *
302201 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTT-TCATTATTAATGGG
302265 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
* **
302329 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-TTCATTATTAATGGG
302392 AGTGCATCGATGCACT
1 A-TGCATCGATGCACT
302408 TCCTGTTGCA
Statistics
Matches: 130, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
63 3 0.02
64 122 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:305613 original size:31 final size:31
Alignment explanation
Indices: 305575--305635 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
305565 CCGAAGGACC
*
305575 AGTCCATA-GATCCCGAAGAACCTAGGTAAAT
1 AGTCCATATG-TCCCGAAGAACATAGGTAAAT
*
305606 AGTCCATATGTTCCGAAGAACATAGGTAAA
1 AGTCCATATGTCCCGAAGAACATAGGTAAA
305636 CCCTCGACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (31 bp):
AGTCCATATGTCCCGAAGAACATAGGTAAAT
Found at i:306401 original size:64 final size:64
Alignment explanation
Indices: 306293--306499 Score: 276
Period size: 64 Copynumber: 3.2 Consensus size: 64
306283 TAATGAAGGT
* * ** * * *
306293 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTT-TCATTATTAATGGG
306357 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
* **
306421 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-TTCATTATTAATGGG
306484 AGTGCATCGATGCACT
1 A-TGCATCGATGCACT
306500 TCCTGTTGCA
Statistics
Matches: 130, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
63 3 0.02
64 122 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:309705 original size:31 final size:31
Alignment explanation
Indices: 309667--309727 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
309657 CCGAAGGACC
*
309667 AGTCCATA-GATCCCGAAGAACCTAGGTAAAT
1 AGTCCATATG-TCCCGAAGAACATAGGTAAAT
*
309698 AGTCCATATGTTCCGAAGAACATAGGTAAA
1 AGTCCATATGTCCCGAAGAACATAGGTAAA
309728 CCCTCGACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (31 bp):
AGTCCATATGTCCCGAAGAACATAGGTAAAT
Found at i:310498 original size:64 final size:64
Alignment explanation
Indices: 310385--310605 Score: 259
Period size: 64 Copynumber: 3.5 Consensus size: 64
310375 TAATGAAGGT
* * ** * * *
310385 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTT-TAATTATTAATGGG
*
310449 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCAATGTTTAATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTAATTATTAATGGG
* * **
310513 ATACATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-TTAATTATTAATGGG
* * *
310576 AGTGCATCGATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
310606 ACACTTCAAA
Statistics
Matches: 137, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
63 3 0.02
64 129 0.94
65 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTAATTATTAATGGG
Found at i:318329 original size:26 final size:26
Alignment explanation
Indices: 318300--318354 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
318290 TGCTCAACTT
318300 GACTAGAAAAGTGTAAAACTGAGCTC
1 GACTAGAAAAGTGTAAAACTGAGCTC
*
318326 GACTGGAAAAGTGTAAAACTGAGCTC
1 GACTAGAAAAGTGTAAAACTGAGCTC
318352 GAC
1 GAC
318355 CTGACTCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.40, C:0.16, G:0.25, T:0.18
Consensus pattern (26 bp):
GACTAGAAAAGTGTAAAACTGAGCTC
Found at i:320572 original size:17 final size:19
Alignment explanation
Indices: 320550--320584 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
320540 GCTTTTGTTC
320550 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
320567 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
320585 GAGGTGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:336099 original size:24 final size:25
Alignment explanation
Indices: 336048--336170 Score: 207
Period size: 25 Copynumber: 5.0 Consensus size: 25
336038 GAGTAGGGGA
*
336048 TTAGGGTTTGAAACCCTAAT-TGGTT
1 TTAGGGTTTGAAACCCTAATCT-GAT
336073 TTAGGGTTTGAAA-CCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
336097 TTAGGG-TTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
336121 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
336146 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
336171 GGGTTGTTGG
Statistics
Matches: 94, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
23 6 0.06
24 31 0.33
25 57 0.61
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:336664 original size:87 final size:89
Alignment explanation
Indices: 336497--336704 Score: 287
Period size: 87 Copynumber: 2.4 Consensus size: 89
336487 CGTCTAAGGG
* * * * * * *
336497 TGACATGGCTCCTACGTGATGAGGAGATCTGGTCATCTTAGGGATGATAACTCGGTTCCTACGTA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAAGGATGATAACACGGTTCCTACGTA
336562 ATGAGGACGACGGTTATC-A-GGT
66 ATGAGGACGACGGTTATCTATGGT
* * *
336584 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGG-TGATAGCACGGTTCCTACGTG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAAGGATGATAACACGGTTCCTACGTA
*
336648 ATGAGGACGGCTGGTTATCTATGGT
66 ATGAGGACGAC-GGTTATCTATGGT
336673 TGACACGGCTCATACGTGATGAAGAGATCTGG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG
336705 TCTGGGGATG
Statistics
Matches: 107, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
86 28 0.26
87 44 0.41
88 1 0.01
89 34 0.32
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (89 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAAGGATGATAACACGGTTCCTACGTA
ATGAGGACGACGGTTATCTATGGT
Found at i:336694 original size:43 final size:42
Alignment explanation
Indices: 336556--336694 Score: 115
Period size: 46 Copynumber: 3.2 Consensus size: 42
336546 ACTCGGTTCC
* *
336556 TACGTAATGAGGACGAC-GGTTATC-AGGTTGACACGGCTCT
1 TACGTGATGAGGACGACTGGTTATCTAGGTTGACACGGCTCA
* ** * *
336596 TACGTGATGAAGA-GATCTGGCCATCTAAAGG-TGATAGCACGGTTCC
1 TACGTGATGAGGACGA-CTGGTTATCT--AGGTTG--A-CACGGCTCA
*
336642 TACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCA
1 TACGTGATGAGGACGACTGGTTATCTA-GGTTGACACGGCTCA
336685 TACGTGATGA
1 TACGTGATGA
336695 AGAGATCTGG
Statistics
Matches: 76, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
39 2 0.03
40 12 0.16
41 5 0.07
43 19 0.25
44 5 0.07
45 3 0.04
46 29 0.38
47 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (42 bp):
TACGTGATGAGGACGACTGGTTATCTAGGTTGACACGGCTCA
Found at i:336705 original size:43 final size:43
Alignment explanation
Indices: 336472--336706 Score: 158
Period size: 43 Copynumber: 5.4 Consensus size: 43
336462 CTCATACGCA
* * * *
336472 ATGAAGAGGTCTGGTCGTCTAAGGGTGACATGGCTCCTACGTG
1 ATGAAGAGATCTGGTCATCTAAGGTTGACACGGCTCCTACGTG
* * * * * *
336515 ATGAGGAGATCTGGTCATCTTAGGGATGATAACTCGGTTCCTACGTA
1 ATGAAGAGATCTGGTCATC-TAAGG-T--TGACACGGCTCCTACGTG
* * *
336562 ATGAGGACGA-C-GGTTATC--AGGTTGACACGGCTCTTACGTG
1 ATGAAGA-GATCTGGTCATCTAAGGTTGACACGGCTCCTACGTG
* *
336602 ATGAAGAGATCTGGCCATCTAAAGG-TGATAGCACGGTTCCTACGTG
1 ATGAAGAGATCTGGTCATCT-AAGGTTG--A-CACGGCTCCTACGTG
* * * * *
336648 ATGAGGACG-GCTGGTTATCTATGGTTGACACGGCTCATACGTG
1 ATGAAGA-GATCTGGTCATCTAAGGTTGACACGGCTCCTACGTG
336691 ATGAAGAGATCTGGTC
1 ATGAAGAGATCTGGTC
336707 TGGGGATGAC
Statistics
Matches: 144, Mismatches: 32, Indels: 32
0.69 0.15 0.15
Matches are distributed among these distances:
39 2 0.01
40 20 0.14
41 5 0.03
42 2 0.01
43 44 0.31
44 8 0.06
45 4 0.03
46 35 0.24
47 22 0.15
48 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (43 bp):
ATGAAGAGATCTGGTCATCTAAGGTTGACACGGCTCCTACGTG
Found at i:337785 original size:7 final size:8
Alignment explanation
Indices: 337756--337792 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
337746 CCCTCTATTT
337756 ATTTTTTC
1 ATTTTTTC
*
337764 TTCTTTTTC
1 AT-TTTTTC
337773 ATTTTTTC
1 ATTTTTTC
337781 ATTTTTTC
1 ATTTTTTC
337789 ATTT
1 ATTT
337793 CCTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTC
Done.