Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000250.1 Hibiscus syriacus cultivar Beakdansim tig00000452_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: 2850692
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 12
Found at i:2355748 original size:36 final size:36
Alignment explanation
Indices: 2355703--2355817 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
2355693 GGTCTCAAGC
*
2355703 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* * ** * **
2355739 GAAATAAATCTTCTTTCGAGAAAAACAGTCTCAAGT
1 GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* *
2355775 GAGACAAAGT-ATGTTTTAAGAAAAACAAAT-TTGAGT
1 GAGATAAA-TCTTGTTTTAAGAAAAAC-AATCTTGAGT
2355811 GAGATAA
1 GAGATAA
2355818 TCATCTGCAT
Statistics
Matches: 59, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
36 56 0.95
37 3 0.05
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.28
Consensus pattern (36 bp):
GAGATAAATCTTGTTTTAAGAAAAACAATCTTGAGT
Found at i:2355790 original size:72 final size:75
Alignment explanation
Indices: 2355643--2355817 Score: 200
Period size: 72 Copynumber: 2.4 Consensus size: 75
2355633 TAAAATCTTC
** * **
2355643 TTAA-AAAAACAGCCTTGAGTGAAATGAAATGCCTCTTTTCGAGTGAAAATGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAATGCCTCTTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
2355707 CAAATCTTGTT
65 CAAATCATGTT
* *
2355718 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTC-TTTCGAG-AAAAACAGTCTCAAGTGAGAC
1 TTAAGAAAAACAATCTTGAGTGAAATAAATGCCTCTTTTCGAGTAAAAACAGTCTCAAGCGAGAC
2355780 AAAGT-ATGTT
66 AAA-TCATGTT
*
2355790 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
2355818 TCATCTGCAT
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
72 47 0.53
73 11 0.12
74 3 0.03
75 8 0.09
76 19 0.22
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (75 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATGCCTCTTTTCGAGTAAAAACAGTCTCAAGCGAGAC
AAATCATGTT
Found at i:2357266 original size:183 final size:183
Alignment explanation
Indices: 2356958--2357494 Score: 941
Period size: 183 Copynumber: 2.9 Consensus size: 183
2356948 ATCAGGTTTA
* * *
2356958 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTAACAAAAGTAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGAAGTGGAGCAAACACCGAATT
* * **
2357023 GCCAAGTGTCTGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
2357087 TTCCTCTATAACCAATTGCCTTAGTGGAATAACTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* * *
2357141 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGAAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGAAGTGGAGCAAACACCGAATT
2357206 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
2357271 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
2357324 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGAAGTGGAGCAAACATCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGAAGTGGAGCAAACACCGAATT
2357389 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
2357454 TCCTCTATAACCAATTACCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
2357495 CGGATTTAAT
Statistics
Matches: 338, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
183 337 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGAAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:2361031 original size:19 final size:19
Alignment explanation
Indices: 2360998--2361034 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2360988 TGCAGATGAT
2360998 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
2361017 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
2361035 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:2362155 original size:21 final size:20
Alignment explanation
Indices: 2362126--2362165 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2362116 GAAAAATAAA
* *
2362126 ATAATAAAATAAATAAGTAAG
1 ATAAGAAAAAAAAT-AGTAAG
2362147 ATAAGAAAAAAAATAGTAA
1 ATAAGAAAAAAAATAGTAA
2362166 AGTAATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (20 bp):
ATAAGAAAAAAAATAGTAAG
Found at i:2362429 original size:11 final size:10
Alignment explanation
Indices: 2362412--2362471 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 10
2362402 TTTTTTAAAA
2362412 AAATAATAAT
1 AAATAATAAT
2362422 ATAATAATAAT
1 A-AATAATAAT
* * *
2362433 GAATAAAAAAA
1 AAAT-AATAAT
2362444 AAATAATAA-
1 AAATAATAAT
2362453 AAATAAT-AT
1 AAATAATAAT
2362462 AAATATATAA
1 AAATA-ATAA
2362472 AGTTATAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
8 1 0.03
9 12 0.30
10 10 0.25
11 17 0.43
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (10 bp):
AAATAATAAT
Found at i:2362466 original size:29 final size:32
Alignment explanation
Indices: 2362408--2362466 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2362398 AGGATTTTTT
*
2362408 AAAAAAATAATAATATAATAATAATGAATAAA
1 AAAAAAATAATAATATAATAATAATAAATAAA
2362440 AAAAAAATAATAA-A-AATAAT-ATAAATA
1 AAAAAAATAATAATATAATAATAATAAATA
2362467 TATAAAGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.23
30 6 0.23
31 1 0.04
32 13 0.50
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (32 bp):
AAAAAAATAATAATATAATAATAATAAATAAA
Found at i:2362721 original size:48 final size:49
Alignment explanation
Indices: 2362650--2362743 Score: 122
Period size: 48 Copynumber: 1.9 Consensus size: 49
2362640 ATATTAAAGA
*
2362650 AATATATATATATAATAAAATATAGTAAAAAATAA-ATGAA-AATAATTT
1 AATATATATATATAATAAAATATAAT-AAAAATAACATGAATAATAATTT
* *
2362698 AATATATATATAT-ATATACATATAATAATAATAACATGAATAATAA
1 AATATATATATATAATA-AAATATAATAAAAATAACATGAATAATAA
2362744 AATTAAATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
47 10 0.25
48 25 0.62
49 5 0.12
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (49 bp):
AATATATATATATAATAAAATATAATAAAAATAACATGAATAATAATTT
Found at i:2362740 original size:18 final size:18
Alignment explanation
Indices: 2362719--2362761 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
2362709 ATATATACAT
2362719 ATAATAATAA-TAACATGA
1 ATAATAATAATTAA-ATGA
2362737 ATAATAA-AATTAAATGA
1 ATAATAATAATTAAATGA
2362754 ATAA-AATA
1 ATAATAATA
2362762 TCCATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.09
17 11 0.48
18 10 0.43
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (18 bp):
ATAATAATAATTAAATGA
Found at i:2363160 original size:37 final size:37
Alignment explanation
Indices: 2363110--2363216 Score: 126
Period size: 37 Copynumber: 2.9 Consensus size: 37
2363100 GTGCTTGTGG
* * * * *
2363110 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACT-CT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATGCT
* *
2363147 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATGCT
2363184 ATCCTATTTTTTAGGAGTTTGAATCCTAGTAAA
1 ATCCTA-TTTTTAGGAGTTTGAATCCTAGTAAA
2363217 CGAAAATGTG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
36 3 0.05
37 32 0.53
38 25 0.42
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATGCT
Found at i:2363731 original size:18 final size:18
Alignment explanation
Indices: 2363708--2363750 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2363698 CGATAAACTC
2363708 AATAAATTAACTTTTAAT
1 AATAAATTAACTTTTAAT
**
2363726 AATAAATT-TTTTTTAAT
1 AATAAATTAACTTTTAAT
2363743 AA-AAATTA
1 AATAAATTA
2363751 TCCTATAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 9 0.41
18 8 0.36
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAAATTAACTTTTAAT
Found at i:2363904 original size:19 final size:17
Alignment explanation
Indices: 2363880--2363918 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 17
2363870 CCAATAAATT
2363880 ATAAAAGAACAATTTAATA
1 ATAAAA-AA-AATTTAATA
2363899 AT-AAAAAAATTTAATA
1 ATAAAAAAAATTTAATA
2363915 ATAA
1 ATAA
2363919 TAATAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.58
17 3 0.16
18 3 0.16
19 2 0.11
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (17 bp):
ATAAAAAAAATTTAATA
Found at i:2364574 original size:181 final size:182
Alignment explanation
Indices: 2364257--2364708 Score: 671
Period size: 181 Copynumber: 2.5 Consensus size: 182
2364247 CACTTTTTTA
* * **
2364257 TTACCGATTTTGTTATTTCGAGATTGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCG
1 TTACCGGTTTTGTCATTTCGAGAACGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCG
* * *
2364322 ATA-TTTTTTATAAAGTATCGACACTTTATTGGCACTATAACTTCTTTTATTTTAAATTTCCAAA
66 ATACATTTTTATAAAGTATCGACACTTTATTAGCACTATAACTTCTTCTATTTTAAATTTCCAAA
* *
2364386 GTGTCGATACTTATAATAAAGTAT-AGACACTATCAACATA-CCGGTAGCTCT
131 GTGTCGATACTTATAATAAAATATCA-ACACTATCAACATATCCGGTAGCGCT
* *
2364437 TTACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATTG
1 TTACCGGTTTTGTCATTTCGAGAACGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCG
* * *
2364502 ATACATTTTTATAAAATATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAA-TTCCAAA
66 ATACATTTTTATAAAGTATCGACACTTTATTAGCACTATAACTTCTTCTATTTTAAATTTCC-AA
2364566 AGTGTCGATACTTATAATAAAATATCAACACTATCAACATATCCGGTAGCGCT
130 AGTGTCGATACTTATAATAAAATATCAACACTATCAACATATCCGGTAGCGCT
* ** * * *
2364619 TTACCTGTTTTGTCATTTATAAAACGATTTTGTCATTTTTTTA-CTGTTTTATTGTTATGGATCG
1 TTACCGGTTTTGTCATTTCGAGAACGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCG
2364683 ATACATTTTTATAAAGTATCGACACT
66 ATACATTTTTATAAAGTATCGACACT
2364709 ATCAACATAT
Statistics
Matches: 246, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
180 67 0.27
181 131 0.53
182 48 0.20
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (182 bp):
TTACCGGTTTTGTCATTTCGAGAACGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCG
ATACATTTTTATAAAGTATCGACACTTTATTAGCACTATAACTTCTTCTATTTTAAATTTCCAAA
GTGTCGATACTTATAATAAAATATCAACACTATCAACATATCCGGTAGCGCT
Found at i:2364838 original size:112 final size:112
Alignment explanation
Indices: 2364582--2365155 Score: 925
Period size: 112 Copynumber: 5.1 Consensus size: 112
2364572 GATACTTATA
* * * * * * *
2364582 ATAAAATATCAACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAAACGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
2364647 TTTGTCATTTTTTTA-CTGTTTTATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
2364693 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
2364758 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
2364805 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTTATTTATAGACTGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
2364870 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
2364917 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTGTTATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
2364982 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATAGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
2365029 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
** * *
2365094 TTTGTCATTTTTTTATTTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
2365141 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
2365156 AAACCGACAA
Statistics
Matches: 434, Mismatches: 28, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
111 75 0.17
112 359 0.83
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:2368262 original size:43 final size:43
Alignment explanation
Indices: 2368206--2368634 Score: 529
Period size: 43 Copynumber: 10.0 Consensus size: 43
2368196 AAACCTCAAT
* * *
2368206 AGGTCAAGATCTATAGTGGCGTTTTTGGAATAAACGCCGCAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * *
2368249 AAGTCGATATCTATAGTGGCGTTTTTGGAACAAACGCCGCAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* *
2368292 AGGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCCACAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* ** * *
2368335 AGGTCGAGATCGATAAAGACGTTTTTGGAACAAACGCCGTAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * * *
2368378 ATGTCAAGATCTATAGCGGTGTTTTTGGAACAAACGACGCAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * * *
2368421 AGGTC-AGATATATAACGGCGTTTTTGGAACAAACACCACAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* ** *
2368463 ATGTCGAGATCTATAGCGGTATTTTTTGAACAAACGCCGCAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * *
2368506 AGGTCGAGATCTATAACGGCATTTTTGGAACAAATGCCGCAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
** ** *
2368549 ATATCGAGATCTATAAAGGCGTTTTTGGAACAAACGTCGCAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* *
2368592 AGGTC-AGATCTATAGCGGCGTTTTTGGAAAAAATGCCGCAAA
1 AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
2368634 A
1 A
2368635 AGTAAGTTTA
Statistics
Matches: 327, Mismatches: 58, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
42 68 0.21
43 259 0.79
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (43 bp):
AGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
Found at i:2368496 original size:171 final size:171
Alignment explanation
Indices: 2368208--2368620 Score: 576
Period size: 171 Copynumber: 2.4 Consensus size: 171
2368198 ACCTCAATAG
* * * * *
2368208 GTCAAGATCTATAGTGGCGTTTTTGGAATAAACGCCGCAAAAAGTC-GATATCTATAGTGGCGTT
1 GTCAAGATCTATAGAGGCGTTTTTGGAACAAACGACGCAAAAGGTCAGATA--TATAGCGGCGTT
* *
2368272 TTTGGAACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCCACAAAAG
64 TTTGGAACAAACACCACAAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCCACAAAAG
* *
2368337 GTCGAGATCGATAAAGACGTTTTTGGAACAAACGCCGTAAAAT
129 GTCGAGATCGATAAAGACATTTTTGGAACAAACGCCGCAAAAT
* * *
2368380 GTCAAGATCTATAGCGGTGTTTTTGGAACAAACGACGCAAAAGGTCAGATATATAACGGCGTTTT
1 GTCAAGATCTATAGAGGCGTTTTTGGAACAAACGACGCAAAAGGTCAGATATATAGCGGCGTTTT
* * * *
2368445 TGGAACAAACACCACAAAATGTCGAGATCTATAGCGGTATTTTTTGAACAAACGCCGCAAAAGGT
66 TGGAACAAACACCACAAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCCACAAAAGGT
* * * *
2368510 CGAGATCTATAACGGCATTTTTGGAACAAATGCCGCAAAAT
131 CGAGATCGATAAAGACATTTTTGGAACAAACGCCGCAAAAT
* * * * *
2368551 ATCGAGATCTATAAAGGCGTTTTTGGAACAAACGTCGCAAAAGGTCAGATCTATAGCGGCGTTTT
1 GTCAAGATCTATAGAGGCGTTTTTGGAACAAACGACGCAAAAGGTCAGATATATAGCGGCGTTTT
2368616 TGGAA
66 TGGAA
2368621 AAAATGCCGC
Statistics
Matches: 213, Mismatches: 27, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
171 168 0.79
172 41 0.19
173 4 0.02
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (171 bp):
GTCAAGATCTATAGAGGCGTTTTTGGAACAAACGACGCAAAAGGTCAGATATATAGCGGCGTTTT
TGGAACAAACACCACAAAAGGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCCACAAAAGGT
CGAGATCGATAAAGACATTTTTGGAACAAACGCCGCAAAAT
Found at i:2378098 original size:2 final size:2
Alignment explanation
Indices: 2378059--2378083 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2378049 CATACCTTTA
2378059 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2378084 CAAGTTTTTA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2379774 original size:3 final size:3
Alignment explanation
Indices: 2379756--2379849 Score: 127
Period size: 3 Copynumber: 31.7 Consensus size: 3
2379746 TGTAAATTAA
*
2379756 AAT AAT ATT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * **
2379803 GAT AAT AAT AAT GAT AAT AAT AAT TAT TGT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2379850 ACCTCGGGCA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
2 2 0.03
3 78 0.98
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2380170 original size:104 final size:104
Alignment explanation
Indices: 2380027--2380273 Score: 305
Period size: 104 Copynumber: 2.4 Consensus size: 104
2380017 ACTTTTGAAG
* * * * * * *
2380027 ATGACATTATTCCTTCTTGTTGAGGAGATCGAGTCAATCCAAATATAATATGGTTTTGAAGACGA
1 ATGACGTTGTTCCTTCTTGTTGAGGAAATCGGGTCAATCCAAAGATAATATGGTGTTGAAAACGA
* *
2380092 TACTCCCCATCCATGTTGAAGAGTTATGGCCATTTTCAT
66 CACTCCCCATCCATGTTGAAGAGTTATGGCCACTTTCAT
** * *
2380131 ATGACGTTGTTCCTTCTCATTGAGGAAACCGGGTCAATCCAGAGATAATATGGTGTTGAAAACGA
1 ATGACGTTGTTCCTTCTTGTTGAGGAAATCGGGTCAATCCAAAGATAATATGGTGTTGAAAACGA
* * * * * *
2380196 CACTGCTCTTCTATGTTGAAGAGTTCTGGTCACTTTCAT
66 CACTCCCCATCCATGTTGAAGAGTTATGGCCACTTTCAT
* *
2380235 ATGACGATGTTCCTTCTTGTTGAGGAAGTCGGGTCAATC
1 ATGACGTTGTTCCTTCTTGTTGAGGAAATCGGGTCAATC
2380274 TAGATAATTT
Statistics
Matches: 119, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
104 119 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (104 bp):
ATGACGTTGTTCCTTCTTGTTGAGGAAATCGGGTCAATCCAAAGATAATATGGTGTTGAAAACGA
CACTCCCCATCCATGTTGAAGAGTTATGGCCACTTTCAT
Found at i:2380668 original size:137 final size:135
Alignment explanation
Indices: 2380276--2380670 Score: 459
Period size: 137 Copynumber: 2.9 Consensus size: 135
2380266 GGTCAATCTA
* * * * * * *
2380276 GATAATTTAAAGATAACATGGTTCGTTCGCGTTGAGGAAGTCTGATTGTCTGAGTATGACACTGG
1 GATAATTTAGAGACAACA-CGTTCCTTCGCGTTGAGGAAGTTTGATTGTCTGAGGATGACACTGC
* ** * * * *
2380341 TCCTTTACGTTGAGGAGATATAGTCAGTAAACCACATTGATCATTCTTGTTGATGATGTCTAGCT
65 TCCTTTGCGTTGAGGAGATATAGTCAGTAAATGACATTGTTCATTC-TGTTGAGGATGCCTAGAT
2380406 ATAGTTG
129 ATAGTTG
* * *
2380413 GATAATTTGGAGACAACGCGATTCCTTCGTGTTGAGGAAGTTTGATTGTCTGAGGATGACACTGC
1 GATAATTTAGAGACAACACG-TTCCTTCGCGTTGAGGAAGTTTGATTGTCTGAGGATGACACTGC
* * *
2380478 TCCTTTGCGTTGAGGAGATATGGTCAGTAAATGACATTTTTCATTCTAATTGAGGATGCCT-GTA
65 TCCTTTGCGTTGAGGAGATATAGTCAGTAAATGACATTGTTCATTCT-GTTGAGGATGCCTAG-A
*
2380542 TATATTTG
128 TATAGTTG
* * *
2380550 GATAATTTAGAGACACCACAGTTCCTTCGCATTGAGGAAGTTTGATTGTATGAGGATGACACTGC
1 GATAATTTAGAGACAACAC-GTTCCTTCGCGTTGAGGAAGTTTGATTGTCTGAGGATGACACTGC
* * * * *
2380615 TCCTTTGTGTTGAGGAGATCTAGTCGGTGAATGACATTGTTCCTTCGTGTTGAGGA
65 TCCTTTGCGTTGAGGAGATATAGTCAGTAAATGACATTGTTCATTC-TGTTGAGGA
2380671 CGTCTACTCG
Statistics
Matches: 218, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
136 3 0.01
137 213 0.98
138 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (135 bp):
GATAATTTAGAGACAACACGTTCCTTCGCGTTGAGGAAGTTTGATTGTCTGAGGATGACACTGCT
CCTTTGCGTTGAGGAGATATAGTCAGTAAATGACATTGTTCATTCTGTTGAGGATGCCTAGATAT
AGTTG
Found at i:2381193 original size:100 final size:101
Alignment explanation
Indices: 2381054--2381288 Score: 341
Period size: 100 Copynumber: 2.3 Consensus size: 101
2381044 AAAATTTATT
** * *
2381054 TTCAAGGGAAAACTATCTCAAACGAGATGAAATTTG-TTTTTAGGAAAACAATCTCAAGT-ATGA
1 TTCAAGGG-AAACTATCTCAAGTGAGATGAAATTGGTTTTTTA-AAAAACAATCTCAAGTGA-GA
*
2381117 TCAATTTTGTTTCAAGTGAAACAACTC-GAAATTTTGGC
63 TCAATTTTGTTTCAAGTGAAACAACTCTGAAATTTAGGC
* *
2381155 TTCAAGGGAAACTGTCTCAAGTGAGATGAAGTTGGTTTTTTAAAAAACAATCTCAAGTGAGATCA
1 TTCAAGGGAAACTATCTCAAGTGAGATGAAATTGGTTTTTTAAAAAACAATCTCAAGTGAGATCA
2381220 ATTTTGTTTCAAGTGAAACAACTCTGAAATTTAGGC
66 ATTTTGTTTCAAGTGAAACAACTCTGAAATTTAGGC
* *
2381256 TTCAAGGTAAACTATCTCAAGTGAGACGAAATT
1 TTCAAGGGAAACTATCTCAAGTGAGATGAAATT
2381289 TTGTTTCGAG
Statistics
Matches: 120, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
100 66 0.55
101 54 0.45
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (101 bp):
TTCAAGGGAAACTATCTCAAGTGAGATGAAATTGGTTTTTTAAAAAACAATCTCAAGTGAGATCA
ATTTTGTTTCAAGTGAAACAACTCTGAAATTTAGGC
Found at i:2381280 original size:101 final size:100
Alignment explanation
Indices: 2381018--2381288 Score: 332
Period size: 100 Copynumber: 2.7 Consensus size: 100
2381008 GGTAAGATAA
* * * * ** **
2381018 AATTTTGTTTCGAGGGAAACAATTTCAAAATTTA-TTTTCAAGGGAAAACTATCTCAAACGAGAT
1 AATTTTGTTTCAAGTGAAACAA-CTCGAAATTTAGGCTTCAA-GGAAAACTATCTCAAGTGAGAT
* *
2381082 GAAATTTGTTTTTAGGAAAACAATCTCAAGTATGATC
64 GAAATTGGTTTTTAGAAAAACAATCTCAAGTATGATC
* * *
2381119 AATTTTGTTTCAAGTGAAACAACTCGAAATTTTGGCTTCAAGGGAAACTGTCTCAAGTGAGATGA
1 AATTTTGTTTCAAGTGAAACAACTCGAAATTTAGGCTTCAAGGAAAACTATCTCAAGTGAGATGA
*
2381184 AGTTGGTTTTTTA-AAAAACAATCTCAAGTGA-GATC
66 AATTGG-TTTTTAGAAAAACAATCTCAAGT-ATGATC
* *
2381219 AATTTTGTTTCAAGTGAAACAACTCTGAAATTTAGGCTTCAAGGTAAACTATCTCAAGTGAGACG
1 AATTTTGTTTCAAGTGAAACAACTC-GAAATTTAGGCTTCAAGGAAAACTATCTCAAGTGAGATG
2381284 AAATT
65 AAATT
2381289 TTGTTTCGAG
Statistics
Matches: 147, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
100 76 0.52
101 71 0.48
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (100 bp):
AATTTTGTTTCAAGTGAAACAACTCGAAATTTAGGCTTCAAGGAAAACTATCTCAAGTGAGATGA
AATTGGTTTTTAGAAAAACAATCTCAAGTATGATC
Found at i:2383147 original size:25 final size:24
Alignment explanation
Indices: 2383111--2383172 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
2383101 TTTTATTTTC
*
2383111 AAAA-TTTGAAAAATA-TCAATTA
1 AAAATTTTGAAAAATATTCAATCA
*
2383133 AAAGCATTTTGAAAAATATTTAATCA
1 AAA--ATTTTGAAAAATATTCAATCA
2383159 AAAATTTTGAAAAA
1 AAAATTTTGAAAAA
2383173 AATATTACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 3 0.09
24 12 0.35
25 11 0.32
26 8 0.24
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.32
Consensus pattern (24 bp):
AAAATTTTGAAAAATATTCAATCA
Found at i:2384064 original size:17 final size:19
Alignment explanation
Indices: 2384038--2384081 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2384028 CCCTCTATTT
2384038 TTTG-TCTTCGCA-TTG-A
1 TTTGATCTTCGCACTTGTA
2384054 TTTGATCTTCGCACTTTGTA
1 TTTGATCTTCGCAC-TTGTA
2384074 TTTGATCT
1 TTTGATCT
2384082 ACTTTTCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.17
17 8 0.33
19 3 0.12
20 9 0.38
ACGTcount: A:0.14, C:0.18, G:0.16, T:0.52
Consensus pattern (19 bp):
TTTGATCTTCGCACTTGTA
Found at i:2389229 original size:14 final size:14
Alignment explanation
Indices: 2389210--2389252 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
2389200 AAATATAAAT
* *
2389210 TAAAATATTATTAA
1 TAAAATAATAATAA
2389224 TAAAATAATAATAA
1 TAAAATAATAATAA
2389238 TAATAATAATAATAA
1 TAA-AATAATAATAA
2389253 ACCCCGGGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAATAATAATAA
Found at i:2389233 original size:3 final size:3
Alignment explanation
Indices: 2389221--2389252 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2389211 AAAATATTAT
2389221 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2389253 ACCCCGGGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2392022 original size:14 final size:14
Alignment explanation
Indices: 2392003--2392033 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2391993 GAACAAAGAT
2392003 TAAGATAATAAAAA
1 TAAGATAATAAAAA
*
2392017 TAAGATAATAAAGA
1 TAAGATAATAAAAA
2392031 TAA
1 TAA
2392034 AGAAAGACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (14 bp):
TAAGATAATAAAAA
Found at i:2392517 original size:51 final size:51
Alignment explanation
Indices: 2392439--2392553 Score: 149
Period size: 51 Copynumber: 2.3 Consensus size: 51
2392429 GTAACTATTG
* * * * *
2392439 AATAAAACAATAATAAACTAAAGATAATGTTTTGATTCTATCATAATTCCT
1 AATAAAACAATAATAAACTAAAAATAATATTTTAAATCTACCATAATTCCT
* * *
2392490 AATAAAATAATAATAAATTAAAAATAATATTTTAAATCTACCTTAATTCCT
1 AATAAAACAATAATAAACTAAAAATAATATTTTAAATCTACCATAATTCCT
*
2392541 AATGAAACAATAA
1 AATAAAACAATAA
2392554 ATCTAATACT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.34
Consensus pattern (51 bp):
AATAAAACAATAATAAACTAAAAATAATATTTTAAATCTACCATAATTCCT
Found at i:2393017 original size:22 final size:23
Alignment explanation
Indices: 2392964--2393031 Score: 86
Period size: 22 Copynumber: 2.9 Consensus size: 23
2392954 AGGGTGCCAA
*
2392964 AGTGCATCCATGCACCCATGCA-T
1 AGTGCATCGATGCA-CCATGCACT
2392987 GCAGTGCATCGATGCACC-TGCACT
1 --AGTGCATCGATGCACCATGCACT
2393011 AGTGCATCGATGCACCATGCA
1 AGTGCATCGATGCACCATGCA
2393032 GTGCATCCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
22 16 0.40
23 8 0.20
24 3 0.08
25 13 0.32
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.21
Consensus pattern (23 bp):
AGTGCATCGATGCACCATGCACT
Found at i:2393036 original size:20 final size:20
Alignment explanation
Indices: 2392984--2393045 Score: 81
Period size: 22 Copynumber: 3.0 Consensus size: 20
2392974 TGCACCCATG
2392984 CATGCAGTGCATCGATGCAC
1 CATGCAGTGCATCGATGCAC
2393004 C-TGCACTAGTGCATCGATGCAC
1 CATG--C-AGTGCATCGATGCAC
*
2393026 CATGCAGTGCATCCATGCAC
1 CATGCAGTGCATCGATGCAC
2393046 TCCAATTCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
19 2 0.05
20 15 0.41
21 2 0.05
22 16 0.43
23 2 0.05
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (20 bp):
CATGCAGTGCATCGATGCAC
Found at i:2393117 original size:20 final size:20
Alignment explanation
Indices: 2393066--2393110 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
2393056 ATGCATTTAG
2393066 TGCATCGATGCATCCTGATA
1 TGCATCGATGCATCCTGATA
*
2393086 TGCATCGATGCATCCTGATG
1 TGCATCGATGCATCCTGATA
2393106 TGCAT
1 TGCAT
2393111 TCATGCACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (20 bp):
TGCATCGATGCATCCTGATA
Found at i:2394757 original size:19 final size:20
Alignment explanation
Indices: 2394733--2394780 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2394723 AACGATTTTC
*
2394733 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
2394752 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
2394772 TTTTGAAAA
1 TTTTGAAAA
2394781 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:2394836 original size:24 final size:24
Alignment explanation
Indices: 2394790--2394836 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2394780 AAGGATTTAG
* *
2394790 AGTTTTCAAAAATAAAAAGTTGAA
1 AGTTTTCAAAAAGAAAAACTTGAA
* *
2394814 AGTTTTGAAAAAGAAAATCTTGA
1 AGTTTTCAAAAAGAAAAACTTGA
2394837 TTTAAAAGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (24 bp):
AGTTTTCAAAAAGAAAAACTTGAA
Found at i:2396243 original size:22 final size:23
Alignment explanation
Indices: 2396188--2396265 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 23
2396178 AGGGTATCAA
2396188 AGTGCATCCATGCACCATTG--C-
1 AGTGCATCCATGCACCA-TGCACT
*
2396209 AGTGTATCCATGCACC-TGCACT
1 AGTGCATCCATGCACCATGCACT
*
2396231 AGTGCATCGATGCACCATG--C-
1 AGTGCATCCATGCACCATGCACT
2396251 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
2396266 TCTATTTCGA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.04
20 14 0.29
21 17 0.35
22 14 0.29
23 2 0.04
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.23
Consensus pattern (23 bp):
AGTGCATCCATGCACCATGCACT
Found at i:2396256 original size:20 final size:19
Alignment explanation
Indices: 2396188--2396417 Score: 125
Period size: 20 Copynumber: 11.7 Consensus size: 19
2396178 AGGGTATCAA
*
2396188 AGTGCATCCATGCACCATTGC
1 AGTGCATCGATGCACC--TGC
* *
2396209 AGTGTATCCATGCACCTGCAC
1 AGTGCATCGATGCACCTG--C
2396230 TAGTGCATCGATGCACCATGC
1 -AGTGCATCGATGCACC-TGC
*
2396251 AGTGCATCCATGCA-CT-C
1 AGTGCATCGATGCACCTGC
* *
2396268 TA-T--TTCGAATGCA-CT-T
1 -AGTGCATCG-ATGCACCTGC
* *
2396284 AGTGCATCAATGCATACTG-
1 AGTGCATCGATGCA-CCTGC
*
2396303 ATGTGCATCGATGCATCATGC
1 A-GTGCATCGATGCA-CCTGC
* *
2396324 TGTGCATCGATGCATCCTGT
1 AGTGCATCGATGCA-CCTGC
*
2396344 TGTGCATCGATGCATCCTGC
1 AGTGCATCGATGCA-CCTGC
* *
2396364 TGTGCATCGATGCATCCTGT
1 AGTGCATCGATGCA-CCTGC
*
2396384 TGTGCATCGATGCATCCTGC
1 AGTGCATCGATGCA-CCTGC
*
2396404 TGTGCATCGATGCA
1 AGTGCATCGATGCA
2396418 TCCTATTGTG
Statistics
Matches: 177, Mismatches: 18, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
15 3 0.02
16 8 0.05
17 7 0.04
18 4 0.02
19 6 0.03
20 116 0.66
21 17 0.10
22 14 0.08
23 2 0.01
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.29
Consensus pattern (19 bp):
AGTGCATCGATGCACCTGC
Found at i:2396329 original size:40 final size:40
Alignment explanation
Indices: 2396285--2396437 Score: 243
Period size: 40 Copynumber: 3.8 Consensus size: 40
2396275 AATGCACTTA
* * * *
2396285 GTGCATCAATGCATACTGATGTGCATCGATGCATCATGCT
1 GTGCATCGATGCATCCTGTTGTGCATCGATGCATCCTGCT
2396325 GTGCATCGATGCATCCTGTTGTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGTTGTGCATCGATGCATCCTGCT
2396365 GTGCATCGATGCATCCTGTTGTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGTTGTGCATCGATGCATCCTGCT
* * *
2396405 GTGCATCGATGCATCCTATTGTGTATCCATGCA
1 GTGCATCGATGCATCCTGTTGTGCATCGATGCA
2396438 CGAAGGCTGC
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 106 1.00
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (40 bp):
GTGCATCGATGCATCCTGTTGTGCATCGATGCATCCTGCT
Found at i:2396427 original size:20 final size:20
Alignment explanation
Indices: 2396285--2396421 Score: 220
Period size: 20 Copynumber: 6.8 Consensus size: 20
2396275 AATGCACTTA
* * *
2396285 GTGCATCAATGCATACTGAT
1 GTGCATCGATGCATCCTGCT
*
2396305 GTGCATCGATGCATCATGCT
1 GTGCATCGATGCATCCTGCT
*
2396325 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGCT
2396345 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
2396365 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGCT
2396385 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
2396405 GTGCATCGATGCATCCT
1 GTGCATCGATGCATCCT
2396422 ATTGTGTATC
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 108 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:2396436 original size:20 final size:20
Alignment explanation
Indices: 2396285--2396437 Score: 216
Period size: 20 Copynumber: 7.7 Consensus size: 20
2396275 AATGCACTTA
* * *
2396285 GTGCATCAATGCATACTGAT
1 GTGCATCGATGCATCCTGTT
* *
2396305 GTGCATCGATGCATCATGCT
1 GTGCATCGATGCATCCTGTT
2396325 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGTT
*
2396345 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGTT
2396365 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCTGTT
*
2396385 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGTT
*
2396405 GTGCATCGATGCATCCTATT
1 GTGCATCGATGCATCCTGTT
* *
2396425 GTGTATCCATGCA
1 GTGCATCGATGCA
2396438 CGAAGGCTGC
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 120 1.00
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGTT
Found at i:2398950 original size:18 final size:18
Alignment explanation
Indices: 2398927--2398961 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2398917 AGGGATTATC
*
2398927 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
2398945 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
2398962 AATATTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2402051 original size:17 final size:17
Alignment explanation
Indices: 2402011--2402051 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
2402001 GAAGAAGAGC
*
2402011 ATAGTTCGCACCTGAAG
1 ATAGTTTGCACCTGAAG
2402028 ATAGTTTGCACCTGAAG
1 ATAGTTTGCACCTGAAG
2402045 ATAGTTT
1 ATAGTTT
2402052 TACAGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (17 bp):
ATAGTTTGCACCTGAAG
Found at i:2405764 original size:17 final size:17
Alignment explanation
Indices: 2405742--2405800 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
2405732 ACATAGTGGT
2405742 TTGTTTTGCTCTTTGCG
1 TTGTTTTGCTCTTTGCG
*
2405759 TTGTTTTGTTCTTTTTGCG
1 TTGTTTTG--CTCTTTGCG
*
2405778 TTG-TTTGTTCTTTTGCG
1 TTGTTTTGCTC-TTTGCG
2405795 TTGTTT
1 TTGTTT
2405801 GTTCTTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 1 0.03
17 17 0.49
18 6 0.17
19 11 0.31
ACGTcount: A:0.00, C:0.12, G:0.22, T:0.66
Consensus pattern (17 bp):
TTGTTTTGCTCTTTGCG
Found at i:2405801 original size:17 final size:17
Alignment explanation
Indices: 2405753--2405808 Score: 94
Period size: 17 Copynumber: 3.2 Consensus size: 17
2405743 TGTTTTGCTC
2405753 TTTGCGTTGTTTTGTTCTT
1 TTTGCGTTG-TTTGTTC-T
2405772 TTTGCGTTGTTTGTTCT
1 TTTGCGTTGTTTGTTCT
2405789 TTTGCGTTGTTTGTTCT
1 TTTGCGTTGTTTGTTCT
2405806 TTT
1 TTT
2405809 TGCTGGAGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
17 21 0.57
18 7 0.19
19 9 0.24
ACGTcount: A:0.00, C:0.11, G:0.21, T:0.68
Consensus pattern (17 bp):
TTTGCGTTGTTTGTTCT
Found at i:2408398 original size:259 final size:259
Alignment explanation
Indices: 2407929--2408451 Score: 994
Period size: 259 Copynumber: 2.0 Consensus size: 259
2407919 ATGTGGCTTA
*
2407929 TTTTAATAATAAACATGTCACATAGGACTTATAACTAAAAATATAATTATATGTTTACTCACTTT
1 TTTTAATAATAAACATGTCACATAGGACTTATAACTAAAAAGATAATTATATGTTTACTCACTTT
*
2407994 CTCTCCTATTTTTCTCAGTATACTTTTAATTTTTTTCAATTAATATAGCAACATCATAATGCAAT
66 CTCTCCTATTTTACTCAGTATACTTTTAATTTTTTTCAATTAATATAGCAACATCATAATGCAAT
2408059 TAGAAACTTAACGGTCGAGTGACAAAAAAATTCAATGTCTAAATTTAGTGAGCTAATTGAAAAAA
131 TAGAAACTTAACGGTCGAGTGACAAAAAAATTCAATGTCTAAATTTAGTGAGCTAATTGAAAAAA
2408124 TTAAAAGTATAGTGAGTGAAATAGAAGAGAATAAAGTTCAGTGAGTAAGTGTGT-TTTATCCTT
196 TTAAAAGTATAGTGAGTGAAATAGAAGAGAATAAAGTTCAGTGAGTAAGTGTGTATTTATCCTT
2408187 TTTTAATAATAAAACATGTCACATAGGACTTATAACTAAAAAGATAATTATATGTTTACTCACTT
1 TTTTAATAAT-AAACATGTCACATAGGACTTATAACTAAAAAGATAATTATATGTTTACTCACTT
2408252 TCTCTCCTATTTTACTCAGTATACTTTTAATTTTTTTCAATTAATATAGCAACATCATAATGCAA
65 TCTCTCCTATTTTACTCAGTATACTTTTAATTTTTTTCAATTAATATAGCAACATCATAATGCAA
2408317 TTAGAAACTTAACGGTCGAGTGACAAAAAAATTCAATGTCTAAATTTAGTGAGCTAATTGAAAAA
130 TTAGAAACTTAACGGTCGAGTGACAAAAAAATTCAATGTCTAAATTTAGTGAGCTAATTGAAAAA
*
2408382 ATTAAAAGTATAGTGAGTGAAATAGAAGAGAATAAAGTTTAGTGAGTAAGTGTGTAATTTATCCT
195 ATTAAAAGTATAGTGAGTGAAATAGAAGAGAATAAAGTTCAGTGAGTAAGTGTGT-ATTTATCCT
2408447 T
259 T
2408448 TTTT
1 TTTT
2408452 TATTATTTCA
Statistics
Matches: 259, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
258 10 0.04
259 236 0.91
261 13 0.05
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (259 bp):
TTTTAATAATAAACATGTCACATAGGACTTATAACTAAAAAGATAATTATATGTTTACTCACTTT
CTCTCCTATTTTACTCAGTATACTTTTAATTTTTTTCAATTAATATAGCAACATCATAATGCAAT
TAGAAACTTAACGGTCGAGTGACAAAAAAATTCAATGTCTAAATTTAGTGAGCTAATTGAAAAAA
TTAAAAGTATAGTGAGTGAAATAGAAGAGAATAAAGTTCAGTGAGTAAGTGTGTATTTATCCTT
Found at i:2408973 original size:31 final size:31
Alignment explanation
Indices: 2408935--2409004 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
2408925 ACTTTTAAAA
*
2408935 TTACAATACAATCTCC-CAACATTTAGTCTGT
1 TTACAATACAATC-CCTCAACATTTAGCCTGT
***
2408966 TTACAATATGGTCCCTCAACATTTAGCCTGT
1 TTACAATACAATCCCTCAACATTTAGCCTGT
*
2408997 TTGCAATA
1 TTACAATA
2409005 TGGTCCCCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (31 bp):
TTACAATACAATCCCTCAACATTTAGCCTGT
Found at i:2409005 original size:31 final size:31
Alignment explanation
Indices: 2408951--2409011 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2408941 TACAATCTCC
*
2408951 CAACATTTAGTCTGTTTACAATATGGTCCCT
1 CAACATTTAGCCTGTTTACAATATGGTCCCT
*
2408982 CAACATTTAGCCTGTTTGCAATATGGTCCC
1 CAACATTTAGCCTGTTTACAATATGGTCCC
2409012 CGACGTAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (31 bp):
CAACATTTAGCCTGTTTACAATATGGTCCCT
Found at i:2411308 original size:18 final size:20
Alignment explanation
Indices: 2411268--2411308 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
2411258 TTCAAAATAT
2411268 ATAATTAAATATATTCATGA
1 ATAATTAAATATATTCATGA
*
2411288 ATAATTAAA-AT-TTCTTGA
1 ATAATTAAATATATTCATGA
2411306 ATA
1 ATA
2411309 CAATTTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (20 bp):
ATAATTAAATATATTCATGA
Found at i:2414522 original size:11 final size:11
Alignment explanation
Indices: 2414506--2414531 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2414496 AGCAAATAAA
2414506 ACATAATAATT
1 ACATAATAATT
2414517 ACATAATAATT
1 ACATAATAATT
2414528 ACAT
1 ACAT
2414532 GCCACTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (11 bp):
ACATAATAATT
Found at i:2415336 original size:11 final size:11
Alignment explanation
Indices: 2415320--2415345 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2415310 AGCAAATAAA
2415320 ACATAATAATT
1 ACATAATAATT
2415331 ACATAATAATT
1 ACATAATAATT
2415342 ACAT
1 ACAT
2415346 GCCACTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (11 bp):
ACATAATAATT
Found at i:2416022 original size:830 final size:812
Alignment explanation
Indices: 2414440--2416087 Score: 3001
Period size: 830 Copynumber: 2.0 Consensus size: 812
2414430 AGTAACAGCG
2414440 AAAATACATATACATTCATAAAATTCCATTTTCTTGTTTCCAATTTTGTTCAACAAAGCAAATAA
1 AAAATACATATACATTCATAAAATTCCATTTTCTTGTTTCCAATTTTGTTCAACAAAGCAAATAA
2414505 AACATAATAATTACATAATAATTACATGCCACTAATTAAATCTACATTACATTTTAGGATGTCTT
66 AACATAATAATTACATAATAATTACATGCCACTAATTAAATCTACATTACATTTTAGGATGTCTT
*
2414570 ACTGATAAAGAAATATACTTGATGTTTGATGTTGCCTTGAACTCTCTATTCTTCTACGAGCTTTT
131 ACTGATAAAGAAATATACTTGATGCTTGATGTTGCCTTGAACTCTCTATTCTTCTACGAGCTTTT
*
2414635 ACCTACGCGTAAAAATCATCACACTAAGTATATACTTATGAGGCAATTAAAACATTTTACAGTGT
196 ACCTACGCGTAAAAATCATCACACTAAGTATATACTTATGAGGCAATTAAAACATTTTACAGTGC
2414700 AATACAATCATGCATAATTTTATTATAAAAACCAAATACCTTACAATCATATTATCAGCATATCC
261 AATACAATCATGCATAATTTTATTATAAAAACCAAATACCTTACAATCATATTATCAGCATATCC
*
2414765 ATATTTTACCATGATCAAAATAATATAACTGAATATAAAATTCCTTACCAATATACTTGCCCTTA
326 ATATTTTACCATGATCAAAATAATATAACTGAATATAAAATTCCTTACCAATATACTTGCCATTA
*
2414830 ATTTCTTAGCTCGTAAGCTTATTTCGTGCTTACCATTATTAACCAATATGTATAAACCATAGACA
391 ATTTCTAAGCTCGTAAGCTTATTTCGTGCTTACCATTATTAACCAATATGTATAAACCATAGACA
* * *
2414895 ATAGCCCAATATACAACCCTTAGGACCCTGGGTATACGAGTAGAATACATGCACCGTAGTGCTAA
456 ATAGACCAATATACAACCCTAAGGACCCTGGGTATACGAGTAAAATACATGCACCGTAGTGCTAA
*
2414960 ACCTGCACTAAGCTTACGCCATAGCTAATCCGGACAATACACATAAGGTCGTACCCACCACCTAC
521 ACCTGCACTAAGCTTACGCCATAGCTAATCCGGACAATACACAAAAGGTCGTACCCACCACCTAC
*
2415025 ACTAAGTTTACGCTATAGTGCTAATCCGGACATAAACCTGCACTTAGTGTCCTTACACACTATAG
586 ACTAAGCTTACGCTATAGTGCTAATCCGGACATAAACCTGCACTTAGTGTCCTTACACACTATAG
*
2415090 TGCTAATATAACCTGCAGCTGCTGTACTCTATGACATGCCAACTATATCCTGTCCCTCAATGACT
651 TGCTAATATAACCTGCAGCTGCTATACTCTATGACATGCCAACTATATCCTGTCCCTCAATGACT
2415155 TATTCGGGCATATAGTCTACTTTATTCAATTCATTCATGGCAAAGTATATTATTATAATTTAACA
716 TATTCGGGCATATAGTCTACTTTATTCAATTCATTCATGGC-AAGTATATTATTATAATTTAAC-
2415220 TTGGGCAGTTCATACCCGAAATAACATTCATGGT
779 TTGGGCAGTTCATACCCGAAATAACATTCATGGT
2415254 AAAATACATATACATTCATAAAATTCCATTTTCTTGTTTCCAATTTTGTTCAACAAAGCAAATAA
1 AAAATACATATACATTCATAAAATTCCATTTTCTTGTTTCCAATTTTGTTCAACAAAGCAAATAA
2415319 AACATAATAATTACATAATAATTACATGCCACTAATTAAATCTACATTACATTTTAGGATGTCTT
66 AACATAATAATTACATAATAATTACATGCCACTAATTAAATCTACATTACATTTTAGGATGTCTT
2415384 ACTGATAAAGAAATATACTTCTTGATGCTTGATGTTGCCTTGAACTCTCTATTCTTCTACGAGCT
131 ACTGATAAAGAAATATA---CTTGATGCTTGATGTTGCCTTGAACTCTCTATTCTTCTACGAGC-
2415449 TTTTACCTACGCGTAAAAATCATCACACGCTAAGTATATACTTAGTGAGGCAATTAAAACATTTT
192 TTTTACCTACGCGTAAAAATCATCACA--CTAAGTATATACTTA-TGAGGCAATTAAAACATTTT
2415514 ACAGTGCAATACAATTCATGCATAATTTTATTATAAAAACCAAATACCTTACAATCATATTATCA
254 ACAGTGCAATACAA-TCATGCATAATTTTATTATAAAAACCAAATACCTTACAATCATATTATCA
2415579 GCATATCCAATATTTTACCATGATCAAAAATAATATAACTGAATATAAAATTCCTTACCAATATA
318 GCATATCC-ATATTTTACCATGATC-AAAATAATATAACTGAATATAAAATTCCTTACCAATATA
2415644 CTTGCCATTAATTTCTAAGCTCGTAAGCTTAATTTCGTGCTTACCATTTATTAACCAATAATGTA
381 CTTGCCATTAATTTCTAAGCTCGTAAGCTT-ATTTCGTGCTTACCA-TTATTAACCAAT-ATGTA
2415709 TAAAACCATAGACAATAGACCAATATACAACCCTAAGGACCCTGGGTATACGAGTAAAATACATG
443 T-AAACCATAGACAATAGACCAATATACAACCCTAAGGACCCTGGGTATACGAGTAAAATACATG
2415774 CACCGTAGTGCTAAACCTGCACTAAGCTTACGCCATAGTGCTAATCCGGACAATACACAAAAGGT
507 CACCGTAGTGCTAAACCTGCACTAAGCTTACGCCATA--GCTAATCCGGACAATACACAAAAGGT
2415839 CGTACCCACCACCTACACTAAGCTTACGCTATAGTGCTAATCCGGACAT-AACCTGCACTTAGTG
570 CGTACCCACCACCTACACTAAGCTTACGCTATAGTGCTAATCCGGACATAAACCTGCACTTAGTG
* *
2415903 TCCTTACACACTATAGTGCTAATATAAACCTGCAGCTGCTATACTCTATGGCGTGCCAACTATAT
635 TCCTTACACACTATAGTGCTAATAT-AACCTGCAGCTGCTATACTCTATGACATGCCAACTATAT
*
2415968 CCTGTCTCTCAATGACTTATTCGGGCATATAGTCTACTTTATTCAATTCATTCATGGCAAGTATA
699 CCTGTCCCTCAATGACTTATTCGGGCATATAGTCTACTTTATTCAATTCATTCATGGCAAGTATA
2416033 TTATTATAATTTAACTTGGGCAGTTCATACCCGAAATAACATTCATGGT
764 TTATTATAATTTAACTTGGGCAGTTCATACCCGAAATAACATTCATGGT
2416082 AAAATA
1 AAAATA
2416088 TCACATTTTC
Statistics
Matches: 804, Mismatches: 13, Indels: 20
0.96 0.02 0.02
Matches are distributed among these distances:
814 147 0.18
817 43 0.05
818 27 0.03
820 15 0.02
821 33 0.04
822 58 0.07
823 16 0.02
824 67 0.08
825 15 0.02
826 12 0.01
827 6 0.01
828 137 0.17
829 62 0.08
830 166 0.21
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.32
Consensus pattern (812 bp):
AAAATACATATACATTCATAAAATTCCATTTTCTTGTTTCCAATTTTGTTCAACAAAGCAAATAA
AACATAATAATTACATAATAATTACATGCCACTAATTAAATCTACATTACATTTTAGGATGTCTT
ACTGATAAAGAAATATACTTGATGCTTGATGTTGCCTTGAACTCTCTATTCTTCTACGAGCTTTT
ACCTACGCGTAAAAATCATCACACTAAGTATATACTTATGAGGCAATTAAAACATTTTACAGTGC
AATACAATCATGCATAATTTTATTATAAAAACCAAATACCTTACAATCATATTATCAGCATATCC
ATATTTTACCATGATCAAAATAATATAACTGAATATAAAATTCCTTACCAATATACTTGCCATTA
ATTTCTAAGCTCGTAAGCTTATTTCGTGCTTACCATTATTAACCAATATGTATAAACCATAGACA
ATAGACCAATATACAACCCTAAGGACCCTGGGTATACGAGTAAAATACATGCACCGTAGTGCTAA
ACCTGCACTAAGCTTACGCCATAGCTAATCCGGACAATACACAAAAGGTCGTACCCACCACCTAC
ACTAAGCTTACGCTATAGTGCTAATCCGGACATAAACCTGCACTTAGTGTCCTTACACACTATAG
TGCTAATATAACCTGCAGCTGCTATACTCTATGACATGCCAACTATATCCTGTCCCTCAATGACT
TATTCGGGCATATAGTCTACTTTATTCAATTCATTCATGGCAAGTATATTATTATAATTTAACTT
GGGCAGTTCATACCCGAAATAACATTCATGGT
Found at i:2417903 original size:18 final size:19
Alignment explanation
Indices: 2417867--2417904 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2417857 TTGTTACACT
*
2417867 ATAAACATTTCAATTTGCC
1 ATAAACATTTCAATATGCC
*
2417886 ATAAA-ATTTCCATATGCC
1 ATAAACATTTCAATATGCC
2417904 A
1 A
2417905 CCATCCATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (19 bp):
ATAAACATTTCAATATGCC
Found at i:2419659 original size:18 final size:19
Alignment explanation
Indices: 2419623--2419660 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2419613 TTGTTACACT
*
2419623 ATAAACATTTCAATTTGCC
1 ATAAACATTTCAATATGCC
*
2419642 ATAAA-ATTTCCATATGCC
1 ATAAACATTTCAATATGCC
2419660 A
1 A
2419661 CCCATCCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.34
Consensus pattern (19 bp):
ATAAACATTTCAATATGCC
Found at i:2420471 original size:26 final size:26
Alignment explanation
Indices: 2420435--2420487 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2420425 TAAAATTGAG
2420435 TTACCATATTCTTTGAGAGATCGAGC
1 TTACCATATTCTTTGAGAGATCGAGC
2420461 TTACCATATTCTTTGAGAGATCGAGC
1 TTACCATATTCTTTGAGAGATCGAGC
2420487 T
1 T
2420488 AGAGCATGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (26 bp):
TTACCATATTCTTTGAGAGATCGAGC
Found at i:2429511 original size:138 final size:139
Alignment explanation
Indices: 2429257--2429511 Score: 381
Period size: 138 Copynumber: 1.8 Consensus size: 139
2429247 CCGATACGAT
* **
2429257 AATTCACAAACTCATTATGAATTCCTTGGGTTACACACCTAGCGCCAGAAGTACACATAGTACTG
1 AATTCACAAACTCATTATGAATACAATGGGTTACACACCTAGCGCCAGAAGTACACATAGTACTG
* *
2429322 ATATGAAAATGCACCCTTATGCATTAAACAAAATCAATCGATAAATTTTATACATAATTGTAAGT
66 ATACGAAAATGCACCCTTATGCATTAAACAAAATCAATCGATAAATATTATACATAATTGTAAGT
2429387 CAAAATGGC
131 CAAAATGGC
* * * *
2429396 AATTCACAAACTCATTATGAATACAAT-GGTTGCAC-CTCTAGTG-CTGAAAGTCCACATAGTAC
1 AATTCACAAACTCATTATGAATACAATGGGTTACACAC-CTAGCGCCAG-AAGTACACATAGTAC
*
2429458 TGATACGAAAATGCACCCTTATGCATTAAACAAAATCAATCGATAACTATTATA
64 TGATACGAAAATGCACCCTTATGCATTAAACAAAATCAATCGATAAATATTATA
2429512 TACAATTTAT
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
137 3 0.03
138 77 0.74
139 24 0.23
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.28
Consensus pattern (139 bp):
AATTCACAAACTCATTATGAATACAATGGGTTACACACCTAGCGCCAGAAGTACACATAGTACTG
ATACGAAAATGCACCCTTATGCATTAAACAAAATCAATCGATAAATATTATACATAATTGTAAGT
CAAAATGGC
Found at i:2436295 original size:228 final size:229
Alignment explanation
Indices: 2435897--2436330 Score: 728
Period size: 228 Copynumber: 1.9 Consensus size: 229
2435887 AGTGCCAAAA
*
2435897 GTACACAGAGTACTGATACGAAAATGCACCCTTATGCATTAAACAAAATCGATCGATAACTTTTA
1 GTACACAGAGTACTGATACGAAAATGCACCCTTATGCATTAAACAAAATCAATCGATAACTTTTA
* ** *
2435962 TATACAATTTATGTCGAAATGTGCCTATGACTCTCAACGCACATACAATGGGCTTTTAAGTCAAA
66 TATACAATTTATGTCAAAATGCACCTATGACTCTCAACGCACATACAATGGGATTTTAAGTCAAA
* *
2436027 TTCACAGATTAAACATTTATTTCTAAAACCTCGATAACCATTAAAACAACATAAACATTCATCTA
131 TTCACAGATTAAACATTTATTTCAAAAACATCGATAACCATTAAAACAACATAAACATTCATCTA
2436092 TTCAATTTAGATGAATGTTTATGTTTTTTTAATC
196 TTCAATTTAGATGAATGTTTATGTTTTTTTAATC
* *
2436126 GTACACATAGTTCTGATACGAAAATGCACCCTTATGCATTAAACAAAAT-AATCGATAACTTTTA
1 GTACACAGAGTACTGATACGAAAATGCACCCTTATGCATTAAACAAAATCAATCGATAACTTTTA
* *
2436190 TATACAATTTATGTCAAAATGCACCTATGACTCTCAATGCGCATACAATGGGATTTTAAGTCAAA
66 TATACAATTTATGTCAAAATGCACCTATGACTCTCAACGCACATACAATGGGATTTTAAGTCAAA
*
2436255 TTCACAGATTAAACATTTATTT-AAGAAACATCGATAACCATTAAAACAACATAAGCATTCATCT
131 TTCACAGATTAAACATTTATTTCAA-AAACATCGATAACCATTAAAACAACATAAACATTCATCT
*
2436319 ATTCATTTTAGA
195 ATTCAATTTAGA
2436331 GTAGTTCATA
Statistics
Matches: 191, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
227 1 0.01
228 143 0.75
229 47 0.25
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (229 bp):
GTACACAGAGTACTGATACGAAAATGCACCCTTATGCATTAAACAAAATCAATCGATAACTTTTA
TATACAATTTATGTCAAAATGCACCTATGACTCTCAACGCACATACAATGGGATTTTAAGTCAAA
TTCACAGATTAAACATTTATTTCAAAAACATCGATAACCATTAAAACAACATAAACATTCATCTA
TTCAATTTAGATGAATGTTTATGTTTTTTTAATC
Found at i:2445910 original size:15 final size:16
Alignment explanation
Indices: 2445892--2445923 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2445882 TGACAAAAAC
2445892 AATATTAAAA-AAATT
1 AATATTAAAATAAATT
2445907 AATATTAAAATAAATT
1 AATATTAAAATAAATT
2445923 A
1 A
2445924 GTGATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATTAAAATAAATT
Found at i:2447139 original size:24 final size:22
Alignment explanation
Indices: 2447112--2447157 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
2447102 TTGAAAGCAT
2447112 CTTTTTTATGTTTTCATATTTTCA
1 CTTTTTTATGTTTT--TATTTTCA
*
2447136 CTTTTTTTTGTTTTTATTTTCA
1 CTTTTTTATGTTTTTATTTTCA
2447158 ATAAATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
24 13 0.62
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.72
Consensus pattern (22 bp):
CTTTTTTATGTTTTTATTTTCA
Found at i:2447856 original size:65 final size:63
Alignment explanation
Indices: 2447787--2447947 Score: 223
Period size: 65 Copynumber: 2.5 Consensus size: 63
2447777 GAATAAATTG
* * *
2447787 AACATCGAATGCATTTCATGCATCGATGCACATATCATGCATCGATGCACTCAGGGTTTTATGAA
1 AACATCGAATGCATTTCATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGCTTTT-TCAA
* *
2447852 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCAGGCTTTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTTTTTCAA
* * *
2447916 AATATCGAATGCATTTTATGCATTGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
2447948 CTTAGTGCAC
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
63 2 0.02
64 30 0.34
65 53 0.61
66 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTTTTTCAA
Found at i:2447963 original size:64 final size:64
Alignment explanation
Indices: 2447787--2447966 Score: 215
Period size: 65 Copynumber: 2.8 Consensus size: 64
2447777 GAATAAATTG
* *
2447787 AACATCGAATGCATTTCATGCATCGATGCACA-TATCATGCATCGATGCACTCAGGGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-T-ATGCATCGATGCACTCAGGCTTTTATCA
2447851 A
64 A
* *
2447852 AACATCGAATGCATTTGATGCATCGATGCACCAGC-CATGCATCGATGCACTCAGGCTTTT-TCA
1 AACATCGAATGCATTTCATGCATCGATGCA-CA-CTTATGCATCGATGCACTCAGGCTTTTATCA
2447915 A
64 A
* * *
2447916 AATATCGAATGCATTTTATGCATTGATGCACACTTAGTGCA-CTGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACACTTA-TGCATC-GATGCACT
2447967 AAGTGTTTCA
Statistics
Matches: 101, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 42 0.42
65 52 0.51
66 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCATCGATGCACTCAGGCTTTTATCAA
Found at i:2456683 original size:64 final size:66
Alignment explanation
Indices: 2456524--2456683 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 66
2456514 GAATAAATTG
* * * * *
2456524 AACATCAAATGCATTTCATGCATCGATGCA-CATATCATGCATTGATGCACTCAGGGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGGCTTTTATCA
2456588 A
66 A
* * * *
2456589 AACATCGATTGCATTTGATGCATCGATGCACCA-GCCATGTATCGATGCACTCAGGCTTTT-TCA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGGCTTTTATCA
2456652 A
66 A
* *
2456653 AACATCGAATGCATTTTATGCATCGGTGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
2456684 ACTTACTGCA
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 31 0.38
65 49 0.60
66 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGGCTTTTATCA
A
Found at i:2456699 original size:64 final size:64
Alignment explanation
Indices: 2456524--2456703 Score: 195
Period size: 65 Copynumber: 2.8 Consensus size: 64
2456514 GAATAAATTG
* * * *
2456524 AACATCAAATGCATTTCATGCATCGATGCACA-TATCATGCATTGATGCACTCAGGGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACACTA-C-TGCATCGATGCACTCAGGCTTTTATCA
2456588 A
64 A
* * * *
2456589 AACATCGATTGCATTTGATGCATCGATGCACCAGCCA-TGTATCGATGCACTCAGGCTTTT-TCA
1 AACATCGAATGCATTTCATGCATCGATGCA-CA-CTACTGCATCGATGCACTCAGGCTTTTATCA
2456652 A
64 A
* * *
2456653 AACATCGAATGCATTTTATGCATCGGTGCACACTTACTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACAC-TACTGCATCGATGCACT
2456704 AAGTGTTTCA
Statistics
Matches: 96, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 42 0.44
65 47 0.49
66 2 0.02
68 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTACTGCATCGATGCACTCAGGCTTTTATCAA
Found at i:2460442 original size:2 final size:2
Alignment explanation
Indices: 2460435--2460459 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2460425 TAATTAGATC
2460435 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2460460 AATAAAAGTT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2464441 original size:19 final size:18
Alignment explanation
Indices: 2464419--2464483 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 18
2464409 AAGGTTAATA
2464419 AAAATAATAAACAAAAAAT
1 AAAATAATAAA-AAAAAAT
2464438 AAAAAATAATAATTAAATAAAAT
1 --AAAATAATAA--AAA-AAAAT
*
2464461 AAAATGAATAAAATAAAAT
1 AAAAT-AATAAAAAAAAAT
2464480 AAAA
1 AAAA
2464484 AAGTAAAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 9 0.23
20 2 0.05
21 15 0.38
22 7 0.18
23 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (18 bp):
AAAATAATAAAAAAAAAT
Found at i:2464454 original size:14 final size:14
Alignment explanation
Indices: 2464415--2464491 Score: 63
Period size: 14 Copynumber: 5.5 Consensus size: 14
2464405 ATTAAAGGTT
*
2464415 AATAAAAATAATAA
1 AATAAAATTAATAA
*
2464429 ACA-AAAAATAA-AA
1 A-ATAAAATTAATAA
2464442 AATAATAATTAAATAA
1 AATAA-AATT-AATAA
*
2464458 AATAAAATGAATAA
1 AATAAAATTAATAA
2464472 AATAAAA-TAA-AA
1 AATAAAATTAATAA
2464484 AAGTAAAA
1 AA-TAAAA
2464492 GGGTTAGTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
12 5 0.09
13 12 0.22
14 24 0.44
15 6 0.11
16 7 0.13
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (14 bp):
AATAAAATTAATAA
Found at i:2464455 original size:18 final size:19
Alignment explanation
Indices: 2464433--2464483 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2464423 TAATAAACAA
2464433 AAAATAAAA-AATAAT-AAT
1 AAAATAAAATAA-AATGAAT
*
2464451 TAAATAAAATAAAATGAAT
1 AAAATAAAATAAAATGAAT
2464470 AAAATAAAATAAAA
1 AAAATAAAATAAAA
2464484 AAGTAAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAATAAAATAAAATGAAT
Found at i:2464460 original size:5 final size:5
Alignment explanation
Indices: 2464440--2464483 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
2464430 CAAAAAATAA
* *
2464440 AAAAT AATAAT TAAAT AAAAT AAAAT -GAAT AAAAT AAAAT AAAA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
2464484 AAGTAAAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 3 0.09
5 26 0.79
6 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:2464540 original size:3 final size:3
Alignment explanation
Indices: 2464532--2464559 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2464522 TAAAACAGTG
2464532 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2464560 ATAGAAAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2465659 original size:16 final size:16
Alignment explanation
Indices: 2465650--2465710 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 16
2465640 AAAAATAAGG
2465650 AATAAAAAAAAAAAAA
1 AATAAAAAAAAAAAAA
*
2465666 AAT-AAAAAATAAAAA
1 AATAAAAAAAAAAAAA
* * *
2465681 TATAAATAACAAAAAAT
1 AATAAA-AAAAAAAAAA
2465698 AATAACAAAAAAA
1 AATAA-AAAAAAA
2465711 TATTTTTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 13 0.37
16 5 0.14
17 16 0.46
18 1 0.03
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
AATAAAAAAAAAAAAA
Found at i:2465669 original size:29 final size:28
Alignment explanation
Indices: 2465622--2465712 Score: 76
Period size: 30 Copynumber: 3.0 Consensus size: 28
2465612 GACCCTGGAC
* *
2465622 AAAAAACAAACAAAGAATAAAAATAAGGAAT
1 AAAAAA-AAA-AAAAAATAAAAATAA-AAAT
2465653 AAAAAAAAAAAAAAATAAAAAATAAAAAT
1 AAAAAAAAAAAAAAAT-AAAAATAAAAAT
* *
2465682 ATAAATAACAAAAAATAATAACAA-AAAAAT
1 A-AAA-AA-AAAAAAAAATAAAAATAAAAAT
2465712 A
1 A
2465713 TTTTTAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
29 10 0.19
30 21 0.40
31 12 0.23
32 9 0.17
ACGTcount: A:0.80, C:0.04, G:0.03, T:0.12
Consensus pattern (28 bp):
AAAAAAAAAAAAAAATAAAAATAAAAAT
Found at i:2465672 original size:14 final size:14
Alignment explanation
Indices: 2465655--2465712 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
2465645 TAAGGAATAA
2465655 AAAAAAAAAAAAAT
1 AAAAAAAAAAAAAT
*
2465669 AAAAAATAAAAATAT
1 AAAAAA-AAAAAAAT
* *
2465684 AAATAACAAAAAAT
1 AAAAAAAAAAAAAT
* *
2465698 AATAACAAAAAAAT
1 AAAAAAAAAAAAAT
2465712 A
1 A
2465713 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAAAAAT
Found at i:2465685 original size:8 final size:8
Alignment explanation
Indices: 2465650--2465708 Score: 50
Period size: 8 Copynumber: 7.2 Consensus size: 8
2465640 AAAAATAAGG
2465650 AATAAAAA
1 AATAAAAA
*
2465658 AAAAAAAA
1 AATAAAAA
2465666 AAT-AAAA
1 AATAAAAA
2465673 AATAAAAA
1 AATAAAAA
*
2465681 TATAAATAA
1 AATAAA-AA
*
2465690 CAA-AAAAT
1 -AATAAAAA
2465698 AATAACAAA
1 AATAA-AAA
2465707 AA
1 AA
2465709 AATATTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
7 9 0.22
8 21 0.52
9 9 0.22
10 1 0.03
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (8 bp):
AATAAAAA
Found at i:2465695 original size:36 final size:35
Alignment explanation
Indices: 2465622--2465709 Score: 97
Period size: 36 Copynumber: 2.5 Consensus size: 35
2465612 GACCCTGGAC
* *
2465622 AAAAAACAAACAAAGAATAAAAATAAGGAATAAAAA
1 AAAAAAAAAACAAAAAATAAAAATAA-GAATAAAAA
* *
2465658 AAAAAAAAAATAAAAAATAAAAATATA-AATAACAA
1 AAAAAAAAAACAAAAAATAAAAATA-AGAATAAAAA
* *
2465693 AAAATAATAACAAAAAA
1 AAAAAAAAAACAAAAAA
2465710 ATATTTTTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
35 21 0.48
36 22 0.50
37 1 0.02
ACGTcount: A:0.81, C:0.05, G:0.03, T:0.11
Consensus pattern (35 bp):
AAAAAAAAAACAAAAAATAAAAATAAGAATAAAAA
Found at i:2465701 original size:13 final size:14
Alignment explanation
Indices: 2465662--2465709 Score: 62
Period size: 13 Copynumber: 3.4 Consensus size: 14
2465652 TAAAAAAAAA
* *
2465662 AAAAAATAAAAAAT
1 AAAAAATAAATAAC
2465676 AAAAATATAAATAAC
1 AAAAA-ATAAATAAC
2465691 AAAAAAT-AATAAC
1 AAAAAATAAATAAC
2465704 AAAAAA
1 AAAAAA
2465710 ATATTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
13 12 0.39
14 7 0.23
15 12 0.39
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAAATAAATAAC
Found at i:2465701 original size:19 final size:19
Alignment explanation
Indices: 2465637--2465694 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
2465627 ACAAACAAAG
2465637 AATAAAAATA-AGGAATAAAA
1 AATAAAAATATA--AATAAAA
2465657 AA-AAAAA-A-AAATAAAA
1 AATAAAAATATAAATAAAA
2465673 AATAAAAATATAAATAACAA
1 AATAAAAATATAAATAA-AA
2465693 AA
1 AA
2465695 AATAATAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.26
17 5 0.15
18 3 0.09
19 11 0.32
20 6 0.18
ACGTcount: A:0.81, C:0.02, G:0.03, T:0.14
Consensus pattern (19 bp):
AATAAAAATATAAATAAAA
Found at i:2465795 original size:38 final size:36
Alignment explanation
Indices: 2465714--2466086 Score: 310
Period size: 37 Copynumber: 9.9 Consensus size: 36
2465704 AAAAAAATAT
* * ** *
2465714 TTTTAAAAACATATAATATATA-AATTTCCAAAATG
1 TTTTAAAAACTTATATTATATATGTTTTCAAAAATG
*
2465749 TTTTAAAAATCTTATATCATATATGTTTTCAAAAATG
1 TTTTAAAAA-CTTATATTATATATGTTTTCAAAAATG
* * *
2465786 TTTTAAAAAAATTATATAATATATATATTTGCAAAAATG
1 TTTT-AAAAACTTATAT--TATATATGTTTTCAAAAATG
2465825 TTTTAAAAAACTATATATTATATA--TTTTC-AAAATG
1 TTTT-AAAAACT-TATATTATATATGTTTTCAAAAATG
* *
2465860 TTTTTTTAAAAACTATATAATATATAAAAGTTTTC-AAAATG
1 ---TTTTAAAAACT-TAT-AT-TATATATGTTTTCAAAAATG
* *
2465901 TTTTCAAAACTATATATTATATAAGTTTTCAAAAAATG
1 TTTTAAAAACT-TATATTATATATGTTTTC-AAAAATG
* *
2465939 TTTTCAAAAACTTTATATTATATAAGTTTTC-CAAATG
1 TTTT-AAAAAC-TTATATTATATATGTTTTCAAAAATG
* * *
2465976 ATTTAAAAAACTATATATTATATATATTTTCTAAAATG
1 -TTTTAAAAACT-TATATTATATATGTTTTCAAAAATG
* *
2466014 TTTTAAAAACTATATATTATATATATTTT-GAAAATG
1 TTTTAAAAACT-TATATTATATATGTTTTCAAAAATG
*
2466050 TTTTAAAAATTTTATATTATATATGTATTTTCAAAAA
1 TTTTAAAAA-CTTATATTATATATG--TTTTCAAAAA
2466087 CCATTTGCAA
Statistics
Matches: 288, Mismatches: 26, Indels: 44
0.80 0.07 0.12
Matches are distributed among these distances:
35 15 0.05
36 54 0.19
37 89 0.31
38 53 0.18
39 60 0.21
40 6 0.02
41 11 0.04
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTAAAAACTTATATTATATATGTTTTCAAAAATG
Found at i:2466114 original size:75 final size:75
Alignment explanation
Indices: 2465714--2466114 Score: 380
Period size: 75 Copynumber: 5.3 Consensus size: 75
2465704 AAAAAAATAT
* * *
2465714 TTTTAAAAAC-ATATAATATATAAATTTCCAAAATGTTTTAAAAATCT-TATATCATATATG--T
1 TTTTAAAAACTATATAATATATATATTTTCAAAATGTTTTAAAAA-CTATATATTATATATGTAT
2465775 TTTCAAAAATG
65 TTTCAAAAATG
* *
2465786 TTTTAAAAAAATTATATAATATATATATTTGCAAAAATGTTTTAAAAAACTATATA-T-TATA--
1 TTTT--AAAAACTATATAATATATATATTTTC-AAAATGTTTT-AAAAACTATATATTATATATG
2465847 TATTTTC-AAAATG
62 TATTTTCAAAAATG
* * *
2465860 TTTTTTTAAAAACTATATAATATATAAAAGTTTTCAAAATGTTTTCAAAACTATATATTATATAA
1 ---TTTTAAAAACTATATAATATAT-ATA-TTTTCAAAATGTTTTAAAAACTATATATTATATAT
2465925 G--TTTTCAAAAAATG
61 GTATTTTC-AAAAATG
* * * *
2465939 TTTTCAAAAACTTTATATTATATA-AGTTTTCCAAATGATTTAAAAAACTATATATTATATA--T
1 TTTT-AAAAACTATATAATATATATA-TTTTCAAAATG-TTTTAAAAACTATATATTATATATGT
*
2466001 ATTTTCTAAAATG
63 ATTTTCAAAAATG
* * * *
2466014 TTTTAAAAACTATATATTATATATATTTTGAAAATGTTTTAAAAATTTTATATTATATATGTATT
1 TTTTAAAAACTATATAATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATGTATT
**
2466079 TTCAAAAACC
66 TTCAAAAATG
* **
2466089 ATTTGCAAACTATATAATATATATAT
1 TTTTAAAAACTATATAATATATATAT
2466115 AGATATATAT
Statistics
Matches: 276, Mismatches: 27, Indels: 49
0.78 0.08 0.14
Matches are distributed among these distances:
72 4 0.01
73 20 0.07
74 38 0.14
75 110 0.40
76 56 0.20
77 42 0.15
79 6 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (75 bp):
TTTTAAAAACTATATAATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATGTATT
TTCAAAAATG
Found at i:2466763 original size:84 final size:84
Alignment explanation
Indices: 2466585--2467479 Score: 882
Period size: 84 Copynumber: 10.7 Consensus size: 84
2466575 GATCCGAATT
* * * * * *
2466585 TAATCGAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTAGTCTTGA-TTCAT-TTGCAAAAG
1 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCT-ATGTTGCAAATG
* *
2466648 ATGTGCCTTTGAGCTGAGTG
65 ATGTGCCTTGGAGCTGAGCG
* *
2466668 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTTCCTTGAGCTATGTTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGA
* *
2466733 TGTGCCTTTGAGCTGAGTG
66 TGTGCCTTGGAGCTGAGCG
* * * * * *
2466752 TAATTGAACTCGAAGGTC-ATTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTT
1 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAA--T
*
2466816 GATATGCCTTTGAGCTGAATGTGAGCTGAGCG
64 G--ATG----TG-CCT---TG-GAGCTGAGCG
* * * * *
2466848 TAATCAAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGATGCAAATGA
1 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGA
* * *
2466909 TATGCCTTGGAGCCGAGCA
66 TGTGCCTTGGAGCTGAGCG
* * * * *
2466928 TAGTCAAACTCGAAGGTCTTTTTTTGGCAAATAGCCCTTCTTTCCTTGAGCTATGTTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGA
2466993 TGTGCCTTGGAGCTGAGCG
66 TGTGCCTTGGAGCTGAGCG
* * * * * * * *
2467012 TAGTCGAACTCGAAGGTCTTTTATTGGCAGATAAACTTTCTAGCCTTGAGTTATGCTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGA
*
2467077 TGTGTCTTGGAGCTGAGCG
66 TGTGCCTTGGAGCTGAGCG
* * * * * *
2467096 TAGTCGAACTCGAAGGTATTTTATTGGCAAATAGCCCTTCTTGCCTTGAGATATGTTGTAAATGA
1 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGA
* *
2467161 TGTGCCTTGGAGCAGAGCA
66 TGTGCCTTGGAGCTGAGCG
* * ** * * * ** *
2467180 TAGTCAAACTCGAAGGTCTTTTGTTGGCAGGTAACACTTCTAGCCTTGAGTTATACTACAAATGA
1 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGA
* *
2467245 TATGCCTTGGAGATGAGCG
66 TGTGCCTTGGAGCTGAGCG
* * *
2467264 TAATCGAACTAGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTTCAAGTGA
1 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGA
*
2467329 TGTACCTTGGAGCTGAGCG
66 TGTGCCTTGGAGCTGAGCG
* * * * *
2467348 TAGTCGATCTTGAAGGTCTTTTATTGGC-AATAACCCTTCTCGCCTTGAGCTATGTTGCAAATGA
1 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGA
* *
2467412 TGTACCTTGGAGCTGAGCA
66 TGTGCCTTGGAGCTGAGCG
* * * *
2467431 TAGTCGAACTCGAA------TTGTTGGCATATAACCCTTCTAGCCTTGAGTTATG
1 TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATG
2467480 CTGCCAATAG
Statistics
Matches: 683, Mismatches: 109, Indels: 45
0.82 0.13 0.05
Matches are distributed among these distances:
77 7 0.01
78 23 0.03
80 25 0.04
81 2 0.00
83 145 0.21
84 405 0.59
85 4 0.01
87 3 0.00
89 2 0.00
91 4 0.01
92 2 0.00
93 34 0.05
94 1 0.00
95 1 0.00
96 25 0.04
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (84 bp):
TAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATGTTGCAAATGA
TGTGCCTTGGAGCTGAGCG
Found at i:2471382 original size:22 final size:24
Alignment explanation
Indices: 2471346--2471390 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2471336 AAAAAAAATA
*
2471346 AAAAAACATACT-AAAATTAAAAG
1 AAAAAACATAATAAAAATTAAAAG
2471369 AAAAAA-ATAATAAAAATTAAAA
1 AAAAAACATAATAAAAATTAAAA
2471391 ATGCTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (24 bp):
AAAAAACATAATAAAAATTAAAAG
Found at i:2477093 original size:25 final size:25
Alignment explanation
Indices: 2477058--2477181 Score: 194
Period size: 25 Copynumber: 5.0 Consensus size: 25
2477048 TATTTTCACC
* *
2477058 CGAAAGTGCCTCGTAGAATTGCACT
1 CGAAAGTACCTCGTAGGATTGCACT
* *
2477083 TGAAAGTGCCTCGTAGGATTGCACT
1 CGAAAGTACCTCGTAGGATTGCACT
2477108 CGAAAGTACCTCGTAGGATTGCACT
1 CGAAAGTACCTCGTAGGATTGCACT
2477133 CGAAAGTACCTCGTAGGATTGCACT
1 CGAAAGTACCTCGTAGGATTGCACT
* *
2477158 CGAAAGTACCTTGTAAGATTGCAC
1 CGAAAGTACCTCGTAGGATTGCAC
2477182 CATAGGTGCC
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 93 1.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (25 bp):
CGAAAGTACCTCGTAGGATTGCACT
Found at i:2477467 original size:24 final size:26
Alignment explanation
Indices: 2477438--2477496 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 26
2477428 CCCAAAATTA
2477438 TATAAAAATA-ATTT-AGTAAA-TCAT
1 TATAAAAATATATTTCA-TAAATTCAT
2477462 TATAAAAA-ATATTTCATAAATTCAT
1 TATAAAAATATATTTCATAAATTCAT
2477487 TA-AAAAATAT
1 TATAAAAATAT
2477497 TTGAAGTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
23 1 0.03
24 21 0.68
25 9 0.29
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (26 bp):
TATAAAAATATATTTCATAAATTCAT
Found at i:2477486 original size:25 final size:24
Alignment explanation
Indices: 2477434--2477498 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 24
2477424 CATACCCAAA
2477434 ATTATATAAAAATAATTTAGTAAATC
1 ATTATA-AAAAAT-ATTTAGTAAATC
2477460 ATTATAAAAAATATTTCA-TAAATTC
1 ATTATAAAAAATATTT-AGTAAA-TC
2477485 A-T-TAAAAAATATTT
1 ATTATAAAAAATATTT
2477499 GAAGTTGGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
23 12 0.32
24 9 0.24
25 10 0.27
26 6 0.16
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.40
Consensus pattern (24 bp):
ATTATAAAAAATATTTAGTAAATC
Found at i:2477833 original size:86 final size:86
Alignment explanation
Indices: 2477688--2477857 Score: 340
Period size: 86 Copynumber: 2.0 Consensus size: 86
2477678 TAGATCTACG
2477688 TTTTACTAGAAAATTTTCAGATTGGGGAGTCGTTTACGATCGAGGAAAGATGAGAACCCTTGAGT
1 TTTTACTAGAAAATTTTCAGATTGGGGAGTCGTTTACGATCGAGGAAAGATGAGAACCCTTGAGT
2477753 CACCTTTTCGGTACCAATCTA
66 CACCTTTTCGGTACCAATCTA
2477774 TTTTACTAGAAAATTTTCAGATTGGGGAGTCGTTTACGATCGAGGAAAGATGAGAACCCTTGAGT
1 TTTTACTAGAAAATTTTCAGATTGGGGAGTCGTTTACGATCGAGGAAAGATGAGAACCCTTGAGT
2477839 CACCTTTTCGGTACCAATC
66 CACCTTTTCGGTACCAATC
2477858 GATTACCCGA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (86 bp):
TTTTACTAGAAAATTTTCAGATTGGGGAGTCGTTTACGATCGAGGAAAGATGAGAACCCTTGAGT
CACCTTTTCGGTACCAATCTA
Found at i:2478019 original size:6 final size:6
Alignment explanation
Indices: 2478010--2478053 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
2478000 ATAAATTTAA
*
2478010 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAATAA AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG AAAAAG A
2478054 TTTAGGGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 30 0.86
7 5 0.14
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:2478031 original size:18 final size:19
Alignment explanation
Indices: 2478007--2478053 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
2477997 AAAATAAATT
2478007 TAAAAAAAGAAAAAGAAAA
1 TAAAAAAAGAAAAAGAAAA
*
2478026 -AGAAAAAGAAAAAGAAAA
1 TAAAAAAAGAAAAAGAAAA
2478044 TAAAAAAAGA
1 TAAAAAAAGA
2478054 TTTAGGGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (19 bp):
TAAAAAAAGAAAAAGAAAA
Found at i:2480226 original size:27 final size:28
Alignment explanation
Indices: 2480187--2480240 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
2480177 GTCTAGAGGT
2480187 ATTTTAGGTCATTTTACACTTTAAGGGC
1 ATTTTAGGTCATTTTACACTTTAAGGGC
*
2480215 ATTTT-GGTCATTTTAGACTTTAAGGG
1 ATTTTAGGTCATTTTACACTTTAAGGG
2480241 TAATTCTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.44
Consensus pattern (28 bp):
ATTTTAGGTCATTTTACACTTTAAGGGC
Found at i:2481230 original size:23 final size:23
Alignment explanation
Indices: 2481192--2481264 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
2481182 ACTATTAACA
* *
2481192 GTTGACTAG-TCAAAGTCAATCG
1 GTTGACTCGATCAAAGTCAATAG
*
2481214 GTTGACTCGATCAAAGTCAATGG
1 GTTGACTCGATCAAAGTCAATAG
*
2481237 GTTGACTCAATCAAAGTCAATAG
1 GTTGACTCGATCAAAGTCAATAG
2481260 GTTGA
1 GTTGA
2481265 ATCTATGATT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 8 0.17
23 38 0.83
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (23 bp):
GTTGACTCGATCAAAGTCAATAG
Found at i:2484362 original size:28 final size:27
Alignment explanation
Indices: 2484331--2484395 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
2484321 TATTCTAGGG
*
2484331 TTTAGAGGTATTTTAGGTTATTTTACAC
1 TTTAGAGGTATTTT-GGTCATTTTACAC
* *
2484359 TTTA-AGGGCATTTTGGTCGTTTTACAC
1 TTTAGA-GGTATTTTGGTCATTTTACAC
2484386 TTTAGAGGTA
1 TTTAGAGGTA
2484396 ATTCTATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
27 19 0.61
28 12 0.39
ACGTcount: A:0.23, C:0.09, G:0.22, T:0.46
Consensus pattern (27 bp):
TTTAGAGGTATTTTGGTCATTTTACAC
Found at i:2485330 original size:22 final size:23
Alignment explanation
Indices: 2485281--2485338 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
2485271 TTTCGGTCAA
* *
2485281 AGTCAAAGGTCAACGGTCTCACT
1 AGTCAAAGGTCAACGGTCACACC
* *
2485304 GGTCAAA-GTCAACGGTCAGACC
1 AGTCAAAGGTCAACGGTCACACC
*
2485326 AGTCAACGGTCAA
1 AGTCAAAGGTCAA
2485339 TAAATTGACT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (23 bp):
AGTCAAAGGTCAACGGTCACACC
Found at i:2485336 original size:29 final size:28
Alignment explanation
Indices: 2485274--2485338 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
2485264 TTGACTTTTT
* *
2485274 CGGTCAAAGTCAAAGGTCAACGGTCTCA
1 CGGTCAAAGTCAAAGGTCAACAGTCTAA
*
2485302 CTGGTCAAAGTCAACGGTCAGACCAGTC-AA
1 C-GGTCAAAGTCAAAGGTCA-A-CAGTCTAA
2485332 CGGTCAA
1 CGGTCAA
2485339 TAAATTGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 23 0.74
30 3 0.10
31 4 0.13
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (28 bp):
CGGTCAAAGTCAAAGGTCAACAGTCTAA
Found at i:2488316 original size:23 final size:23
Alignment explanation
Indices: 2488267--2488318 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2488257 ACAATTAATG
*
2488267 GGTTGACTCGGTAAAGGTCAACG
1 GGTTGACTCGGTAAAGGTCAACA
* *
2488290 GGTTTACTCGGTCAAA-GTTAACA
1 GGTTGACTCGGT-AAAGGTCAACA
2488313 GGTTGA
1 GGTTGA
2488319 TTAGGTGGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (23 bp):
GGTTGACTCGGTAAAGGTCAACA
Found at i:2493762 original size:29 final size:30
Alignment explanation
Indices: 2493729--2493795 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 30
2493719 GGTCAATCTC
*
2493729 AAAGTCAATGGTCAAC-GGTCTGAC-CAGTA
1 AAAGTCAATGATCAACGGGT-TGACTCAGTA
2493758 AAAGTCAATGATCAACGGGTTGACTCAGTA
1 AAAGTCAATGATCAACGGGTTGACTCAGTA
2493788 AAAGTCAA
1 AAAGTCAA
2493796 CGGGTTGACT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 19 0.54
30 16 0.46
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (30 bp):
AAAGTCAATGATCAACGGGTTGACTCAGTA
Found at i:2493799 original size:23 final size:23
Alignment explanation
Indices: 2493769--2493828 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2493759 AAGTCAATGA
2493769 TCAACGGGTTGACTCAGTAAAAG
1 TCAACGGGTTGACTCAGTAAAAG
* *
2493792 TCAACGGGTTGACTCGGTCAAAG
1 TCAACGGGTTGACTCAGTAAAAG
* *
2493815 TTAACAGGTTGACT
1 TCAACGGGTTGACT
2493829 TGGTGGGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (23 bp):
TCAACGGGTTGACTCAGTAAAAG
Found at i:2496526 original size:23 final size:23
Alignment explanation
Indices: 2496496--2496553 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 23
2496486 AAGTCAACGA
*
2496496 TCAACGGGTTGACTCGGT-AAAGG
1 TCAACGGGTTGACTCGATCAAA-G
2496519 TCAACGGGTTGACTCGATCAAAG
1 TCAACGGGTTGACTCGATCAAAG
*
2496542 TCAACAGGTTGA
1 TCAACGGGTTGA
2496554 TTAGGTGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 29 0.91
24 3 0.09
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.22
Consensus pattern (23 bp):
TCAACGGGTTGACTCGATCAAAG
Found at i:2499171 original size:23 final size:22
Alignment explanation
Indices: 2499113--2499172 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
2499103 ATGGTCTGAT
*
2499113 CAGTCAAAGTCAACGGTTAGAC
1 CAGTCAAAGTCAACGATTAGAC
*
2499135 CAGTCAACGTTCAACGAATT-GAC
1 CAGTCAAAG-TCAACG-ATTAGAC
*
2499158 TCGGTCAAAGTCAAC
1 -CAGTCAAAGTCAAC
2499173 AGGTGACAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 8 0.26
23 14 0.45
24 9 0.29
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (22 bp):
CAGTCAAAGTCAACGATTAGAC
Found at i:2502029 original size:29 final size:30
Alignment explanation
Indices: 2501995--2502063 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
2501985 GGTCTAACTC
* *
2501995 AAAGTCAATGGTCAACG-GTCTGAC-CAGTA
1 AAAGTCAACGATCAACGAGT-TGACTCAGTA
*
2502024 AAAGTCAACGATCAACGAGTTGACTCGGTA
1 AAAGTCAACGATCAACGAGTTGACTCAGTA
*
2502054 AAAGACAACG
1 AAAGTCAACG
2502064 GGTTGACTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.17
Consensus pattern (30 bp):
AAAGTCAACGATCAACGAGTTGACTCAGTA
Found at i:2502068 original size:23 final size:23
Alignment explanation
Indices: 2502036--2502094 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
2502026 AGTCAACGAT
*
2502036 CAACGAGTTGACTCGGTAAAAGA
1 CAACGGGTTGACTCGGTAAAAGA
* *
2502059 CAACGGGTTGACTCGGTCAAAGT
1 CAACGGGTTGACTCGGTAAAAGA
* *
2502082 TAACAGGTTGACT
1 CAACGGGTTGACT
2502095 TGGTGGGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (23 bp):
CAACGGGTTGACTCGGTAAAAGA
Found at i:2506381 original size:21 final size:21
Alignment explanation
Indices: 2506352--2506394 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
2506342 AATTATTAAT
2506352 AATATATATACTATAATATAAAC
1 AATATATATA-TAT-ATATAAAC
2506375 AATATATATATATATATAAA
1 AATATATATATATATATAAA
2506395 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 10 0.50
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
AATATATATATATATATAAAC
Found at i:2506470 original size:2 final size:2
Alignment explanation
Indices: 2506453--2506501 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
2506443 TTTTAAAAAC
2506453 AT AT A- AT AT AT A- 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
2506493 AT AT AT AT A
1 AT AT AT AT A
2506502 GTTTAGGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2506664 original size:71 final size:71
Alignment explanation
Indices: 2506589--2506802 Score: 178
Period size: 71 Copynumber: 3.1 Consensus size: 71
2506579 TTGTTTTCTG
2506589 TATTTTATTTTTCTGGGACACTTCTGAAGAGACTATGTTTACAAGTCTAGATTGAATTTGGGGGT
1 TATTTTATTTTTCTGGGACACTTCTGAAGAGACTATGTTTACAAGTCTAGATTGAATTTGGGGGT
2506654 AGCCGA
66 AGCCGA
* ** ** * ***
2506660 TATTTT-TCTTCTTCT-GGTCA-TT-TG-A-TCAC-ATACTTACAAG-CTCG-TTCTTCTTTGAT
1 TATTTTAT-TT-TTCTGGGACACTTCTGAAGAGACTATGTTTACAAGTCTAGATT-GAATTTG--
** * ** *
2506716 TTGTTTTCTG-
61 GGGGTAGCCGA
2506726 TATTTTATTTTTCTGGGACACTTCTGAAGAGACTATGTTTACAAGTCTAGATTGAATTTGGGGGT
1 TATTTTATTTTTCTGGGACACTTCTGAAGAGACTATGTTTACAAGTCTAGATTGAATTTGGGGGT
2506791 AGCCGA
66 AGCCGA
2506797 TATTTT
1 TATTTT
2506803 TTCTTCTTCT
Statistics
Matches: 98, Mismatches: 30, Indels: 30
0.62 0.19 0.19
Matches are distributed among these distances:
64 2 0.02
65 11 0.11
66 21 0.21
67 9 0.09
68 3 0.03
69 3 0.03
70 9 0.09
71 27 0.28
72 11 0.11
73 2 0.02
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.44
Consensus pattern (71 bp):
TATTTTATTTTTCTGGGACACTTCTGAAGAGACTATGTTTACAAGTCTAGATTGAATTTGGGGGT
AGCCGA
Found at i:2506798 original size:137 final size:139
Alignment explanation
Indices: 2506552--2506829 Score: 533
Period size: 137 Copynumber: 2.0 Consensus size: 139
2506542 ATTCTACTCA
2506552 ATACTTACAAGCTCGTTCTTCTTTGATTTGTTTTCTGTATTTTATTTTTCTGGGACACTTCTGAA
1 ATACTTACAAGCTCGTTCTTCTTTGATTTGTTTTCTGTATTTTATTTTTCTGGGACACTTCTGAA
2506617 GAGACTATGTTTACAAGTCTAGATTGAATTTGGGGGTAGCCGATA-TTTTTCTTCTTCTGGTC-A
66 GAGACTATGTTTACAAGTCTAGATTGAATTTGGGGGTAGCCGATATTTTTTCTTCTTCTGGTCAA
*
2506680 TTTGATCAC
131 ATTGATCAC
2506689 ATACTTACAAGCTCGTTCTTCTTTGATTTGTTTTCTGTATTTTATTTTTCTGGGACACTTCTGAA
1 ATACTTACAAGCTCGTTCTTCTTTGATTTGTTTTCTGTATTTTATTTTTCTGGGACACTTCTGAA
2506754 GAGACTATGTTTACAAGTCTAGATTGAATTTGGGGGTAGCCGATATTTTTTCTTCTTCTGGTCAA
66 GAGACTATGTTTACAAGTCTAGATTGAATTTGGGGGTAGCCGATATTTTTTCTTCTTCTGGTCAA
2506819 ATTGATCAC
131 ATTGATCAC
2506828 AT
1 AT
2506830 GGGACATTAT
Statistics
Matches: 138, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
137 110 0.80
138 17 0.12
139 11 0.08
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (139 bp):
ATACTTACAAGCTCGTTCTTCTTTGATTTGTTTTCTGTATTTTATTTTTCTGGGACACTTCTGAA
GAGACTATGTTTACAAGTCTAGATTGAATTTGGGGGTAGCCGATATTTTTTCTTCTTCTGGTCAA
ATTGATCAC
Found at i:2507081 original size:134 final size:134
Alignment explanation
Indices: 2506863--2507130 Score: 527
Period size: 134 Copynumber: 2.0 Consensus size: 134
2506853 CTATTTTATT
2506863 ATTTGGAGTATCTTGGGTTTATCGAGGAAACAAAATGATCGACTTCTCAAGACAATAATATCACC
1 ATTTGGAGTATCTTGGGTTTATCGAGGAAACAAAATGATCGACTTCTCAAGACAATAATATCACC
2506928 CTTAGAGAAGAAATCATTTTGCTTTAGGATTCCAAGAGATGGATGGGATAACGAATTCTCAAGCT
66 CTTAGAGAAGAAATCATTTTGCTTTAGGATTCCAAGAGATGGATGGGATAACGAATTCTCAAGCT
2506993 TCGA
131 TCGA
*
2506997 ATTTGGAGTATCTTGGGTTTATCGAGGAAAGAAAATGATCGACTTCTCAAGACAATAATATCACC
1 ATTTGGAGTATCTTGGGTTTATCGAGGAAACAAAATGATCGACTTCTCAAGACAATAATATCACC
2507062 CTTAGAGAAGAAATCATTTTGCTTTAGGATTCCAAGAGATGGATGGGATAACGAATTCTCAAGCT
66 CTTAGAGAAGAAATCATTTTGCTTTAGGATTCCAAGAGATGGATGGGATAACGAATTCTCAAGCT
2507127 TCGA
131 TCGA
2507131 GGTGGATGAT
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 133 1.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (134 bp):
ATTTGGAGTATCTTGGGTTTATCGAGGAAACAAAATGATCGACTTCTCAAGACAATAATATCACC
CTTAGAGAAGAAATCATTTTGCTTTAGGATTCCAAGAGATGGATGGGATAACGAATTCTCAAGCT
TCGA
Found at i:2513472 original size:16 final size:16
Alignment explanation
Indices: 2513451--2513484 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2513441 TATTGTCTTG
2513451 AATTTTCTCTAATTCA
1 AATTTTCTCTAATTCA
*
2513467 AATTTTCTCTTATTCA
1 AATTTTCTCTAATTCA
2513483 AA
1 AA
2513485 CAACAACCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTTCTCTAATTCA
Found at i:2553781 original size:45 final size:44
Alignment explanation
Indices: 2553725--2553984 Score: 358
Period size: 45 Copynumber: 5.8 Consensus size: 44
2553715 AAATCTATGA
* *
2553725 ATCGGTATAAAAGATGCCACTAATAAAGATGCATAATGGTGCATT
1 ATCGGCATAAAAGGTGCCACTAATAAA-ATGCATAATGGTGCATT
* * *
2553770 ATAGGCATAAAAGGTGTCACTAATGAAAATGCATAACGGTGCATT
1 ATCGGCATAAAAGGTGCCACTAAT-AAAATGCATAATGGTGCATT
* *
2553815 ATCGGCATAAAAGGTGCCACTAATGAAGATGCATAATGGTTCATT
1 ATCGGCATAAAAGGTGCCACTAAT-AAAATGCATAATGGTGCATT
*
2553860 ATCGGCATAAAAGGTGCCACTAATAAAATACATAATGGTGCATT
1 ATCGGCATAAAAGGTGCCACTAATAAAATGCATAATGGTGCATT
* *
2553904 ATCGGCATAAAAAGTGCCACTAATGAAAATGCATAACGGTGCATT
1 ATCGGCATAAAAGGTGCCACTAAT-AAAATGCATAATGGTGCATT
* * *
2553949 ATCGGCATAAAAAGTGCCATTAATGAAAATGTATAA
1 ATCGGCATAAAAGGTGCCACTAAT-AAAATGCATAA
2553985 CAGAACTTGC
Statistics
Matches: 195, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
44 40 0.21
45 152 0.78
46 3 0.02
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (44 bp):
ATCGGCATAAAAGGTGCCACTAATAAAATGCATAATGGTGCATT
Found at i:2553936 original size:89 final size:90
Alignment explanation
Indices: 2553725--2553978 Score: 370
Period size: 89 Copynumber: 2.8 Consensus size: 90
2553715 AAATCTATGA
* * *
2553725 ATCGGTAT-AAAAGATGCCACTAAT-AAAGATGCATAATGGTGCATTATAGGCATAAAAGGTGTC
1 ATCGGCATAAAAAG-TGCCACTAATGAAA-ATGCATAATGGTGCATTATCGGCATAAAAGGTGCC
*
2553788 ACTAATGAAAATGCATAACGGTGCATT
64 ACTAATGAAAATACATAACGGTGCATT
* * *
2553815 ATCGGCATAAAAGGTGCCACTAATGAAGATGCATAATGGTTCATTATCGGCATAAAAGGTGCCAC
1 ATCGGCATAAAAAGTGCCACTAATGAAAATGCATAATGGTGCATTATCGGCATAAAAGGTGCCAC
*
2553880 TAAT-AAAATACATAATGGTGCATT
66 TAATGAAAATACATAACGGTGCATT
* * *
2553904 ATCGGCATAAAAAGTGCCACTAATGAAAATGCATAACGGTGCATTATCGGCATAAAAAGTGCCAT
1 ATCGGCATAAAAAGTGCCACTAATGAAAATGCATAATGGTGCATTATCGGCATAAAAGGTGCCAC
2553969 TAATGAAAAT
66 TAATGAAAAT
2553979 GTATAACAGA
Statistics
Matches: 147, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
89 81 0.55
90 60 0.41
91 6 0.04
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (90 bp):
ATCGGCATAAAAAGTGCCACTAATGAAAATGCATAATGGTGCATTATCGGCATAAAAGGTGCCAC
TAATGAAAATACATAACGGTGCATT
Found at i:2553966 original size:134 final size:135
Alignment explanation
Indices: 2553725--2553984 Score: 423
Period size: 134 Copynumber: 1.9 Consensus size: 135
2553715 AAATCTATGA
* * * *
2553725 ATCGGTATAAAAGATGCCACTAATAAAGATGCATAATGGTGCATTATAGGCATAAAAGGTGTCAC
1 ATCGGCATAAAAGATGCCACTAATAAAGATACATAATGGTGCATTATAGGCATAAAAAGTGCCAC
* *
2553790 TAATGAAAATGCATAACGGTGCATTATCGGCATAAAAGGTGCCACTAATGAAGATGCATAATGGT
66 TAATGAAAATGCATAACGGTGCATTATCGGCATAAAAAGTGCCACTAATGAAAATGCATAATGGT
2553855 TCATT
131 TCATT
* *
2553860 ATCGGCATAAAAGGTGCCACTAATAAA-ATACATAATGGTGCATTATCGGCATAAAAAGTGCCAC
1 ATCGGCATAAAAGATGCCACTAATAAAGATACATAATGGTGCATTATAGGCATAAAAAGTGCCAC
* *
2553924 TAATGAAAATGCATAACGGTGCATTATCGGCATAAAAAGTGCCATTAATGAAAATGTATAA
66 TAATGAAAATGCATAACGGTGCATTATCGGCATAAAAAGTGCCACTAATGAAAATGCATAA
2553985 CAGAACTTGC
Statistics
Matches: 115, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
134 90 0.78
135 25 0.22
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (135 bp):
ATCGGCATAAAAGATGCCACTAATAAAGATACATAATGGTGCATTATAGGCATAAAAAGTGCCAC
TAATGAAAATGCATAACGGTGCATTATCGGCATAAAAAGTGCCACTAATGAAAATGCATAATGGT
TCATT
Found at i:2557606 original size:45 final size:45
Alignment explanation
Indices: 2557537--2557819 Score: 386
Period size: 45 Copynumber: 6.3 Consensus size: 45
2557527 GAATCGACAA
* * * *
2557537 AAAAGGTGTCACTAATGAAGATGCATAACGGTTCATTATCGGTAT
1 AAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGGCAT
** * *
2557582 AAAAGGTGTAAATGATGAAAATGCATAACGGTGCATTATCGGCAT
1 AAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGGCAT
* * *
2557627 AAAATGTGCCACTAATGAAATTGCATAATGGTGCATTATCGGCAT
1 AAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGGCAT
* * *
2557672 AAAAGGTGACACTAATGAAAATGCATAATGGTGAATTATCGGCAT
1 AAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGGCAT
* * *
2557717 AAAAGGTGCCATTAATGAAAATGCATAATGGTGCATTATCGACAT
1 AAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGGCAT
* *
2557762 AAAAGGTACCACTAATGAAAATGCATAACGGTGCATTATCGACAT
1 AAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGGCAT
*
2557807 AAAAGGTTCCACT
1 AAAAGGTGCCACT
2557820 TATTACATTC
Statistics
Matches: 213, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 213 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (45 bp):
AAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATCGGCAT
Found at i:2558660 original size:18 final size:17
Alignment explanation
Indices: 2558628--2558662 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2558618 TTATCTTACA
2558628 TATTATATATAATATTT
1 TATTATATATAATATTT
*
2558645 TATTATTATATTATATTT
1 TATTA-TATATAATATTT
2558663 ACAAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTATATATAATATTT
Found at i:2563602 original size:24 final size:24
Alignment explanation
Indices: 2563574--2563646 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
2563564 GCAAGTTTAT
2563574 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACGAGCTTA
* * *
2563598 TGGTACAAAT--G-GTA--AGTATTT
1 TGGTA-AAATAAGCTTACGAG-CTTA
2563619 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACGAGCTTA
2563643 TGGT
1 TGGT
2563647 TAATAAATGG
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 6 0.17
21 7 0.19
22 3 0.08
23 3 0.08
24 11 0.31
25 6 0.17
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (24 bp):
TGGTAAAATAAGCTTACGAGCTTA
Found at i:2563622 original size:45 final size:45
Alignment explanation
Indices: 2563560--2563646 Score: 149
Period size: 45 Copynumber: 1.9 Consensus size: 45
2563550 GTTATGGAAT
2563560 AATGGCAAGTTTATTGGTAAAATAAGCTTACGAGCTTATGGTACA
1 AATGGCAAGTTTATTGGTAAAATAAGCTTACGAGCTTATGGTACA
*
2563605 AATGGTAAGTATT-TTGGTAAAATAAGCTTACGAGCTTATGGT
1 AATGGCAAGT-TTATTGGTAAAATAAGCTTACGAGCTTATGGT
2563647 TAATAAATGG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 38 0.95
46 2 0.05
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.33
Consensus pattern (45 bp):
AATGGCAAGTTTATTGGTAAAATAAGCTTACGAGCTTATGGTACA
Found at i:2565581 original size:3 final size:3
Alignment explanation
Indices: 2565562--2565632 Score: 60
Period size: 3 Copynumber: 24.0 Consensus size: 3
2565552 TGTCTGTTTC
* *
2565562 TAT TAT TAA TGT T-T TAT TAT TAT TAT TAT TA- TAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
2565606 ATAT ATAA TAT T-T TAT TAT TA- TAT TAT
1 -TAT -TAT TAT TAT TAT TAT TAT TAT TAT
2565633 ATTTACAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
2 8 0.14
3 40 0.70
4 9 0.16
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2565616 original size:16 final size:15
Alignment explanation
Indices: 2565585--2565635 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
2565575 TTATTATTAT
*
2565585 TATTATTATATTATA
1 TATTATTATATAATA
2565600 TATTATATATATAATA
1 TATTAT-TATATAATA
* *
2565616 TTTTATTATTATATTA
1 TATTATTA-TATAATA
2565632 TATT
1 TATT
2565636 TACAAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTATATAATA
Found at i:2576045 original size:6 final size:6
Alignment explanation
Indices: 2576034--2576069 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
2576024 ATAATAGGAT
2576034 TATTAA TATTAA TATTAA TATTAA TATTAAA TATTA
1 TATTAA TATTAA TATTAA TATTAA TATT-AA TATTA
2576070 TTAAGTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTAA
Found at i:2576055 original size:18 final size:19
Alignment explanation
Indices: 2576009--2576069 Score: 70
Period size: 18 Copynumber: 3.2 Consensus size: 19
2575999 CTATATAGTT
2576009 TTAATATTCAATATTATAATA
1 TTAATATT-AATATTA-AATA
** *
2576030 GGATTATTAATATT-AATA
1 TTAATATTAATATTAAATA
2576048 TTAATATTAATATTAAATA
1 TTAATATTAATATTAAATA
2576067 TTA
1 TTA
2576070 TTAAGTAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 15 0.45
19 7 0.21
20 6 0.18
21 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (19 bp):
TTAATATTAATATTAAATA
Found at i:2581023 original size:21 final size:21
Alignment explanation
Indices: 2580978--2581036 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
2580968 TCCTTAGGGA
2580978 AAGGGATCGATCA-TTTGCCTG
1 AAGGGATCGATCATTTTGCC-G
*
2580999 AAGGGATCGATCATTTTG-AG
1 AAGGGATCGATCATTTTGCCG
*
2581019 CAAGGGCTCGATCATTTT
1 -AAGGGATCGATCATTTT
2581037 TATGAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.85
22 4 0.12
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (21 bp):
AAGGGATCGATCATTTTGCCG
Found at i:2605087 original size:63 final size:63
Alignment explanation
Indices: 2605010--2605180 Score: 315
Period size: 63 Copynumber: 2.7 Consensus size: 63
2605000 ATTTTATTTA
*
2605010 TGTAACCTATATATATTGGTGTCGAATACACATGCATATATATAAATGAGATTAAACACAGTC
1 TGTAACCTATATATATTGGGGTCGAATACACATGCATATATATAAATGAGATTAAACACAGTC
2605073 TGTAACCTATATATATTGGGGTCGAATACACATGCATATATATAAATGAGATTAAACACAGTC
1 TGTAACCTATATATATTGGGGTCGAATACACATGCATATATATAAATGAGATTAAACACAGTC
* *
2605136 TGTAAACTATATATATTGGGGTCGAAAACACATGCATATATATAA
1 TGTAACCTATATATATTGGGGTCGAATACACATGCATATATATAA
2605181 CATCTTACCT
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 105 1.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (63 bp):
TGTAACCTATATATATTGGGGTCGAATACACATGCATATATATAAATGAGATTAAACACAGTC
Found at i:2605242 original size:17 final size:18
Alignment explanation
Indices: 2605220--2605259 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2605210 AAGTATAAAC
2605220 ATAAAAAACA-GAAAGAA
1 ATAAAAAACATGAAAGAA
*
2605237 ATAAAAAACATGAAATAA
1 ATAAAAAACATGAAAGAA
2605255 ATAAA
1 ATAAA
2605260 TTATAAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.12
Consensus pattern (18 bp):
ATAAAAAACATGAAAGAA
Found at i:2609080 original size:41 final size:41
Alignment explanation
Indices: 2609035--2609112 Score: 93
Period size: 41 Copynumber: 1.9 Consensus size: 41
2609025 TTGACCTTGG
* *
2609035 CAGCAGGTACTAATTCACAATTCAATTCAATTCAATCCTAA
1 CAGCAGGCAATAATTCACAATTCAATTCAATTCAATCCTAA
* * * **
2609076 CAGCATGCAATAGTTCACCATTTGATTCAATTCAATC
1 CAGCAGGCAATAATTCACAATTCAATTCAATTCAATC
2609113 ATGGAAGCAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (41 bp):
CAGCAGGCAATAATTCACAATTCAATTCAATTCAATCCTAA
Found at i:2609122 original size:41 final size:41
Alignment explanation
Indices: 2609045--2609298 Score: 226
Period size: 41 Copynumber: 6.2 Consensus size: 41
2609035 CAGCAGGTAC
* * *
2609045 TAATTCACAATTCAATTCAATTCAATCCT-AACAGCATGCAA
1 TAATTCACCATTCAATTCAATTCAATCATGGA-AGCATGCAA
* ** **
2609086 TAGTTCACCATTTGATTCAATTCAATCATGGAAGCATAAAA
1 TAATTCACCATTCAATTCAATTCAATCATGGAAGCATGCAA
* * * * *
2609127 TAATTCAACATTAAACTT-GATTCGATCATGGTAGCATGCAA
1 TAATTCACCATTCAA-TTCAATTCAATCATGGAAGCATGCAA
* * * *
2609168 TAATTCACAATTCTATTCAATTCAATCATGAAAGGATGCAA
1 TAATTCACCATTCAATTCAATTCAATCATGGAAGCATGCAA
* * * *
2609209 TAGTTCATCATTCGATTTAATTCAATCATGGAAGCATGCAA
1 TAATTCACCATTCAATTCAATTCAATCATGGAAGCATGCAA
* * * *
2609250 TAATTTATCATTCAATTTAATTCAATCATGGTAA-CATGCAT
1 TAATTCACCATTCAATTCAATTCAATCATGG-AAGCATGCAA
*
2609291 TTATTCAC
1 TAATTCAC
2609299 AACCCAATTA
Statistics
Matches: 169, Mismatches: 40, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
40 2 0.01
41 162 0.96
42 5 0.03
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (41 bp):
TAATTCACCATTCAATTCAATTCAATCATGGAAGCATGCAA
Found at i:2609278 original size:123 final size:123
Alignment explanation
Indices: 2609045--2609300 Score: 343
Period size: 123 Copynumber: 2.1 Consensus size: 123
2609035 CAGCAGGTAC
* *
2609045 TAATTCACAATTCAATTCAATTCAATCCTAACAGCATGCAATAGTTCACCATTTGATTCAATTCA
1 TAATTCACAATTCAATTCAATTCAATCATAACAGCATGCAATAGTTCACCATTCGATTCAATTCA
* * *
2609110 ATCATGGAAGCATAAAATAATTCAACATTAAACTTGATTCGATCATGGTAGCATGCAA
66 ATCATGGAAGCATAAAATAATTCAACATTAAACTTAATTCAATCATGGTAACATGCAA
* * * *
2609168 TAATTCACAATTCTATTCAATTCAATCATGAA-AGGATGCAATAGTTCATCATTCGATTTAATTC
1 TAATTCACAATTCAATTCAATTCAATCAT-AACAGCATGCAATAGTTCACCATTCGATTCAATTC
** * * * * *
2609232 AATCATGGAAGCATGCAATAATTTATCATTCAATTTAATTCAATCATGGTAACATGCAT
65 AATCATGGAAGCATAAAATAATTCAACATTAAACTTAATTCAATCATGGTAACATGCAA
*
2609291 TTATTCACAA
1 TAATTCACAA
2609301 CCCAATTAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
123 113 0.98
124 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (123 bp):
TAATTCACAATTCAATTCAATTCAATCATAACAGCATGCAATAGTTCACCATTCGATTCAATTCA
ATCATGGAAGCATAAAATAATTCAACATTAAACTTAATTCAATCATGGTAACATGCAA
Found at i:2609307 original size:41 final size:40
Alignment explanation
Indices: 2609262--2609353 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 40
2609252 ATTTATCATT
* *
2609262 CAATTTAATTCAATCATGGTAACATGCATTTATTCACAACC
1 CAATTAAATTCAATCATGGTAACATGCA-TTATTCACAAAC
* **
2609303 CAATTAAATT-AGGTCATGGTAGTATGCATTAGTTCACAAAC
1 CAATTAAATTCA-ATCATGGTAACATGCATTA-TTCACAAAC
2609344 CAATTAAATT
1 CAATTAAATT
2609354 AGGTCATGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
40 4 0.09
41 40 0.91
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (40 bp):
CAATTAAATTCAATCATGGTAACATGCATTATTCACAAAC
Found at i:2609389 original size:41 final size:41
Alignment explanation
Indices: 2609275--2609381 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
2609265 TTTAATTCAA
** * *
2609275 TCATGGTAACATGCATTTATTCACAACCCAATTAAATTAGG
1 TCATGGTAGTATGCATTAATTCACAAACCAATTAAATTAGG
*
2609316 TCATGGTAGTATGCATTAGTTCACAAACCAATTAAATTAGG
1 TCATGGTAGTATGCATTAATTCACAAACCAATTAAATTAGG
*
2609357 TCATGGTAGTATGGATTAATTCACA
1 TCATGGTAGTATGCATTAATTCACA
2609382 TTTCAATTCA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (41 bp):
TCATGGTAGTATGCATTAATTCACAAACCAATTAAATTAGG
Done.