Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold197
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: 1875808
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 64134 characters in sequence are not A, C, G, or T
File 5 of 6
Found at i:1361874 original size:12 final size:12
Alignment explanation
Indices: 1361857--1361889 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1361847 TAAATTAGTT
1361857 AGCAGTTAGCAG
1 AGCAGTTAGCAG
1361869 AGCAGTTAGCAG
1 AGCAGTTAGCAG
*
1361881 AGTAGTTAG
1 AGCAGTTAG
1361890 TATTAGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.21
Consensus pattern (12 bp):
AGCAGTTAGCAG
Found at i:1363029 original size:30 final size:27
Alignment explanation
Indices: 1362970--1363035 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 27
1362960 ATTAGAAATA
* * *
1362970 AATTAAAAACTTTAAAACATGTTTGTT
1 AATTAAAAACTTAAAAACATGCTTATT
1362997 AATTAAAAACTTGAAAATAACATGCTTATT
1 AATTAAAAACTT--AAA-AACATGCTTATT
1363027 AATTAAAAA
1 AATTAAAAA
1363036 TATTAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 12 0.36
29 2 0.06
30 19 0.58
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.35
Consensus pattern (27 bp):
AATTAAAAACTTAAAAACATGCTTATT
Found at i:1363208 original size:28 final size:28
Alignment explanation
Indices: 1363157--1363210 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1363147 AAGGAAGTGT
*
1363157 GTTTGGTATAAAGTGTTTTCTAAAAGCG
1 GTTTGGTATAAACTGTTTTCTAAAAGCG
*
1363185 GTTTGGTATACACTGCTTTT-TAAAAG
1 GTTTGGTATAAACTG-TTTTCTAAAAG
1363211 TACCTTTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (28 bp):
GTTTGGTATAAACTGTTTTCTAAAAGCG
Found at i:1363517 original size:22 final size:21
Alignment explanation
Indices: 1363476--1363518 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1363466 ATAATAGAGC
*
1363476 ATAAATTTTTATTTATTTGTG
1 ATAAATTTTTATTTAATTGTG
*
1363497 ATAATTTTTTATTTGAATTGTG
1 ATAAATTTTTATTT-AATTGTG
1363519 TTATTGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (21 bp):
ATAAATTTTTATTTAATTGTG
Found at i:1369799 original size:20 final size:20
Alignment explanation
Indices: 1369724--1369787 Score: 87
Period size: 19 Copynumber: 3.3 Consensus size: 20
1369714 GATGCGTAAT
1369724 AGAGGCACCAAAGTGCAAAC
1 AGAGGCACCAAAGTGCAAAC
* * *
1369744 AG-GGAACCGAAGTG-TAAC
1 AGAGGCACCAAAGTGCAAAC
1369762 AGAGGCACCAAAGTGCAAAC
1 AGAGGCACCAAAGTGCAAAC
1369782 AGAGGC
1 AGAGGC
1369788 GCCGAAATGC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 5 0.14
19 20 0.56
20 11 0.31
ACGTcount: A:0.42, C:0.22, G:0.30, T:0.06
Consensus pattern (20 bp):
AGAGGCACCAAAGTGCAAAC
Found at i:1370468 original size:17 final size:17
Alignment explanation
Indices: 1370446--1370484 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1370436 AAAATTCCCT
1370446 ATCAATTCTAA-CATTTA
1 ATCAATTC-AATCATTTA
*
1370463 ATCAATTCAATCCTTTA
1 ATCAATTCAATCATTTA
1370480 ATCAA
1 ATCAA
1370485 AAACTAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (17 bp):
ATCAATTCAATCATTTA
Found at i:1373602 original size:17 final size:16
Alignment explanation
Indices: 1373568--1373600 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1373558 TTCTCTTCTC
1373568 TATTTTCCCTTTTTTT
1 TATTTTCCCTTTTTTT
*
1373584 TATTTTCTCTTTTTTT
1 TATTTTCCCTTTTTTT
1373600 T
1 T
1373601 TAAAAGCAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TATTTTCCCTTTTTTT
Found at i:1375269 original size:40 final size:40
Alignment explanation
Indices: 1375229--1375313 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 40
1375219 TTTTAGTCAT
*
1375229 TTATTAT-TA-AATTGGTTGTTTTAATAT-TTATTATTATCA
1 TTATTATATATAATT-GCTGTTTTAA-ATGTTATTATTATCA
* *
1375268 TTATGATATATCATTGCTGTTTTAAATGTTATTATTATCA
1 TTATTATATATAATTGCTGTTTTAAATGTTATTATTATCA
1375308 TTATTA
1 TTATTA
1375314 GTTTTATTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
39 8 0.21
40 28 0.72
41 3 0.08
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (40 bp):
TTATTATATATAATTGCTGTTTTAAATGTTATTATTATCA
Found at i:1402256 original size:128 final size:128
Alignment explanation
Indices: 1402026--1402277 Score: 495
Period size: 128 Copynumber: 2.0 Consensus size: 128
1402016 GCACTTCAAA
1402026 GCTCAAACTTTTTATCCCTTGAATCTATTTCTACCCCTTTGATCTAGAACCACCTAGTCTGTATT
1 GCTCAAACTTTTTATCCCTTGAATCTATTTCTACCCCTTTGATCTAGAACCACCTAGTCTGTATT
1402091 GTGCTAAGAGTCAGATGGTATTTAGTAAAATAAGCCATATAACATTTTCTCAACAATTGAAGT
66 GTGCTAAGAGTCAGATGGTATTTAGTAAAATAAGCCATATAACATTTTCTCAACAATTGAAGT
1402154 GCTCAAACTTTTTATCCCTTGAATCTATTTCTACCCCTTTGATCTAGAACCACCTAGTCTGTATT
1 GCTCAAACTTTTTATCCCTTGAATCTATTTCTACCCCTTTGATCTAGAACCACCTAGTCTGTATT
*
1402219 GTGCTAAGAGTCAGATGGTATTTAGTAAAATATGCCATATAACATTTTCTCAACAATTG
66 GTGCTAAGAGTCAGATGGTATTTAGTAAAATAAGCCATATAACATTTTCTCAACAATTG
1402278 CCAGTAAGTT
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 123 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (128 bp):
GCTCAAACTTTTTATCCCTTGAATCTATTTCTACCCCTTTGATCTAGAACCACCTAGTCTGTATT
GTGCTAAGAGTCAGATGGTATTTAGTAAAATAAGCCATATAACATTTTCTCAACAATTGAAGT
Found at i:1403670 original size:7 final size:7
Alignment explanation
Indices: 1403658--1403687 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1403648 TATGTCTAAT
1403658 GAGAAGA
1 GAGAAGA
1403665 GAGAAGA
1 GAGAAGA
1403672 GAGAAGA
1 GAGAAGA
1403679 GAGAAGA
1 GAGAAGA
1403686 GA
1 GA
1403688 TTGGTGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
GAGAAGA
Found at i:1409205 original size:43 final size:42
Alignment explanation
Indices: 1409158--1409343 Score: 178
Period size: 43 Copynumber: 4.3 Consensus size: 42
1409148 ACGTCGCTAA
* * *
1409158 CTTTTGCGGCGTTTTTAGAAACAAACGTCGCTAAAGGTCATGA-
1 CTTTTGCGGCGCTTTT--AAACAAACGCCGCTAAAGGTCAGGAC
* *
1409201 CTTTTAGCGGCGCTTTTAAA-AAACGCCGCAAAAGGCCAGGAC
1 CTTTT-GCGGCGCTTTTAAACAAACGCCGCTAAAGGTCAGGAC
* * **
1409243 CTTTAGTGGCGCTTTTCTTACAAACGCCGCTAAAGGTCAGGAC
1 CTTTTGCGGCGCTTTT-AAACAAACGCCGCTAAAGGTCAGGAC
* * * * *
1409286 CTTTAGCGACGCTTTTATTACAAACGCCGCTAAAAGATCATGAC
1 CTTTTGCGGCGCTTTTA-AACAAACGCCGCT-AAAGGTCAGGAC
1409330 CTTTTGCGGCGCTT
1 CTTTTGCGGCGCTT
1409344 CTGCCAAAAA
Statistics
Matches: 119, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
41 27 0.23
42 8 0.07
43 52 0.44
44 32 0.27
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (42 bp):
CTTTTGCGGCGCTTTTAAACAAACGCCGCTAAAGGTCAGGAC
Found at i:1416440 original size:230 final size:230
Alignment explanation
Indices: 1416037--1418527 Score: 4626
Period size: 230 Copynumber: 10.9 Consensus size: 230
1416027 TTGCTTACCT
1416037 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1416102 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
66 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
1416167 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
131 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
1416232 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
196 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
1416267 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1416332 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
66 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
1416397 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
131 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
1416462 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
196 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
1416497 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1416562 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
66 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
1416627 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
131 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
1416692 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
196 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
1416727 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1416792 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
66 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
1416857 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
131 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
1416922 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
196 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
1416957 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1417022 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
66 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
1417087 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
131 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
1417152 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
196 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
1417187 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1417252 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
66 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
1417317 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
131 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
1417382 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
196 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
1417417 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1417482 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
66 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
1417547 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
131 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
1417612 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
196 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
1417647 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1417712 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
66 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
1417777 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
131 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
1417842 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
196 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
1417877 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1417942 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
66 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
1418007 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
131 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
1418072 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
196 AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
1418107 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
1418172 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
66 TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
* * * * *
1418237 AAGCTTAAAAAAGGGCGTCGTTGGGCTTAGG--TTTTTTTGCGGCGCTTTCCCAAAAA-TGCCGC
131 AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACT-CCGC
* * * *
1418299 TAAAACCCTGAGCATTAGCGGCGCTTT-CTTAAAAAC
195 TAAAGCCCTGGGTATTAGCGGCGCTTTAC-CAAAAAC
* * * * *
1418335 GCTGCTAAATCCCCGAAAGCTCAGAAAATGGCATCGTTGGGCTTAGGTTTTTTTGCGGCGC-TTC
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
* * * * * * * * *
1418399 CCAAAAACGCCGCTAAAGCCCT-GATCATTAGCGACGCTTTCTTATAAACTCCTCTAAATCCTCG
66 TCAAAAACGCCGCTAAAGCCTTAG-GCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCG
** *
1418463 AAAGCTC-GAGAAACGACGTCGTTGGGCTTAGG---TTTTTTGCGGCGC-TTTCTCAAAAACGCC
130 AAAGCTCAGA-AAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTC-CAAAAACTCC
1418523 GCTAA
193 GCTAA
1418528 TGCTTATTTT
Statistics
Matches: 2226, Mismatches: 29, Indels: 16
0.98 0.01 0.01
Matches are distributed among these distances:
225 3 0.00
226 28 0.01
227 83 0.04
228 115 0.05
230 1997 0.90
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (230 bp):
GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCATTGTTGGGCTTAGGTTTTTTTGCGGCGCTTTA
TCAAAAACGCCGCTAAAGCCTTAGGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGA
AAGCTCAGAAAACGGTGTCGTTGGGCTTAGGTTTTTTTTTGCGGCGCTTTTCCAAAAACTCCGCT
AAAGCCCTGGGTATTAGCGGCGCTTTACCAAAAAC
Found at i:1419658 original size:25 final size:25
Alignment explanation
Indices: 1419630--1419686 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
1419620 ATGAGCCTTT
* *
1419630 AAATCAATTTGAATAAAATAAAATC
1 AAATCAATTGGAACAAAATAAAATC
** * *
1419655 AAATTGATTGGAACCAAATCAAATC
1 AAATCAATTGGAACAAAATAAAATC
1419680 AAATCAA
1 AAATCAA
1419687 GATATATGTC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.25
Consensus pattern (25 bp):
AAATCAATTGGAACAAAATAAAATC
Found at i:1425572 original size:23 final size:24
Alignment explanation
Indices: 1425532--1425586 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
1425522 TATGGGTATA
*
1425532 AAATGTAACTTAAATTGGAATATG
1 AAATGTAACATAAATTGGAATATG
1425556 AAATGTAA-ATAAATTGGAATATG
1 AAATGTAACATAAATTGGAATATG
1425579 AAATGTAA
1 AAATGTAA
1425587 GCTAATAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.31
Consensus pattern (24 bp):
AAATGTAACATAAATTGGAATATG
Found at i:1426037 original size:37 final size:37
Alignment explanation
Indices: 1425982--1426114 Score: 144
Period size: 37 Copynumber: 3.6 Consensus size: 37
1425972 ACTCCCTGTT
* * *
1425982 TTGGTGTGTTTTCGGTTGGACTAGCTCTTTAGAGCAA
1 TTGGCGTGTTTTTGGTTGGATTAGCTCTTTAGAGCAA
* *
1426019 TTGGCGTGTTTTTGGTTGGATTAGCTCTTCAAAGCAA
1 TTGGCGTGTTTTTGGTTGGATTAGCTCTTTAGAGCAA
* * *
1426056 TTGGCGTG-TATTGGTTGGATTAACTC-TTATGAGCAT
1 TTGGCGTGTTTTTGGTTGGATTAGCTCTTTA-GAGCAA
* * *
1426092 TTGGCGTATTTTCGGATGGATTA
1 TTGGCGTGTTTTTGGTTGGATTA
1426115 CTGTGCTTGT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
35 2 0.03
36 27 0.34
37 51 0.64
ACGTcount: A:0.18, C:0.12, G:0.29, T:0.41
Consensus pattern (37 bp):
TTGGCGTGTTTTTGGTTGGATTAGCTCTTTAGAGCAA
Found at i:1438729 original size:27 final size:27
Alignment explanation
Indices: 1438699--1438753 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1438689 ACAAGTTGCA
1438699 AAGTACAAAGTGTGACAATAGATATAT
1 AAGTACAAAGTGTGACAATAGATATAT
*
1438726 AAGTACAAAGTGTGGCAATAGATATAT
1 AAGTACAAAGTGTGACAATAGATATAT
1438753 A
1 A
1438754 CATGTCTAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (27 bp):
AAGTACAAAGTGTGACAATAGATATAT
Found at i:1448014 original size:12 final size:12
Alignment explanation
Indices: 1447997--1448024 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1447987 AAAAAAAGGG
1447997 AAAATAAAGAAA
1 AAAATAAAGAAA
1448009 AAAATAAAGAAA
1 AAAATAAAGAAA
1448021 AAAA
1 AAAA
1448025 GAAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAATAAAGAAA
Found at i:1450277 original size:84 final size:83
Alignment explanation
Indices: 1450125--1450287 Score: 211
Period size: 84 Copynumber: 2.0 Consensus size: 83
1450115 TTTTGGGTAA
* * *
1450125 ATGGATTTGGTAAGATAATGACAGATTTGGTCCTTGTATTTCAACAAAAATTCTAATATAGTACT
1 ATGGATTTGGTAAGATAATGACAGACTTGGACCTTGTATTTCAACAAAAATTCTAATATAGTAAT
1450190 TTTACTTTCAAAATGTCG
66 TTTACTTTCAAAATGTCG
* * * * ** *
1450208 ATGGGTTTGGTAAGATAATGACGGCCTTGGACTTTGTACTTT-ACACAAATCTTCTAATGTAGTA
1 ATGGATTTGGTAAGATAATGACAGACTTGGACCTTGTA-TTTCA-ACAAAAATTCTAATATAGTA
1450272 ATTTTACTTTCAAAAT
64 ATTTTACTTTCAAAAT
1450288 ACCCATTAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
83 33 0.49
84 35 0.51
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.39
Consensus pattern (83 bp):
ATGGATTTGGTAAGATAATGACAGACTTGGACCTTGTATTTCAACAAAAATTCTAATATAGTAAT
TTTACTTTCAAAATGTCG
Found at i:1451521 original size:3 final size:3
Alignment explanation
Indices: 1451515--1451574 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
1451505 CGACGACGAC
* * *
1451515 GAA GAA GAA GAA GAA GAA GAG GAA GAG GAA GAA GAA GAA GAA GAA GAG
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1451563 GAA GAA GAA GAA
1 GAA GAA GAA GAA
1451575 AATGAACTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1457864 original size:14 final size:14
Alignment explanation
Indices: 1457845--1457877 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1457835 TTACCTCCGT
1457845 CCTCCACCGATCCA
1 CCTCCACCGATCCA
*
1457859 CCTCCACCGGTCCA
1 CCTCCACCGATCCA
1457873 CCTCC
1 CCTCC
1457878 GGTCTACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.61, G:0.09, T:0.15
Consensus pattern (14 bp):
CCTCCACCGATCCA
Found at i:1458177 original size:14 final size:14
Alignment explanation
Indices: 1458157--1458197 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1458147 CACCGAGCAT
1458157 CGATCCACCTCCAC
1 CGATCCACCTCCAC
* *
1458171 TGATCCACTTCCAC
1 CGATCCACCTCCAC
*
1458185 CGGTCCACCTCCA
1 CGATCCACCTCCA
1458198 GTCCTGCACC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.20, C:0.51, G:0.10, T:0.20
Consensus pattern (14 bp):
CGATCCACCTCCAC
Found at i:1458521 original size:44 final size:44
Alignment explanation
Indices: 1458468--1458573 Score: 176
Period size: 44 Copynumber: 2.4 Consensus size: 44
1458458 AAGAAGTAGA
*
1458468 GATATTGAGCATGTTTTGGGATGACTCGGTATTTTGAGTTTAGGT
1 GATA-TGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGT
1458513 GATATGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGT
1 GATATGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGT
* *
1458557 GATTTGAGCATTTTTTG
1 GATATGAGCATGTTTTG
1458574 AAAGCCTACA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
44 54 0.93
45 4 0.07
ACGTcount: A:0.21, C:0.07, G:0.29, T:0.43
Consensus pattern (44 bp):
GATATGAGCATGTTTTGGGATGACTCAGTATTTTGAGTTTAGGT
Found at i:1458861 original size:12 final size:12
Alignment explanation
Indices: 1458844--1458870 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1458834 TAGAATCTTA
1458844 ATTTTAGGAATC
1 ATTTTAGGAATC
1458856 ATTTTAGGAATC
1 ATTTTAGGAATC
1458868 ATT
1 ATT
1458871 AGCTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (12 bp):
ATTTTAGGAATC
Found at i:1462639 original size:25 final size:25
Alignment explanation
Indices: 1462593--1462651 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
1462583 TTCAGCTTAT
*
1462593 ATGAGCTTACCGATACTGAGCTCGA
1 ATGAGCTTACCGATACTAAGCTCGA
* * *
1462618 ATGAGCTTACCGTTATTAAGCTTGA
1 ATGAGCTTACCGATACTAAGCTCGA
*
1462643 AGGAGCTTA
1 ATGAGCTTA
1462652 TTGATTACAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (25 bp):
ATGAGCTTACCGATACTAAGCTCGA
Found at i:1463152 original size:17 final size:17
Alignment explanation
Indices: 1463130--1463165 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1463120 TTATAGTGAT
1463130 TTGGAAGCTCGTTCGAG
1 TTGGAAGCTCGTTCGAG
* *
1463147 TTGGAAGCTTGTTGGAG
1 TTGGAAGCTCGTTCGAG
1463164 TT
1 TT
1463166 ATATCACACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.11, G:0.36, T:0.36
Consensus pattern (17 bp):
TTGGAAGCTCGTTCGAG
Found at i:1465589 original size:25 final size:24
Alignment explanation
Indices: 1465561--1465620 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
1465551 AAAATATTTT
* *
1465561 GGTTTAAAAATAATTAAAAACTAA
1 GGTTTAAAAATAAGTAAAAAATAA
*
1465585 GGGTTAAAAACTAAGTAAAAAATAA
1 GGTTTAAAAA-TAAGTAAAAAATAA
1465610 --TTTAAAAATAA
1 GGTTTAAAAATAA
1465621 AAAGGTTCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 3 0.10
23 7 0.23
24 9 0.29
25 12 0.39
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.27
Consensus pattern (24 bp):
GGTTTAAAAATAAGTAAAAAATAA
Found at i:1465616 original size:11 final size:11
Alignment explanation
Indices: 1465564--1465620 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
1465554 ATATTTTGGT
1465564 TTAAAAATAA-
1 TTAAAAATAAG
1465574 TTAAAAACTAAGGG
1 TTAAAAA-TAA--G
1465588 TTAAAAACTAAG
1 TTAAAAA-TAAG
* *
1465600 TAAAAAATAAT
1 TTAAAAATAAG
1465611 TTAAAAATAA
1 TTAAAAATAA
1465621 AAAGGTTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 7 0.17
11 15 0.38
12 7 0.17
14 11 0.28
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (11 bp):
TTAAAAATAAG
Found at i:1485549 original size:37 final size:37
Alignment explanation
Indices: 1485503--1485646 Score: 137
Period size: 37 Copynumber: 4.1 Consensus size: 37
1485493 ATTCGAAAAA
1485503 TAATA-TTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATACTTATTTTAATAGTATT-ATATT-AATTTAATAT
*
1485539 TAATACTTATTTTAATAGTATTTTATTAATTTAATAT
1 TAATACTTATTTTAATAGTATTATATTAATTTAATAT
* * **
1485576 TAA-AGTGA--TT-ATCCTA--ATATTAAATTTAAT-T
1 TAATACTTATTTTAATAGTATTATATT-AATTTAATAT
*
1485607 TAATACTTATTTTAATAGTATTTTATTAATTTAATAT
1 TAATACTTATTTTAATAGTATTATATTAATTTAATAT
1485644 TAA
1 TAA
1485647 AGTGATTAAG
Statistics
Matches: 86, Mismatches: 11, Indels: 21
0.73 0.09 0.18
Matches are distributed among these distances:
31 8 0.09
32 11 0.13
33 4 0.05
34 4 0.05
35 4 0.05
36 24 0.28
37 29 0.34
38 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (37 bp):
TAATACTTATTTTAATAGTATTATATTAATTTAATAT
Found at i:1485570 original size:31 final size:31
Alignment explanation
Indices: 1485533--1485642 Score: 105
Period size: 31 Copynumber: 3.4 Consensus size: 31
1485523 AATATTAAAT
1485533 TTAATTTAATACTTATTTTAATAGTATTTTA
1 TTAATTTAATACTTATTTTAATAGTATTTTA
** * **
1485564 TTAATTTAATA-TTAAAGTGATTATCCTAATATTAAA
1 TTAATTTAATACTT--A-T--TT-TAATAGTATTTTA
1485600 TTTAATTTAATACTTATTTTAATAGTATTTTA
1 -TTAATTTAATACTTATTTTAATAGTATTTTA
1485632 TTAATTTAATA
1 TTAATTTAATA
1485643 TTAAAGTGAT
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
30 2 0.03
31 22 0.36
32 9 0.15
33 3 0.05
35 3 0.05
36 9 0.15
37 11 0.18
38 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (31 bp):
TTAATTTAATACTTATTTTAATAGTATTTTA
Found at i:1485576 original size:11 final size:11
Alignment explanation
Indices: 1485503--1485646 Score: 61
Period size: 12 Copynumber: 12.8 Consensus size: 11
1485493 ATTCGAAAAA
*
1485503 TAATATTATTT
1 TAATATTAATT
1485514 TAATAGTTTAATAT
1 TAATA--TTAAT-T
1485528 TAA-ATTTAATT
1 TAATA-TTAATT
*
1485539 TAATACTTATTT
1 TAATA-TTAATT
*
1485551 TAATAGT-ATT
1 TAATATTAATT
1485561 T--TATTAATT
1 TAATATTAATT
*
1485570 TAATATTAAAGT
1 TAATATT-AATT
* *
1485582 GATTATCCTAATAT
1 TAATAT--TAAT-T
1485596 TAA-ATTTAATT
1 TAATA-TTAATT
*
1485607 TAATACTTATTT
1 TAATA-TTAATT
*
1485619 TAATAGT-ATT
1 TAATATTAATT
1485629 T--TATTAATT
1 TAATATTAATT
1485638 TAATATTAA
1 TAATATTAA
1485647 AGTGATTAAG
Statistics
Matches: 100, Mismatches: 17, Indels: 32
0.67 0.11 0.21
Matches are distributed among these distances:
8 6 0.06
9 8 0.08
10 6 0.06
11 25 0.25
12 39 0.39
13 8 0.08
14 8 0.08
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (11 bp):
TAATATTAATT
Found at i:1485586 original size:20 final size:18
Alignment explanation
Indices: 1485504--1485611 Score: 62
Period size: 19 Copynumber: 5.8 Consensus size: 18
1485494 TTCGAAAAAT
* *
1485504 AATATTATTTTAATAGTTT
1 AATATTAATTTAATA-TTA
1485523 AATATTAAATTTAAT-TT-
1 AATATT-AATTTAATATTA
* *
1485540 AATACTTATTTTAATAGTA
1 AATA-TTAATTTAATATTA
**
1485559 TTTTATTAATTTAATATTA
1 -AATATTAATTTAATATTA
*
1485578 AAGTGATT-ATCCTAATATTA
1 AA-T-ATTAAT-TTAATATTA
1485598 AAT-TTAATTTAATA
1 AATATTAATTTAATA
1485612 CTTATTTTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
17 18 0.26
18 7 0.10
19 22 0.32
20 22 0.32
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (18 bp):
AATATTAATTTAATATTA
Found at i:1485599 original size:68 final size:68
Alignment explanation
Indices: 1485522--1485654 Score: 266
Period size: 68 Copynumber: 2.0 Consensus size: 68
1485512 TTTAATAGTT
1485522 TAATATTAAATTTAATTTAATACTTATTTTAATAGTATTTTATTAATTTAATATTAAAGTGATTA
1 TAATATTAAATTTAATTTAATACTTATTTTAATAGTATTTTATTAATTTAATATTAAAGTGATTA
1485587 TCC
66 TCC
1485590 TAATATTAAATTTAATTTAATACTTATTTTAATAGTATTTTATTAATTTAATATTAAAGTGATTA
1 TAATATTAAATTTAATTTAATACTTATTTTAATAGTATTTTATTAATTTAATATTAAAGTGATTA
1485655 AGTTAAATCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (68 bp):
TAATATTAAATTTAATTTAATACTTATTTTAATAGTATTTTATTAATTTAATATTAAAGTGATTA
TCC
Found at i:1493653 original size:202 final size:203
Alignment explanation
Indices: 1493297--1493702 Score: 805
Period size: 202 Copynumber: 2.0 Consensus size: 203
1493287 TAATATTAAA
1493297 GTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCCTTATATAAAGAGAGCCTTAGCTCAT
1 GTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCCTTATATAAAGAGAGCCTTAGCTCAT
1493362 TATTTCACACACTTGAATTTAAGAGAAAGTTGTAGAGAGAAAAATCTTTTAAGAGATTATTCCAA
66 TATTTCACACACTTGAATTTAAGAGAAAGTTGTAGAGAGAAAAATCTTTTAAGAGATTATTCCAA
1493427 AAAATTTGTAAAGATATTTTTCTGATTTACAACTTAACCCAAAATTTTAAAGAAATTACAAAATT
131 AAAATTTGTAAAGATATTTTTCTGATTTACAACTTAACCCAAAATTTTAAAGAAATTACAAAATT
1493492 ACCCCATT
196 ACCCCATT
1493500 GTGATTAAG-TTAATCATAGTTGAACTCTCTAAACTCTCCTTATATAAAGAGAGCCTTAGCTCAT
1 GTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCCTTATATAAAGAGAGCCTTAGCTCAT
1493564 TATTTCACACACTTGAATTTAAGAGAAAGTTGTAGAGAGAAAAATCTTTTAAGAGATTATTCCAA
66 TATTTCACACACTTGAATTTAAGAGAAAGTTGTAGAGAGAAAAATCTTTTAAGAGATTATTCCAA
1493629 AAAATTTGTAAAGATATTTTTCTGATTTACAACTTAACCCAAAATTTTAAAGAAATTACAAAATT
131 AAAATTTGTAAAGATATTTTTCTGATTTACAACTTAACCCAAAATTTTAAAGAAATTACAAAATT
1493694 ACCCCATT
196 ACCCCATT
1493702 G
1 G
1493703 GTAATTTTGT
Statistics
Matches: 203, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
202 194 0.96
203 9 0.04
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (203 bp):
GTGATTAAGTTTAATCATAGTTGAACTCTCTAAACTCTCCTTATATAAAGAGAGCCTTAGCTCAT
TATTTCACACACTTGAATTTAAGAGAAAGTTGTAGAGAGAAAAATCTTTTAAGAGATTATTCCAA
AAAATTTGTAAAGATATTTTTCTGATTTACAACTTAACCCAAAATTTTAAAGAAATTACAAAATT
ACCCCATT
Found at i:1497166 original size:9 final size:9
Alignment explanation
Indices: 1497152--1497198 Score: 76
Period size: 9 Copynumber: 5.2 Consensus size: 9
1497142 GTAGTGATTC
1497152 AATTCGGTT
1 AATTCGGTT
*
1497161 AATTCGGGT
1 AATTCGGTT
1497170 AATTCGGTT
1 AATTCGGTT
*
1497179 AATTTGGTT
1 AATTCGGTT
1497188 AATTCGGTT
1 AATTCGGTT
1497197 AA
1 AA
1497199 CAGATAGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:1501187 original size:9 final size:9
Alignment explanation
Indices: 1501175--1501201 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1501165 TGTTCTTGAT
1501175 GTTAGTTAA
1 GTTAGTTAA
1501184 GTTAGTTAA
1 GTTAGTTAA
1501193 GTTAGTTAA
1 GTTAGTTAA
1501202 CACTGTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (9 bp):
GTTAGTTAA
Found at i:1513994 original size:22 final size:22
Alignment explanation
Indices: 1513969--1514013 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1513959 ATTTGTTTGT
1513969 TTGCATATTTCGAAAATAATCC
1 TTGCATATTTCGAAAATAATCC
1513991 TTGCATATTTCGAAAATAATCC
1 TTGCATATTTCGAAAATAATCC
1514013 T
1 T
1514014 ACTCTGCGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.38
Consensus pattern (22 bp):
TTGCATATTTCGAAAATAATCC
Found at i:1521540 original size:8 final size:8
Alignment explanation
Indices: 1521527--1521554 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1521517 AATCATTAAC
1521527 TTTAAATG
1 TTTAAATG
1521535 TTTAAATG
1 TTTAAATG
1521543 TTTAAATG
1 TTTAAATG
1521551 TTTA
1 TTTA
1521555 TGTAAGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (8 bp):
TTTAAATG
Found at i:1523706 original size:25 final size:25
Alignment explanation
Indices: 1523618--1523712 Score: 111
Period size: 25 Copynumber: 3.8 Consensus size: 25
1523608 GATGCAGCAA
* * *
1523618 AGGAGTGTCGACGGTC-ATGCGGCAA
1 AGGAGTGTTGACGG-CGATGCGACAG
*
1523643 AGGAGTGTTGACGGCAATGCGACAG
1 AGGAGTGTTGACGGCGATGCGACAG
*
1523668 AGGAGTGTTGACGGCGATGTGACAG
1 AGGAGTGTTGACGGCGATGCGACAG
**
1523693 AGGAGTGTCAACGGCGATGC
1 AGGAGTGTTGACGGCGATGC
1523713 AGTATAGGGG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
24 1 0.02
25 60 0.98
ACGTcount: A:0.25, C:0.17, G:0.41, T:0.17
Consensus pattern (25 bp):
AGGAGTGTTGACGGCGATGCGACAG
Found at i:1523835 original size:34 final size:35
Alignment explanation
Indices: 1523751--1523839 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 35
1523741 GTAGACGGTC
* * ** *
1523751 GGGGAAAATC-TAAGGGATTTGGGGAGTTTTGATTT
1 GGGGAAAAACATAAGGGATTCGGGGAAATTT-ATTA
1523786 GGGGAAAAA-ATTAAGGGATTCGGGGAAATTT-TTA
1 GGGGAAAAACA-TAAGGGATTCGGGGAAATTTATTA
1523820 GGGGAAAAACATAAGGGATT
1 GGGGAAAAACATAAGGGATT
1523840 TCGTGGATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 20 0.43
35 9 0.20
36 17 0.37
ACGTcount: A:0.35, C:0.03, G:0.35, T:0.27
Consensus pattern (35 bp):
GGGGAAAAACATAAGGGATTCGGGGAAATTTATTA
Found at i:1523991 original size:41 final size:41
Alignment explanation
Indices: 1523915--1524069 Score: 204
Period size: 41 Copynumber: 3.8 Consensus size: 41
1523905 TGATTAAAAC
* * *
1523915 GCCGCTATTGCTT-ACCTTTTGCAGCATTTTTCTCATAAAT
1 GCCGCTACTGCTTGACCTTTTGCGGCGTTTTTCTCATAAAT
* * *
1523955 GCCGCTACTGCTTGACTTTTTGCGGCGTTTTCCTCATAAAC
1 GCCGCTACTGCTTGACCTTTTGCGGCGTTTTTCTCATAAAT
*
1523996 GCCACTACTGCTTGACCTTTTGCGGCGTTTTTCTCATAAAT
1 GCCGCTACTGCTTGACCTTTTGCGGCGTTTTTCTCATAAAT
* * * *
1524037 GCCGCTACTACTTTACCTATTGCGGCATTTTTC
1 GCCGCTACTGCTTGACCTTTTGCGGCGTTTTTC
1524070 CATTAGCGCC
Statistics
Matches: 99, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 12 0.12
41 87 0.88
ACGTcount: A:0.17, C:0.28, G:0.16, T:0.39
Consensus pattern (41 bp):
GCCGCTACTGCTTGACCTTTTGCGGCGTTTTTCTCATAAAT
Found at i:1525096 original size:2 final size:2
Alignment explanation
Indices: 1525089--1525118 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1525079 CTATTGAGAA
*
1525089 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1525119 GGAATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1536803 original size:21 final size:22
Alignment explanation
Indices: 1536762--1536803 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1536752 ATATTATTAG
*
1536762 ATTAAATTTAATATTAAATTTT
1 ATTAAATTTAATATGAAATTTT
1536784 ATTAAA-TTAATA-GAATATTT
1 ATTAAATTTAATATGAA-ATTT
1536804 ATCTACATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.56
22 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAAATTTAATATGAAATTTT
Found at i:1536880 original size:39 final size:37
Alignment explanation
Indices: 1536832--1536904 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 37
1536822 AAATTAAATT
1536832 TAATATTAAGAT-AGTCACTTTAATATTAAATTAATAAAA
1 TAATATTAAGATAAGT-A-TTTAAT-TTAAATTAATAAAA
*
1536871 TAATATTAAGATAAGTATTTAATTTAATTTAATA
1 TAATATTAAGATAAGTATTTAATTTAAATTAATA
1536905 TTAAATCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 10 0.31
38 6 0.19
39 13 0.41
40 3 0.09
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.42
Consensus pattern (37 bp):
TAATATTAAGATAAGTATTTAATTTAAATTAATAAAA
Found at i:1536893 original size:19 final size:20
Alignment explanation
Indices: 1536828--1536897 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 20
1536818 CATTAAATTA
1536828 AATTTAATATTAAGAT-AGT
1 AATTTAATATTAAGATAAGT
*
1536847 CACTTTAATATTAA-ATTAA-T
1 -AATTTAATATTAAGA-TAAGT
**
1536867 AAAATAATATTAAGATAAGT
1 AATTTAATATTAAGATAAGT
1536887 -ATTTAAT-TTAA
1 AATTTAATATTAA
1536898 TTTAATATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 4 0.10
19 19 0.47
20 16 0.40
21 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (20 bp):
AATTTAATATTAAGATAAGT
Found at i:1538909 original size:16 final size:16
Alignment explanation
Indices: 1538888--1538921 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1538878 TTTCATCATA
1538888 ATCACAATACAATGTT
1 ATCACAATACAATGTT
*
1538904 ATCACAATATAATGTT
1 ATCACAATACAATGTT
1538920 AT
1 AT
1538922 TGCTTCTTTC
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:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (16 bp):
ATCACAATACAATGTT
Found at i:1541828 original size:13 final size:12
Alignment explanation
Indices: 1541806--1541839 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1541796 TTGATCCTCA
1541806 CTTTTCTTTTTT
1 CTTTTCTTTTTT
*
1541818 TTTTTCATTTTTT
1 CTTTTC-TTTTTT
1541831 CTTTTCTTT
1 CTTTTCTTT
1541840 AAGCACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (12 bp):
CTTTTCTTTTTT
Found at i:1549836 original size:3 final size:3
Alignment explanation
Indices: 1549828--1549855 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1549818 CTTGAATTCA
1549828 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1549856 CTCCTCTGAT
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):
AAT
Found at i:1550433 original size:27 final size:27
Alignment explanation
Indices: 1550401--1550454 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
1550391 ATTTATGAGA
*
1550401 ATGCACCAGTAATTTTGCCATATTTAT
1 ATGCACCACTAATTTTGCCATATTTAT
1550428 ATGCACCACTAATTTTGCCATATTTAT
1 ATGCACCACTAATTTTGCCATATTTAT
1550455 TGAATTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (27 bp):
ATGCACCACTAATTTTGCCATATTTAT
Found at i:1550530 original size:30 final size:32
Alignment explanation
Indices: 1550467--1550528 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 32
1550457 AATTTTGTGC
*
1550467 AGGAATACAATTTGGGGCTAAATAGAAGAAAA
1 AGGAATACAATTTGGGGCCAAATAGAAGAAAA
*
1550499 AGGAA-ACAA-TT-GGGCCAAATTGAAGAAAA
1 AGGAATACAATTTGGGGCCAAATAGAAGAAAA
1550528 A
1 A
1550529 AGCAAAGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 17 0.61
30 2 0.07
31 4 0.14
32 5 0.18
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (32 bp):
AGGAATACAATTTGGGGCCAAATAGAAGAAAA
Found at i:1559432 original size:20 final size:18
Alignment explanation
Indices: 1559385--1559433 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
1559375 CAAGATAAAC
1559385 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
1559402 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
1559422 ATTAAATTAATA
1 ATTAAATTAATA
1559434 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:1559928 original size:19 final size:19
Alignment explanation
Indices: 1559895--1559934 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1559885 AAAATAGCAT
*
1559895 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
1559914 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
1559933 AT
1 AT
1559935 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:1560897 original size:362 final size:362
Alignment explanation
Indices: 1560232--1560955 Score: 1448
Period size: 362 Copynumber: 2.0 Consensus size: 362
1560222 ACTTAATCAT
1560232 AGGGGCAGTCCACAAGAAGTACCATGATTGAAAACTCCTTATTGTATACTCTTTACGAAAGCAAT
1 AGGGGCAGTCCACAAGAAGTACCATGATTGAAAACTCCTTATTGTATACTCTTTACGAAAGCAAT
1560297 TCATCCAGCTGGTTTGTCCAATGACCTCGTCATGTGTGTGTTACCCTCATATGATATCCTTGATT
66 TCATCCAGCTGGTTTGTCCAATGACCTCGTCATGTGTGTGTTACCCTCATATGATATCCTTGATT
1560362 CCTTTGAGTTAAATATGTCCACTCAATACAATCCTATTTTCTCTCATTGTCACCATTGTGTCTTC
131 CCTTTGAGTTAAATATGTCCACTCAATACAATCCTATTTTCTCTCATTGTCACCATTGTGTCTTC
1560427 TTAATGATAAATATGATCATTTTCAACAAATGACTGTAATAAATTGCTCGTTCGAGAACAAGTAA
196 TTAATGATAAATATGATCATTTTCAACAAATGACTGTAATAAATTGCTCGTTCGAGAACAAGTAA
1560492 CCCGTGGTCACATTCCATATTCATCAATCCACACAATGCCAATGAATTCTACTATTGAATTCTAC
261 CCCGTGGTCACATTCCATATTCATCAATCCACACAATGCCAATGAATTCTACTATTGAATTCTAC
1560557 TGTTGCTAGTAAAACCATGCCATACACAAGTCATGTA
326 TGTTGCTAGTAAAACCATGCCATACACAAGTCATGTA
1560594 AGGGGCAGTCCACAAGAAGTACCATGATTGAAAACTCCTTATTGTATACTCTTTACGAAAGCAAT
1 AGGGGCAGTCCACAAGAAGTACCATGATTGAAAACTCCTTATTGTATACTCTTTACGAAAGCAAT
1560659 TCATCCAGCTGGTTTGTCCAATGACCTCGTCATGTGTGTGTTACCCTCATATGATATCCTTGATT
66 TCATCCAGCTGGTTTGTCCAATGACCTCGTCATGTGTGTGTTACCCTCATATGATATCCTTGATT
1560724 CCTTTGAGTTAAATATGTCCACTCAATACAATCCTATTTTCTCTCATTGTCACCATTGTGTCTTC
131 CCTTTGAGTTAAATATGTCCACTCAATACAATCCTATTTTCTCTCATTGTCACCATTGTGTCTTC
1560789 TTAATGATAAATATGATCATTTTCAACAAATGACTGTAATAAATTGCTCGTTCGAGAACAAGTAA
196 TTAATGATAAATATGATCATTTTCAACAAATGACTGTAATAAATTGCTCGTTCGAGAACAAGTAA
1560854 CCCGTGGTCACATTCCATATTCATCAATCCACACAATGCCAATGAATTCTACTATTGAATTCTAC
261 CCCGTGGTCACATTCCATATTCATCAATCCACACAATGCCAATGAATTCTACTATTGAATTCTAC
1560919 TGTTGCTAGTAAAACCATGCCATACACAAGTCATGTA
326 TGTTGCTAGTAAAACCATGCCATACACAAGTCATGTA
1560956 CCTAACATAT
Statistics
Matches: 362, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
362 362 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (362 bp):
AGGGGCAGTCCACAAGAAGTACCATGATTGAAAACTCCTTATTGTATACTCTTTACGAAAGCAAT
TCATCCAGCTGGTTTGTCCAATGACCTCGTCATGTGTGTGTTACCCTCATATGATATCCTTGATT
CCTTTGAGTTAAATATGTCCACTCAATACAATCCTATTTTCTCTCATTGTCACCATTGTGTCTTC
TTAATGATAAATATGATCATTTTCAACAAATGACTGTAATAAATTGCTCGTTCGAGAACAAGTAA
CCCGTGGTCACATTCCATATTCATCAATCCACACAATGCCAATGAATTCTACTATTGAATTCTAC
TGTTGCTAGTAAAACCATGCCATACACAAGTCATGTA
Found at i:1561464 original size:16 final size:16
Alignment explanation
Indices: 1561443--1561473 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1561433 CCATGCATGC
*
1561443 AAAATATAAAAGACAG
1 AAAATAAAAAAGACAG
1561459 AAAATAAAAAAGACA
1 AAAATAAAAAAGACA
1561474 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.06, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATAAAAAAGACAG
Found at i:1569902 original size:17 final size:18
Alignment explanation
Indices: 1569869--1569904 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1569859 TAATGGGCAC
*
1569869 CTAAAACTGGTTTAAGCA
1 CTAAAAATGGTTTAAGCA
1569887 CTAAAAATGG-TTAAGCA
1 CTAAAAATGGTTTAAGCA
1569904 C
1 C
1569905 ATGACATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (18 bp):
CTAAAAATGGTTTAAGCA
Found at i:1577743 original size:22 final size:21
Alignment explanation
Indices: 1577713--1577822 Score: 103
Period size: 22 Copynumber: 5.0 Consensus size: 21
1577703 GCTTGTACAG
*
1577713 GATTTGCACTGTGGTGCCTACT
1 GATTCGCACT-TGGTGCCTACT
*
1577735 GATTCGCACTTCGGTGCCTATT
1 GATTCGCACTT-GGTGCCTACT
* * *
1577757 GCTTCACACTACGGTGCCTACT
1 GATTCGCACT-TGGTGCCTACT
*
1577779 GATTCGCACTTTGATGCCTACT
1 GATTCGCAC-TTGGTGCCTACT
* *
1577801 GTTTAGCACTTCGGTGCCTACT
1 GATTCGCACTT-GGTGCCTACT
1577823 ACTGTGGTAT
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
21 3 0.04
22 67 0.94
23 1 0.01
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.35
Consensus pattern (21 bp):
GATTCGCACTTGGTGCCTACT
Found at i:1577788 original size:44 final size:44
Alignment explanation
Indices: 1577725--1577822 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
1577715 TTTGCACTGT
* *
1577725 GGTGCCTACTGATTCGCACTTCGGTGCCTATTGCTTCA-CACTAC
1 GGTGCCTACTGATTCGCACTTCGATGCCTACTG-TTCAGCACTAC
* * *
1577769 GGTGCCTACTGATTCGCACTTTGATGCCTACTGTTTAGCACTTC
1 GGTGCCTACTGATTCGCACTTCGATGCCTACTGTTCAGCACTAC
1577813 GGTGCCTACT
1 GGTGCCTACT
1577823 ACTGTGGTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 3 0.06
44 45 0.94
ACGTcount: A:0.15, C:0.30, G:0.21, T:0.34
Consensus pattern (44 bp):
GGTGCCTACTGATTCGCACTTCGATGCCTACTGTTCAGCACTAC
Found at i:1609646 original size:18 final size:19
Alignment explanation
Indices: 1609623--1609659 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1609613 ATATTTATTT
1609623 TTTGTTT-ATTTATTTTTA
1 TTTGTTTAATTTATTTTTA
*
1609641 TTTGTTTAATTTCTTTTTA
1 TTTGTTTAATTTATTTTTA
1609660 GGTCGTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTGTTTAATTTATTTTTA
Found at i:1617617 original size:19 final size:19
Alignment explanation
Indices: 1617593--1617635 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1617583 CTGAAAAGAA
*
1617593 AATAAAAG-AGAAACTAAAT
1 AATAAAAGAAGAAAAT-AAT
1617612 AAT-AAAGAAGAAAATAAT
1 AATAAAAGAAGAAAATAAT
1617630 AATAAA
1 AATAAA
1617636 GTGAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (19 bp):
AATAAAAGAAGAAAATAAT
Found at i:1618676 original size:36 final size:36
Alignment explanation
Indices: 1618624--1618697 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
1618614 AGTAAACTCT
* * *
1618624 ATTCAGTTAAGTAGCCTTTCGGGTCAATTCTGACTG
1 ATTCAGTTAAGCAGCCTTTCAGATCAATTCTGACTG
* *
1618660 ATTCAGTTGAGCAGCCTTTCAGATCTATTCTGACTG
1 ATTCAGTTAAGCAGCCTTTCAGATCAATTCTGACTG
1618696 AT
1 AT
1618698 GCGCTCCTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (36 bp):
ATTCAGTTAAGCAGCCTTTCAGATCAATTCTGACTG
Found at i:1628957 original size:29 final size:28
Alignment explanation
Indices: 1628924--1628998 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
1628914 CCAATTTACT
1628924 ATATAATATGATATATTAATT-TTAATTTG
1 ATATAAT-T-ATATATTAATTATTAATTTG
* *
1628953 ATATAATTATCTATTAATTAATTAATTTTA
1 ATATAATTATATATTAATT-ATTAA-TTTG
*
1628983 ATTTAATTATATATTA
1 ATATAATTATATATTA
1628999 GAGTATTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
27 10 0.26
28 1 0.03
29 11 0.28
30 17 0.44
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (28 bp):
ATATAATTATATATTAATTATTAATTTG
Found at i:1629360 original size:52 final size:52
Alignment explanation
Indices: 1629282--1629385 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
1629272 AGCGAGTATC
*
1629282 GTCTCAAGAGAGTAATTTGATCTGCACCTCAATCTTTGTCACCCTATTTTAA
1 GTCTCAAGAGAGCAATTTGATCTGCACCTCAATCTTTGTCACCCTATTTTAA
1629334 GTCTCAAGAGAGCAATTTGATCTGCACCTCAATCTTTGTCACCCTATTTTAA
1 GTCTCAAGAGAGCAATTTGATCTGCACCTCAATCTTTGTCACCCTATTTTAA
1629386 CTATCAAAGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (52 bp):
GTCTCAAGAGAGCAATTTGATCTGCACCTCAATCTTTGTCACCCTATTTTAA
Found at i:1635541 original size:40 final size:40
Alignment explanation
Indices: 1635464--1635539 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
1635454 TAGAAATTTT
* *
1635464 CGCTAAAGATCGAGCATTAACAGCGTTTTTTGAAAAACGC
1 CGCTAAAAATCGAGCATTAACAGCGTTTTTCGAAAAACGC
*
1635504 CGCTAAAAAT-GAGCATTAGC-GACGTTTTTCGAAAAA
1 CGCTAAAAATCGAGCATTAACAG-CGTTTTTCGAAAAA
1635540 ACTCCGCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.03
39 22 0.69
40 9 0.28
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (40 bp):
CGCTAAAAATCGAGCATTAACAGCGTTTTTCGAAAAACGC
Found at i:1635648 original size:41 final size:41
Alignment explanation
Indices: 1635587--1635858 Score: 323
Period size: 41 Copynumber: 6.7 Consensus size: 41
1635577 TGACCTTTTA
1635587 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* * * ***
1635628 AGGTTTTAGCGGCATTTTTGAAAAAGCATTGC--ATGCTCG
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* * * *
1635667 GGGCTTTAGAGGCGTTTTTAAAAAAGTGCTGCTAATGCTCG
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* * * * *
1635708 GGGCTTTAGCTGTGTTTTTAAAAAAGCACCGCTAATGCTAG
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* *
1635749 GGGATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTAG
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
* ** * *
1635790 GGGATTTAATGGCATTTTTGAAAAATCGCCGCTAATGCTCG
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
*
1635831 GGGCTTTAGCAGCGTTTTTGAAAAAGCG
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCG
1635859 TCGCAAAAAA
Statistics
Matches: 192, Mismatches: 37, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
39 31 0.16
41 161 0.84
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCG
Found at i:1636289 original size:14 final size:14
Alignment explanation
Indices: 1636272--1636305 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1636262 GATTTAAGGT
1636272 TTAGGGGTT-AGACG
1 TTAGGGGTTAAGA-G
1636286 TTAGGGGTTAAGAG
1 TTAGGGGTTAAGAG
1636300 TTAGGG
1 TTAGGG
1636306 ATTTAGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.24, C:0.03, G:0.44, T:0.29
Consensus pattern (14 bp):
TTAGGGGTTAAGAG
Found at i:1641053 original size:20 final size:21
Alignment explanation
Indices: 1641030--1641068 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1641020 TAAATTTCAA
1641030 TTTAACCAAAAA-TATTTATT
1 TTTAACCAAAAATTATTTATT
*
1641050 TTTACCCAAAAATTATTTA
1 TTTAACCAAAAATTATTTA
1641069 AAACCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAACCAAAAATTATTTATT
Found at i:1642838 original size:40 final size:40
Alignment explanation
Indices: 1642783--1642861 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
1642773 GTGTCCAGGA
*
1642783 TTGTTCTAATTGTTATCACTTTCTACAGCAGATTAAAAGC
1 TTGTTCTAATTGTTATCACTTTCTACAGCAGATGAAAAGC
1642823 TTGTTCTAATTGTTATCACTTTCTACAGCAGATGAAAAG
1 TTGTTCTAATTGTTATCACTTTCTACAGCAGATGAAAAG
1642862 TTGAGCTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (40 bp):
TTGTTCTAATTGTTATCACTTTCTACAGCAGATGAAAAGC
Found at i:1653570 original size:15 final size:15
Alignment explanation
Indices: 1653534--1653572 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1653524 GCAAATATCG
*
1653534 TGATAACAAATACAA
1 TGATAATAAATACAA
1653549 T-AGTAATAAATACAA
1 TGA-TAATAAATACAA
1653564 TGATAATAA
1 TGATAATAA
1653573 TTTTAACGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.26
Consensus pattern (15 bp):
TGATAATAAATACAA
Found at i:1653901 original size:16 final size:17
Alignment explanation
Indices: 1653870--1653902 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1653860 ATTAGTTGAA
1653870 AAAAATATAAATATGTAC
1 AAAAATAT-AATATGTAC
1653888 AAAAATAT-ATATGTA
1 AAAAATATAATATGTA
1653903 TATAGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (17 bp):
AAAAATATAATATGTAC
Found at i:1655422 original size:44 final size:44
Alignment explanation
Indices: 1655359--1655906 Score: 231
Period size: 44 Copynumber: 12.8 Consensus size: 44
1655349 TTTGATGTGA
**
1655359 TCTGCTCTGCTGCAACTTCAGAGAGATAAGACTTGCCTACTTAG
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGCCTACTTAG
* * * * * *
1655403 TCTGCTCCACTTCAACTTCAGGGAGATAAGACTAG-ATGC-GA-
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGCCTACTTAG
* * * * * *
1655444 TCTACT-CTCTGCAACTTCAGAAAGATAAGA--T-CCAAGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGCCTA---CTTAG
** * * *
1655487 TCCACTCCACTGCAACTTCATGA-AGATAGGATTTGCTTACTTAG
1 TCTGCTCCACTGCAACTTCA-GAGAGATAAGACTTGCCTACTTAG
* * * * *
1655531 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGC-GA-
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGCCTACTTAG
* * * *
1655572 TCTGCT-CTCTGCAACTTCAGAGAGATAAGA--T-CCAAGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGCCTA---CTTAG
** * * *
1655615 TCCACTCCACTGCAACTTCATGA-AGATAGGATTTGCTTACTTAG
1 TCTGCTCCACTGCAACTTCA-GAGAGATAAGACTTGCCTACTTAG
* * *
1655659 --T--T---CTGCAACTTCAGGGAGATAAGATTTG-CTATCTTCAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGCCTA-CTT-AG
*
1655697 TCTGC-CTCACTGCAACTTCAG-GAGGATAAGACTTTCCTACTTAG
1 TCTGCTC-CACTGCAACTTCAGAGA-GATAAGACTTGCCTACTTAG
* * * * *
1655741 TCTGCTCCATTGCAACTTCAGGGAGATAAGATTATCGGCT--TTAA
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACT-T-GCCTACTTAG
* * * * * * *
1655785 CCTGCTCCACTACAACTTTAGGGAGATAAGATTTTCC-ATCTTCAT
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGCCTA-CTT-AG
* *
1655830 TCTGC-CTCACTGCAACTTCA-AAAGGATAAGACTTGCTTACTTAG
1 TCTGCTC-CACTGCAACTTCAGAGA-GATAAGACTTGCCTACTTAG
* * *
1655874 TCTACTCCACTACAACTTCAGGGAGATAAGACT
1 TCTGCTCCACTGCAACTTCAGAGAGATAAGACT
1655907 AGATGCGATA
Statistics
Matches: 371, Mismatches: 84, Indels: 98
0.67 0.15 0.18
Matches are distributed among these distances:
36 3 0.01
37 25 0.07
38 1 0.00
40 44 0.12
41 11 0.03
42 5 0.01
43 15 0.04
44 192 0.52
45 63 0.17
46 8 0.02
47 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGCCTACTTAG
Found at i:1655598 original size:128 final size:128
Alignment explanation
Indices: 1655368--1655664 Score: 515
Period size: 128 Copynumber: 2.3 Consensus size: 128
1655358 ATCTGCTCTG
* * * *
1655368 CTGCAACTTCA-GAGAGATAAGACTTGCCTACTTAGTCTGCTCCACTTCAACTTCAGGGAGATAA
1 CTGCAACTTCATGA-AGATAGGATTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA
1655432 GACTAGATGCGATCTACTCTCTGCAACTTCAGAAAGATAAGATCCAAGGTTTTAATCCACTCCA
65 GACTAGATGCGATCTACTCTCTGCAACTTCAGAAAGATAAGATCCAAGGTTTTAATCCACTCCA
1655496 CTGCAACTTCATGAAGATAGGATTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
1 CTGCAACTTCATGAAGATAGGATTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
* *
1655561 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCACTCCA
66 ACTAGATGCGATCTACTCTCTGCAACTTCAGAAAGATAAGATCCAAGGTTTTAATCCACTCCA
1655624 CTGCAACTTCATGAAGATAGGATTTGCTTACTTAGTTCTGC
1 CTGCAACTTCATGAAGATAGGATTTGCTTACTTAG-TCTGC
1655665 AACTTCAGGG
Statistics
Matches: 161, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
128 154 0.96
129 7 0.04
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (128 bp):
CTGCAACTTCATGAAGATAGGATTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
ACTAGATGCGATCTACTCTCTGCAACTTCAGAAAGATAAGATCCAAGGTTTTAATCCACTCCA
Found at i:1655834 original size:89 final size:89
Alignment explanation
Indices: 1655661--1655849 Score: 201
Period size: 89 Copynumber: 2.1 Consensus size: 89
1655651 TTACTTAGTT
* * *
1655661 CTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAA
1 CTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAACCTGCCTCACTACAACTTCAGGAGGATAA
1655726 GACTTTCCTACTTAGTCTG-CTCCA
66 GACTTTCCTACTTAGTCTGCCT-CA
* * * *
1655750 TTGCAACTTCAGGGAGATAAGATTAT-C-GGCTTTAACCTG-CTCCACTACAACTTTAGG-GAGA
1 CTGCAACTTCAGGGAGATAAGATT-TGCTAGCTTCAACCTGCCT-CACTACAACTTCAGGAG-GA
* *
1655811 TAAGATTTTCC-ATCTTCATTCTGCCTCA
63 TAAGACTTTCCTA-CTT-AGTCTGCCTCA
1655839 CTGCAACTTCA
1 CTGCAACTTCA
1655850 AAAGGATAAG
Statistics
Matches: 84, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
87 4 0.05
88 36 0.43
89 41 0.49
90 3 0.04
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (89 bp):
CTGCAACTTCAGGGAGATAAGATTTGCTAGCTTCAACCTGCCTCACTACAACTTCAGGAGGATAA
GACTTTCCTACTTAGTCTGCCTCA
Found at i:1655840 original size:133 final size:133
Alignment explanation
Indices: 1655664--1655904 Score: 383
Period size: 133 Copynumber: 1.8 Consensus size: 133
1655654 CTTAGTTCTG
* **
1655664 CAACTTCAGGGAGATAAGATTTGCTATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGAC
1 CAACTTCAGGGAGATAAGATTTGCCATCTTCAATCTGCCTCACTGCAACTTCAAAAGGATAAGAC
* * * *
1655729 TTTCCTACTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGATTATCGGCTTTAACCTGCTCCA
66 TTGCCTACTTAGTCTACTCCACTACAACTTCAGGGAGATAAGATTATCGGCTTTAACCTGCTCCA
1655794 CTA
131 CTA
* * *
1655797 CAACTTTAGGGAGATAAGATTTTCCATCTTCATTCTGCCTCACTGCAACTTCAAAAGGATAAGAC
1 CAACTTCAGGGAGATAAGATTTGCCATCTTCAATCTGCCTCACTGCAACTTCAAAAGGATAAGAC
*
1655862 TTGCTTACTTAGTCTACTCCACTACAACTTCAGGGAGATAAGA
66 TTGCCTACTTAGTCTACTCCACTACAACTTCAGGGAGATAAGA
1655905 CTAGATGCGA
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
133 97 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (133 bp):
CAACTTCAGGGAGATAAGATTTGCCATCTTCAATCTGCCTCACTGCAACTTCAAAAGGATAAGAC
TTGCCTACTTAGTCTACTCCACTACAACTTCAGGGAGATAAGATTATCGGCTTTAACCTGCTCCA
CTA
Found at i:1683301 original size:32 final size:30
Alignment explanation
Indices: 1683248--1683314 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 30
1683238 ATCACTTTAA
*
1683248 TATTAAATTAATAAAATACTATTAAGATAAT
1 TATTAAATTAATAAAATACTATTAAAAT-AT
*
1683279 TATTAAATTTAATATTAA-ACTATTAAAATAT
1 TATTAAA-TTAATA-AAATACTATTAAAATAT
1683310 TATTA
1 TATTA
1683315 TTTTTTGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 14 0.44
32 16 0.50
33 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (30 bp):
TATTAAATTAATAAAATACTATTAAAATAT
Found at i:1685721 original size:27 final size:26
Alignment explanation
Indices: 1685691--1685776 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 26
1685681 ATTCCTATAA
*
1685691 AGTTCACCATACTTACTGCATCTTTAG
1 AGTTCACCATACTTACT-CATCTTCAG
* *
1685718 AGTTCGCCATA-TATA-TTATTCCTTCAG
1 AGTTCACCATACT-TACTCA-T-CTTCAG
*
1685745 AGTTCACCATACTTACTACACCTTCAG
1 AGTTCACCATACTTACT-CATCTTCAG
1685772 AGTTC
1 AGTTC
1685777 GCCAAGAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
25 1 0.02
26 3 0.06
27 40 0.85
28 2 0.04
29 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (26 bp):
AGTTCACCATACTTACTCATCTTCAG
Found at i:1685721 original size:54 final size:54
Alignment explanation
Indices: 1685656--1685780 Score: 153
Period size: 54 Copynumber: 2.3 Consensus size: 54
1685646 ACGAAGCCTT
** *
1685656 TCTTTCAGAGTTCGCTGTACACATTATTCCTAT-AAAGTTCACCATACTTACTGCA
1 TCTTT-AGAGTTCGCCATACACATTATTCCT-TCAAAGTTCACCATACTTACTACA
* * *
1685711 TCTTTAGAGTTCGCCATATATATTATTCCTTCAGAGTTCACCATACTTACTACA
1 TCTTTAGAGTTCGCCATACACATTATTCCTTCAAAGTTCACCATACTTACTACA
* *
1685765 CCTTCAGAGTTCGCCA
1 TCTTTAGAGTTCGCCA
1685781 AGAATACCAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.02
54 55 0.90
55 5 0.08
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.36
Consensus pattern (54 bp):
TCTTTAGAGTTCGCCATACACATTATTCCTTCAAAGTTCACCATACTTACTACA
Found at i:1697227 original size:29 final size:29
Alignment explanation
Indices: 1697194--1697250 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1697184 GTGGGATGAC
*
1697194 AGGGGTAGTAAAAGT-TTTGGGAGAAAGTG
1 AGGGGAAGTAAAAGTATTTGGG-GAAAGTG
1697223 AGGGGAAGTAAAAGTATTTGGGGAAAGT
1 AGGGGAAGTAAAAGTATTTGGGGAAAGT
1697251 AAAAAGGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (29 bp):
AGGGGAAGTAAAAGTATTTGGGGAAAGTG
Found at i:1700508 original size:15 final size:14
Alignment explanation
Indices: 1700488--1700519 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1700478 TTTCAAGTTT
1700488 TACTTATATATATCA
1 TACTTATATATAT-A
1700503 TACTTATATATATA
1 TACTTATATATATA
1700517 TAC
1 TAC
1700520 ACTTATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (14 bp):
TACTTATATATATA
Found at i:1707858 original size:8 final size:8
Alignment explanation
Indices: 1707845--1707870 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1707835 TTTCGAGTAA
1707845 TTATTCTT
1 TTATTCTT
1707853 TTATTCTT
1 TTATTCTT
1707861 TTATTCTT
1 TTATTCTT
1707869 TT
1 TT
1707871 TCCACATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTATTCTT
Found at i:1712518 original size:88 final size:88
Alignment explanation
Indices: 1712408--1712582 Score: 278
Period size: 88 Copynumber: 2.0 Consensus size: 88
1712398 TTCAGCCTTA
* * * * *
1712408 TCTCCTTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCTTGTATTGGCAGCGAA
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGGCAGCGAA
* *
1712473 GTAGATCGAAGATACCAGTCTTG
66 GCAGATCGAAGACACCAGTCTTG
*
1712496 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGGCAGTGAA
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGGCAGCGAA
1712561 GCAGATCGAAGACACCAGTCTT
66 GCAGATCGAAGACACCAGTCTT
1712583 CTCGCCTTGA
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (88 bp):
TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGGCAGCGAA
GCAGATCGAAGACACCAGTCTTG
Found at i:1712539 original size:44 final size:44
Alignment explanation
Indices: 1712408--1712539 Score: 140
Period size: 44 Copynumber: 3.0 Consensus size: 44
1712398 TTCAGCCTTA
*
1712408 TCTCCTTGAGCAGTAGTGGAGTAGGTTGAAAATAGCAGATCTTG
1 TCTCCTTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
* *** * * * * * *
1712452 TCTTCTTGTATTGGCAGCGAAGTAGATCGAAGATACCAG-TCTTG
1 TCTCCTTG-AGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
*
1712496 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
1 TCTCCTTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
1712540 CCTTCCTGTA
Statistics
Matches: 64, Mismatches: 22, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
43 21 0.33
44 23 0.36
45 20 0.31
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (44 bp):
TCTCCTTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTG
Found at i:1712557 original size:45 final size:45
Alignment explanation
Indices: 1712422--1712558 Score: 145
Period size: 45 Copynumber: 3.1 Consensus size: 45
1712412 CTTGAGCAGT
* *
1712422 AGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCTTGTATTGGC
1 AGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTACTGGC
* * * * * * * *
1712467 AGCGAAGTAGATCGAAGATACCAG-TCTTGTCTCCCTG-AGC-AGC
1 AGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTA-CTGGC
*
1712510 AGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGGC
1 AGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTACTGGC
1712555 AGTG
1 AGTG
1712559 AAGCAGATCG
Statistics
Matches: 69, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
43 21 0.30
44 23 0.33
45 25 0.36
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (45 bp):
AGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTACTGGC
Found at i:1712900 original size:100 final size:100
Alignment explanation
Indices: 1712782--1712992 Score: 343
Period size: 100 Copynumber: 2.1 Consensus size: 100
1712772 ATTACAGTGG
* * *
1712782 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGG-TAGTGTAGTGGAATAGATTGAAGCT
1 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGGCT-GTGCAGTGGAACAGATTGAAGCT
1712846 ACGACGGCGAATCTTGTTTCCCCGACATTGCAATTA
65 ACGACGGCGAATCTTGTTTCCCCGACATTGCAATTA
* *
1712882 AATAGATTGAAGCCACAACGGTGAATTTTACTTCCCCGGCTGTGCAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGGCTGTGCAGTGGAACAGATTGAAGCTA
*
1712947 CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
66 CGACGGCGAATCTTGTTTCCCCGACATTGCAATTA
*
1712982 AACAGATTGAA
1 AATAGATTGAA
1712993 TGTACCAATC
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 102 0.99
101 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (100 bp):
AATAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGGCTGTGCAGTGGAACAGATTGAAGCTA
CGACGGCGAATCTTGTTTCCCCGACATTGCAATTA
Found at i:1712978 original size:50 final size:50
Alignment explanation
Indices: 1712771--1712979 Score: 213
Period size: 50 Copynumber: 4.2 Consensus size: 50
1712761 ATCTCTTTGG
* * *
1712771 CATTACAGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGG
1 CATTGCAGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
* * * * * **
1712821 TAGTGTAGTGGAATAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGA
1 CATTGCAGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
* ** * * *
1712871 CATTGCAATTAAATAGATTGAAGCCACAACGGTGAATTTTACTTCCCCGG
1 CATTGCAGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
* * * **
1712921 C-TGTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGA
1 CAT-TGCAGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
1712971 CATTGCAGT
1 CATTGCAGT
1712980 TAAACAGATT
Statistics
Matches: 123, Mismatches: 34, Indels: 4
0.76 0.21 0.02
Matches are distributed among these distances:
49 1 0.01
50 121 0.98
51 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (50 bp):
CATTGCAGTGGAATAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
Found at i:1713138 original size:44 final size:44
Alignment explanation
Indices: 1713004--1713157 Score: 145
Period size: 44 Copynumber: 3.6 Consensus size: 44
1712994 GTACCAATCC
* * *
1713004 TATCTCTCTGAAGCTACAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAACCACAGATCT
* *** *** *
1713048 CATCTCTCTGAAGTTGTC-GTAGAATAGA-TCGTATC-CAG-TCT
1 TATCTCTCTGAAGTTG-CAGTAGAGCGGATTAAAACCACAGATCT
* *
1713089 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAACCACAGATCT
*
1713133 TATCTCTCTAAAGTTGCAGTAGAGC
1 TATCTCTCTGAAGTTGCAGTAGAGC
1713158 AGATCGCATA
Statistics
Matches: 81, Mismatches: 24, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
40 1 0.01
41 23 0.28
42 6 0.07
43 6 0.07
44 44 0.54
45 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
TATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAACCACAGATCT
Found at i:1713147 original size:85 final size:85
Alignment explanation
Indices: 1713004--1713189 Score: 257
Period size: 85 Copynumber: 2.2 Consensus size: 85
1712994 GTACCAATCC
* * * *
1713004 TATCTCTCTGAAGCTACAGTGGAGCGGATTAAAACCACAGATCTCATCTCTCTGAAGTTGTC-GT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTCATCTCTCTAAAGTTG-CAGT
* * **
1713068 AGAATAGATCGTATCCAGTCT
65 AGAACAGATCGCATAAAGTCT
*
1713089 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTCATCTCTCTAAAGTTGCAGTA
*
1713154 GAGCAGATCGCATAAAGTCT
66 GAACAGATCGCATAAAGTCT
*
1713174 TATCTCCATGAAGTTG
1 TATCTCCCTGAAGTTG
1713190 TAGTAGAGTA
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 1 0.01
85 88 0.99
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (85 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTCATCTCTCTAAAGTTGCAGTA
GAACAGATCGCATAAAGTCT
Found at i:1714904 original size:19 final size:18
Alignment explanation
Indices: 1714880--1714919 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1714870 TTTCATTTTT
1714880 TATATACATATTATACATA
1 TATATACATATTATA-ATA
* *
1714899 TATATACGTATTTTAATA
1 TATATACATATTATAATA
1714917 TAT
1 TAT
1714920 GCATATACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (18 bp):
TATATACATATTATAATA
Found at i:1735268 original size:51 final size:50
Alignment explanation
Indices: 1735206--1735402 Score: 184
Period size: 51 Copynumber: 3.9 Consensus size: 50
1735196 CTATTATCAT
*
1735206 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCATTAATA
1 TCGATACACGTAGTAGCCTACACATAGTACTACACACGTGACCATTAATA
* * *
1735256 TCTGATACACGTAGTAGCCTACACATAGTACTACACATGTGATCGA--AGCTA
1 TC-GATACACGTAGTAGCCTACACATAGTACTACACACGTGA-CCATTA-ATA
* * * * * * * * * * *
1735307 TCCAGTACGCATAGTAGCCTGCATATAGTACGAGACATGCGACCTTTCAT-
1 TCGA-TACACGTAGTAGCCTACACATAGTACTACACACGTGACCATTAATA
*
1735357 TCCGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCAT
1 T-CGATACACGTAGTAGCCTACACATAGTACTACACACGTGACCAT
1735403 CACTTTCACT
Statistics
Matches: 113, Mismatches: 27, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
50 38 0.34
51 73 0.65
52 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (50 bp):
TCGATACACGTAGTAGCCTACACATAGTACTACACACGTGACCATTAATA
Found at i:1735650 original size:16 final size:16
Alignment explanation
Indices: 1735625--1735669 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1735615 ATCCAGTCCA
*
1735625 AAAATCACATTTTGGC
1 AAAATTACATTTTGGC
1735641 AAAATTACATTTTGGC
1 AAAATTACATTTTGGC
1735657 AAAATTACATTTT
1 AAAATTACATTTT
1735670 TGCCCCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (16 bp):
AAAATTACATTTTGGC
Found at i:1739146 original size:51 final size:50
Alignment explanation
Indices: 1739070--1739253 Score: 183
Period size: 51 Copynumber: 3.6 Consensus size: 50
1739060 TATAAACACG
* **
1739070 TGTGTAGTACTAAGTGCAGGCTACTACGTGTGTC-AATAGATAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA-AGAT-ATGGTCACA
* * * *
1739121 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAGGCTTTGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GAAAGATATGGTCACA
* * * ** *
1739172 TGTGTAGTACTATGTGCAGGCTACTACGTGAATCGGAAAG-TTTTATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTA-CCGAAAGATATGGTCACA
* *
1739222 TGTGTAGTACTATGTGAAGACTACTACGTGTA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTA
1739254 TTGAATGATA
Statistics
Matches: 113, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
50 36 0.32
51 72 0.64
52 3 0.03
53 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.32
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAAGATATGGTCACA
Found at i:1739247 original size:50 final size:51
Alignment explanation
Indices: 1739116--1739251 Score: 184
Period size: 51 Copynumber: 2.7 Consensus size: 51
1739106 TAGATAATGG
* * * *
1739116 TCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAGGCTTTGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAGCTTTGA
* *
1739167 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGAATCGGAAAG-TTTTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAGCTTTGA
* * *
1739217 TCACGTGTGTAGTACTATGTGAAGACTACTACGTG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTG
1739252 TATTGAATGA
Statistics
Matches: 76, Mismatches: 9, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
50 35 0.46
51 41 0.54
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGAACCGGAAAGCTTTGA
Found at i:1741620 original size:28 final size:28
Alignment explanation
Indices: 1741570--1741630 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
1741560 TACTTAAAAT
* * *
1741570 ATAGTCCTAACGAACTTCCACATTTAAG
1 ATAGTCATAACGAACCTCCACATATAAG
* * *
1741598 ATAGTCATAACGGACCTCGACATATACG
1 ATAGTCATAACGAACCTCCACATATAAG
1741626 ATAGT
1 ATAGT
1741631 ACTAACTTCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (28 bp):
ATAGTCATAACGAACCTCCACATATAAG
Found at i:1741683 original size:24 final size:24
Alignment explanation
Indices: 1741617--1741683 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
1741607 ACGGACCTCG
*
1741617 ACATATACGATAGTACTAACTTCC
1 ACATATACGATAGTACTGACTTCC
* *
1741641 ACATATATGATAGTTCTGACTTCC
1 ACATATACGATAGTACTGACTTCC
* * *
1741665 AGATATACAATAGTCCTGA
1 ACATATACGATAGTACTGA
1741684 TAGACTTCCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (24 bp):
ACATATACGATAGTACTGACTTCC
Found at i:1741705 original size:28 final size:28
Alignment explanation
Indices: 1741674--1741727 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1741664 CAGATATACA
*
1741674 ATAGTCCTGATAGACTTCCACATTTATG
1 ATAGTCCTGACAGACTTCCACATTTATG
* **
1741702 ATAGTCTTGACAGACTTTTACATTTA
1 ATAGTCCTGACAGACTTCCACATTTA
1741728 CGGTAATGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (28 bp):
ATAGTCCTGACAGACTTCCACATTTATG
Found at i:1745972 original size:23 final size:23
Alignment explanation
Indices: 1745946--1745991 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1745936 GGTATGTTCT
1745946 TCATGGGCAATTTGAAGCTTACA
1 TCATGGGCAATTTGAAGCTTACA
1745969 TCATGGGCAATTTGAAGCTTACA
1 TCATGGGCAATTTGAAGCTTACA
1745992 CTCTGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (23 bp):
TCATGGGCAATTTGAAGCTTACA
Found at i:1750210 original size:27 final size:29
Alignment explanation
Indices: 1750147--1750212 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 29
1750137 ATCTTTTTCT
1750147 TTTTTCTTTT--CTTTTTCATTTTCCTTC
1 TTTTTCTTTTCCCTTTTTCATTTTCCTTC
*
1750174 ATTTTC--TTCCCTTTTTC-TTTT-CTTC
1 TTTTTCTTTTCCCTTTTTCATTTTCCTTC
1750199 TTTTTCTTTTCCCT
1 TTTTTCTTTTCCCT
1750213 AGCCGCCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
25 11 0.33
26 4 0.12
27 18 0.55
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (29 bp):
TTTTTCTTTTCCCTTTTTCATTTTCCTTC
Found at i:1753792 original size:94 final size:94
Alignment explanation
Indices: 1753671--1753854 Score: 260
Period size: 94 Copynumber: 2.0 Consensus size: 94
1753661 ATTACAGCCC
* * * * **
1753671 AAGTTCATTGATTTATGATCACAAACAATCTTCTCTAAGTTAGCTTATTTATGATTGCAACTCCA
1 AAGTTCATTGATTAACGATCACAAACAATCTTCTCTAAGTTAGCTGATTTACGATCACAACTCCA
* *
1753736 AACAGCTTGCTGATTTACGTTCACAAGCT
66 AACAACTTGCTGATTTACGATCACAAGCT
** * *
1753765 AAGTTCATTGATTAACGATCAGGAACAATCTTCTCTGAGTTAGCTGATTTACGATCATAACTCCA
1 AAGTTCATTGATTAACGATCACAAACAATCTTCTCTAAGTTAGCTGATTTACGATCACAACTCCA
1753830 AACAACTTGCTGATTTACGATCACA
66 AACAACTTGCTGATTTACGATCACA
1753855 TTTGATATTA
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
94 78 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.34
Consensus pattern (94 bp):
AAGTTCATTGATTAACGATCACAAACAATCTTCTCTAAGTTAGCTGATTTACGATCACAACTCCA
AACAACTTGCTGATTTACGATCACAAGCT
Found at i:1753913 original size:130 final size:130
Alignment explanation
Indices: 1753745--1754126 Score: 487
Period size: 130 Copynumber: 2.9 Consensus size: 130
1753735 AAACAGCTTG
* * * *
1753745 CTGATTTACGTTCACAAG-CTAAGTTCATTGATTAACGATCAGGAACAATCTTCTCTGAGTTAGC
1 CTGATTTACGATCAC-AGCCTAAGTTCATTGATTTACGATCACGAACAATCTTTTCTGAGTTAGC
** * * * **
1753809 TGATTTACGATCATAACTCCAAACAACTTGCTGATTTACGATCACATTTGATATTATTAAGGCTC
65 TGATTTACGATCGCAACTCCAAATAGCTCGCTGATTTACGATCACAACTGATATTATTAAGGCTC
1753874 C
130 C
* *
1753875 CTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCACAAACAATCTTTTCTAAGTTAGCT
1 CTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCACGAACAATCTTTTCTGAGTTAGCT
* * * * * * *
1753940 GATTTACGATCGCAACTCCAAATAGCTCGTTAATTTATGATCACAACTGTTATTAATAAGGTTCG
66 GATTTACGATCGCAACTCCAAATAGCTCGCTGATTTACGATCACAACTGATATTATTAAGGCTCC
* * * * * *
1754005 CTGATTTATGATCACAACCTAAGTTCATTGATTTACGATAATGAACAATTTTTTTTGAGTTAGCT
1 CTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCACGAACAATCTTTTCTGAGTTAGCT
* * *
1754070 GATTTACAATCGCAATTCCAAATAGCTCGCTGATTTACAATCACAACTGATATTATT
66 GATTTACGATCGCAACTCCAAATAGCTCGCTGATTTACGATCACAACTGATATTATT
1754127 TGTAACACTG
Statistics
Matches: 215, Mismatches: 36, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
129 2 0.01
130 213 0.99
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (130 bp):
CTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCACGAACAATCTTTTCTGAGTTAGCT
GATTTACGATCGCAACTCCAAATAGCTCGCTGATTTACGATCACAACTGATATTATTAAGGCTCC
Found at i:1753942 original size:63 final size:62
Alignment explanation
Indices: 1753744--1754076 Score: 168
Period size: 63 Copynumber: 5.2 Consensus size: 62
1753734 CAAACAGCTT
* * * * * * *
1753744 GCTGATTTACGTTCACAAGCTAAGTTCATTGATTAACGATCAGGAACAATCTTCTCTGAGTTA
1 GCTGATTTACGATCACAACCTAAGTTCATTGATTTACGATCA-CAACAATCTTTTATAAGTTA
* * *** * *** * *
1753807 GCTGATTTACGATCATAACTCCAAACAACTTGCTGATTTACGATCACATTTGATATTATTA-AGG
1 GCTGATTTACGATCACAA--CCTAAGTTCAT--TGATTTACGATCACA-ACAATCTT-TTATAAG
* *
1753871 CTC
60 TTA
* * *
1753874 CCTGATTTACGATCACAGCCTAAGTTCATTGATTTACGATCACAAACAATCTTTTCTAAGTTA
1 GCTGATTTACGATCACAACCTAAGTTCATTGATTTACGATCAC-AACAATCTTTTATAAGTTA
* * * * * * *
1753937 GCTGATTTACGATCGCAACTCCAAATAGCTCGTTAATTTATGATCACAAC--TGTTATTAATAAG
1 GCTGATTTACGATCACAA--CC-TA-AGTTCATTGATTTACGATCACAACAATCTT-TT-ATAA-
*
1754000 GTTC
59 GTTA
* * * * * *
1754004 GCTGATTTATGATCACAACCTAAGTTCATTGATTTACGATAATGAACAATTTTTTTTGAGTTA
1 GCTGATTTACGATCACAACCTAAGTTCATTGATTTACGATCA-CAACAATCTTTTATAAGTTA
1754067 GCTGATTTAC
1 GCTGATTTAC
1754077 AATCGCAATT
Statistics
Matches: 191, Mismatches: 61, Indels: 36
0.66 0.21 0.12
Matches are distributed among these distances:
62 2 0.01
63 79 0.41
64 10 0.05
65 19 0.10
66 11 0.06
67 69 0.36
68 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (62 bp):
GCTGATTTACGATCACAACCTAAGTTCATTGATTTACGATCACAACAATCTTTTATAAGTTA
Found at i:1755192 original size:20 final size:20
Alignment explanation
Indices: 1755143--1755189 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1755133 AAAACACTAA
*
1755143 AAGAAGAAAT-TTAAAAACT
1 AAGAAAAAATATTAAAAACT
*
1755162 AAGAATAAATATTAAAAA-T
1 AAGAAAAAATATTAAAAACT
1755181 AAGAAAAAA
1 AAGAAAAAA
1755190 ATAAAAGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (20 bp):
AAGAAAAAATATTAAAAACT
Found at i:1761466 original size:14 final size:14
Alignment explanation
Indices: 1761432--1761474 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1761422 TTGAAAAATT
**
1761432 ATTTAATTGGTTAA
1 ATTTAATTAATTAA
1761446 A-TTAATTAATTAA
1 ATTTAATTAATTAA
*
1761459 ATTTAATTATTTAA
1 ATTTAATTAATTAA
1761473 AT
1 AT
1761475 AATTAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
ATTTAATTAATTAA
Found at i:1764676 original size:20 final size:19
Alignment explanation
Indices: 1764651--1764720 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 19
1764641 AAATCAATTT
1764651 AAAATGATTTTAACCTAGTC
1 AAAATGATTTTAACC-AGTC
* *
1764671 AAAATGATTTCAACCAAGTT
1 AAAATGATTTTAACC-AGTC
*
1764691 AAAATCATTTTAACACA-TC
1 AAAATGATTTTAAC-CAGTC
1764710 AAAATGATTTT
1 AAAATGATTTT
1764721 CAAACAAGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 11 0.26
20 30 0.71
21 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.34
Consensus pattern (19 bp):
AAAATGATTTTAACCAGTC
Found at i:1764693 original size:40 final size:40
Alignment explanation
Indices: 1764649--1764731 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
1764639 TAAAATCAAT
* *
1764649 TTAAAATGATTTTAAC-CTAGTCAAAATGA-TTTCAACCAAG
1 TTAAAATCATTTTAACAC-A-TCAAAATGATTTTCAAACAAG
1764689 TTAAAATCATTTTAACACATCAAAATGATTTTCAAACAAG
1 TTAAAATCATTTTAACACATCAAAATGATTTTCAAACAAG
1764729 TTA
1 TTA
1764732 GAATTGCTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 9 0.23
40 29 0.74
41 1 0.03
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (40 bp):
TTAAAATCATTTTAACACATCAAAATGATTTTCAAACAAG
Found at i:1765859 original size:24 final size:24
Alignment explanation
Indices: 1765832--1765879 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1765822 AAGATTTAGT
1765832 ATTTATTAGTATAATATATTTGAC
1 ATTTATTAGTATAATATATTTGAC
* * *
1765856 ATTTATTAGTGTAGTTTATTTGAC
1 ATTTATTAGTATAATATATTTGAC
1765880 TTACTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.52
Consensus pattern (24 bp):
ATTTATTAGTATAATATATTTGAC
Found at i:1766305 original size:30 final size:30
Alignment explanation
Indices: 1766269--1766330 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1766259 AAAATTCATC
1766269 AAAGTTCAAATTAAAATCATATGCAAAACA
1 AAAGTTCAAATTAAAATCATATGCAAAACA
1766299 AAAGTTCAAATTAAAATCATATGCAAAACA
1 AAAGTTCAAATTAAAATCATATGCAAAACA
1766329 AA
1 AA
1766331 CACATTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (30 bp):
AAAGTTCAAATTAAAATCATATGCAAAACA
Found at i:1773108 original size:24 final size:24
Alignment explanation
Indices: 1773081--1773128 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1773071 AAGATTTAGT
1773081 ATTTATTAGTATAATATATTTGAC
1 ATTTATTAGTATAATATATTTGAC
* * *
1773105 ATTTATTAGTGTAGTTTATTTGAC
1 ATTTATTAGTATAATATATTTGAC
1773129 TTACTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.52
Consensus pattern (24 bp):
ATTTATTAGTATAATATATTTGAC
Found at i:1777467 original size:24 final size:24
Alignment explanation
Indices: 1777440--1777487 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1777430 AAGATTTAGT
1777440 ATTTATTAGTATAATATATTTGAC
1 ATTTATTAGTATAATATATTTGAC
* * *
1777464 ATTTATTAGTGTAGTTTATTTGAC
1 ATTTATTAGTATAATATATTTGAC
1777488 TTACTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.52
Consensus pattern (24 bp):
ATTTATTAGTATAATATATTTGAC
Found at i:1783459 original size:25 final size:24
Alignment explanation
Indices: 1783431--1783516 Score: 61
Period size: 24 Copynumber: 3.5 Consensus size: 24
1783421 ATCCGGGAAA
1783431 TATAAAGGGAAGCTTACAAAGAGCC
1 TATAAAGGGAAGC-TACAAAGAGCC
* * *
1783456 TATAACGGGTAGCTCCAAAGAGCAC
1 TATAAAGGGAAGCTACAAAGAGC-C
* * *
1783481 T-TAACGGGTAGCTCCGAAA-AGCAC
1 TATAAAGGGAAGCTAC-AAAGAGC-C
1783505 T-TAAAGGGAAGC
1 TATAAAGGGAAGC
1783517 ACCAGATAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
24 38 0.70
25 16 0.30
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (24 bp):
TATAAAGGGAAGCTACAAAGAGCC
Found at i:1783485 original size:24 final size:24
Alignment explanation
Indices: 1783447--1783508 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
1783437 GGGAAGCTTA
1783447 CAAAGAGC-CTATAACGGGTAGCTC
1 CAAAGAGCACT-TAACGGGTAGCTC
1783471 CAAAGAGCACTTAACGGGTAGCTC
1 CAAAGAGCACTTAACGGGTAGCTC
1783495 CGAAA-AGCACTTAA
1 C-AAAGAGCACTTAA
1783509 AGGGAAGCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.16
Consensus pattern (24 bp):
CAAAGAGCACTTAACGGGTAGCTC
Found at i:1801214 original size:12 final size:12
Alignment explanation
Indices: 1801189--1801228 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1801179 TCTGGCTGTT
*
1801189 ACACGGCCTAGC
1 ACACGGCCTGGC
*
1801201 ACATGGCCTGGC
1 ACACGGCCTGGC
1801213 ACACGGCCTGGC
1 ACACGGCCTGGC
1801225 ACAC
1 ACAC
1801229 AGGCATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.23, C:0.40, G:0.28, T:0.10
Consensus pattern (12 bp):
ACACGGCCTGGC
Found at i:1804986 original size:33 final size:33
Alignment explanation
Indices: 1804920--1804986 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
1804910 CGTTCTGAAC
*
1804920 ATTTTAAATTTGAATATTGATATGTTTATATAT
1 ATTTTAAATTTGAATATTGATATGTTTAAATAT
*
1804953 ATTTTAAA-TTGAA-ATTGTTATGTTTTAAAATAT
1 ATTTTAAATTTGAATATTGATATG-TTT-AAATAT
1804986 A
1 A
1804987 AAAGGTTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 8 0.27
32 8 0.27
33 14 0.47
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (33 bp):
ATTTTAAATTTGAATATTGATATGTTTAAATAT
Found at i:1815004 original size:12 final size:12
Alignment explanation
Indices: 1814987--1815011 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1814977 ATATTGGAAC
1814987 AATAAAGAAGAT
1 AATAAAGAAGAT
1814999 AATAAAGAAGAT
1 AATAAAGAAGAT
1815011 A
1 A
1815012 GATGGAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AATAAAGAAGAT
Found at i:1815996 original size:43 final size:43
Alignment explanation
Indices: 1815935--1816020 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
1815925 ACCTTGAGGT
*
1815935 AATGTGACCCCATTAGATTCATGGGTCTAAAATTGGGCTTCGA
1 AATGTGACCCCATCAGATTCATGGGTCTAAAATTGGGCTTCGA
1815978 AATGTGACCCCATCAGATTCATGGGTCTAAAATTGGGCTTCGA
1 AATGTGACCCCATCAGATTCATGGGTCTAAAATTGGGCTTCGA
1816021 GACTCACATC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (43 bp):
AATGTGACCCCATCAGATTCATGGGTCTAAAATTGGGCTTCGA
Found at i:1816714 original size:96 final size:96
Alignment explanation
Indices: 1816595--1816872 Score: 502
Period size: 96 Copynumber: 2.9 Consensus size: 96
1816585 TTTCTAGTTA
* *
1816595 GATATTTAATTGGACACTAGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
1 GATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
*
1816660 AGTGATATCTCAATTGTATTCTCACTATTTG
66 GGTGATATCTCAATTGTATTCTCACTATTTG
*
1816691 GATATTTAATTTGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
1 GATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
*
1816756 GGTGATATCTCAATTGTATTCTCTCTATTTG
66 GGTGATATCTCAATTGTATTCTCACTATTTG
1816787 GATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
1 GATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
*
1816852 GGTGATACCTCAATTGTATTC
66 GGTGATATCTCAATTGTATTC
1816873 CTTATTTCAT
Statistics
Matches: 175, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 175 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (96 bp):
GATATTTAATTGGACATTGGAAACCCTTATGATCTTTTGAACTACACCAATAACATTGCACAAAA
GGTGATATCTCAATTGTATTCTCACTATTTG
Found at i:1819963 original size:12 final size:11
Alignment explanation
Indices: 1819948--1819991 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1819938 ATAAATAAAA
1819948 TTTATTTTTAT
1 TTTATTTTTAT
1819959 GTTTATTTTTAT
1 -TTTATTTTTAT
* **
1819971 TTTAATTACAT
1 TTTATTTTTAT
1819982 TTTATTTTTA
1 TTTATTTTTA
1819992 GTTATAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:1820475 original size:305 final size:306
Alignment explanation
Indices: 1819978--1820588 Score: 1215
Period size: 305 Copynumber: 2.0 Consensus size: 306
1819968 TATTTTAATT
1819978 ACATTTTATTTTTAGTTATAAATAAAATAGATAAATTTTGTCAATAAATAAATGGGTAAATAAAA
1 ACATTTTATTTTTAGTTATAAATAAAATAGATAAATTTTGTCAATAAATAAATGGGTAAATAAAA
1820043 AAATGTAAATAGAACTCCTAATTAAAATTAAGTTAATCTTTTAATTTAAGTGAAATTAGGGTTAG
66 AAATGTAAATAGAACTCCTAATTAAAATTAAGTTAATCTTTTAATTTAAGTGAAATTAGGGTTAG
1820108 TTTTTTTATTTTTCTCTCCTATTGTTATTTTCTTCTTTTGTTTTTCTTTCAGCCACCGCCCTCCT
131 TTTTTTTATTTTTCTCTCCTATTGTTATTTTCTTCTTTTGTTTTTCTTTCAGCCACCGCCCTCCT
1820173 CATTGTCCCGACTAGCCACAGCCCGAACAACATTAGTCGACCCCCCAGCCCTGCAAACTTTTGCG
196 CATTGTCCCGACTAGCCACAGCCCGAACAACATTAGTCGACCCCCCAGCCCTGCAAACTTTTGCG
1820238 AGCACAAACCCTCTAGCAGCAGGCCCTTACACGCTGCACTGTCGTA
261 AGCACAAACCCTCTAGCAGCAGGCCCTTACACGCTGCACTGTCGTA
1820284 ACATTTTA-TTTTAGTTATAAATAAAATAGATAAATTTTGTCAATAAATAAATGGGTAAATAAAA
1 ACATTTTATTTTTAGTTATAAATAAAATAGATAAATTTTGTCAATAAATAAATGGGTAAATAAAA
1820348 AAATGTAAATAGAACTCCTAATTAAAATTAAGTTAATCTTTTAATTTAAGTGAAATTAGGGTTAG
66 AAATGTAAATAGAACTCCTAATTAAAATTAAGTTAATCTTTTAATTTAAGTGAAATTAGGGTTAG
1820413 TTTTTTTATTTTTCTCTCCTATTGTTATTTTCTTCTTTTGTTTTTCTTTCAGCCACCGCCCTCCT
131 TTTTTTTATTTTTCTCTCCTATTGTTATTTTCTTCTTTTGTTTTTCTTTCAGCCACCGCCCTCCT
1820478 CATTGTCCCGACTAGCCACAGCCCGAACAACATTAGTCGACCCCCCAGCCCTGCAAACTTTTGCG
196 CATTGTCCCGACTAGCCACAGCCCGAACAACATTAGTCGACCCCCCAGCCCTGCAAACTTTTGCG
1820543 AGCACAAACCCTCTAGCAGCAGGCCCTTACACGCTGCACTGTCGTA
261 AGCACAAACCCTCTAGCAGCAGGCCCTTACACGCTGCACTGTCGTA
1820589 CACCATCACC
Statistics
Matches: 305, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
305 297 0.97
306 8 0.03
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (306 bp):
ACATTTTATTTTTAGTTATAAATAAAATAGATAAATTTTGTCAATAAATAAATGGGTAAATAAAA
AAATGTAAATAGAACTCCTAATTAAAATTAAGTTAATCTTTTAATTTAAGTGAAATTAGGGTTAG
TTTTTTTATTTTTCTCTCCTATTGTTATTTTCTTCTTTTGTTTTTCTTTCAGCCACCGCCCTCCT
CATTGTCCCGACTAGCCACAGCCCGAACAACATTAGTCGACCCCCCAGCCCTGCAAACTTTTGCG
AGCACAAACCCTCTAGCAGCAGGCCCTTACACGCTGCACTGTCGTA
Found at i:1828483 original size:40 final size:39
Alignment explanation
Indices: 1828434--1828542 Score: 139
Period size: 39 Copynumber: 2.8 Consensus size: 39
1828424 GTTTGGACAA
* *
1828434 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTTAAG
1 AAAACGCCGCTAAAAATAGAGAATTAGCGGCGCTTTT-AG
* * * *
1828474 GAAACGCCGCT-AAAATAGAGTATTAGAGGCGCTTTTTG
1 AAAACGCCGCTAAAAATAGAGAATTAGCGGCGCTTTTAG
1828512 AAAATCGCCGCTAAAAATAGAGAATTAGCGG
1 AAAA-CGCCGCTAAAAATAGAGAATTAGCGG
1828543 AGTTTTCTAG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
38 4 0.07
39 29 0.49
40 26 0.44
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATAGAGAATTAGCGGCGCTTTTAG
Found at i:1828780 original size:42 final size:42
Alignment explanation
Indices: 1828709--1828860 Score: 164
Period size: 41 Copynumber: 3.7 Consensus size: 42
1828699 ATTTCTGAAA
* * *
1828709 AAGCGCCACTAATGCTCT-AGGCTTTAGCGGCGTTTTCCAAT
1 AAGCGCCGCTGATGCGCTGAGGCTTTAGCGGCGTTTTCCAAT
* * ** *
1828750 AAGCGCCGCTGATGCGCTGCGGCTTTAGCGGCATTTTTGAAA
1 AAGCGCCGCTGATGCGCTGAGGCTTTAGCGGCGTTTTCCAAT
* * *
1828792 AAGCGCCACTAATGCTCT-AGGCTTTAGCGGCGTTTTCCAAT
1 AAGCGCCGCTGATGCGCTGAGGCTTTAGCGGCGTTTTCCAAT
* * *
1828833 AAGCGCTGCTGGTGCGCTGGGGCTTTAG
1 AAGCGCCGCTGATGCGCTGAGGCTTTAG
1828861 TAGGGGCTTT
Statistics
Matches: 87, Mismatches: 22, Indels: 3
0.78 0.20 0.03
Matches are distributed among these distances:
41 46 0.53
42 41 0.47
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (42 bp):
AAGCGCCGCTGATGCGCTGAGGCTTTAGCGGCGTTTTCCAAT
Found at i:1828795 original size:83 final size:82
Alignment explanation
Indices: 1828604--1828860 Score: 336
Period size: 83 Copynumber: 3.1 Consensus size: 82
1828594 GAGCTTTTCG
* * * * * * ** *
1828604 GGGCTTTAGCGGCGTTTTTGAAAAAGCGTCGCTAATGCTCT-GAGATTTAGTGGCATTTTTGAAA
1 GGGCTTTAGCGGCATTTTTGAAAAAGCGCCACTAATGCTCTAG-GCTTTAGCGGCGTTTTCCAAT
* * *
1828668 AAGCGTTGCTAATGCTCT
65 AAGCGCTGCTGATGCGCT
* *
1828686 GGGATTTAGCGGCATTTCTGAAAAAGCGCCACTAATGCTCTAGGCTTTAGCGGCGTTTTCCAATA
1 GGGCTTTAGCGGCATTTTTGAAAAAGCGCCACTAATGCTCTAGGCTTTAGCGGCGTTTTCCAATA
*
1828751 AGCGCCGCTGATGCGCT
66 AGCGCTGCTGATGCGCT
1828768 GCGGCTTTAGCGGCATTTTTGAAAAAGCGCCACTAATGCTCTAGGCTTTAGCGGCGTTTTCCAAT
1 G-GGCTTTAGCGGCATTTTTGAAAAAGCGCCACTAATGCTCTAGGCTTTAGCGGCGTTTTCCAAT
*
1828833 AAGCGCTGCTGGTGCGCT
65 AAGCGCTGCTGATGCGCT
1828851 GGGGCTTTAG
1 -GGGCTTTAG
1828861 TAGGGGCTTT
Statistics
Matches: 153, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
82 66 0.43
83 86 0.56
84 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (82 bp):
GGGCTTTAGCGGCATTTTTGAAAAAGCGCCACTAATGCTCTAGGCTTTAGCGGCGTTTTCCAATA
AGCGCTGCTGATGCGCT
Found at i:1828837 original size:41 final size:41
Alignment explanation
Indices: 1828605--1828838 Score: 229
Period size: 41 Copynumber: 5.7 Consensus size: 41
1828595 AGCTTTTCGG
* *
1828605 GGCTTTAGCGGCGTTTTTGAAAAAGCGTCGCTAATGCTCT-
1 GGCTTTAGCGGCGTTTTCGAAAAAGCGCCGCTAATGCTCTA
* * * * ** *
1828645 GAGATTTAGTGGCATTTTTGAAAAAGCGTTGCTAATGCTCTG
1 G-GCTTTAGCGGCGTTTTCGAAAAAGCGCCGCTAATGCTCTA
* * *
1828687 GGATTTAGCGGC-ATTTCTGAAAAAGCGCCACTAATGCTCTA
1 GGCTTTAGCGGCGTTTTC-GAAAAAGCGCCGCTAATGCTCTA
* * * * *
1828728 GGCTTTAGCGGCGTTTTCCAATAAGCGCCGCTGATGCGCTGC
1 GGCTTTAGCGGCGTTTTCGAAAAAGCGCCGCTAATGCTCT-A
* * *
1828770 GGCTTTAGCGGCATTTTTGAAAAAGCGCCACTAATGCTCTA
1 GGCTTTAGCGGCGTTTTCGAAAAAGCGCCGCTAATGCTCTA
* *
1828811 GGCTTTAGCGGCGTTTTCCAATAAGCGC
1 GGCTTTAGCGGCGTTTTCGAAAAAGCGC
1828839 TGCTGGTGCG
Statistics
Matches: 158, Mismatches: 31, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
40 4 0.03
41 116 0.73
42 38 0.24
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (41 bp):
GGCTTTAGCGGCGTTTTCGAAAAAGCGCCGCTAATGCTCTA
Found at i:1829259 original size:14 final size:14
Alignment explanation
Indices: 1829240--1829423 Score: 88
Period size: 14 Copynumber: 12.8 Consensus size: 14
1829230 ATTACTATAT
*
1829240 TTTAGGGTTTTTGG
1 TTTAGGGTTTATGG
*
1829254 TTTAGGGTATATGG
1 TTTAGGGTTTATGG
* *
1829268 TTTAGAGTTTAAGG
1 TTTAGGGTTTATGG
*
1829282 TTTAGGTGTTACCAT--
1 TTTAGG-GTT--TATGG
*
1829297 TTTAAGGTTTATGG
1 TTTAGGGTTTATGG
*
1829311 ATTATGGGTTTATGG
1 TTTA-GGGTTTATGG
* * *
1829326 GTTATGATTTATGG
1 TTTAGGGTTTATGG
* *
1829340 TTTATGGTTTAAAGG
1 TTTAGGGTTT-ATGG
* **
1829355 -TTGGGGTTTAAAG
1 TTTAGGGTTTATGG
1829368 TTTAGAGG-TTATGTG
1 TTTAG-GGTTTATG-G
* *
1829383 CTAAGGGTTTATGAG
1 TTTAGGGTTTATG-G
* *
1829398 TTTATGGTTTTAGGG
1 TTTA-GGGTTTATGG
1829413 TTTAGGGTTTA
1 TTTAGGGTTTA
1829424 AATTAACTAG
Statistics
Matches: 126, Mismatches: 32, Indels: 24
0.69 0.18 0.13
Matches are distributed among these distances:
12 2 0.02
13 3 0.02
14 71 0.56
15 42 0.33
16 7 0.06
17 1 0.01
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTATGG
Done.