Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 55 of 228
Found at i:16418697 original size:23 final size:26
Alignment explanation
Indices: 16418649--16418699 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 26
16418639 ATTAATTAGA
16418649 TAAGTATTATTTAATTAATATTTTAT
1 TAAGTATTATTTAATTAATATTTTAT
*
16418675 TAAG-ATT-TTTAA-TATTATTTTAT
1 TAAGTATTATTTAATTAATATTTTAT
16418698 TA
1 TA
16418700 GTAAATGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 12 0.50
24 5 0.21
25 3 0.12
26 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (26 bp):
TAAGTATTATTTAATTAATATTTTAT
Found at i:16421351 original size:56 final size:50
Alignment explanation
Indices: 16421284--16421562 Score: 224
Period size: 50 Copynumber: 5.5 Consensus size: 50
16421274 TGTGAGCCAG
** *
16421284 TGTAAGACCATGTCTGGGACATGGCATTAGCATTATTGAAATTATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTAGC---ACCG--A-GATGAGAGGTCCCA
* * *
16421340 TGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAGATGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTAGCACCGAGATGAGAGGTCCCA
* * *
16421390 TGTAAGACCATGTTTGGGACAT-G-ATGTTGTCACCGAGATGAGAGGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCAT-TAG-CACCGAGATGAGAGGTCCCA
* * ** * * * **
16421440 CGTAAGACCATGTCTGGGACATGGAATGGGCACTGATATAAGAACTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTAGCACCGAGATGAGAGGTCCCA
* * * * * **
16421490 TGTAAGACCATATCTGGGATATGGCATTAGCA--GTACAGGAAACATCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTAGCACCG-AGATGAGAGGTCCCA
16421539 TGTAAGACCATGTCTGGGACATGG
1 TGTAAGACCATGTCTGGGACATGG
16421563 ATTTGGCATG
Statistics
Matches: 183, Mismatches: 35, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
48 2 0.01
49 34 0.19
50 112 0.61
51 3 0.02
52 2 0.01
53 2 0.01
56 28 0.15
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATTAGCACCGAGATGAGAGGTCCCA
Found at i:16421385 original size:50 final size:50
Alignment explanation
Indices: 16421327--16421570 Score: 233
Period size: 50 Copynumber: 4.9 Consensus size: 50
16421317 TATTGAAATT
* *
16421327 ATGAGAGGTCCCATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* *** *
16421377 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGATGTTGTCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * * * *
16421427 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGAATGGGCACTGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* ** * * * *
16421477 ATAAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTAGCA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AG
* * **
16421526 AGGAAACATCCCATGTAAGACCATGTCTGGGACATGG-ATTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCA-TTGGCA
16421571 TGTTATTATT
Statistics
Matches: 158, Mismatches: 34, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
48 2 0.01
49 36 0.23
50 120 0.76
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:16423452 original size:2 final size:2
Alignment explanation
Indices: 16423445--16423485 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16423435 ATGGTCAAAT
16423445 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
16423486 AGGTAATTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16426619 original size:15 final size:17
Alignment explanation
Indices: 16426584--16426623 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
16426574 TTTCTCACTC
16426584 TCTTTTTCGTTTTCAATT
1 TCTTTTTCG-TTTCAATT
16426602 TCTTTTTC-TTTC-ATT
1 TCTTTTTCGTTTCAATT
16426617 TCTTTTT
1 TCTTTTT
16426624 TTCGCCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.45
16 4 0.18
18 8 0.36
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.72
Consensus pattern (17 bp):
TCTTTTTCGTTTCAATT
Found at i:16430847 original size:30 final size:30
Alignment explanation
Indices: 16430806--16430871 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
16430796 GTTGTCCCAA
*
16430806 CCCTTTTCATAGCTCAATAGTCGAAGCTAT
1 CCCTTTGCATAGCTCAATAGTCGAAGCTAT
*
16430836 CCCTTTGCATAGCTCAATAGTTGAAGCTAT
1 CCCTTTGCATAGCTCAATAGTCGAAGCTAT
16430866 CCCTTT
1 CCCTTT
16430872 TCATTATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (30 bp):
CCCTTTGCATAGCTCAATAGTCGAAGCTAT
Found at i:16430898 original size:30 final size:30
Alignment explanation
Indices: 16430864--16431053 Score: 156
Period size: 30 Copynumber: 6.4 Consensus size: 30
16430854 AGTTGAAGCT
16430864 ATCCCTTTTCATTATTTGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
16430894 ATCCCTTTTCATTA-TTGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* ** * *
16430923 ATCCCTTTTCATAATTTGAT-AAC-TGAAGCT
1 ATCCCTTTTCATTATTTGATGGTCGT-CA-CC
* * ** * *
16430953 ATCCCTTTTCATAATTCGATAATCG-AAGCT
1 ATCCCTTTTCATTATTTGATGGTCGTCA-CC
* * *
16430983 ATCCTTTTTCATTGTTCGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
* * * *
16431013 ATCTCTTTGCATT-GTAGATGGTCGTCACC
1 ATCCCTTTTCATTATTTGATGGTCGTCACC
16431042 ATCCCTTTTCAT
1 ATCCCTTTTCAT
16431054 AATTCGATTC
Statistics
Matches: 133, Mismatches: 21, Indels: 13
0.80 0.13 0.08
Matches are distributed among these distances:
28 1 0.01
29 54 0.41
30 75 0.56
31 3 0.02
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (30 bp):
ATCCCTTTTCATTATTTGATGGTCGTCACC
Found at i:16430927 original size:89 final size:90
Alignment explanation
Indices: 16430834--16431024 Score: 215
Period size: 89 Copynumber: 2.1 Consensus size: 90
16430824 AGTCGAAGCT
* ** * * ** *
16430834 ATCCCTTTGCATAGCTCAATAGTTGAAGCTATCCCTTTTCATTATTTGATGGTCGTCA-CCATCC
1 ATCCCTTTGCATAACTCAATAACTGAAGCTATCCCTTTTCATAATTCGATAATCG-AAGCCATCC
16430898 CTTTTCATTATT-GATGGTCGTCACC
65 CTTTTCATTATTCGATGGTCGTCACC
* * ** * *
16430923 ATCCCTTTTCATAATTTGATAACTGAAGCTATCCCTTTTCATAATTCGATAATCGAAGCTATCCT
1 ATCCCTTTGCATAACTCAATAACTGAAGCTATCCCTTTTCATAATTCGATAATCGAAGCCATCCC
*
16430988 TTTTCATTGTTCGATGGTCGTCACC
66 TTTTCATTATTCGATGGTCGTCACC
*
16431013 ATCTCTTTGCAT
1 ATCCCTTTGCAT
16431025 TGTAGATGGT
Statistics
Matches: 83, Mismatches: 17, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
88 1 0.01
89 59 0.71
90 23 0.28
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (90 bp):
ATCCCTTTGCATAACTCAATAACTGAAGCTATCCCTTTTCATAATTCGATAATCGAAGCCATCCC
TTTTCATTATTCGATGGTCGTCACC
Found at i:16431033 original size:119 final size:119
Alignment explanation
Indices: 16430792--16431083 Score: 354
Period size: 119 Copynumber: 2.5 Consensus size: 119
16430782 GTAAAATCAC
* * ** * * * * * *
16430792 GATGGTTGTC-CCAACCCTTTTCATAGCTCAATAGTCGAAGCTATCCCTTTGCATAGCTCAATAG
1 GATGGTCGTCACCATCCCTTTTCATAATTCGATACTTGAAGCTATCCCTTTTCATAACTCAATAA
* * * *
16430856 TTGAAGCTATCCCTTTTCATTATTTGATGGTCGTCACCATCCCTTTTCATTATT
66 TCGAAGCTATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTGCATTATA
* * *
16430910 GATGGTCGTCACCATCCCTTTTCATAATTTGATAAC-TGAAGCTATCCCTTTTCATAATTCGATA
1 GATGGTCGTCACCATCCCTTTTCATAATTCGAT-ACTTGAAGCTATCCCTTTTCATAACTCAATA
* * * *
16430974 ATCGAAGCTATCCTTTTTCATTGTTCGATGGTCGTCACCATCTCTTTGCATTGTA
65 ATCGAAGCTATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTGCATTATA
* *
16431029 GATGGTCGTCACCATCCCTTTTCATAATTCGATTCTTGAGGCTATCCCTTTTCAT
1 GATGGTCGTCACCATCCCTTTTCATAATTCGATACTTGAAGCTATCCCTTTTCAT
16431084 TATTTTGAGG
Statistics
Matches: 147, Mismatches: 24, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
118 10 0.07
119 136 0.93
120 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (119 bp):
GATGGTCGTCACCATCCCTTTTCATAATTCGATACTTGAAGCTATCCCTTTTCATAACTCAATAA
TCGAAGCTATCCCTTTTCATTATTCGATGGTCGTCACCATCCCTTTGCATTATA
Found at i:16432699 original size:42 final size:42
Alignment explanation
Indices: 16432602--16432826 Score: 263
Period size: 42 Copynumber: 5.3 Consensus size: 42
16432592 AACAAAAATG
* * ** *
16432602 CCGCTAAAGATCATGTTCTTTAGCAGCGTTTTTTTTTCTAAGCG
1 CCGCTAAAGAACATGATCTTTAGC-G-GCATTTTTTTCTAAGCA
*
16432646 CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAGCG
1 CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAGCA
** * *
16432688 CTACTATAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCA
1 CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAGCA
* *
16432730 CCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCTAAGCA
1 CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAGCA
* * * * *
16432772 CCGGTAAAGATCATGTTCTTTAACGGCATTTTTCTCTAAG-A
1 CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAGCA
16432813 GCCGCTAAAGAACA
1 -CCGCTAAAGAACA
16432827 CCACTAAAGA
Statistics
Matches: 158, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
41 1 0.01
42 134 0.85
43 1 0.01
44 22 0.14
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (42 bp):
CCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAGCA
Found at i:16433405 original size:21 final size:21
Alignment explanation
Indices: 16433381--16433431 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
16433371 TTCTTTTGAA
*
16433381 CCTCTGCTTCTCTCGCTACAG
1 CCTCTGCTTCCCTCGCTACAG
* * *
16433402 CCTCCGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTACAG
16433423 CCTCTGCTT
1 CCTCTGCTT
16433432 TAAGTTGTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.04, C:0.49, G:0.16, T:0.31
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTACAG
Found at i:16438941 original size:9 final size:9
Alignment explanation
Indices: 16438927--16439091 Score: 161
Period size: 9 Copynumber: 19.2 Consensus size: 9
16438917 CTTTTATGTA
16438927 TTATGTAAG
1 TTATGTAAG
16438936 TTATGTAAG
1 TTATGTAAG
16438945 TTATGT-A-
1 TTATGTAAG
16438952 TTATGTAAG
1 TTATGTAAG
16438961 -TACTGTAAG
1 TTA-TGTAAG
*
16438970 TAATGTAAG
1 TTATGTAAG
16438979 TTATGTAAG
1 TTATGTAAG
*
16438988 TAATGT-A-
1 TTATGTAAG
16438995 TTATGTAAG
1 TTATGTAAG
*
16439004 TTGTGT-A-
1 TTATGTAAG
* *
16439011 TAAAGTAAG
1 TTATGTAAG
*
16439020 TTAAG-AAGG
1 TTATGTAA-G
16439029 TTATGT-A-
1 TTATGTAAG
*
16439036 TAATGTAAG
1 TTATGTAAG
16439045 TTATGTAAG
1 TTATGTAAG
* *
16439054 TTATTTAAT
1 TTATGTAAG
16439063 TTATGTAAG
1 TTATGTAAG
16439072 TTATGTAAG
1 TTATGTAAG
16439081 TTATGTAAG
1 TTATGTAAG
16439090 TT
1 TT
16439092 GTCTTGGCTT
Statistics
Matches: 128, Mismatches: 16, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
7 19 0.15
8 11 0.09
9 97 0.76
10 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:16438954 original size:25 final size:27
Alignment explanation
Indices: 16438927--16439091 Score: 161
Period size: 25 Copynumber: 6.4 Consensus size: 27
16438917 CTTTTATGTA
16438927 TTATGTAAGTTATGTAAGTTATGT-A-
1 TTATGTAAGTTATGTAAGTTATGTAAG
*
16438952 TTATGTAAG-TACTGTAAGTAATGTAAG
1 TTATGTAAGTTA-TGTAAGTTATGTAAG
*
16438979 TTATGTAAGTAATGT-A-TTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAG
* * * *
16439004 TTGTGT-A-TAAAGTAAGTTAAG-AAGG
1 TTATGTAAGTTATGTAAGTTATGTAA-G
*
16439029 TTATGT-A-TAATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAG
* *
16439054 TTATTTAATTTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATGTAAG
16439081 TTATGTAAGTT
1 TTATGTAAGTT
16439092 GTCTTGGCTT
Statistics
Matches: 117, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
23 5 0.04
24 6 0.05
25 62 0.53
26 5 0.04
27 38 0.32
28 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.44
Consensus pattern (27 bp):
TTATGTAAGTTATGTAAGTTATGTAAG
Found at i:16439067 original size:84 final size:86
Alignment explanation
Indices: 16438931--16439093 Score: 226
Period size: 84 Copynumber: 1.9 Consensus size: 86
16438921 TATGTATTAT
* *
16438931 GTAAGTTATGTAAGTTATGTATTATGTAAGTACTGTAAGTAATGTAAGTTATGTAAGTAATGT-A
1 GTAAGTTAAGTAAGTTATGTATAATGTAAGTACTGTAAGTAATGTAAGTTATGTAAGTAATGTAA
16438995 -TTATGTAAGTTGTGTATAAA
66 GTTATGTAAGTTGTGTATAAA
* * * *
16439015 GTAAGTTAAG-AAGGTTATGTATAATGTAAGTTA-TGTAAGTTATTTAATTTATGTAAGTTATGT
1 GTAAGTTAAGTAA-GTTATGTATAATGTAAG-TACTGTAAGTAATGTAAGTTATGTAAGTAATGT
16439078 AAGTTATGTAAGTTGT
64 AAGTTATGTAAGTTGT
16439094 CTTGGCTTGC
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
83 2 0.03
84 51 0.74
85 3 0.04
86 13 0.19
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (86 bp):
GTAAGTTAAGTAAGTTATGTATAATGTAAGTACTGTAAGTAATGTAAGTTATGTAAGTAATGTAA
GTTATGTAAGTTGTGTATAAA
Found at i:16439272 original size:9 final size:9
Alignment explanation
Indices: 16439258--16439535 Score: 62
Period size: 9 Copynumber: 32.1 Consensus size: 9
16439248 TATTAATAAT
16439258 TTATGTAAG
1 TTATGTAAG
16439267 TTATGTAAG
1 TTATGTAAG
16439276 TGT-TGT-A-
1 T-TATGTAAG
16439283 TTATGTAAGG
1 TTATGTAA-G
**
16439293 CAAAT-TAAG
1 -TTATGTAAG
*
16439302 TTATGTAGG
1 TTATGTAAG
*
16439311 CTATGT-A-
1 TTATGTAAG
*
16439318 TTATGCAAG
1 TTATGTAAG
*
16439327 TTATTTAAG
1 TTATGTAAG
*
16439336 TTGTGTAAG
1 TTATGTAAG
16439345 TGT-TGTATTA-
1 T-TATGTA--AG
*
16439355 TGTAAGTAAG
1 T-TATGTAAG
*
16439365 TTAT-TTA-
1 TTATGTAAG
16439372 TTATGTAAG
1 TTATGTAAG
16439381 TT-T-TAAG
1 TTATGTAAG
16439388 TCAAATATGTAAG
1 T----TATGTAAG
**
16439401 -T-TGTATT
1 TTATGTAAG
*
16439408 TTATGAAAG
1 TTATGTAAG
*
16439417 TTATATAAG
1 TTATGTAAG
*
16439426 TTATGTAGG
1 TTATGTAAG
* *
16439435 CTATGT--T
1 TTATGTAAG
* *
16439442 TTATGCAAT
1 TTATGTAAG
* *
16439451 TTATTTAAT
1 TTATGTAAG
*
16439460 TTCTGTAAG
1 TTATGTAAG
16439469 TGT-TGT-A-
1 T-TATGTAAG
16439476 TTATGTAAG
1 TTATGTAAG
*
16439485 TTGTGT-A-
1 TTATGTAAG
16439492 TTATGTAAG
1 TTATGTAAG
*
16439501 ATATGTAAG
1 TTATGTAAG
**
16439510 -T-TGTATT
1 TTATGTAAG
16439517 TTATGTAAG
1 TTATGTAAG
16439526 TTATGTAAG
1 TTATGTAAG
16439535 T
1 T
16439536 AACGAGTTAT
Statistics
Matches: 193, Mismatches: 42, Indels: 68
0.64 0.14 0.22
Matches are distributed among these distances:
6 2 0.01
7 38 0.20
8 18 0.09
9 113 0.59
10 10 0.05
11 7 0.04
12 1 0.01
13 4 0.02
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:16439484 original size:16 final size:16
Alignment explanation
Indices: 16439463--16439500 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
16439453 ATTTAATTTC
16439463 TGTAAG-TGTTGTATTA
1 TGTAAGTTG-TGTATTA
16439479 TGTAAGTTGTGTATTA
1 TGTAAGTTGTGTATTA
16439495 TGTAAG
1 TGTAAG
16439501 ATATGTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 19 0.90
17 2 0.10
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (16 bp):
TGTAAGTTGTGTATTA
Found at i:16439505 original size:25 final size:25
Alignment explanation
Indices: 16439477--16439535 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
16439467 AGTGTTGTAT
*
16439477 TATGTAAGTTGTGTATTATGTAAGA
1 TATGTAAGTTGTATATTATGTAAGA
* *
16439502 TATGTAAGTTGTATTTTATGTAAGT
1 TATGTAAGTTGTATATTATGTAAGA
16439527 TATGTAAGT
1 TATGTAAGT
16439536 AACGAGTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (25 bp):
TATGTAAGTTGTATATTATGTAAGA
Found at i:16439507 original size:16 final size:16
Alignment explanation
Indices: 16439472--16439507 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16439462 CTGTAAGTGT
* *
16439472 TGTATTATGTAAGTTG
1 TGTATTATGTAAGATA
16439488 TGTATTATGTAAGATA
1 TGTATTATGTAAGATA
16439504 TGTA
1 TGTA
16439508 AGTTGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (16 bp):
TGTATTATGTAAGATA
Found at i:16439607 original size:22 final size:22
Alignment explanation
Indices: 16439582--16439653 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
16439572 ATAATATAAG
16439582 TTATGTATTAAGTTATTATG-TA
1 TTATGTA-TAAGTTATTATGTTA
*
16439604 TTATG--TAATTTATTATGTTA
1 TTATGTATAAGTTATTATGTTA
* * *
16439624 TTATATATAAGTTATGGAAGTTA
1 TTATGTATAAGTTAT-TATGTTA
16439647 TTATGTA
1 TTATGTA
16439654 AGTTATGCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
22 12 0.30
23 11 0.28
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (22 bp):
TTATGTATAAGTTATTATGTTA
Found at i:16439638 original size:19 final size:18
Alignment explanation
Indices: 16439569--16439735 Score: 55
Period size: 19 Copynumber: 8.9 Consensus size: 18
16439559 GTTATGCAAG
16439569 ATTATAATATAAGTTATGT
1 ATTAT-ATATAAGTTATGT
16439588 ATTA-AGT-T-A-TTATGT
1 ATTATA-TATAAGTTATGT
* *
16439603 ATTATGTAATTTA-TTATGTT
1 ATTATAT-A-TAAGTTATG-T
*
16439623 ATTATATATAAGTTATGGA
1 ATTATATATAAGTTAT-GT
* *
16439642 AGTTATTATGTAAGTTATGCAAG
1 A-TTA-TATATAAGTTATG---T
*
16439665 ATTATAAAATAAGTTATGT
1 ATTAT-ATATAAGTTATGT
*
16439684 ATTATGT-T-A-TTATGT
1 ATTATATATAAGTTATGT
* *
16439699 ATTATGTAATTTA-TTATGTT
1 ATTATAT-A-TAAGTTATG-T
16439719 ATTATATATAAGTTATG
1 ATTATATATAAGTTATG
16439736 GAAGTTATTA
Statistics
Matches: 114, Mismatches: 13, Indels: 42
0.67 0.08 0.25
Matches are distributed among these distances:
15 24 0.21
16 2 0.02
17 3 0.03
18 7 0.06
19 33 0.29
20 19 0.17
21 12 0.11
22 13 0.11
23 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.50
Consensus pattern (18 bp):
ATTATATATAAGTTATGT
Found at i:16439648 original size:31 final size:32
Alignment explanation
Indices: 16439603--16439748 Score: 104
Period size: 31 Copynumber: 4.6 Consensus size: 32
16439593 GTTATTATGT
* *
16439603 ATTATGTAATTTATTATGTTATTATATATAAG
1 ATTATGGAAGTTATTATGTTATTATATATAAG
* * **
16439635 -TTATGGAAGTTATTATGTAAGT-TATGCAAG
1 ATTATGGAAGTTATTATGTTATTATATATAAG
* * * * *
16439665 ATTAT-AAAATAAGTTATG-TATTATGTTATTATG
1 ATTATGGAAGTTA-TTATGTTATTAT-ATA-TAAG
* *
16439698 TATTATGTAATTTATTATGTTATTATATATAAG
1 -ATTATGGAAGTTATTATGTTATTATATATAAG
16439731 -TTATGGAAGTTATTATGT
1 ATTATGGAAGTTATTATGT
16439749 AAGTTATGCA
Statistics
Matches: 84, Mismatches: 22, Indels: 17
0.68 0.18 0.14
Matches are distributed among these distances:
30 12 0.14
31 44 0.52
32 1 0.01
33 5 0.06
34 12 0.14
35 10 0.12
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.49
Consensus pattern (32 bp):
ATTATGGAAGTTATTATGTTATTATATATAAG
Found at i:16439655 original size:96 final size:96
Alignment explanation
Indices: 16439555--16439802 Score: 428
Period size: 96 Copynumber: 2.6 Consensus size: 96
16439545 TGTAAACTAG
*
16439555 GTAAGTTATGCAAGATTATAATATAAGTTATGTATTAAGTTATTATGTATTATGTAATTTATTAT
1 GTAAGTTATGCAAGATTATAATATAAGTTATGTATTATGTTATTATGTATTATGTAATTTATTAT
16439620 GTTATTATATATAAGTTATGGAAGTTATTAT
66 GTTATTATATATAAGTTATGGAAGTTATTAT
*
16439651 GTAAGTTATGCAAGATTATAAAATAAGTTATGTATTATGTTATTATGTATTATGTAATTTATTAT
1 GTAAGTTATGCAAGATTATAATATAAGTTATGTATTATGTTATTATGTATTATGTAATTTATTAT
16439716 GTTATTATATATAAGTTATGGAAGTTATTAT
66 GTTATTATATATAAGTTATGGAAGTTATTAT
* * *
16439747 GTAAGTTATGCAAGCTTAT-ATACCAA-TTATGTATTATGTTATTATGTATTAAGTAA
1 GTAAGTTATGCAAGATTATAATA-TAAGTTATGTATTATGTTATTATGTATTATGTAA
16439803 GCAAATGATT
Statistics
Matches: 145, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
95 31 0.21
96 114 0.79
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (96 bp):
GTAAGTTATGCAAGATTATAATATAAGTTATGTATTATGTTATTATGTATTATGTAATTTATTAT
GTTATTATATATAAGTTATGGAAGTTATTAT
Found at i:16439677 original size:22 final size:21
Alignment explanation
Indices: 16439630--16439682 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
16439620 GTTATTATAT
* * *
16439630 ATAAGTTATGGAAGTTATTAT
1 ATAAGTTATGCAAGTTATAAA
*
16439651 GTAAGTTATGCAAGATTATAAA
1 ATAAGTTATGCAAG-TTATAAA
16439673 ATAAGTTATG
1 ATAAGTTATG
16439683 TATTATGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.38
Consensus pattern (21 bp):
ATAAGTTATGCAAGTTATAAA
Found at i:16439696 original size:8 final size:7
Alignment explanation
Indices: 16439678--16439723 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
16439668 ATAAAATAAG
16439678 TTATGTA
1 TTATGTA
16439685 TTATGTTA
1 TTATG-TA
16439693 TTATGTA
1 TTATGTA
16439700 TTATGTA
1 TTATGTA
*
16439707 --ATTTA
1 TTATGTA
16439712 TTATGTTA
1 TTATG-TA
16439720 TTAT
1 TTAT
16439724 ATATAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 4 0.12
7 16 0.48
8 13 0.39
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (7 bp):
TTATGTA
Found at i:16439698 original size:15 final size:15
Alignment explanation
Indices: 16439678--16439723 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
16439668 ATAAAATAAG
16439678 TTATGTATTATGTTA
1 TTATGTATTATGTTA
16439693 TTATGTATTATG-TA
1 TTATGTATTATGTTA
*
16439707 --ATTTATTATGTTA
1 TTATGTATTATGTTA
16439720 TTAT
1 TTAT
16439724 ATATAAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 2 0.07
15 14 0.52
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (15 bp):
TTATGTATTATGTTA
Found at i:16439972 original size:61 final size:61
Alignment explanation
Indices: 16439883--16440026 Score: 175
Period size: 61 Copynumber: 2.4 Consensus size: 61
16439873 AAAAATATAA
* * * * * * *
16439883 TTATTTATAAAACTTTTAAAATTGATACTTATAAA-TTTTATTAATAATAAATCTAGAACACT
1 TTATTTAGAAAACTTATAAATTTAATACTAATAAATTTTTA-TAACAATAAATCTAGAA-AAT
* *
16439945 TT-TTTAGAAAACTTATAAATTTAATACTAATAAATTTTTATACCAATAAATTTAGAAAAT
1 TTATTTAGAAAACTTATAAATTTAATACTAATAAATTTTTATAACAATAAATCTAGAAAAT
16440005 TTATTTAGAAAACTTATAAATT
1 TTATTTAGAAAACTTATAAATT
16440027 CAGAAAAGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
60 4 0.06
61 60 0.85
62 7 0.10
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (61 bp):
TTATTTAGAAAACTTATAAATTTAATACTAATAAATTTTTATAACAATAAATCTAGAAAAT
Found at i:16439992 original size:16 final size:16
Alignment explanation
Indices: 16439959--16439997 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
16439949 TAGAAAACTT
*
16439959 ATAAA-TTTAATACTA
1 ATAAATTTTAATACCA
*
16439974 ATAAATTTTTATACCA
1 ATAAATTTTAATACCA
16439990 ATAAATTT
1 ATAAATTT
16439998 AGAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAAATTTTAATACCA
Found at i:16440026 original size:30 final size:30
Alignment explanation
Indices: 16439990--16440046 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
16439980 TTTTATACCA
* * *
16439990 ATAAATTTAGAAAATTTATTTAGAAAACTT
1 ATAAATTCAGAAAAGTTATATAGAAAACTT
16440020 ATAAATTCAGAAAAGTTATATAGAAAA
1 ATAAATTCAGAAAAGTTATATAGAAAA
16440047 TAAAACAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (30 bp):
ATAAATTCAGAAAAGTTATATAGAAAACTT
Found at i:16441922 original size:15 final size:16
Alignment explanation
Indices: 16441902--16441936 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
16441892 TTCAAATTTA
*
16441902 TAAATACTCTCAAT-T
1 TAAATACTATCAATAT
16441917 TAAATACTATCAATAT
1 TAAATACTATCAATAT
16441933 TAAA
1 TAAA
16441937 ATTGATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATACTATCAATAT
Found at i:16443009 original size:8 final size:7
Alignment explanation
Indices: 16442968--16443052 Score: 64
Period size: 7 Copynumber: 12.0 Consensus size: 7
16442958 ACTAAAGTGG
16442968 CCTAAAC
1 CCTAAAC
*
16442975 CCCAAAC
1 CCTAAAC
* *
16442982 CCCAAAT
1 CCTAAAC
*
16442989 CTTAAAC
1 CCTAAAC
16442996 CCTAAAC
1 CCTAAAC
16443003 TCCTAAAC
1 -CCTAAAC
16443011 CCTAAAC
1 CCTAAAC
*
16443018 CCAAAAC
1 CCTAAAC
*
16443025 ACC-AAAA
1 -CCTAAAC
* *
16443032 CCTACAT
1 CCTAAAC
*
16443039 CATAAAC
1 CCTAAAC
16443046 CCTAAAC
1 CCTAAAC
16443053 TTAAAACTCT
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
6 2 0.03
7 50 0.82
8 9 0.15
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.14
Consensus pattern (7 bp):
CCTAAAC
Found at i:16443524 original size:115 final size:112
Alignment explanation
Indices: 16443331--16443925 Score: 540
Period size: 115 Copynumber: 5.2 Consensus size: 112
16443321 AACTCTGCAC
*
16443331 TTTGGTTAAGATATTTTGCGGCACTTCTCAAAAAGCGCCGCTAATACTATGCTTTAGCGGCGATT
1 TTTGGTTAAGATATTTTGCGGCGCTTCTC-AAAAGCGCCGCTAATACTATGCTTTAGCGGC-ATT
* * * * *
16443396 TCTCGT-GGACGCCACTAATTCTAGTATACATCAAGACTTAAATGCTGCAT
64 TCCCATAAG-CGCCACTAATTCTAGTATACATCAAGAC-AAAATGCTGCGT
* * *
16443446 TTTGGTTAATATATTTTGCGGCGCTTCTCAAAGCGCGCCGCTAATAGTATGCTTTAGCGGCATGT
1 TTTGGTTAAGATATTTTGCGGCGCTTCTCAAA-AGCGCCGCTAATACTATGCTTTAGCGGCAT-T
* * * *
16443511 TCCCATAAGCGCCACTAATTCTAATACACCTCAAGACCAAACT-CTGCGT
64 TCCCATAAGCGCCACTAATTCTAGTATACATCAAGA-CAAAATGCTGCGT
* * * *
16443560 TTTGG-TGAGCATATTTTGCGGCGCTTTTTGC-AAAGCGCCACTAATACTATGATTTAGCGGCAT
1 TTTGGTTAAG-ATATTTTGCGGCGC-TTCT-CAAAAGCGCCGCTAATACTATGCTTTAGCGGCAT
* * * * *
16443623 TTTCCAGTATA-CGCCACTAATTATAGTATACATAAAGACAAAAACGCTACGT
63 TTCCCA-TA-AGCGCCACTAATTCTAGTATACATCAAGAC-AAAATGCTGCGT
* * * * *
16443675 TTTGGTTAAGAAATTTTGCGGCGCTTCTCCAAACGCGCCGCTAATAGTATGCCTT-GACGGCGTG
1 TTTGGTTAAGATATTTTGCGGCGCTTCT-CAAAAGCGCCGCTAATACTATGCTTTAG-CGGCAT-
** * * *
16443739 TTCCC-TTTGCGCCACTAATTCTAGTATACCTCAAGACCAAACT-CTACGT
63 TTCCCATAAGCGCCACTAATTCTAGTATACATCAAGA-CAAAATGCTGCGT
* * * *
16443788 TTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATAATATGATTTAGCGGCGTTT
1 TTTGGTTAAGATATTTTGCGGCGCTTCTCA-AAAGCGCCGCTAATACTATGCTTTAGCGGC-ATT
* * * * ** * * *
16443853 TCCCGTAAGCGCCATTAACTGTAACATACATCAAGACCAAAACGGTGCGC
64 TCCCATAAGCGCCACTAATTCTAGTATACATCAAGA-CAAAATGCTGCGT
*
16443903 TTTGGTTAGGATATTTTGCGGCG
1 TTTGGTTAAGATATTTTGCGGCG
16443926 TTTTCCCATA
Statistics
Matches: 390, Mismatches: 68, Indels: 44
0.78 0.14 0.09
Matches are distributed among these distances:
112 2 0.01
113 69 0.18
114 145 0.37
115 164 0.42
116 10 0.03
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (112 bp):
TTTGGTTAAGATATTTTGCGGCGCTTCTCAAAAGCGCCGCTAATACTATGCTTTAGCGGCATTTC
CCATAAGCGCCACTAATTCTAGTATACATCAAGACAAAATGCTGCGT
Found at i:16443721 original size:229 final size:226
Alignment explanation
Indices: 16443313--16443925 Score: 739
Period size: 229 Copynumber: 2.7 Consensus size: 226
16443303 ATGCATGGTT
** * *
16443313 AAGACCAAAACTCTGCACTTTGGTTAAGATATTTTGCGGCACTTCTCAAAAAGCGCCGCTAATAC
1 AAGACC-AAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCCGCTAATAC
* * * ** *
16443378 TATGCTTTAGCGGCGA-TTTCTCGTGGACGCCACTAATTCTAGTATACATCAAGACTTAAATGCT
65 TATGATTTAGCGGC-ATTTTC-CGT-AACGCCACTAATTATAGTATACATCAAGACAAAAACGCT
* * *
16443442 GCATTTTGGTTAATATATTTTGCGGCGCTTCTCAAAGCGCGCCGCTAATAGTATG-CTTTAGCGG
127 GCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCAAAGCGCGCCGCTAATAGTATGCCTTGA-CGG
16443506 CATGTTCCCATAAGCGCCACTAATTCTAATACACCTC
191 CATGTTCCC-TAAGCGCCACTAATTCTAATACACCTC
* * ** *
16443543 AAGACCAAACTCTGCGTTTTGG-TGAGCATATTTTGCGGCGCTTTTTGCAAAGCGCCACTAATAC
1 AAGACCAAACTCTGCGTTTTGGTTAAG-ATATTTTGCGGCGCTTCTCACAAAGCGCCGCTAATAC
* *
16443607 TATGATTTAGCGGCATTTTCCAGTATACGCCACTAATTATAGTATACATAAAGACAAAAACGCTA
65 TATGATTTAGCGGCATTTTCC-GTA-ACGCCACTAATTATAGTATACATCAAGACAAAAACGCTG
*
16443672 CGTTTTGGTTAAGAAATTTTGCGGCGCTTCTCCAAA-CGCGCCGCTAATAGTATGCCTTGACGGC
128 CGTTTTGGTTAAGATATTTTGCGGCGCTTCT-CAAAGCGCGCCGCTAATAGTATGCCTTGACGGC
* ** * *
16443736 GTGTTCCCTTTGCGCCACTAATTCTAGTATACCTC
192 ATGTTCCCTAAGCGCCACTAATTCTAATACACCTC
* * *
16443771 AAGACCAAACTCTACGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATAAT
1 AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCCGCTAATACT
* * * * ** * *
16443836 ATGATTTAGCGGCGTTTTCCCGTAAGCGCCATTAACTGTAACATACATCAAGACCAAAACGGTGC
66 ATGATTTAGCGGCATTTT-CCGTAA-CGCCACTAATTATAGTATACATCAAGACAAAAACGCTGC
* *
16443901 GCTTTGGTTAGGATATTTTGCGGCG
129 GTTTTGGTTAAGATATTTTGCGGCG
16443926 TTTTCCCATA
Statistics
Matches: 327, Mismatches: 47, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
227 1 0.00
228 153 0.47
229 159 0.49
230 14 0.04
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (226 bp):
AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAGCGCCGCTAATACT
ATGATTTAGCGGCATTTTCCGTAACGCCACTAATTATAGTATACATCAAGACAAAAACGCTGCGT
TTTGGTTAAGATATTTTGCGGCGCTTCTCAAAGCGCGCCGCTAATAGTATGCCTTGACGGCATGT
TCCCTAAGCGCCACTAATTCTAATACACCTC
Found at i:16443909 original size:228 final size:229
Alignment explanation
Indices: 16443313--16443925 Score: 745
Period size: 228 Copynumber: 2.7 Consensus size: 229
16443303 ATGCATGGTT
** *
16443313 AAGACCAAAACTCTGCACTTTGGTTAAGATATTTTGCGGCACTTCTCA-AAAAGCGCCGCTAATA
1 AAGACC-AAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAA-CGCCGCTAATA
* * * * * ** *
16443377 CTATGCTTTAGCGGCGATTTCTCGT-GGACGCCACTAATTCTAGTATACATCAAGACTTAAATGC
64 CTATGATTTAGCGGCGTTTTCCCGTAAG-CGCCACTAATTATAGTATACATCAAGACAAAAACGC
* * *
16443441 TGCATTTTGGTTAATATATTTTGCGGCGCTTCTCAAAGCGCGCCGCTAATAGTATGCTTTAGCGG
128 TGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCAAAGCGCGCCGCTAATAGTATGCTTGAGCGG
16443506 CATGTTCCCATAAGCGCCACTAATTCTAATACACCTC
193 CATGTTCCCATAAGCGCCACTAATTCTAATACACCTC
* * ** * *
16443543 AAGACCAAACTCTGCGTTTTGG-TGAGCATATTTTGCGGCGCTTTTTGCAAAGCGCCACTAATAC
1 AAGACCAAACTCTGCGTTTTGGTTAAG-ATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATAC
* * *
16443607 TATGATTTAGCGGCATTTTCCAGTATA-CGCCACTAATTATAGTATACATAAAGACAAAAACGCT
65 TATGATTTAGCGGCGTTTTCCCGTA-AGCGCCACTAATTATAGTATACATCAAGACAAAAACGCT
* *
16443671 ACGTTTTGGTTAAGAAATTTTGCGGCGCTTCTCCAAA-CGCGCCGCTAATAGTATGCCTTGA-CG
129 GCGTTTTGGTTAAGATATTTTGCGGCGCTTCT-CAAAGCGCGCCGCTAATAGTATG-CTTGAGCG
* ** * *
16443734 GCGTGTTCCC-TTTGCGCCACTAATTCTAGTATACCTC
192 GCATGTTCCCATAAGCGCCACTAATTCTAATACACCTC
* *
16443771 AAGACCAAACTCTACGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATAAT
1 AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATACT
* * * ** * *
16443836 ATGATTTAGCGGCGTTTTCCCGTAAGCGCCATTAACTGTAACATACATCAAGACCAAAACGGTGC
66 ATGATTTAGCGGCGTTTTCCCGTAAGCGCCACTAATTATAGTATACATCAAGACAAAAACGCTGC
* *
16443901 GCTTTGGTTAGGATATTTTGCGGCG
131 GTTTTGGTTAAGATATTTTGCGGCG
16443926 TTTTCCCATA
Statistics
Matches: 323, Mismatches: 52, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
227 1 0.00
228 153 0.47
229 152 0.47
230 17 0.05
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (229 bp):
AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATACT
ATGATTTAGCGGCGTTTTCCCGTAAGCGCCACTAATTATAGTATACATCAAGACAAAAACGCTGC
GTTTTGGTTAAGATATTTTGCGGCGCTTCTCAAAGCGCGCCGCTAATAGTATGCTTGAGCGGCAT
GTTCCCATAAGCGCCACTAATTCTAATACACCTC
Found at i:16444132 original size:112 final size:112
Alignment explanation
Indices: 16443932--16444205 Score: 329
Period size: 112 Copynumber: 2.4 Consensus size: 112
16443922 GGCGTTTTCC
* * * * ** *
16443932 CATAAGCGCCACAAATTCTAATATACCTCTAGACCAAACTCTGCATTTTGGTTAACATATCTTAC
1 CATAAGCGCCACTAATTCTAATATACATCAAGACAAAACGATGCATTTTCGTTAACATATCTTAC
* *
16443997 GGCGCTTTTCATAAGCGCGGCTAATACTTGCTTTAGCGGCAGGTTT-T
66 GGCGCTTTTCATAAGCGCCGCTAATACTTGCTTCAGCGGCA-GTTTAT
* * * * *
16444044 CGTAAGCGCCACTAATTCTAATATACAGCAAGACAAAACGATGCATTTTCGTTAAGAT-TTTTGC
1 CATAAGCGCCACTAATTCTAATATACATCAAGACAAAACGATGCATTTTCGTTAACATATCTTAC
*
16444108 GGCGC-TTTCGATAATGCGCCGCTAATACTTGCTTCAGCGGCATTTTAT
66 GGCGCTTTTC-ATAA-GCGCCGCTAATACTTGCTTCAGCGGCAGTTTAT
* * *
16444156 CATAATCGCCACTAATTCTAGTATACATCAAGACCAAAACGATGCGTTTT
1 CATAAGCGCCACTAATTCTAATATACATCAAGA-CAAAACGATGCATTTT
16444206 GGTCTTGAGA
Statistics
Matches: 138, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
110 4 0.03
111 16 0.12
112 103 0.75
113 15 0.11
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (112 bp):
CATAAGCGCCACTAATTCTAATATACATCAAGACAAAACGATGCATTTTCGTTAACATATCTTAC
GGCGCTTTTCATAAGCGCCGCTAATACTTGCTTCAGCGGCAGTTTAT
Found at i:16446799 original size:19 final size:20
Alignment explanation
Indices: 16446764--16446809 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
16446754 TTCATTGATG
**
16446764 AGTTTG-TGATATTTTTA-A
1 AGTTTGATGATAGATTTATA
16446782 AGTTTGATGATAGATTTATA
1 AGTTTGATGATAGATTTATA
*
16446802 AGCTTGAT
1 AGTTTGAT
16446810 AATTAAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 6 0.26
19 9 0.39
20 8 0.35
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (20 bp):
AGTTTGATGATAGATTTATA
Found at i:16447003 original size:13 final size:13
Alignment explanation
Indices: 16446985--16447009 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16446975 CTGTGGAAGA
16446985 TTTGGCTAGCATT
1 TTTGGCTAGCATT
16446998 TTTGGCTAGCAT
1 TTTGGCTAGCAT
16447010 AAATAGTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (13 bp):
TTTGGCTAGCATT
Found at i:16448153 original size:19 final size:20
Alignment explanation
Indices: 16448115--16448155 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
16448105 TTTTTTATAT
16448115 AAGTATCGATAAAATAGACCA
1 AAGTATCGAT-AAATAGACCA
*
16448136 AAGTATCGAT-ACTAGACCA
1 AAGTATCGATAAATAGACCA
16448155 A
1 A
16448156 TTGAACAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
21 10 0.53
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.20
Consensus pattern (20 bp):
AAGTATCGATAAATAGACCA
Found at i:16452214 original size:24 final size:24
Alignment explanation
Indices: 16452157--16452214 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
16452147 ATGCTCATGC
*
16452157 GAGCATATAACGAGTAGCTCCGAA
1 GAGCATTTAACGAGTAGCTCCGAA
* * * *
16452181 AAGCACTTAACGGGTAGCTCCGAG
1 GAGCATTTAACGAGTAGCTCCGAA
16452205 GAGCATTTAA
1 GAGCATTTAA
16452215 TCAGGAAACA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (24 bp):
GAGCATTTAACGAGTAGCTCCGAA
Found at i:16463549 original size:95 final size:93
Alignment explanation
Indices: 16463396--16463586 Score: 328
Period size: 95 Copynumber: 2.0 Consensus size: 93
16463386 AAAAGCAAAC
* **
16463396 CAAACGCTAGAAGAATCGAGAAAAAACCCAGTCTCTTTGTGCTAAAAATCACAACACTAAAGTTA
1 CAAACGCTAGAAGAATCAAGAAAAAACCCAGTCTCTCCGTGCTAAAAATCACAACACTAAAGTTA
16463461 GAAAAATCTCCTAATTTGGATTATATGA
66 GAAAAATCTCCTAATTTGGATTATATGA
16463489 CAAACGCTAGAAGAATCAAGAAAAAACCCACAGTCTCTCCGTGCTAAAAATCACAACACTAAAGT
1 CAAACGCTAGAAGAATCAAGAAAAAA-CC-CAGTCTCTCCGTGCTAAAAATCACAACACTAAAGT
*
16463554 TAGGAAAATCTCCTAATTTGGATTATATGA
64 TAGAAAAATCTCCTAATTTGGATTATATGA
16463584 CAA
1 CAA
16463587 TGAGTGAACA
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
93 25 0.27
94 2 0.02
95 65 0.71
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (93 bp):
CAAACGCTAGAAGAATCAAGAAAAAACCCAGTCTCTCCGTGCTAAAAATCACAACACTAAAGTTA
GAAAAATCTCCTAATTTGGATTATATGA
Found at i:16466143 original size:25 final size:25
Alignment explanation
Indices: 16466115--16466173 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
16466105 CGAACATGTA
*
16466115 AACGGGAAGCTC-TTTCGAGCCATAT
1 AACGGGAAGCTCATGT-GAGCCATAT
*
16466140 AACGGGAAGCTCATGTGAGCTATAT
1 AACGGGAAGCTCATGTGAGCCATAT
16466165 AACGGGAAG
1 AACGGGAAG
16466174 TTCAATCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (25 bp):
AACGGGAAGCTCATGTGAGCCATAT
Found at i:16468431 original size:16 final size:16
Alignment explanation
Indices: 16468407--16468440 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
16468397 GGTAGGAAAC
16468407 TATGGTATAAAATTTA
1 TATGGTATAAAATTTA
*
16468423 TATGTTATAAAATTTA
1 TATGGTATAAAATTTA
16468439 TA
1 TA
16468441 ATTTAATTAT
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:0.00, G:0.09, T:0.47
Consensus pattern (16 bp):
TATGGTATAAAATTTA
Found at i:16468443 original size:7 final size:7
Alignment explanation
Indices: 16468433--16468477 Score: 63
Period size: 7 Copynumber: 6.3 Consensus size: 7
16468423 TATGTTATAA
16468433 AATTTAT
1 AATTTAT
16468440 AATTTAAT
1 AATTT-AT
*
16468448 TATTTAT
1 AATTTAT
*
16468455 AATGTAT
1 AATTTAT
16468462 AATTTAT
1 AATTTAT
16468469 AATTTAT
1 AATTTAT
16468476 AA
1 AA
16468478 ATGAAAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (7 bp):
AATTTAT
Found at i:16470230 original size:15 final size:16
Alignment explanation
Indices: 16470204--16470236 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
16470194 CACAAAGGAA
*
16470204 TTGGCATATTAACATG
1 TTGGCATATTAAAATG
16470220 TTGGC-TATTAAAATG
1 TTGGCATATTAAAATG
16470235 TT
1 TT
16470237 TTGTTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.42
Consensus pattern (16 bp):
TTGGCATATTAAAATG
Found at i:16491203 original size:19 final size:18
Alignment explanation
Indices: 16491179--16491255 Score: 66
Period size: 19 Copynumber: 4.1 Consensus size: 18
16491169 CACAGTTATT
16491179 ATTTTAGAATATTTTTAAA
1 ATTTTAGAAT-TTTTTAAA
* *
16491198 ATTTTA-ACTTTTTATATAT
1 ATTTTAGAATTTTT-TA-AA
*
16491217 TTTTTAGAATTTTTTTAAA
1 ATTTTAGAA-TTTTTTAAA
*
16491236 AGTTTGAGAATTTTTTAAA
1 A-TTTTAGAATTTTTTAAA
16491255 A
1 A
16491256 ATATAAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
17 4 0.09
18 4 0.09
19 23 0.50
20 10 0.22
21 5 0.11
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTTTAGAATTTTTTAAA
Found at i:16503801 original size:15 final size:15
Alignment explanation
Indices: 16503764--16503805 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
16503754 TGAATATGGA
*
16503764 GATAATAATAGTAAT
1 GATAATAATAATAAT
*
16503779 GATGATAATATATAAT
1 GATAATAATA-ATAAT
16503795 -ATAATAATAAT
1 GATAATAATAAT
16503806 GTTTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 17 0.74
16 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (15 bp):
GATAATAATAATAAT
Found at i:16509495 original size:19 final size:20
Alignment explanation
Indices: 16509456--16509495 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
16509446 TTTACAAAAT
*
16509456 TTCATATTATCCATAATGTA
1 TTCACATTATCCATAATGTA
*
16509476 TTCACATTAT-CATTATGTA
1 TTCACATTATCCATAATGTA
16509495 T
1 T
16509496 GTATGTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCACATTATCCATAATGTA
Found at i:16510847 original size:20 final size:22
Alignment explanation
Indices: 16510796--16510853 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
16510786 TTATTATTAG
*
16510796 ATATATTTTAATAACAATAAAA
1 ATATAATTTAATAACAATAAAA
* *
16510818 ATAAAATTTAATAA-AAT-AAT
1 ATATAATTTAATAACAATAAAA
16510838 ATATAATTTAATAACA
1 ATATAATTTAATAACA
16510854 TTCTTAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 15 0.48
21 4 0.13
22 12 0.39
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATAATTTAATAACAATAAAA
Found at i:16510909 original size:23 final size:21
Alignment explanation
Indices: 16510883--16510925 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16510873 TAAAATATGA
16510883 ATTAAAAAATCATAATATATAAT
1 ATTAAAAAA--ATAATATATAAT
*
16510906 ATTATAAAAATAATATATAA
1 ATTAAAAAAATAATATATAA
16510926 CCTACGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAAATAATATATAAT
Found at i:16514054 original size:16 final size:16
Alignment explanation
Indices: 16514030--16514067 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
16514020 TAATAAAATT
*
16514030 AAAACTAATTGTTATC
1 AAAATTAATTGTTATC
*
16514046 AAAATTAATTGTTATT
1 AAAATTAATTGTTATC
16514062 AAAATT
1 AAAATT
16514068 GTATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (16 bp):
AAAATTAATTGTTATC
Found at i:16514306 original size:52 final size:52
Alignment explanation
Indices: 16514228--16514331 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
16514218 ATTGCATGTT
* *
16514228 CACCATCCTGTTCACTGGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
1 CACCATCCTATTCACTAGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
*
16514280 CACCATCCTATTCACTAGACATTGAATCATTTGGGTCTCTTTCTATTAAACA
1 CACCATCCTATTCACTAGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
16514332 ATTAAAAGGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.36
Consensus pattern (52 bp):
CACCATCCTATTCACTAGACATTGAATCACTTGGGTCTCTTTCTATTAAACA
Found at i:16514531 original size:15 final size:15
Alignment explanation
Indices: 16514511--16514541 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16514501 TTTATAGCAA
16514511 TAAACATACTTAATT
1 TAAACATACTTAATT
16514526 TAAACATACTTAATT
1 TAAACATACTTAATT
16514541 T
1 T
16514542 TATCCTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAACATACTTAATT
Found at i:16514749 original size:9 final size:9
Alignment explanation
Indices: 16514737--16514762 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
16514727 AACATCATCC
16514737 TCATCGTCG
1 TCATCGTCG
16514746 TCATCGTCG
1 TCATCGTCG
16514755 TCATCGTC
1 TCATCGTC
16514763 CCTTTTGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.19, T:0.35
Consensus pattern (9 bp):
TCATCGTCG
Found at i:16517050 original size:45 final size:45
Alignment explanation
Indices: 16516986--16517081 Score: 158
Period size: 45 Copynumber: 2.1 Consensus size: 45
16516976 AGCAAGGCAA
16516986 TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAATAGGC
1 TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAATAGGC
* *
16517031 TAATGTGAAATTT-TGAGCTAATTTTCCATTATATAAACAATCGGC
1 TAATGTGAAATTTCT-AGCTAATGTTCCATTATATAAACAATAGGC
16517076 TAATGT
1 TAATGT
16517082 TCCATTTATA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 1 0.02
45 47 0.98
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (45 bp):
TAATGTGAAATTTCTAGCTAATGTTCCATTATATAAACAATAGGC
Found at i:16518534 original size:10 final size:10
Alignment explanation
Indices: 16518519--16518550 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
16518509 GCCTAAAATT
16518519 ATATATAATG
1 ATATATAATG
*
16518529 ATATATAATA
1 ATATATAATG
16518539 ATATATAATG
1 ATATATAATG
16518549 AT
1 AT
16518551 GGGGATGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (10 bp):
ATATATAATG
Found at i:16520134 original size:43 final size:43
Alignment explanation
Indices: 16520073--16520160 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
16520063 TTTTATCTTG
16520073 TATATTTAGAGATGCCATGTTATACACCAGATGCTTATGTCCA
1 TATATTTAGAGATGCCATGTTATACACCAGATGCTTATGTCCA
16520116 TATATTTAGAGATGCCATGTTATACACCAGATGCTTATGTCCA
1 TATATTTAGAGATGCCATGTTATACACCAGATGCTTATGTCCA
16520159 TA
1 TA
16520161 CTTTACTTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (43 bp):
TATATTTAGAGATGCCATGTTATACACCAGATGCTTATGTCCA
Found at i:16533254 original size:30 final size:29
Alignment explanation
Indices: 16533188--16533259 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
16533178 ATACTCTTCA
* *
16533188 TATATTT-AGAATTTAGTCTCTTTATTTT
1 TATATTTAAGAATTTAATCCCTTTATTTT
*
16533216 TATTTTTAAGAATTTAATCCCTTTACTTTT
1 TATATTTAAGAATTTAATCCCTTTA-TTTT
*
16533246 T-TAATTTAAAAATT
1 TAT-ATTTAAGAATT
16533260 CAGGTGCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.17
29 16 0.44
30 14 0.39
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (29 bp):
TATATTTAAGAATTTAATCCCTTTATTTT
Found at i:16539598 original size:19 final size:19
Alignment explanation
Indices: 16539574--16539611 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
16539564 TTGCGGATTT
16539574 TTTAAAGAAA-ATTATTTTA
1 TTTAAA-AAATATTATTTTA
16539593 TTTAAAAAATATTATTTTA
1 TTTAAAAAATATTATTTTA
16539612 ATGAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTAAAAAATATTATTTTA
Found at i:16540692 original size:18 final size:17
Alignment explanation
Indices: 16540664--16540702 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
16540654 TAATGCATGA
16540664 TATTTAAAG-TTATTAAT
1 TATTTAAAGTTTATT-AT
16540681 TATTTAAAAGTTTATTAT
1 TATTT-AAAGTTTATTAT
16540699 TATT
1 TATT
16540703 AGTATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 10 0.50
19 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TATTTAAAGTTTATTAT
Found at i:16541071 original size:32 final size:31
Alignment explanation
Indices: 16541029--16541110 Score: 78
Period size: 32 Copynumber: 2.6 Consensus size: 31
16541019 AATACATCTA
*
16541029 AAAAATATATAAAAATAAAAAAAATAATTGTTG
1 AAAAA-ATATAAAAATAAAAAAAAT-ATTGTTC
* *
16541062 AAAAAATATATAACAAT-ACAAAAATATTTTTC
1 AAAAAATATA-AA-AATAAAAAAAATATTGTTC
*
16541094 AAAAAAT-TAATAATAAA
1 AAAAAATATAAAAATAAA
16541111 TTTAAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
29 3 0.07
30 2 0.05
31 2 0.05
32 17 0.41
33 14 0.34
34 3 0.07
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (31 bp):
AAAAAATATAAAAATAAAAAAAATATTGTTC
Found at i:16541279 original size:17 final size:18
Alignment explanation
Indices: 16541249--16541294 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
16541239 ATTTAAATTG
16541249 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
16541267 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
16541283 --GTCGCGGTCGCG
1 CGGTCGCGGTCGCG
16541295 GACATAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 3 0.11
17 6 0.22
18 7 0.26
ACGTcount: A:0.00, C:0.30, G:0.41, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:16542303 original size:3 final size:3
Alignment explanation
Indices: 16542295--16542327 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
16542285 GTAGTTTACT
16542295 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16542328 ACGTCAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16545072 original size:21 final size:21
Alignment explanation
Indices: 16545048--16545092 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
16545038 TCCTCCCAAC
16545048 ACCCACAACC-GAGCAACCACA
1 ACCC-CAACCTGAGCAACCACA
*
16545069 ACCCCTACCTGAGCAACCACA
1 ACCCCAACCTGAGCAACCACA
16545090 ACC
1 ACC
16545093 TCCGCTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.38, C:0.49, G:0.09, T:0.04
Consensus pattern (21 bp):
ACCCCAACCTGAGCAACCACA
Found at i:16546299 original size:125 final size:126
Alignment explanation
Indices: 16545945--16546461 Score: 692
Period size: 124 Copynumber: 4.1 Consensus size: 126
16545935 GGCCAAACAT
* *
16545945 GAACTACTGTAGAAAAAGAGCGT-C-CATGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCGTC
1 GAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * *
16546008 CCGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * * * *
16546069 GAACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTTCA-TCAATTTTGCTAATAGTGCA
1 GAACTACTGTAGAAAAAGAGCGTCCACATGAGAGC-TTTTTTCAGT-AATTTTGCTGACAGTGCA
* *
16546133 TCTTGCTTGAAGCGTTTTTGACACTA-TTGTTCAGAAACGTCTTCTCAAATTTATTTTTT-AG
64 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * *
16546194 GAACTATTGTAGAAAAAGAGCATCCACATGAGAGCTTTTTTCA-TCAATTTAGCTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGT-AATTTTGCTGACAGTGCAT
* * *
16546258 CCTGCTTGAAGCGTTTTTGATACTATTTGTTTAGAACCGTCTTCTC-AAATTATTTTTTCAG
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
* * * * * *
16546319 AAATTACTATAG-AAAAGAGCGTCCACGTGAGAGCTTTTTTTAGTAGTTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* *
16546383 TTGCTTGAAGCATTTTTGACACTATTTGTTCAG-AACTGTCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAAC-GTCTTCTCAAAATTATTTTTTCAG
16546444 GAACTACTGTAGAGAAAA
1 GAACTACTGTAGA-AAAA
16546462 ACCAATATCC
Statistics
Matches: 342, Mismatches: 40, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
123 2 0.01
124 164 0.48
125 85 0.25
126 40 0.12
127 51 0.15
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACATGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAG
Found at i:16546725 original size:15 final size:15
Alignment explanation
Indices: 16546702--16546740 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
16546692 TTATTTTAAC
* *
16546702 AAAAA-CCTAACCCT
1 AAAAACCCTAAACCA
16546716 AAAAACCCTAAACCA
1 AAAAACCCTAAACCA
16546731 AAAAACCCTA
1 AAAAACCCTA
16546741 GGGACTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.56, C:0.33, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAACCCTAAACCA
Found at i:16546726 original size:42 final size:43
Alignment explanation
Indices: 16546632--16546726 Score: 131
Period size: 42 Copynumber: 2.2 Consensus size: 43
16546622 AAAAATTCCT
* *
16546632 AAAACCCAGAACCCTAAATTATTTTAACAAAACCCTAAACCCTA
1 AAAACCC-TAACCCTAAATTATTTTAACAAAAACCTAAACCCTA
* *
16546676 CAAA-CCTAACCTTAAATTATTTTAACAAAAACCT-AACCCTA
1 AAAACCCTAACCCTAAATTATTTTAACAAAAACCTAAACCCTA
16546717 AAAACCCTAA
1 AAAACCCTAA
16546727 ACCAAAAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
41 10 0.22
42 30 0.67
43 2 0.04
44 3 0.07
ACGTcount: A:0.48, C:0.28, G:0.01, T:0.22
Consensus pattern (43 bp):
AAAACCCTAACCCTAAATTATTTTAACAAAAACCTAAACCCTA
Found at i:16547207 original size:16 final size:16
Alignment explanation
Indices: 16547167--16547224 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
16547157 GGTTGGGGTG
* *
16547167 AATAGAATAGGGTTAT
1 AATAGAATAAGATTAT
*
16547183 AAT-GAAATAGAGA-TGT
1 AATAG-AATA-AGATTAT
16547199 AATAGAATAAGATTAT
1 AATAGAATAAGATTAT
16547215 AATAGAATAA
1 AATAGAATAA
16547225 AACTATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 4 0.12
16 28 0.82
17 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (16 bp):
AATAGAATAAGATTAT
Found at i:16547231 original size:16 final size:16
Alignment explanation
Indices: 16547198--16547233 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16547188 AATAGAGATG
* *
16547198 TAATAGAATAAGATTA
1 TAATAGAATAAAACTA
16547214 TAATAGAATAAAACTA
1 TAATAGAATAAAACTA
16547230 TAAT
1 TAAT
16547234 CAGTAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (16 bp):
TAATAGAATAAAACTA
Found at i:16550106 original size:192 final size:192
Alignment explanation
Indices: 16549867--16550249 Score: 721
Period size: 192 Copynumber: 2.0 Consensus size: 192
16549857 CTCGGGTTAG
16549867 GTTACTATACTTAAATCTAAATGAACTAAATTATGTATGAGCTATATATGGAACTCACTCCAATA
1 GTTACTATACTTAAATCTAAATGAACTAAATTATGTATGAGCTATATATGGAACTCACTCCAATA
* *
16549932 CCTTGATTAATTTCCACCTTTGATTTGTAGAATTAGCTGTAATTAACTTTGCATTTTTAAATAGT
66 CCTTGATTAATTTCCACATTTGATTTGTAGAATTAGCTCTAATTAACTTTGCATTTTTAAATAGT
*
16549997 ACATCTTGTAAGCGTATGATAACATTTAAAACATTATGAGATAATCTGCTAACAGTTTCCCT
131 ACATCTTGTAAGCGTATGATAACATTTAAAACATTATGAGATAATCTGCGAACAGTTTCCCT
16550059 GTTACTATACTTAAATCTAAATGAACTAAATTATGTATGAGCTATATATGGAACTCACTCCAATA
1 GTTACTATACTTAAATCTAAATGAACTAAATTATGTATGAGCTATATATGGAACTCACTCCAATA
* *
16550124 CCTTGATTAATTTCCAGATTTGATTTGTAGAATTAGCTCTAATTGACTTTGCATTTTTAAATAGT
66 CCTTGATTAATTTCCACATTTGATTTGTAGAATTAGCTCTAATTAACTTTGCATTTTTAAATAGT
16550189 ACATCTTGTAAGCGTATGATAACATTTAAAACATTATGAGATAATCTGCGAACAGTTTCCC
131 ACATCTTGTAAGCGTATGATAACATTTAAAACATTATGAGATAATCTGCGAACAGTTTCCC
16550250 CGGACCTATT
Statistics
Matches: 186, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
192 186 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (192 bp):
GTTACTATACTTAAATCTAAATGAACTAAATTATGTATGAGCTATATATGGAACTCACTCCAATA
CCTTGATTAATTTCCACATTTGATTTGTAGAATTAGCTCTAATTAACTTTGCATTTTTAAATAGT
ACATCTTGTAAGCGTATGATAACATTTAAAACATTATGAGATAATCTGCGAACAGTTTCCCT
Found at i:16552460 original size:19 final size:19
Alignment explanation
Indices: 16552436--16552529 Score: 161
Period size: 19 Copynumber: 4.8 Consensus size: 19
16552426 AATTTTTGAG
16552436 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
16552455 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
16552474 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
16552493 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
16552514 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
16552530 ATATATGATT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
19 52 0.73
21 19 0.27
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:16552511 original size:40 final size:38
Alignment explanation
Indices: 16552436--16552536 Score: 161
Period size: 40 Copynumber: 2.7 Consensus size: 38
16552426 AATTTTTGAG
16552436 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
*
16552474 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATG--ATATGCAATCCTAGATAT
16552514 GATATGCAATCTTAGA-AT-ATATG
1 GATATGCAATCTTAGATATGATATG
16552537 ATTTTGTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
36 5 0.08
38 20 0.33
39 2 0.03
40 33 0.55
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
Found at i:16553268 original size:13 final size:14
Alignment explanation
Indices: 16553245--16553291 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
16553235 TTATTTTATT
16553245 TTATTTATTTATAA
1 TTATTTATTTATAA
16553259 TTATTT-TTTATAA
1 TTATTTATTTATAA
* *
16553272 TCTATATATGTTATAT
1 T-TATTTAT-TTATAA
16553288 TTAT
1 TTAT
16553292 CTTTGTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 8 0.29
14 10 0.36
15 4 0.14
16 6 0.21
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (14 bp):
TTATTTATTTATAA
Found at i:16553726 original size:19 final size:20
Alignment explanation
Indices: 16553699--16553739 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
16553689 TTCTAGGCCT
* *
16553699 TTGTAATATTTATTATTGCA
1 TTGTAATATTTAATATAGCA
16553719 TTGT-ATATTTAATATAGCA
1 TTGTAATATTTAATATAGCA
16553738 TT
1 TT
16553740 ACATCATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.54
Consensus pattern (20 bp):
TTGTAATATTTAATATAGCA
Found at i:16554113 original size:98 final size:98
Alignment explanation
Indices: 16553980--16554174 Score: 336
Period size: 98 Copynumber: 2.0 Consensus size: 98
16553970 CTAAAAACAA
* * * *
16553980 TAAAAGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTG
1 TAAAAGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGGGTGATTTC
16554045 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
16554078 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGGGTGATTTC
1 TAAAAGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGGGTGATTTC
16554143 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
16554175 ATTTTATTGT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.36
Consensus pattern (98 bp):
TAAAAGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGGGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:16563632 original size:14 final size:14
Alignment explanation
Indices: 16563610--16563697 Score: 70
Period size: 14 Copynumber: 6.3 Consensus size: 14
16563600 GGGATAATCA
* *
16563610 GCATGTATGAATTT
1 GCATCTATGAATTC
16563624 GCATCTATGAATTC
1 GCATCTATGAATTC
* *
16563638 GTATCTATGAATCC
1 GCATCTATGAATTC
* *
16563652 ACA-CATATGAATAC
1 GCATC-TATGAATTC
* *
16563666 GAATGTATGAATTC
1 GCATCTATGAATTC
* *
16563680 GCATTTATGAATCC
1 GCATCTATGAATTC
16563694 GCAT
1 GCAT
16563698 AAGTTTATTT
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
13 1 0.02
14 57 0.98
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (14 bp):
GCATCTATGAATTC
Found at i:16563688 original size:28 final size:28
Alignment explanation
Indices: 16563612--16563691 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 28
16563602 GATAATCAGC
* * * *
16563612 ATGTATGAATTTGCATCTATGAATTCGT
1 ATGTATGAATTCGCATATATGAATACGA
* * * *
16563640 ATCTATGAATCCACACATATGAATACGA
1 ATGTATGAATTCGCATATATGAATACGA
*
16563668 ATGTATGAATTCGCATTTATGAAT
1 ATGTATGAATTCGCATATATGAAT
16563692 CCGCATAAGT
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (28 bp):
ATGTATGAATTCGCATATATGAATACGA
Found at i:16569932 original size:85 final size:86
Alignment explanation
Indices: 16569818--16569986 Score: 241
Period size: 85 Copynumber: 2.0 Consensus size: 86
16569808 CAAAAAAGTG
* * *
16569818 GTGGATCGTCCACAAAACCCAGTGACAATTTGTTTAATCTGTAAATATGTTGTGCACTCACAACA
1 GTGGATCGTCCACAAAACCCAGTGACAATTTGTTTAATCTGCAAACATGTTATGCACTCACAACA
* *
16569883 AGTGGCAGTTACTGCAAATAT
66 AGTGACAGTAACTGCAAATAT
* * * *
16569904 GTGGCTCGTCCAC-AAACCCAGTGGCAATTTGTTTAATTTGCAACCATGTTATGCACTCACAACA
1 GTGGATCGTCCACAAAACCCAGTGACAATTTGTTTAATCTGCAAACATGTTATGCACTCACAACA
*
16569968 AGTGATAGTAACTGCAAAT
66 AGTGACAGTAACTGCAAAT
16569987 TTTTTTATCT
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 61 0.84
86 12 0.16
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (86 bp):
GTGGATCGTCCACAAAACCCAGTGACAATTTGTTTAATCTGCAAACATGTTATGCACTCACAACA
AGTGACAGTAACTGCAAATAT
Found at i:16572778 original size:17 final size:18
Alignment explanation
Indices: 16572753--16572786 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16572743 AATAATGTGG
16572753 AAAATAAAAAAATATTTT
1 AAAATAAAAAAATATTTT
*
16572771 AAAA-AAAAATATATTT
1 AAAATAAAAAAATATTT
16572787 GGTACATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATAAAAAAATATTTT
Found at i:16572844 original size:36 final size:36
Alignment explanation
Indices: 16572802--16572877 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
16572792 ATTACCAATG
16572802 AAGTTTTTAAATTCTCAAATAGGGTTAAGAGTATGA-
1 AAGTTTTTAAATTCTCAAATAGGGTTAAGAGT-TGAC
16572838 AAGTTTTTAAATTCTCAAATAGGGTTAAGAGTTGAC
1 AAGTTTTTAAATTCTCAAATAGGGTTAAGAGTTGAC
16572874 AAGT
1 AAGT
16572878 GTCATGTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 3 0.08
36 36 0.92
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (36 bp):
AAGTTTTTAAATTCTCAAATAGGGTTAAGAGTTGAC
Found at i:16572979 original size:16 final size:17
Alignment explanation
Indices: 16572948--16572982 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16572938 AAGACACGTT
16572948 ATTAAAATACATTTAAAA
1 ATTAAAATA-ATTTAAAA
16572966 ATTAAAAT-ATTTAAAA
1 ATTAAAATAATTTAAAA
16572982 A
1 A
16572983 CAAATCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
ATTAAAATAATTTAAAA
Found at i:16573501 original size:26 final size:27
Alignment explanation
Indices: 16573472--16573523 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
16573462 GTAATAGGTT
16573472 TTTAAAC-CAATAAAAAT-ACTTTAAAA
1 TTTAAACACAATAAAAATCA-TTTAAAA
*
16573498 TTTAAACATAATAAAAATCATTTAAA
1 TTTAAACACAATAAAAATCATTTAAA
16573524 TAATGAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 15 0.65
28 1 0.04
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.33
Consensus pattern (27 bp):
TTTAAACACAATAAAAATCATTTAAAA
Found at i:16584188 original size:23 final size:26
Alignment explanation
Indices: 16584157--16584225 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
16584147 AGCTAAAGAA
*
16584157 CGGTAAGCTC-TATTGAGCTGA-A-AT
1 CGGTAAGCTCATA-AGAGCTGATATAT
16584181 -GGTAAGCTCATAAGAGCTGATATAT
1 CGGTAAGCTCATAAGAGCTGATATAT
* *
16584206 CGGTAAGCTCGTACGAGCTG
1 CGGTAAGCTCATAAGAGCTG
16584226 TGGTGAGTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
23 16 0.42
24 3 0.08
25 2 0.05
26 17 0.45
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (26 bp):
CGGTAAGCTCATAAGAGCTGATATAT
Found at i:16587198 original size:18 final size:18
Alignment explanation
Indices: 16587162--16587204 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16587152 ACAGTTTGGA
*
16587162 AAATTAATACAGTTCACC
1 AAATTAATACAGATCACC
* *
16587180 ATATTAATACAGATGACC
1 AAATTAATACAGATCACC
16587198 AAATTAA
1 AAATTAA
16587205 CACACTTCGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (18 bp):
AAATTAATACAGATCACC
Found at i:16587441 original size:15 final size:16
Alignment explanation
Indices: 16587409--16587441 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
16587399 CATTATCAAT
16587409 AAAATTCATATGTTATA
1 AAAATTCATA-GTTATA
16587426 AAAATTCATA-TTATA
1 AAAATTCATAGTTATA
16587441 A
1 A
16587442 TATTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAATTCATAGTTATA
Found at i:16589011 original size:32 final size:31
Alignment explanation
Indices: 16588946--16589012 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
16588936 ACCTAAAATT
* * *
16588946 ATTAATTCTAATTATTATAATATTTTATTTA
1 ATTAATTCTAATTATTATAATATATAATCTA
16588977 ATTAATTCCTAATTATT-TAATTATATAATCTA
1 ATTAATT-CTAATTATTATAA-TATATAATCTA
16589009 ATTA
1 ATTA
16589013 CAGTTTTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 10 0.32
32 21 0.68
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTAATTCTAATTATTATAATATATAATCTA
Found at i:16589273 original size:31 final size:31
Alignment explanation
Indices: 16589238--16589299 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
16589228 TTCAAAATGC
16589238 TCACTAAACTATTCAAAAGTTTACATTTAAA
1 TCACTAAACTATTCAAAAGTTTACATTTAAA
* * * **
16589269 TCACTGAGCTATTCGAAAGTTTTTATTTAAA
1 TCACTAAACTATTCAAAAGTTTACATTTAAA
16589300 CATTGGGTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.39
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAGTTTACATTTAAA
Found at i:16604723 original size:14 final size:15
Alignment explanation
Indices: 16604704--16604736 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16604694 AAAATCTAAA
*
16604704 AAAATTTAAAAA-AT
1 AAAATTCAAAAATAT
16604718 AAAATTCAAAAATAT
1 AAAATTCAAAAATAT
16604733 AAAA
1 AAAA
16604737 AATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATTCAAAAATAT
Found at i:16604728 original size:23 final size:23
Alignment explanation
Indices: 16604665--16604743 Score: 81
Period size: 22 Copynumber: 3.4 Consensus size: 23
16604655 TTTAAAAAGT
*
16604665 AAAATAAAAATAAAAATAATTTTAA
1 AAAATAAAATTAAAAA-AA-TTTAA
*
16604690 TAAA-AAAATCTAAAAAAATTTAA
1 AAAATAAAAT-TAAAAAAATTTAA
* *
16604713 AAAATAAAATT-CAAAAATATAA
1 AAAATAAAATTAAAAAAATTTAA
16604735 AAAATAAAA
1 AAAATAAAA
16604744 ATAGTCAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
22 18 0.38
23 9 0.19
24 11 0.23
25 9 0.19
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAATAAAATTAAAAAAATTTAA
Found at i:16619721 original size:21 final size:19
Alignment explanation
Indices: 16619672--16619720 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
16619662 TTATATTTTG
16619672 TATTTATTTTAATATTATA
1 TATTTATTTTAATATTATA
* *
16619691 AATGTATTTTAATTTATTATA
1 TATTTATTTTAA--TATTATA
16619712 TATTT-TTTT
1 TATTTATTTT
16619721 TGCAAAATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 10 0.42
20 4 0.17
21 10 0.42
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTATTTTAATATTATA
Found at i:16627644 original size:14 final size:14
Alignment explanation
Indices: 16627625--16627652 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16627615 GCACACATTT
16627625 GTTCTTCTCTGCTG
1 GTTCTTCTCTGCTG
16627639 GTTCTTCTCTGCTG
1 GTTCTTCTCTGCTG
16627653 CTGCTGGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.29, G:0.21, T:0.50
Consensus pattern (14 bp):
GTTCTTCTCTGCTG
Found at i:16627729 original size:11 final size:11
Alignment explanation
Indices: 16627695--16627729 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
16627685 TCTAAATTTT
*
16627695 GTTCTCTGCTA
1 GTTCTCTGCTG
*
16627706 GTTCTCTGTTG
1 GTTCTCTGCTG
16627717 GTTCTCTGCTG
1 GTTCTCTGCTG
16627728 GT
1 GT
16627730 GTTGGTGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.03, C:0.23, G:0.26, T:0.49
Consensus pattern (11 bp):
GTTCTCTGCTG
Found at i:16630048 original size:18 final size:18
Alignment explanation
Indices: 16630025--16630072 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
16630015 AAAATATGAG
*
16630025 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
16630043 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
16630061 AAATGATGTTCA
1 AAATGATGTTCA
16630073 AATTGATGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:16630594 original size:72 final size:72
Alignment explanation
Indices: 16630495--16630665 Score: 258
Period size: 72 Copynumber: 2.4 Consensus size: 72
16630485 CTGGCAATGC
* * *
16630495 TAAA-CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTA
1 TAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTA
*
16630559 TTTATGT
66 TTTATAT
*
16630566 GT-AATCTAGTTTTATTAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTT
1 -TAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTT
*
16630630 ATTTTTAT
65 ATTTATAT
16630638 TAAAT-TAGTTTTATCAATAGTTGTTTAT
1 TAAATCTAGTTTTATCAATAGTTGTTTAT
16630666 ATATGATTTT
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
71 25 0.28
72 65 0.72
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.56
Consensus pattern (72 bp):
TAAATCTAGTTTTATCAATAGTTGTTTATGTTTGGTCTTTAGATATTGAATTTATGTTCTACTTA
TTTATAT
Found at i:16640035 original size:8 final size:9
Alignment explanation
Indices: 16640011--16640036 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
16640001 CTAGAAATAT
16640011 TTGAAAAAC
1 TTGAAAAAC
16640020 TTGAAAAAC
1 TTGAAAAAC
16640029 TTGAAAAA
1 TTGAAAAA
16640037 ATTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.12, T:0.23
Consensus pattern (9 bp):
TTGAAAAAC
Found at i:16643009 original size:17 final size:17
Alignment explanation
Indices: 16642980--16643033 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
16642970 ACCGTGAACA
*
16642980 CAAGCCTGCGAGCTCAC
1 CAAGACTGCGAGCTCAC
*
16642997 CAAGACTGTGAGCTCAC
1 CAAGACTGCGAGCTCAC
* *
16643014 CAATAGTGCGAGCTCAC
1 CAAGACTGCGAGCTCAC
16643031 CAA
1 CAA
16643034 ACTTGTGATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.30, C:0.33, G:0.22, T:0.15
Consensus pattern (17 bp):
CAAGACTGCGAGCTCAC
Found at i:16644847 original size:38 final size:38
Alignment explanation
Indices: 16644803--16644879 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
16644793 AGTAGCATAT
16644803 ACCAACTCACTAGATGAAACCAAGTTATAGCATAGAAG
1 ACCAACTCACTAGATGAAACCAAGTTATAGCATAGAAG
*
16644841 ACCAACTCACTAGATGAAACCAAGTTATGGCATAGAAG
1 ACCAACTCACTAGATGAAACCAAGTTATAGCATAGAAG
16644879 A
1 A
16644880 ATGGGACATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (38 bp):
ACCAACTCACTAGATGAAACCAAGTTATAGCATAGAAG
Found at i:16648846 original size:23 final size:23
Alignment explanation
Indices: 16648801--16648856 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
16648791 GGTAAAGGCA
16648801 GTAAATGAGGAGGAAAAAAAAGGG
1 GTAAATGAGGA-GAAAAAAAAGGG
16648825 GTAAATGAGGA-AAAAAAGAAGGG
1 GTAAATGAGGAGAAAAAA-AAGGG
16648848 G-AATATGAG
1 GTAA-ATGAG
16648857 TGTCTACGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.27
23 11 0.37
24 11 0.37
ACGTcount: A:0.54, C:0.00, G:0.36, T:0.11
Consensus pattern (23 bp):
GTAAATGAGGAGAAAAAAAAGGG
Found at i:16649451 original size:268 final size:267
Alignment explanation
Indices: 16648965--16649505 Score: 845
Period size: 268 Copynumber: 2.0 Consensus size: 267
16648955 AGTATAATAA
** * *
16648965 AAATATGTTTGACTCATTATAATAAGAATATATATAATATTTGTCTAGTTAATGTATTTATTAGA
1 AAATATGTGAGACCCATTATAATAAGAATATATATAATATTTGTCTAGTTAATGTACTTATTAGA
16649030 TTAAAAATATTTTTTTAAAAATTAATTTTAATTATAAATTAATAAACATATGTGTGACCCAAATT
66 TTAAAAATATTTTTTT-AAAATTAATTTTAATTATAAATTAATAAACATATGTGTGACCCAAATT
* ** * *
16649095 CTTGTCAAATAAAATAAGACATTGTTTGCAATTCAAGTTAAACATAATATATTTTCTTTCTAGAA
130 CTTATCAAATAAAATAAGACATTACTTGCAAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAA
* * *
16649160 GATTTAGTATTTATTAGTATAATATATTTTACATTTATTAGCATAATTTATTTGACCTATGAATT
195 GATTTAGTATCTATTAATATAATATATTTTACATTTATTAGCATAATTTATTTGACCTACGAATT
16649225 TAATCTAT
260 TAATCTAT
16649233 AAATATGTGAGACCCATTATAATAAGAATATATATATGTAATATTTGTCTAGTTAATGTACTTAT
1 AAATATGTGAGACCCATTATAATAAG-A-ATATATA--TAATATTTGTCTAGTTAATGTACTTAT
*
16649298 TAGATTAAAAATATTTTTTT-AAATTAATTTTAATTATAAATTAAT-AA-ATATGTGTTACCCAA
62 TAGATTAAAAATATTTTTTTAAAATTAATTTTAATTATAAATTAATAAACATATGTGTGACCCAA
* *
16649360 ATTCTTATTAAATAAAATAAGAGATTACTTGCAAGTCAAGTTAAACAAAATATATTTTCTTTCTA
127 ATTCTTATCAAATAAAATAAGACATTACTTGCAAGTCAAGTTAAACAAAATATATTTTCTTTCTA
** *
16649425 GAAGATTTAGTATCTATTAATATAATATATTTTGTATTTATTAGTATAATTTATTTGACCTACGA
192 GAAGATTTAGTATCTATTAATATAATATATTTTACATTTATTAGCATAATTTATTTGACCTACGA
*
16649490 ATTTAGTCTAT
257 ATTTAATCTAT
16649501 AAATA
1 AAATA
16649506 GACACTTTTA
Statistics
Matches: 250, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
268 169 0.68
269 3 0.01
270 32 0.13
272 46 0.18
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (267 bp):
AAATATGTGAGACCCATTATAATAAGAATATATATAATATTTGTCTAGTTAATGTACTTATTAGA
TTAAAAATATTTTTTTAAAATTAATTTTAATTATAAATTAATAAACATATGTGTGACCCAAATTC
TTATCAAATAAAATAAGACATTACTTGCAAGTCAAGTTAAACAAAATATATTTTCTTTCTAGAAG
ATTTAGTATCTATTAATATAATATATTTTACATTTATTAGCATAATTTATTTGACCTACGAATTT
AATCTAT
Found at i:16649456 original size:24 final size:24
Alignment explanation
Indices: 16649429--16649480 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
16649419 TTTCTAGAAG
16649429 ATTTAGTATCTATTAATATAATAT
1 ATTTAGTATCTATTAATATAATAT
* * * *
16649453 ATTTTGTATTTATTAGTATAATTT
1 ATTTAGTATCTATTAATATAATAT
16649477 ATTT
1 ATTT
16649481 GACCTACGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
ATTTAGTATCTATTAATATAATAT
Found at i:16656274 original size:2 final size:2
Alignment explanation
Indices: 16656267--16656307 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
16656257 GCAAGAAGAA
16656267 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
16656308 ACCTAGGATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16665583 original size:24 final size:24
Alignment explanation
Indices: 16665568--16665619 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16665558 AATCAAATTC
16665568 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
16665592 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
16665616 AAAT
1 AAAT
16665620 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:16670784 original size:21 final size:22
Alignment explanation
Indices: 16670740--16670782 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
16670730 GTCCTAGGTA
*
16670740 TATATTATATTTTTTGAAAAAAT
1 TATATTATATTTTAT-AAAAAAT
16670763 TATATTATATTTTATAAAAA
1 TATATTATATTTTATAAAAA
16670783 TTTCAGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATTATATTTTATAAAAAAT
Found at i:16671382 original size:31 final size:30
Alignment explanation
Indices: 16671346--16671417 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
16671336 GATTAAATCA
*
16671346 AAATTAAAGTTTAAAGTATACATTTGAACC
1 AAATTAAAGTTTAAAGTATACAATTGAACC
* * * * *
16671376 ACAATTAGAGTTTCAGGTATATAATTGCACC
1 A-AATTAAAGTTTAAAGTATACAATTGAACC
16671407 AAATTAAAGTT
1 AAATTAAAGTT
16671418 CATTTATACA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (30 bp):
AAATTAAAGTTTAAAGTATACAATTGAACC
Found at i:16671459 original size:29 final size:27
Alignment explanation
Indices: 16671395--16671459 Score: 67
Period size: 31 Copynumber: 2.3 Consensus size: 27
16671385 GTTTCAGGTA
* *
16671395 TATAATTGCACCAAATTAAAGTTCATT
1 TATAATTGCACCAAATCAAAGTTCATG
*
16671422 TATACAATTGCACACTAAATCAAAGTTTATG
1 TAT--AATTGCAC-C-AAATCAAAGTTCATG
16671453 TATAATT
1 TATAATT
16671460 TTGAGATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 3 0.10
29 12 0.39
30 1 0.03
31 15 0.48
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.37
Consensus pattern (27 bp):
TATAATTGCACCAAATCAAAGTTCATG
Found at i:16671546 original size:21 final size:21
Alignment explanation
Indices: 16671516--16671570 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
16671506 TATTTTTCTA
16671516 AAAT-AAAATATTTTAATTAAT
1 AAATAAAAATATTTTAA-TAAT
*
16671537 -AATAAAAATAAATTTAATAAT
1 AAATAAAAAT-ATTTTAATAAT
16671558 AAATAAATAATAT
1 AAATAAA-AATAT
16671571 AATAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 3 0.11
21 9 0.32
22 13 0.46
23 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAAAAATATTTTAATAAT
Found at i:16671562 original size:22 final size:23
Alignment explanation
Indices: 16671527--16671569 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
16671517 AATAAAATAT
16671527 TTTAATTAATAATAAA-AATAAA
1 TTTAATTAATAATAAATAATAAA
16671549 TTTAA-TAATAAATAAATAATA
1 TTTAATTAAT-AATAAATAATA
16671570 TAATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TTTAATTAATAATAAATAATAAA
Found at i:16671563 original size:16 final size:16
Alignment explanation
Indices: 16671536--16671581 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 16
16671526 TTTTAATTAA
16671536 TAATAA-AAATAAATT
1 TAATAATAAATAAATT
16671551 TAATAATAAATAAA--
1 TAATAATAAATAAATT
16671565 TAAT-AT-AATAAATT
1 TAATAATAAATAAATT
16671579 TAA
1 TAA
16671582 ATATGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 6 0.21
13 2 0.07
14 7 0.25
15 6 0.21
16 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAATAAATAAATT
Found at i:16675198 original size:18 final size:18
Alignment explanation
Indices: 16675177--16675237 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
16675167 ATTCATATGT
*
16675177 ATTTTATAGTATATATAC
1 ATTTTATAATATATATAC
* *
16675195 ATTTCATAATATTTATAC
1 ATTTTATAATATATATAC
*
16675213 ATTTTCTATAATATACATAC
1 A-TTT-TATAATATATATAC
16675233 ATTTT
1 ATTTT
16675238 TATATCTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 17 0.49
19 6 0.17
20 12 0.34
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51
Consensus pattern (18 bp):
ATTTTATAATATATATAC
Found at i:16675223 original size:20 final size:20
Alignment explanation
Indices: 16675181--16675241 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
16675171 ATATGTATTT
*
16675181 TATAGTATATATACA-TTTC
1 TATAATATATATACATTTTC
*
16675200 -ATAATATTTATACATTTTC
1 TATAATATATATACATTTTC
*
16675219 TATAATATACATACATTTT-
1 TATAATATATATACATTTTC
16675238 TATA
1 TATA
16675242 TCTTTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 12 0.33
19 8 0.22
20 16 0.44
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (20 bp):
TATAATATATATACATTTTC
Found at i:16681248 original size:47 final size:46
Alignment explanation
Indices: 16681191--16681279 Score: 133
Period size: 47 Copynumber: 1.9 Consensus size: 46
16681181 AAAAGGTGGG
* * *
16681191 ACCAAGGTGAAAGCCTACAAAGGGCGCTTTGAGTCAAAAAAAAAGAC
1 ACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGT-AAAAAAAAAGAC
*
16681238 ACCAGGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAA
1 ACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAA
16681280 TAGAGAGGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
46 8 0.21
47 30 0.79
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (46 bp):
ACCAAGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAGAC
Found at i:16682818 original size:91 final size:89
Alignment explanation
Indices: 16682571--16683878 Score: 1158
Period size: 91 Copynumber: 14.5 Consensus size: 89
16682561 TTCAAAGTCA
* * * * * *
16682571 ACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC-AAAGAAAGCAGATCTTGCCTTCATGT
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAAAAAAGCAGATCTTGTCTTCATGT
16682635 A-TCGGCGTGAAGTAGATCAAAG-T
66 ACT-GGCGTGAAGTAGATCAAAGAT
* * * * *
16682658 CAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC-AAAGAAAGCAGATCTTGTCTTCAT
1 --ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAAAAAAGCAGATCTTGTCTTCAT
*
16682722 GTACTGGCGTGAAGTAGATCAAATAT
64 GTACTGGCGTGAAGTAGATCAAAGAT
* *
16682748 ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCAT
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAA--AAAAAGCAGATCTTGTCTTCAT
16682813 GTACTGGCGTGAAGTAGATCAAAGAT
64 GTACTGGCGTGAAGTAGATCAAAGAT
* * * * **
16682839 ACAGATCTCGCCTTCCTATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTCCCC
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAA--AAAAAGCAGATCTTGTCTTCAT
* * * * * *
16682904 ATACTGGTGGCGAAGCAGATCGAAGGAAAA
64 GTACTGG-CGTGAAGTAGATC-AA--AGAT
*** * * * * * * * ***
16682934 AGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC-AAAGATA-CAGATCTCGCCTTCCCA
1 A-CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAAAAAAGCAGATCTTGTCTTCATG
* * * *
16682996 TACTGGTGGCGAAGCAGATCGAAAGAAAA
65 TACTGG-CGTGAAGTAGATC-AAAG--AT
*** **** * * * * * ***
16683025 AGCAGATCTTGTCTTCATGTACT-GACATGAAGTAGATC-AAAGATA-CAGATCTCGCCTTCCCA
1 A-CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAAAAAAGCAGATCTTGTCTTCATG
* * * *
16683087 TACTGGTGGCGAAGTAGATCGAAGGAAAA
65 TACTGG-CGTGAAGTAGATC-AA--AGAT
*
16683116 AGCAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCA
1 A-CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAA--AAAAAGCAGATCTTGTCTTCA
16683181 TGTACTGGCGTGAAGTAGATCAAAGAT
63 TGTACTGGCGTGAAGTAGATCAAAGAT
* *
16683208 ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCAT
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAA--AAAAAGCAGATCTTGTCTTCAT
*
16683273 GTACTAGCGTGAAGTAGATCAAAGAT
64 GTACTGGCGTGAAGTAGATCAAAGAT
* * *
16683299 ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAACAGATCTTGTCTTCAT
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAA--AAAAAGCAGATCTTGTCTTCAT
*
16683364 GTACTGGCGTGAAGTAGATCAAATAT
64 GTACTGGCGTGAAGTAGATCAAAGAT
* *
16683390 ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCAT
1 ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAA--AAAAAGCAGATCTTGTCTTCAT
16683455 GTACTGGCGTGAAGTAGATCAAAGAT
64 GTACTGGCGTGAAGTAGATCAAAGAT
* * * * * *
16683481 AACAGATCTCGCCTTCCCATATTGGTGGCGAAGCAGATCGAAAGAAAGTAGATATTGTCTTCATG
1 -ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAAAAAAGCAGATCTTGTCTTCATG
*
16683546 TA-TCAGCGTGAAGTAGATCAAAG-T
65 TACT-GGCGTGAAGTAGATCAAAGAT
* * * * * * * *
16683570 CAACAGATCTTATCTCCCCATACTGGTGGTGGAGTAGATC-AAAGAAAGTAGATCTTGCCTTCAT
1 --ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAAAAAAGCAGATCTTGTCTTCAT
16683634 GTA-TCGGCGTGAAGTAGATCAAAG-T
64 GTACT-GGCGTGAAGTAGATCAAAGAT
* * * * * *
16683659 CAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC-AAAGAAAGCAAATCTTGTCTTCAT
1 --ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAAAAAAGCAGATCTTGTCTTCAT
*
16683723 GTATTGGCGTGAAGTAGATCAAAGA-
64 GTACTGGCGTGAAGTAGATCAAAGAT
* * * * * * *
16683748 AGCAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGGTCGAAGAAAA-CAGATCGTGTCTTCATG
1 A-CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAAAAAAGCAGATCTTGTCTTCATG
16683812 TACTGGCGTGAAGTAGATCAAAGAT
65 TACTGGCGTGAAGTAGATCAAAGAT
* * * * * * **
16683837 AGTAGGTCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAA
1 A-CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAA
16683879 TATACATCTT
Statistics
Matches: 1089, Mismatches: 102, Indels: 56
0.87 0.08 0.04
Matches are distributed among these distances:
87 1 0.00
88 106 0.10
89 251 0.23
90 75 0.07
91 517 0.47
92 66 0.06
93 5 0.00
94 4 0.00
95 27 0.02
96 37 0.03
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (89 bp):
ACAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAAAAAAGCAGATCTTGTCTTCATGT
ACTGGCGTGAAGTAGATCAAAGAT
Found at i:16682911 original size:139 final size:138
Alignment explanation
Indices: 16682749--16683452 Score: 669
Period size: 139 Copynumber: 5.1 Consensus size: 138
16682739 ATCAAATATA
* *
16682749 CAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATG
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAA-CAGATCTTGTCTTCATG
* *
16682814 TACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCTATACTGGTGGCGAAGCAGATCGA
65 TACTGGCGTGAAGTAGATCAAAAATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
16682879 AGGAAAAAG
130 AGGAAAAAG
*
16682888 CAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATG
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAA-CAGATCTTGTCTTCATG
*
16682953 TACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
65 TACTGGCGTGAAGTAGATCAAAAATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
*
16683018 AAGAAAAAG
130 AGGAAAAAG
*** **** * * * * * ***
16683027 CAGATCTTGTCTTCATGTACT-GACATGAAGTAGATC-AA--AGATACAGATCTCGCCTTCCCAT
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAACAGATCTTGTCTTCATGT
* * * * * *
16683088 ACTGGTGGCGAAGTAGATCGAAGGAAAAAGCAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGA
66 ACTGG-CGTGAAGTAGATC-AA--AAATA-CAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGA
16683153 TCGAAGGAAAAAG
126 TCGAAGGAAAAAG
*** * * * * * * * ***
16683166 CAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC-AA--AGATACAGATCTCGCCTTCCCAT
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAACAGATCTTGTCTTCATGT
* * * * * * *** * * * *
16683227 ACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATGTACTAG-CGTGAAGTAGA
66 ACTGG-CGTGAAGTAGATC-AA--AAATA-CAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGA
* *
16683291 TC-AA--AGATA-
126 TCGAAGGAAAAAG
* *
16683300 CAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAACAGATCTTGTCTTCATG
1 CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAGG-AAAAACAGATCTTGTCTTCATG
*
16683365 TACTGGCGTGAAGTAGATCAAATATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
65 TACTGGCGTGAAGTAGATCAAAAATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
16683430 AGGAAAAAG
130 AGGAAAAAG
16683439 CAGATCTTGTCTTC
1 CAGATCTTGTCTTC
16683453 ATGTACTGGC
Statistics
Matches: 475, Mismatches: 74, Indels: 32
0.82 0.13 0.06
Matches are distributed among these distances:
134 53 0.11
135 40 0.08
136 6 0.01
137 6 0.01
138 36 0.08
139 333 0.70
140 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (138 bp):
CAGATCTTGTCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAACAGATCTTGTCTTCATGT
ACTGGCGTGAAGTAGATCAAAAATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAA
GGAAAAAG
Found at i:16683061 original size:230 final size:230
Alignment explanation
Indices: 16682661--16683359 Score: 1262
Period size: 230 Copynumber: 3.1 Consensus size: 230
16682651 TCAAAGTCAA
* * * *
16682661 CAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC-AA--AGAAAGCAGATCTTGTCTTCATG
1 CAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATG
*
16682723 TACTGGCGTGAAGTAGATCAAATATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
66 TACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
*
16682788 AGGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTT
131 AGGAAAAAGCAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATACAGATCTCGCCTT
*
16682853 CCTATACTGGTGGCGAAGCAGATCGAAGGAAAAAG
196 CCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAG
16682888 CAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATG
1 CAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATG
16682953 TACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
66 TACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
* *
16683018 AAGAAAAAGCAGATCTTGTCTTCATGTACTGACATGAAGTAGATCAAAGATACAGATCTCGCCTT
131 AGGAAAAAGCAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATACAGATCTCGCCTT
*
16683083 CCCATACTGGTGGCGAAGTAGATCGAAGGAAAAAG
196 CCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAG
16683118 CAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATG
1 CAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATG
16683183 TACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
66 TACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
16683248 AGGAAAAAGCAGATCTTGTCTTCATGTACT-AGCGTGAAGTAGATCAAAGATACAGATCTCGCCT
131 AGGAAAAAGCAGATCTTGTCTTCATGTACTGA-CGTGAAGTAGATCAAAGATACAGATCTCGCCT
*
16683312 TCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAA
195 TCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAG
16683348 CAGATCTTGTCT
1 CAGATCTTGTCT
16683360 TCATGTACTG
Statistics
Matches: 454, Mismatches: 14, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
227 34 0.07
228 2 0.00
229 1 0.00
230 417 0.92
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (230 bp):
CAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATG
TACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGA
AGGAAAAAGCAGATCTTGTCTTCATGTACTGACGTGAAGTAGATCAAAGATACAGATCTCGCCTT
CCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAG
Found at i:16683215 original size:321 final size:319
Alignment explanation
Indices: 16682570--16683527 Score: 1290
Period size: 321 Copynumber: 3.0 Consensus size: 319
16682560 GTTCAAAGTC
* * * * *
16682570 AACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC-AA--AGAAAGCAGATCTTGCCTTCA
1 AACAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCA
* * * * * *
16682632 TGTA-TCGGCGTGAAGTAGATCAAAG-TCAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAG
66 TGTACT-GGCGTGAAGTAGATCAAAGAT--ACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAG
16682695 ATC-AAAG--AAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATATACAGATCTC
128 ATCGAAAGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATATACAGATCTC
* **
16682757 GCCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATGTACTGGCG
193 GCCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTCCACATACTGGCG
* * * * * *
16682822 TGAAGTAGATCAAAGATACAGATCTCGCCTTCCTATACTGGTGGCGAAGCAGATCGAAGGAAA
258 CGAAGCAGATCAAAAAAACAGATCTCGCCTTCATATACTGGTCGCGAAGCAGATCGAA-GAAA
16682885 AAGCAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTC
1 AA-CAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTC
16682950 ATGTACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGAT
65 ATGTACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGAT
* * *
16683015 CGAAAGAAAAAGCAGATCTTGTCTTCATGTACTGACATGAAGTAGATCAAAGATACAGATCTCGC
130 CGAAAGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATATACAGATCTCGC
* * *
16683080 CTTCCCATACTGGTGGCGAAGTAGATCGAAGGAAAAAGCAGATCTTGTCTCCCCATACTGGTGGC
195 CTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTCCACATACTGG-CGC
* * * * * *
16683145 GAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATC-AA-AGA
259 GAAGCAGATC-AA--AAAAA-CAGATCTCGCCTTCATATACTGGTCGCGAAGCAGATCGAAGAAA
* * * *
16683207 TACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCA
1 AACAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCA
*
16683272 TGTACTAGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATC
66 TGTACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATC
* *
16683337 GAAGGAAAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATATACAGATCTCGCC
131 GAAAGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATATACAGATCTCGCC
* ** *
16683402 TTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
196 TTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTCCACATACTGGCGCGA
* * ** * *
16683467 AGTAGATCAAAGATAACAGATCTCGCCTTCCCATATTGGTGGCGAAGCAGATCGAAAGAAA
261 AGCAGATCAAA-AAAACAGATCTCGCCTTCATATACTGGTCGCGAAGCAGATCG-AAGAAA
16683528 GTAGATATTG
Statistics
Matches: 563, Mismatches: 61, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
315 2 0.00
316 34 0.06
317 20 0.04
318 45 0.08
319 48 0.09
320 14 0.02
321 351 0.62
322 13 0.02
323 2 0.00
324 2 0.00
325 13 0.02
326 19 0.03
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (319 bp):
AACAGATCTTGTCTCCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCA
TGTACTGGCGTGAAGTAGATCAAAGATACAGATCTCGCCTTCCCATACTGGTGGCGAAGCAGATC
GAAAGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAATATACAGATCTCGCC
TTCCCATACTGGTGGCGAAGCAGATCGAAGGAAAAAGCAGATCTTGTCTCCACATACTGGCGCGA
AGCAGATCAAAAAAACAGATCTCGCCTTCATATACTGGTCGCGAAGCAGATCGAAGAAA
Found at i:16683852 original size:44 final size:44
Alignment explanation
Indices: 16682601--16683835 Score: 682
Period size: 44 Copynumber: 27.3 Consensus size: 44
16682591 CTGGTGGTGG
*
16682601 AGTAGATCAAAGAAAGCAGATCTTGCCTTCATGTA-TCGGCGTGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACT-GGCGTGA
* * *** * *
16682645 AGTAGATCAAAGTCAA-CAGATCTTGTCTCCCCATACTGGTGGTGG
1 AGTAGATCAAAG-AAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
16682690 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
* * * * *** * *
16682734 AGTAGATCAAATATA-CAGATCTCGCCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* *
16682778 AGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
1 AGTAGATC-AA--AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
* * * * * * *
16682825 AGTAGATCAAAGATA-CAGATCTCGCCTTCCTATACTGGTGGCGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* * * *** * *
16682869 AGCAGATCGAAGGAAAAAGCAGATCTTGTCTCCCCATACTGGTGGCGA
1 AGTAGATC-AA--AGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* *
16682917 AGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
1 AGTAGATC-AA--AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
* * * *** * *
16682964 AGTAGATCAAAGATA-CAGATCTCGCCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* * *
16683008 AGCAGATCGAAAGAAAAAGCAGATCTTGTCTTCATGTACTGACATGA
1 AGTAGATC-AAAG--AAAGCAGATCTTGTCTTCATGTACTGGCGTGA
* * * *** * *
16683055 AGTAGATCAAAGATA-CAGATCTCGCCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* * *** * *
16683099 AGTAGATCGAAGGAAAAAGCAGATCTTGTCTCCCCATACTGGTGGCGA
1 AGTAGATC-AA--AGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* *
16683147 AGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
1 AGTAGATC-AA--AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
* * * *** * *
16683194 AGTAGATCAAAGATA-CAGATCTCGCCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* * *
16683238 AGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATGTACTAGCGTGA
1 AGTAGATC-AA--AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
* * * *** * *
16683285 AGTAGATCAAAGATA-CAGATCTCGCCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* * *
16683329 AGCAGATCGAAGGAAAAAACAGATCTTGTCTTCATGTACTGGCGTGA
1 AGTAGATC-AA--AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
* * * * *** * *
16683376 AGTAGATCAAATATA-CAGATCTCGCCTTCCCATACTGGTGGCGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* *
16683420 AGCAGATCGAAGGAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
1 AGTAGATC-AA--AGAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
* * *** * * *
16683467 AGTAGATCAAAGATAA-CAGATCTCGCCTTCCCATATTGGTGGCGA
1 AGTAGATCAAAGA-AAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* * * *
16683512 AGCAGATCGAAAGAAAGTAGATATTGTCTTCATGTA-TCAGCGTGA
1 AGTAGATC-AAAGAAAGCAGATCTTGTCTTCATGTACT-GGCGTGA
* * * *** * *
16683557 AGTAGATCAAAGTCAA-CAGATCTTATCTCCCCATACTGGTGGTGG
1 AGTAGATCAAAG-AAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* *
16683602 AGTAGATCAAAGAAAGTAGATCTTGCCTTCATGTA-TCGGCGTGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACT-GGCGTGA
* * *** * *
16683646 AGTAGATCAAAGTCAA-CAGATCTTGTCTCCCCATACTGGTGGTGG
1 AGTAGATCAAAG-AAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* *
16683691 AGTAGATCAAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
* *** * *
16683735 AGTAGATCAAAG-AAGCAGATCTTGTCTCCCCATACTGGTGGTGG
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGA
* * * *
16683779 AGTAGGTCGAAGAAAACAGATCGTGTCTTCATGTACTGGCGTGA
1 AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
16683823 AGTAGATCAAAGA
1 AGTAGATCAAAGA
16683836 TAGTAGGTCC
Statistics
Matches: 893, Mismatches: 243, Indels: 110
0.72 0.20 0.09
Matches are distributed among these distances:
43 145 0.16
44 246 0.28
45 165 0.18
46 34 0.04
47 89 0.10
48 214 0.24
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (44 bp):
AGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGA
Found at i:16687702 original size:6 final size:6
Alignment explanation
Indices: 16687691--16687725 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
16687681 TGTTGGCTAC
16687691 TTTGCA TTTGCA TTTGCA TTTTGCA TTTTGCA TTT
1 TTTGCA TTTGCA TTTGCA -TTTGCA -TTTGCA TTT
16687726 TACCCTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 15 0.54
7 13 0.46
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (6 bp):
TTTGCA
Found at i:16687715 original size:7 final size:7
Alignment explanation
Indices: 16687691--16687726 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
16687681 TGTTGGCTAC
16687691 TTTGCA-
1 TTTGCAT
16687697 TTTGCA-
1 TTTGCAT
16687703 TTTGCAT
1 TTTGCAT
16687710 TTTGCAT
1 TTTGCAT
16687717 TTTGCAT
1 TTTGCAT
16687724 TTT
1 TTT
16687727 ACCCTTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.58
Consensus pattern (7 bp):
TTTGCAT
Found at i:16688525 original size:13 final size:13
Alignment explanation
Indices: 16688507--16688532 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16688497 AAAGAGATTT
16688507 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
16688520 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
16688533 AATTAAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:16690492 original size:20 final size:20
Alignment explanation
Indices: 16690467--16690507 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
16690457 GCAAATGTTC
16690467 TTTCATTCTTT-ACGATTTTT
1 TTTCATTCTTTCA-GATTTTT
16690487 TTTCATTCTTTCAGATTTTT
1 TTTCATTCTTTCAGATTTTT
16690507 T
1 T
16690508 CTGCCAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTCATTCTTTCAGATTTTT
Found at i:16691469 original size:7 final size:7
Alignment explanation
Indices: 16691457--16691500 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
16691447 AGAAGTGATG
16691457 TGAAAAA
1 TGAAAAA
16691464 TGAAAAGA
1 TGAAAA-A
16691472 TG-AAAA
1 TGAAAAA
16691478 TGAAAAA
1 TGAAAAA
16691485 TGAAAAA
1 TGAAAAA
16691492 -GTAAAAA
1 TG-AAAAA
16691499 TG
1 TG
16691501 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
6 4 0.12
7 25 0.76
8 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (7 bp):
TGAAAAA
Found at i:16691498 original size:21 final size:21
Alignment explanation
Indices: 16691457--16691500 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16691447 AGAAGTGATG
*
16691457 TGAAAAATGAAAAGATGAAAA
1 TGAAAAATGAAAAGATAAAAA
16691478 TGAAAAATGAAAA-AGTAAAAA
1 TGAAAAATGAAAAGA-TAAAAA
16691499 TG
1 TG
16691501 GAGAGGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (21 bp):
TGAAAAATGAAAAGATAAAAA
Done.