Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009623.1 Hibiscus syriacus cultivar Beakdansim tig00117012_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3488723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 18
Found at i:906759 original size:4 final size:4
Alignment explanation
Indices: 906743--906780 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
906733 ATACAAATTT
* *
906743 TATG TAT- TATG TATG TATG TGTA TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
906781 TTGTTTCTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:906771 original size:16 final size:17
Alignment explanation
Indices: 906745--906778 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
906735 ACAAATTTTA
906745 TGTATTATGTATGTATG
1 TGTATTATGTATGTATG
906762 TGTA-TATGTATGTATG
1 TGTATTATGTATGTATG
906778 T
1 T
906779 ATTTGTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (17 bp):
TGTATTATGTATGTATG
Found at i:914292 original size:3 final size:3
Alignment explanation
Indices: 914284--914334 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
914274 TATTTGTAAT
**
914284 TAA TAA TAA TAA T-A TAAA TAA T-A TAA CGA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
914329 TAA TAA
1 TAA TAA
914335 CGTTAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 31 0.77
4 5 0.12
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:921153 original size:11 final size:11
Alignment explanation
Indices: 921123--921154 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
921113 ACGTACGTAG
*
921123 GAATTTTTCCA
1 GAATTTTTTCA
921134 GAATTTTTTCA
1 GAATTTTTTCA
921145 GAATTTTTTC
1 GAATTTTTTC
921155 GACCTTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (11 bp):
GAATTTTTTCA
Found at i:921464 original size:20 final size:21
Alignment explanation
Indices: 921439--921478 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
921429 TTTTGTATAG
*
921439 TAGTATCGATACCA-AAGGCA
1 TAGTATCGACACCATAAGGCA
921459 TAGTATCGACACCATAAGGC
1 TAGTATCGACACCATAAGGC
921479 CCCAACGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (21 bp):
TAGTATCGACACCATAAGGCA
Found at i:924196 original size:200 final size:200
Alignment explanation
Indices: 923853--924253 Score: 793
Period size: 200 Copynumber: 2.0 Consensus size: 200
923843 CATGTATGTT
923853 AAAAAGATGTTATGTTGAACATTTTAAAGTTTTAATATTTTCATTATTTTTTTGTTCATCATAAT
1 AAAAAGATGTTATGTTGAACATTTTAAAGTTTTAATATTTTCATTATTTTTTTGTTCATCATAAT
*
923918 GAATTTTGGTCAAAATTGATTTTAATGCAAACGATATCTCTCTAACAATTGATATCAACATTTCA
66 GAATTTTGGTCAAAATTGATTTTAATGCAAACGATATCTCTCTAACAATTGATATCAACATTTAA
923983 AATGCTTGATTTTACAAATTTTAAAATTTTGACCTAAAATTAAAGCTTTATGCATTTGTACTTAA
131 AATGCTTGATTTTACAAATTTTAAAATTTTGACCTAAAATTAAAGCTTTATGCATTTGTACTTAA
924048 TTTCA
196 TTTCA
924053 AAAAAGATGTTATGTTGAACATTTTAAAGTTTTAATATTTTCATTATTTTTTTGTTCATCATAAT
1 AAAAAGATGTTATGTTGAACATTTTAAAGTTTTAATATTTTCATTATTTTTTTGTTCATCATAAT
924118 GAATTTTGGTCAAAATTGATTTTAATGCAAACGATATCTCTCTAACAATTGATATCAACATTTAA
66 GAATTTTGGTCAAAATTGATTTTAATGCAAACGATATCTCTCTAACAATTGATATCAACATTTAA
924183 AATGCTTGATTTTACAAATTTTAAAATTTTGACCTAAAATTAAAGCTTTATGCATTTGTACTTAA
131 AATGCTTGATTTTACAAATTTTAAAATTTTGACCTAAAATTAAAGCTTTATGCATTTGTACTTAA
924248 TTTCA
196 TTTCA
924253 A
1 A
924254 CTATTTGTAT
Statistics
Matches: 200, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (200 bp):
AAAAAGATGTTATGTTGAACATTTTAAAGTTTTAATATTTTCATTATTTTTTTGTTCATCATAAT
GAATTTTGGTCAAAATTGATTTTAATGCAAACGATATCTCTCTAACAATTGATATCAACATTTAA
AATGCTTGATTTTACAAATTTTAAAATTTTGACCTAAAATTAAAGCTTTATGCATTTGTACTTAA
TTTCA
Found at i:924903 original size:20 final size:21
Alignment explanation
Indices: 924878--924917 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
924868 TTTTGTATAG
924878 TAGTATCGATACCA-AAGGCA
1 TAGTATCGATACCATAAGGCA
924898 TAGTATCGATACCATAAGGC
1 TAGTATCGATACCATAAGGC
924918 CCTAACGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
TAGTATCGATACCATAAGGCA
Found at i:925897 original size:12 final size:13
Alignment explanation
Indices: 925871--925900 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
925861 AAAAAAACAC
925871 TCTATTTATTCAT
1 TCTATTTATTCAT
925884 TCTATTTA-TCAT
1 TCTATTTATTCAT
925896 TCTAT
1 TCTAT
925901 CAAGTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (13 bp):
TCTATTTATTCAT
Found at i:926922 original size:20 final size:20
Alignment explanation
Indices: 926885--926921 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
926875 TATTGAGTTT
926885 GTATATAAATAACTTTTTGA
1 GTATATAAATAACTTTTTGA
*
926905 GTATATAATTAA-TTTTT
1 GTATATAAATAACTTTTT
926922 TTACACTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (20 bp):
GTATATAAATAACTTTTTGA
Found at i:929080 original size:34 final size:33
Alignment explanation
Indices: 929016--929082 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
929006 TCTCTGTTAT
* *
929016 TTGACTGAGTGAAAGCTCTCTCTACCATCAGTA
1 TTGACTAAGTGAAAGCTCTCTCTACAATCAGTA
* * *
929049 TTGACTAAGTGAAAAGTTTTCTCTGCAATCAGTA
1 TTGACTAAGTG-AAAGCTCTCTCTACAATCAGTA
929083 GATTAATCGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 10 0.36
34 18 0.64
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (33 bp):
TTGACTAAGTGAAAGCTCTCTCTACAATCAGTA
Found at i:931080 original size:33 final size:34
Alignment explanation
Indices: 931043--931111 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
931033 ACAGAAAAAA
*
931043 ATTC-ATCTCAAAAGAAGTGTATAGTAAAAGGAT
1 ATTCAATCTCAAAAGAAGTGTATAGTAAAAGAAT
931076 ATTCAATCTCAAAAGAAGTGTATAGTAAAAGAAT
1 ATTCAATCTCAAAAGAAGTGTATAGTAAAAGAAT
931110 AT
1 AT
931112 GTGAATTATG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 4 0.12
34 30 0.88
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.28
Consensus pattern (34 bp):
ATTCAATCTCAAAAGAAGTGTATAGTAAAAGAAT
Found at i:937198 original size:10 final size:9
Alignment explanation
Indices: 937174--937201 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
937164 TGTAATTGAA
937174 TTAAAAATG
1 TTAAAAATG
937183 TTAAAAATG
1 TTAAAAATG
937192 TTAAAAATG
1 TTAAAAATG
937201 T
1 T
937202 CATTAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.36
Consensus pattern (9 bp):
TTAAAAATG
Found at i:937894 original size:30 final size:31
Alignment explanation
Indices: 937855--937922 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 31
937845 ATAAAAGCCT
*
937855 AAAT-TTTAGGACAAGGTTCATTTTCATCCA
1 AAATATTTAGGACAAGGATCATTTTCATCCA
937885 AAA-ATTTAGGACAAGGATCATTTTCATCCA
1 AAATATTTAGGACAAGGATCATTTTCATCCA
937915 AAATATTT
1 AAATATTT
937923 TTCCCTCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (31 bp):
AAATATTTAGGACAAGGATCATTTTCATCCA
Found at i:953303 original size:18 final size:17
Alignment explanation
Indices: 953276--953390 Score: 73
Period size: 18 Copynumber: 6.6 Consensus size: 17
953266 AAGAATAAAT
953276 AAAA-GAGAAAAAATGAA
1 AAAATGAGAAAAAA-GAA
953293 AAAATGAGAAAAAAG-A
1 AAAATGAGAAAAAAGAA
953309 AAAATGATGGAAAAAACGAA
1 AAAATGA--GAAAAAA-GAA
*
953329 AAGAA--AAAAAAGAAGAA
1 AA-AATGAGAAAA-AAGAA
953346 AAAATG-GAAAAGGGAAGAA
1 AAAATGAGAAAA---AAGAA
*
953365 AAAAT--GAAAAATGAA
1 AAAATGAGAAAAAAGAA
*
953380 AAAAAGAGAAA
1 AAAATGAGAAA
953391 TAAAAGAAGG
Statistics
Matches: 81, Mismatches: 4, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
15 8 0.10
16 10 0.12
17 22 0.27
18 23 0.28
19 13 0.16
20 3 0.04
21 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (17 bp):
AAAATGAGAAAAAAGAA
Found at i:953312 original size:26 final size:26
Alignment explanation
Indices: 953276--953386 Score: 88
Period size: 26 Copynumber: 4.2 Consensus size: 26
953266 AAGAATAAAT
953276 AAAAGAGAAAA-AATGAAAAAATGAGAA
1 AAAAGA-AAAAGAATGAAAAAATGA-AA
*
953303 AAAAGAAAAATG-ATGGAAAAAACGAAA
1 AAAAGAAAAA-GAAT-GAAAAAATGAAA
*
953330 AGAAA-AAAAAGAA-GAAAAAATGGAA
1 A-AAAGAAAAAGAATGAAAAAATGAAA
** *
953355 AAGGGAAGAAAAAATG-AAAAATGAAA
1 AAAAGAA-AAAGAATGAAAAAATGAAA
953381 AAAAGA
1 AAAAGA
953387 GAAATAAAAG
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
24 1 0.01
25 13 0.19
26 23 0.34
27 18 0.27
28 12 0.18
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (26 bp):
AAAAGAAAAAGAATGAAAAAATGAAA
Found at i:953356 original size:19 final size:18
Alignment explanation
Indices: 953291--953384 Score: 63
Period size: 19 Copynumber: 5.3 Consensus size: 18
953281 AGAAAAAATG
953291 AAAAAATGAGAAAAAAGAA
1 AAAAAATG-GAAAAAAGAA
**
953310 AAATGATGGAAAAAACG-A
1 AAAAAATGGAAAAAA-GAA
*
953328 AAAGAA---AAAAAAGAA
1 AAAAAATGGAAAAAAGAA
**
953343 GAAAAAATGGAAAAGGGAA
1 -AAAAAATGGAAAAAAGAA
*
953362 GAAAAAAT-GAAAAATGAA
1 -AAAAAATGGAAAAAAGAA
953380 AAAAA
1 AAAAA
953385 GAGAAATAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.02
15 7 0.12
16 5 0.08
17 5 0.08
18 20 0.33
19 22 0.37
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.06
Consensus pattern (18 bp):
AAAAAATGGAAAAAAGAA
Found at i:953390 original size:44 final size:43
Alignment explanation
Indices: 953284--953390 Score: 112
Period size: 45 Copynumber: 2.5 Consensus size: 43
953274 ATAAAAGAGA
* * *
953284 AAAAATGAAAAAATGAGAAAAAAGAAAAATGATGGAAAAAACG
1 AAAAATGAAAAAAAGAGAAAAAAGAAAAAGGATAGAAAAAACG
* *
953327 -AAAA-GAAAAAAAAGAAGAAAAAATGGAAAAGGGA-AGAAAAAATG
1 AAAAATG-AAAAAAAG-AGAAAAAA--GAAAAAGGATAGAAAAAACG
953371 AAAAATGAAAAAAAGAGAAA
1 AAAAATGAAAAAAAGAGAAA
953391 TAAAAGAAGG
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
41 1 0.02
42 11 0.21
43 8 0.15
44 13 0.25
45 19 0.36
46 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.07
Consensus pattern (43 bp):
AAAAATGAAAAAAAGAGAAAAAAGAAAAAGGATAGAAAAAACG
Found at i:954612 original size:37 final size:37
Alignment explanation
Indices: 954562--954673 Score: 136
Period size: 37 Copynumber: 3.0 Consensus size: 37
954552 TCGAAACAAG
* *
954562 TCAAACTTAAGCCTTCACGAAAGAGTTGTGAAGCAAT
1 TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
* *
954599 TCAAACTTAAGCCTTCACGGAAGAGTGGTGAAGCAAA
1 TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
** * *
954636 TC-ATTTATAAGCCTTCAGGAAAGAATAGTGAAGCAAA
1 TCAAACT-TAAGCCTTCACGAAAGAGTAGTGAAGCAAA
954673 T
1 T
954674 ACATTTTATG
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 2 0.03
37 63 0.97
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (37 bp):
TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
Found at i:958079 original size:6 final size:6
Alignment explanation
Indices: 958015--958098 Score: 57
Period size: 6 Copynumber: 14.0 Consensus size: 6
958005 GCTTCACTTA
* * * *
958015 TTTTTC CTTTTC -TTTTC TTTTCTC TTTCTC TTTTTC TATTTA TTATTTC
1 TTTTTC TTTTTC TTTTTC TTTT-TC TTTTTC TTTTTC TTTTTC TT-TTTC
* * *
958064 TTTTT- GTTTTC TTTTTA TTTTT- TTGTTTA TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC
958099 AACAGAGATT
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
5 11 0.18
6 38 0.62
7 12 0.20
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:958842 original size:26 final size:25
Alignment explanation
Indices: 958800--958856 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
958790 ATGTAAACTT
*
958800 ATAAAATGATTTATCAGTATTCAGAA
1 ATAAAATGATTTATCAG-ACTCAGAA
* *
958826 ATAAAATAGGTTT-TCAGACTCAGAT
1 ATAAAAT-GATTTATCAGACTCAGAA
958851 ATAAAA
1 ATAAAA
958857 CAAAATACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 12 0.44
26 11 0.41
27 4 0.15
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (25 bp):
ATAAAATGATTTATCAGACTCAGAA
Found at i:959289 original size:38 final size:39
Alignment explanation
Indices: 959189--959294 Score: 155
Period size: 39 Copynumber: 2.7 Consensus size: 39
959179 ACTAAAGGGG
*
959189 CTTACCCTGTGCACAAAGCAGAGGAGCCTGAGGTAAGGT
1 CTTATCCTGTGCACAAAGCAGAGGAGCCTGAGGTAAGGT
959228 CTTATCCTGTGCACAAAGCAGAGGAGCCTGCA-GTAAGGT
1 CTTATCCTGTGCACAAAGCAGAGGAGCCTG-AGGTAAGGT
*
959267 CTTATCCT-TGCACATAA-TAGAGGAGCCT
1 CTTATCCTGTGCACA-AAGCAGAGGAGCCT
959295 TGGACACAGT
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
38 16 0.25
39 46 0.73
40 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (39 bp):
CTTATCCTGTGCACAAAGCAGAGGAGCCTGAGGTAAGGT
Found at i:959533 original size:44 final size:44
Alignment explanation
Indices: 959189--959533 Score: 299
Period size: 44 Copynumber: 8.1 Consensus size: 44
959179 ACTAAAGGGG
* *
959189 CTTACCCTGTGCACAAAGCAGAGGAGCCT---G--A-GGTAAGGT
1 CTTACCCT-TGCACATAGCAGAGGAGCCTGCGGTAACGGTAAGGA
* * *
959228 CTTATCCTGTGCACAAAGCAGAGGAGCCTGC----A--GTAAGGT
1 CTTACCCT-TGCACATAGCAGAGGAGCCTGCGGTAACGGTAAGGA
* ** * *
959267 CTTATCCTTGCACATAATAGAGGAGCCT-TGG-ACACAGTAAGGA
1 CTTACCCTTGCACATAGCAGAGGAGCCTGCGGTA-ACGGTAAGGA
* * * ** *
959310 CTTACTCTTGCACCTTA-CATAGGAGCCTG-GAAAATGGTAAGGA
1 CTTACCCTTGCA-CATAGCAGAGGAGCCTGCGGTAACGGTAAGGA
* * *
959353 CATACCCTTGCACATAGCAGAGGAGCATGCGATAACGGTAAGGA
1 CTTACCCTTGCACATAGCAGAGGAGCCTGCGGTAACGGTAAGGA
* * * *
959397 CATACCCTTGCACATAGCAGAGTAGCTTACGGTAACGGTAAGGA
1 CTTACCCTTGCACATAGCAGAGGAGCCTGCGGTAACGGTAAGGA
* * *
959441 CTTACTCTTGCACATAGAAGAGGAGCTTGCGGTAACGGTAAGGA
1 CTTACCCTTGCACATAGCAGAGGAGCCTGCGGTAACGGTAAGGA
*
959485 CTTACCCTTGCACATAGCAGAGGAGCCTGCGGTAACGGTAAGGT
1 CTTACCCTTGCACATAGCAGAGGAGCCTGCGGTAACGGTAAGGA
959529 CTTAC
1 CTTAC
959534 AAGTTAAAAA
Statistics
Matches: 259, Mismatches: 34, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
38 17 0.07
39 43 0.17
40 1 0.00
41 1 0.00
42 3 0.01
43 54 0.21
44 140 0.54
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (44 bp):
CTTACCCTTGCACATAGCAGAGGAGCCTGCGGTAACGGTAAGGA
Found at i:959668 original size:24 final size:24
Alignment explanation
Indices: 959634--959694 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
959624 TAGAATTTAT
*
959634 ATAAGATATCAGAACAGAATCCAG
1 ATAAGAAATCAGAACAGAATCCAG
* *
959658 ATTAGAAATCAGAACAGAATTCAG
1 ATAAGAAATCAGAACAGAATCCAG
959682 ATAAGAAATCAGA
1 ATAAGAAATCAGA
959695 TAAAACATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.52, C:0.13, G:0.16, T:0.18
Consensus pattern (24 bp):
ATAAGAAATCAGAACAGAATCCAG
Found at i:959670 original size:12 final size:12
Alignment explanation
Indices: 959634--959697 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
959624 TAGAATTTAT
*
959634 ATAAGATATCAG
1 ATAAGAAATCAG
959646 A-ACAG-AATCCAG
1 ATA-AGAAAT-CAG
*
959658 ATTAGAAATCAG
1 ATAAGAAATCAG
*
959670 A-ACAGAATTCAG
1 ATA-AGAAATCAG
959682 ATAAGAAATCAG
1 ATAAGAAATCAG
959694 ATAA
1 ATAA
959698 AACATTCATG
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
11 3 0.07
12 34 0.83
13 4 0.10
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (12 bp):
ATAAGAAATCAG
Found at i:970375 original size:18 final size:18
Alignment explanation
Indices: 970352--970386 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
970342 GTTCAGTATT
*
970352 TGTCCCGAAGGACCACTA
1 TGTCCCAAAGGACCACTA
970370 TGTCCCAAAGGACCACT
1 TGTCCCAAAGGACCACT
970387 GGATACGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:970405 original size:22 final size:22
Alignment explanation
Indices: 970353--970426 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
970343 TTCAGTATTT
970353 GTCCCGAAGGACCACT--AT--
1 GTCCCGAAGGACCACTGGATAC
*
970371 GTCCCAAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
970393 GTCTCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
970415 GTCCCGAAGGAC
1 GTCCCGAAGGAC
970427 TAATACCCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.31
20 2 0.04
22 31 0.65
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.15
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:971085 original size:64 final size:65
Alignment explanation
Indices: 970972--971133 Score: 174
Period size: 64 Copynumber: 2.5 Consensus size: 65
970962 TCCCTTGATG
* * * *
970972 GGTGCATTGATGCACTACC-CATGCATCGGTGCATAAATCCTATTCGATGTT-TGT-ATTT-TAT
1 GGTGCATCGATGCACT-CCTTATGCATCGATGCATAAATCCTATTCGATGTTAT-TAATTTAAAT
971033 GCA
64 G-A
* * *
971036 GGTGCATCGATGCACTCCTTATGCATCGATGCATTAATGGC-ATTTGATGTTCATTAATTTAAAT
1 GGTGCATCGATGCACTCCTTATGCATCGATGCATAAAT-CCTATTCGATGTT-ATTAATTTAAAT
971100 GA
64 GA
971102 -GTGCATCGATGCACTCCTTATGCATCGATGCA
1 GGTGCATCGATGCACTCCTTATGCATCGATGCA
971134 CCTTCAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
63 2 0.02
64 40 0.47
65 34 0.40
66 6 0.07
67 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (65 bp):
GGTGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTATTAATTTAAATGA
Found at i:974413 original size:26 final size:26
Alignment explanation
Indices: 974378--974443 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
974368 ACATAAAATC
974378 AAGA-AAATAAACAACCAAGTTAGTA
1 AAGAGAAATAAACAACCAAGTTAGTA
974403 AAGAGAAATAAACAACCAAGTTAGTA
1 AAGAGAAATAAACAACCAAGTTAGTA
*
974429 GAGAGAAATAAACAA
1 AAGAGAAATAAACAA
974444 TAGTAACAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
25 4 0.10
26 35 0.90
ACGTcount: A:0.61, C:0.11, G:0.15, T:0.14
Consensus pattern (26 bp):
AAGAGAAATAAACAACCAAGTTAGTA
Found at i:976380 original size:65 final size:65
Alignment explanation
Indices: 976276--976398 Score: 210
Period size: 65 Copynumber: 1.9 Consensus size: 65
976266 TGACTGAAAT
*
976276 TAAAGAACATAAAATCTAAAGGATTTAGTATATAATTAAACAAGTGATTAAAATAGGAAGAAAAC
1 TAAAGAACATAAAATCTAAAGGATTTAGCATATAATTAAACAAGTGATTAAAATAGGAAGAAAAC
* * *
976341 TAAAGAACCTAAAATCTAAAGGCTTTAGCGTATAATTAAACAAGTGATTAAAATAGGA
1 TAAAGAACATAAAATCTAAAGGATTTAGCATATAATTAAACAAGTGATTAAAATAGGA
976399 GGATTAGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (65 bp):
TAAAGAACATAAAATCTAAAGGATTTAGCATATAATTAAACAAGTGATTAAAATAGGAAGAAAAC
Found at i:977251 original size:10 final size:11
Alignment explanation
Indices: 977227--977255 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
977217 GGGTATCTTT
977227 CTTATTTTTCA
1 CTTATTTTTCA
977238 CTTATTTTTC-
1 CTTATTTTTCA
977248 CTTATTTT
1 CTTATTTT
977256 CTTGAGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (11 bp):
CTTATTTTTCA
Found at i:977867 original size:19 final size:21
Alignment explanation
Indices: 977833--977881 Score: 68
Period size: 19 Copynumber: 2.4 Consensus size: 21
977823 GGATCTTGTA
977833 TATTT-TTTTGTAAAATGG-T
1 TATTTATTTTGTAAAATGGAT
977852 TATTTATTTTGT-AAATGGAT
1 TATTTATTTTGTAAAATGGAT
977872 TCATTTATTT
1 T-ATTTATTT
977882 GTGGACTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.41
20 8 0.30
21 8 0.30
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (21 bp):
TATTTATTTTGTAAAATGGAT
Found at i:977882 original size:20 final size:19
Alignment explanation
Indices: 977833--977883 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
977823 GGATCTTGTA
*
977833 TATTTTTTTGTAAAATGGT
1 TATTTATTTGTAAAATGGT
977852 TATTTATTTTGT-AAATGGAT
1 TATTTA-TTTGTAAAATGG-T
977872 TCATTTATTTGT
1 T-ATTTATTTGT
977884 GGACTGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 11 0.39
20 12 0.43
21 5 0.18
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (19 bp):
TATTTATTTGTAAAATGGT
Found at i:982198 original size:194 final size:193
Alignment explanation
Indices: 981854--982206 Score: 456
Period size: 194 Copynumber: 1.8 Consensus size: 193
981844 TATGGTGACA
* * * * *
981854 TATGCATAATCATCATTCATAATATTATTAGGTAACACTATATTATGTCATTAAAAATGTGACAG
1 TATGCATAAGCATCATTCATAATATTATTAGGTAACACTATATTACGTCACTAAAAATGTAACAA
* * *
981919 TACCTCTTTCGTCACATATAGATTGATTTTAATGTATTATTCGTGACAATATAAATTATCAATAA
66 TACATCTTTCGTCACATATAGATTGATTTTAATGTATTATCCGTGACAATATAAATCATCAATAA
* * *
981984 TAAAATCTTATATGATTTAGTGACATAATCAACTGTCATAGAATATAAATTATAAAGCAACAT
131 CAAAATCTTACATAATTTAGTGACATAATCAACTGTCATAGAATATAAATTATAAAGCAACAT
* * * * *
982047 TATGCATAAGCGTCGTTCTTAATATTATTTGGTAACATTGATATTACGTCACTAAAAATGTAACA
1 TATGCATAAGCATCATTCATAATATTATTAGGTAACACT-ATATTACGTCACTAAAAATGTAACA
* * ** * *
982112 ATATATCTTTCGTCACTTATAGGA-TGATTTTAATGTATTATCCGTGATGATATATATCATTAAT
65 ATACATCTTTCGTCACATATA-GATTGATTTTAATGTATTATCCGTGACAATATAAATCATCAAT
* * *
982176 AACGAAATTTTACATAATTTAGTGTCATAAT
129 AACAAAATCTTACATAATTTAGTGACATAAT
982207 TAGTTGTAAT
Statistics
Matches: 133, Mismatches: 25, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
193 33 0.25
194 98 0.74
195 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (193 bp):
TATGCATAAGCATCATTCATAATATTATTAGGTAACACTATATTACGTCACTAAAAATGTAACAA
TACATCTTTCGTCACATATAGATTGATTTTAATGTATTATCCGTGACAATATAAATCATCAATAA
CAAAATCTTACATAATTTAGTGACATAATCAACTGTCATAGAATATAAATTATAAAGCAACAT
Found at i:984622 original size:31 final size:32
Alignment explanation
Indices: 984578--984638 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
984568 TTGTTATTAT
*
984578 TTGATTTAATTTTG-TTTTTTATGATGGTTGA
1 TTGATTGAATTTTGATTTTTTATGATGGTTGA
* *
984609 TTGATTGATTTTTGATTTTTTATGGTGGTT
1 TTGATTGAATTTTGATTTTTTATGATGGTT
984639 TTGTTGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.16, C:0.00, G:0.21, T:0.62
Consensus pattern (32 bp):
TTGATTGAATTTTGATTTTTTATGATGGTTGA
Found at i:984645 original size:29 final size:30
Alignment explanation
Indices: 984578--984647 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 30
984568 TTGTTATTAT
* *
984578 TTGATTTAATTTTGTTTTTTATGATGGTTGA
1 TTGATTGATTTTTGTTTTTTATGATGGTT-A
*
984609 TTGATTGATTTTTGATTTTTTATGGTGGTT-
1 TTGATTGATTTTTG-TTTTTTATGATGGTTA
984639 TTG-TTGATT
1 TTGATTGATT
984648 ATGGTGGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.17
30 3 0.09
31 12 0.34
32 14 0.40
ACGTcount: A:0.16, C:0.00, G:0.21, T:0.63
Consensus pattern (30 bp):
TTGATTGATTTTTGTTTTTTATGATGGTTA
Found at i:995667 original size:13 final size:13
Alignment explanation
Indices: 995646--995723 Score: 93
Period size: 13 Copynumber: 6.0 Consensus size: 13
995636 AATGACGCGC
995646 AATGCGCGTCATA
1 AATGCGCGTCATA
*
995659 AATGTGCGTCATA
1 AATGCGCGTCATA
*
995672 AATGTGCGTCATA
1 AATGCGCGTCATA
* *
995685 AATACACGTCATA
1 AATGCGCGTCATA
* * *
995698 AATGTGTGTTATA
1 AATGCGCGTCATA
995711 AATGCGCGTCATA
1 AATGCGCGTCATA
995724 GATTTATGAC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 53 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:995670 original size:85 final size:85
Alignment explanation
Indices: 995509--995674 Score: 233
Period size: 85 Copynumber: 2.0 Consensus size: 85
995499 ATACAATCAC
* * *
995509 GACACACGAATGTGTGTCATCTTCATTTATGACGGGGGTTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGCAAGTCATA
* *
995574 CATACGTGTCATAAATTTAT
66 AATACGCGTCATAAATTTAT
* * **
995594 GACACACAAATGTGTGTCATTTTCATTTATGACGGGGGCTTCAATGACGCGCAATGCGCGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGCAAGTCATA
**
995659 AATGTGCGTCATAAAT
66 AATACGCGTCATAAAT
995675 GTGCGTCATA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGCAAGTCATA
AATACGCGTCATAAATTTAT
Found at i:997382 original size:5 final size:5
Alignment explanation
Indices: 997359--997405 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
997349 TATTAAGTTA
* * *
997359 TGGTT AGGTT AGGTTT TGGGT TGGTT TGGTT TGGTT TGGTT TGGTT T
1 TGGTT TGGTT TGG-TT TGGTT TGGTT TGGTT TGGTT TGGTT TGGTT T
997406 TGTAATTGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 33 0.89
6 4 0.11
ACGTcount: A:0.04, C:0.00, G:0.40, T:0.55
Consensus pattern (5 bp):
TGGTT
Found at i:997804 original size:3 final size:3
Alignment explanation
Indices: 997796--997827 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
997786 AAAAAATGTA
997796 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
997828 ACACCAGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:997949 original size:363 final size:353
Alignment explanation
Indices: 997390--998040 Score: 1149
Period size: 363 Copynumber: 1.8 Consensus size: 353
997380 TGGTTTGGTT
* * *
997390 TGGTTTGGTTTGGTTTTGTAATTGAGCTTCAGTTTGGGCCTGCAAAAAATATAAATAATAATAAT
1 TGGTTAGGTTAGGTTTTGTAATTGAGCTTCAATTTGGGCCTGCAAAAAATATAAATAATAATAAT
997455 AATAATAATAAACACCAGACAAAAAATGATGTCAACAGTCATCAAATTATTTTTTTGAAAATCAT
66 AATAATAATAAACACCAGACAAAAAATGATGTCAACAGTCATCAAATTATTTTTTTGAAAATCAT
*
997520 ATATAACAAAAATTATATAATTCTCGAAATAAACAAAAAGGAAACGAAAGATGAAACATAAATCA
131 ATACAACAAAAATTATATAATTCTCGAAATAAACAAAAAGGAAACGAAAGATGAAACATAAATCA
997585 TGGATCAACTAAGCCCTTTTAAGGATTTGCTTAAGAATAAGAAAGAGGAATCTCATGTAAATACC
196 TGGATCAACTAAGCCCTTTTAAGGATTTGCTTAAGAATAAGAAAGAGGAATCTCATGTAAATACC
997650 ATTGAATAAGGTTTGATCCTATTCATGACGGCGGTGTGCTCTGAAAACGACGGTAGAAGCATGAA
261 ATTGAATAAGGTTTGATCCTATTCATGACGGCGGTGTGCTCTGAAAACGACGGTAGAAGCATGAA
997715 GGCTTAGGGTTAGGATTATATTAAGTTA
326 GGCTTAGGGTTAGGATTATATTAAGTTA
997743 TGGTTAGGTTAGGTTTTGTAATTGAGCTTCAATTTGGGCCTGCAAAAAATGTAAATAATAATAAT
1 TGGTTAGGTTAGGTTTTGTAATTGAGCTTCAATTTGGGCCTGC---AAA---AAAT-AT-A-AAT
*
997808 AATAATAATAATAATAATAAACACCAGACAAAAAATGATGTCAACAGTCATCAAATTTTTTTTTT
57 AATAATAATAATAATAATAAACACCAGACAAAAAATGATGTCAACAGTCATCAAA-TTATTTTTT
997873 TGAAAATCATATACAACAAAAATTATATAATTCTCGAAATAAACAAAAAGGAAACGAAAGATGAA
121 TGAAAATCATATACAACAAAAATTATATAATTCTCGAAATAAACAAAAAGGAAACGAAAGATGAA
* *
997938 ACATAAATCATGGATCAACTAAGCCCTTTTGAGGATTTGCTTAAGAATAAGCAAGAGGAATCTCA
186 ACATAAATCATGGATCAACTAAGCCCTTTTAAGGATTTGCTTAAGAATAAGAAAGAGGAATCTCA
998003 TGTAAATACCATTGAATAAGGTTTGATCCTATTCATGA
251 TGTAAATACCATTGAATAAGGTTTGATCCTATTCATGA
998041 GGATTCTGTA
Statistics
Matches: 281, Mismatches: 7, Indels: 10
0.94 0.02 0.03
Matches are distributed among these distances:
353 40 0.14
356 3 0.01
359 4 0.01
360 2 0.01
361 1 0.00
362 58 0.21
363 173 0.62
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (353 bp):
TGGTTAGGTTAGGTTTTGTAATTGAGCTTCAATTTGGGCCTGCAAAAAATATAAATAATAATAAT
AATAATAATAAACACCAGACAAAAAATGATGTCAACAGTCATCAAATTATTTTTTTGAAAATCAT
ATACAACAAAAATTATATAATTCTCGAAATAAACAAAAAGGAAACGAAAGATGAAACATAAATCA
TGGATCAACTAAGCCCTTTTAAGGATTTGCTTAAGAATAAGAAAGAGGAATCTCATGTAAATACC
ATTGAATAAGGTTTGATCCTATTCATGACGGCGGTGTGCTCTGAAAACGACGGTAGAAGCATGAA
GGCTTAGGGTTAGGATTATATTAAGTTA
Found at i:1004051 original size:111 final size:111
Alignment explanation
Indices: 1003786--1004352 Score: 861
Period size: 111 Copynumber: 5.1 Consensus size: 111
1003776 GTTTGTGTCA
* * * * * *
1003786 ATACTTCATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAAATAAAAAAACCGGTCT
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAACCGGTCT
*
1003851 ATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAAGTGACG
65 ATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG-CG
* *
1003899 ATACTTTATAAAAATGTATCTATCCATAACAATATAACAGGTAAAAAAAATGACAAAATCGGTCT
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAACCGGTCT
*
1003964 ATAAATGACAAAACAGGTAAAGCGTTACCGGATATATTGAAAGTG-G
65 ATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGCG
*
1004010 ATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTA
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTA
*
1004075 TAAATGA-AAAACAGGTAAAGTGCTACCGGATATATTGAAAGTGTCG
66 TAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG-CG
*
1004121 ATACTTTATAAAAATGTATCGATCCATAATAATATAACAGGTAAAAAAATGACAAAACCGGTCTA
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTA
* *
1004186 TAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCG
66 TAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG-CG
* * *
1004233 GTACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGT-AAAAAATGACAAAATCGGTCTA
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTA
* * * *
1004297 TAAATGACAAAACAGGTAAAACGCTACTGGATATGTTGATAGTGTCG
66 TAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTG-CG
1004344 ATACTTTAT
1 ATACTTTAT
1004353 TATAAGTATC
Statistics
Matches: 424, Mismatches: 27, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
109 34 0.08
110 29 0.07
111 186 0.44
112 75 0.18
113 100 0.24
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (111 bp):
ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTA
TAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGCG
Found at i:1004281 original size:222 final size:223
Alignment explanation
Indices: 1003786--1004352 Score: 879
Period size: 223 Copynumber: 2.5 Consensus size: 223
1003776 GTTTGTGTCA
* * * * * *
1003786 ATACTTCATAAAAATATATTGATCCATAACAATATAACAAGTAAAAAAAATAAAAAAACCGGTCT
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAACCGGTCT
* *
1003851 ATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAAGTGACGATACTTTATAAAAATGT
65 ATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGT
* *
1003916 ATCTATCCATAACAATATAACAGGTAAAAAAAATGACAAAATCGGTCTATAAATGACAAAACAGG
130 ATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAACCGGTCTATAAATGACAAAACAGG
*
1003981 TAAAGCGTTACCGGATATATTGAAAGTGG
195 TAAAGCGCTACCGGATATATTGAAAGTGG
*
1004010 ATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTA
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTA
*
1004075 TAAATGA-AAAACAGGTAAAGTGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTA
66 TAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTA
*
1004139 TCGATCCATAATAATATAACAGGT-AAAAAAATGACAAAACCGGTCTATAAATGACAAAACAGGT
131 TCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAACCGGTCTATAAATGACAAAACAGGT
* *
1004203 AAAGCGCTACCGGATATGTTGATAGTGTCG
196 AAAGCGCTACCGGATATATTGAAAGTG--G
* * *
1004233 GTACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGT-AAAAAATGACAAAATCGGTCTA
1 ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTA
* * * *
1004297 TAAATGACAAAACAGGTAAAACGCTACTGGATATGTTGATAGTGTCGATACTTTAT
66 TAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT
1004353 TATAAGTATC
Statistics
Matches: 315, Mismatches: 25, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
221 63 0.20
222 104 0.33
223 111 0.35
224 37 0.12
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (223 bp):
ATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTA
TAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTA
TCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAACCGGTCTATAAATGACAAAACAGGT
AAAGCGCTACCGGATATATTGAAAGTGG
Found at i:1004532 original size:182 final size:182
Alignment explanation
Indices: 1004226--1004678 Score: 757
Period size: 182 Copynumber: 2.5 Consensus size: 182
1004216 ATATGTTGAT
* * *
1004226 AGTGTCGGTACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAA-ATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT
** * *
1004290 CGGTCTATAAATGACAAAACAGGTAAAACGCTACTGGATATGTTGATAGTGTCGATACTTTATTA
66 CGGTCTCGAAATGACAAAACCGGTAAAACGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
* *
1004355 TAAGTATCGACACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAA
131 TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
*
1004407 AGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACATGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT
*
1004472 TGGTCTCGAAATGACAAAACCGGTAAAGA-GCTACCGGATATGTTGATAGTGTCGATACTTTATT
66 CGGTCTCGAAATGACAAAACCGGTAAA-ACGCTACCGGATATGTTGATAGTGTCGATACTTTATT
*
1004536 ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
130 ATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
*
1004589 AGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT
*
1004654 CGATCTCGAAATGACAAAACCGGTA
66 CGGTCTCGAAATGACAAAACCGGTA
1004679 GTAAAAATGT
Statistics
Matches: 254, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
181 50 0.20
182 203 0.80
183 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAT
CGGTCTCGAAATGACAAAACCGGTAAAACGCTACCGGATATGTTGATAGTGTCGATACTTTATTA
TAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
Found at i:1005316 original size:23 final size:23
Alignment explanation
Indices: 1005287--1005357 Score: 106
Period size: 23 Copynumber: 3.1 Consensus size: 23
1005277 AAATAGGTCA
1005287 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1005310 ATATAAGCGCTTCCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* * *
1005333 ATAAAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTATTACATT
1005356 AT
1 AT
1005358 TGTATTTGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:1007334 original size:20 final size:19
Alignment explanation
Indices: 1007309--1007353 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1007299 AAATATAATT
1007309 AATAAAA-TAAATATTTATAA
1 AATAAAATTAAA-ATTT-TAA
*
1007329 AATAAAATTCAAATTTTAA
1 AATAAAATTAAAATTTTAA
1007348 AATAAA
1 AATAAA
1007354 CACATATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 11 0.48
21 3 0.13
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAAAATTAAAATTTTAA
Found at i:1007994 original size:2 final size:2
Alignment explanation
Indices: 1007987--1008025 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1007977 TATTTATAAG
1007987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1008026 GAACCCAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1008532 original size:24 final size:24
Alignment explanation
Indices: 1008505--1008577 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
1008495 CGTTCATTTA
1008505 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
1008529 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * *
1008553 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
1008577 C
1 C
1008578 ATTCATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
24 43 0.96
25 2 0.04
ACGTcount: A:0.10, C:0.15, G:0.26, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:1008534 original size:14 final size:14
Alignment explanation
Indices: 1008515--1008570 Score: 84
Period size: 14 Copynumber: 4.3 Consensus size: 14
1008505 CGTTCGTGAA
1008515 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1008529 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1008543 CG-T---TTATGTT
1 CGTTCGGTTATGTT
1008553 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1008567 CGTT
1 CGTT
1008571 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1008590 original size:24 final size:24
Alignment explanation
Indices: 1008516--1008577 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
1008506 GTTCGTGAAC
*
1008516 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
1008540 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
1008564 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1008578 ATTCATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.08, C:0.13, G:0.26, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:1009630 original size:16 final size:15
Alignment explanation
Indices: 1009609--1009659 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
1009599 GTCTCCAACG
1009609 TTTATGTTCGTATTCA
1 TTTATGTTCGT-TTCA
*
1009625 TTTATGTTCGTGTTCG
1 TTTATGTTCGT-TTCA
1009641 TTTATGTTCGTTT-A
1 TTTATGTTCGTTTCA
1009655 TTTAT
1 TTTAT
1009660 TAAATGAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 25 0.78
ACGTcount: A:0.14, C:0.10, G:0.16, T:0.61
Consensus pattern (15 bp):
TTTATGTTCGTTTCA
Found at i:1010539 original size:23 final size:23
Alignment explanation
Indices: 1010509--1010587 Score: 140
Period size: 23 Copynumber: 3.4 Consensus size: 23
1010499 TCTGAATATA
*
1010509 TAAACGAACATGTTCGTAAACGT
1 TAAACGAACATGTTCGTAAGCGT
1010532 TAAACGAACATGTTCGTAAGCGT
1 TAAACGAACATGTTCGTAAGCGT
*
1010555 TAAACGAACATGTTCGTAAGCAT
1 TAAACGAACATGTTCGTAAGCGT
1010578 TAAACGAACA
1 TAAACGAACA
1010588 CTAAATAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (23 bp):
TAAACGAACATGTTCGTAAGCGT
Found at i:1021159 original size:20 final size:20
Alignment explanation
Indices: 1021123--1021161 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1021113 ATCTTTAATA
*
1021123 AAAATAAATTAAGATAAAAG
1 AAAATAAATTAAAATAAAAG
1021143 AAAA-AAATTAATAATAAAA
1 AAAATAAATTAA-AATAAAA
1021162 AATAAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAATAAATTAAAATAAAAG
Found at i:1021168 original size:19 final size:19
Alignment explanation
Indices: 1021118--1021168 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1021108 CTTTTATCTT
1021118 TAAT-AAAAAT-AAATTAA
1 TAATAAAAAATAAAATTAA
* *
1021135 -GATAAAAGAAAAAAATTAA
1 TAATAAAA-AATAAAATTAA
1021154 TAATAAAAAATAAAA
1 TAATAAAAAATAAAA
1021169 ACCTTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
16 2 0.08
17 3 0.12
18 2 0.08
19 13 0.50
20 6 0.23
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (19 bp):
TAATAAAAAATAAAATTAA
Found at i:1023775 original size:13 final size:13
Alignment explanation
Indices: 1023757--1023824 Score: 91
Period size: 13 Copynumber: 5.2 Consensus size: 13
1023747 TGTGTCATAA
*
1023757 ATTTATGACGCGC
1 ATTTATGACACGC
*
1023770 ATTTATGACACAC
1 ATTTATGACACGC
*
1023783 ATTTATGACACAC
1 ATTTATGACACGC
* *
1023796 ATTTATGACGCGT
1 ATTTATGACACGC
1023809 ATTTATGACACGC
1 ATTTATGACACGC
1023822 ATT
1 ATT
1023825 GCGTGTAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:1027733 original size:18 final size:18
Alignment explanation
Indices: 1027691--1027734 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1027681 TTCTTCTTCG
*
1027691 TCATCTCCATTTCCATCA
1 TCATCTTCATTTCCATCA
*
1027709 TCATCTTCATATT-CATCT
1 TCATCTTCAT-TTCCATCA
1027727 TCATCTTC
1 TCATCTTC
1027735 GCCATCATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.20, C:0.34, G:0.00, T:0.45
Consensus pattern (18 bp):
TCATCTTCATTTCCATCA
Found at i:1028307 original size:13 final size:13
Alignment explanation
Indices: 1028289--1028322 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1028279 ATTTAAAACA
1028289 AAATATAATTCCT
1 AAATATAATTCCT
1028302 AAATATAATTCCT
1 AAATATAATTCCT
*
1028315 AAAAATAA
1 AAATATAA
1028323 AAAAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAATTCCT
Found at i:1028423 original size:23 final size:23
Alignment explanation
Indices: 1028397--1028442 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1028387 TGATTGAATC
*
1028397 TTTTAGAAGCTGCTGACTGGGCA
1 TTTTAGAAACTGCTGACTGGGCA
*
1028420 TTTTAGAAACTGTTGACTGGGCA
1 TTTTAGAAACTGCTGACTGGGCA
1028443 CCACATCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (23 bp):
TTTTAGAAACTGCTGACTGGGCA
Found at i:1036737 original size:22 final size:22
Alignment explanation
Indices: 1036712--1036761 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
1036702 GGGGTTTTGG
1036712 TAAAAAGAT-ATTTAAA-TAATAA
1 TAAAAA-ATGATTTAAAGTAA-AA
1036734 T-AAAAATGATTTAAAGTAAAA
1 TAAAAAATGATTTAAAGTAAAA
1036755 TAAAAAA
1 TAAAAAA
1036762 AATTAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.08
21 14 0.56
22 9 0.36
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (22 bp):
TAAAAAATGATTTAAAGTAAAA
Found at i:1036745 original size:21 final size:21
Alignment explanation
Indices: 1036721--1036760 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1036711 GTAAAAAGAT
1036721 ATTTAAA-TAATAATAAAAATG
1 ATTTAAAGTAA-AATAAAAATG
1036742 ATTTAAAGTAAAATAAAAA
1 ATTTAAAGTAAAATAAAAA
1036761 AAATTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
ATTTAAAGTAAAATAAAAATG
Found at i:1044232 original size:52 final size:53
Alignment explanation
Indices: 1044152--1044342 Score: 287
Period size: 53 Copynumber: 3.6 Consensus size: 53
1044142 ATGAGGGATC
* * **
1044152 TGCTTCAGGGAGTATAACTCGAATAATCTTCTGCTTACGGGTTCGGTCCCTCT
1 TGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTCACTCCCTCT
1044205 TGCTTCAGGG-GTAGAACTCGAACAATCTTCTG-TCTACGGGTTCACTCCCTCT
1 TGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCT-TACGGGTTCACTCCCTCT
* * *
1044257 TGCTTCAGGGAGTAGAACTCGAACAATCTTTTGCCTATGGGTTCACTCCCTCT
1 TGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTCACTCCCTCT
*
1044310 TGCTTCAGGGAGTAGAACTTGAACAATCTTCTG
1 TGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1044343 GTGTGATTCT
Statistics
Matches: 126, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
51 1 0.01
52 46 0.37
53 79 0.63
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (53 bp):
TGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCTTACGGGTTCACTCCCTCT
Found at i:1044853 original size:42 final size:42
Alignment explanation
Indices: 1044800--1045030 Score: 275
Period size: 42 Copynumber: 5.5 Consensus size: 42
1044790 TTTATTATCT
* *** *
1044800 TGCTCGAAAGACTCAAAAATGACTCAAATGATTTAATCATCA
1 TGCTCGAAAGACTTACTGATGACCCAAATGATTTAATCATCA
*
1044842 TGCTCGAAAGACTTACTGATGGCCCAAATGATTTAATCATCA
1 TGCTCGAAAGACTTACTGATGACCCAAATGATTTAATCATCA
* * * *
1044884 TGCTCGAAAGACTTACTAATAACCCGAAA-GACTTCATCATCA
1 TGCTCGAAAGACTTACTGATGACCC-AAATGATTTAATCATCA
* * * * * * *
1044926 TGCTTGAAAGACTTACTGATGGCCCGAAGGACTTCATCGTCA
1 TGCTCGAAAGACTTACTGATGACCCAAATGATTTAATCATCA
* *
1044968 TGCTCGAAAGACTTACTGAGGACCCGAATGATTTAATCATCA
1 TGCTCGAAAGACTTACTGATGACCCAAATGATTTAATCATCA
1045010 TGCTCGAAAGACTTACTGATG
1 TGCTCGAAAGACTTACTGATG
1045031 GCACTTACTG
Statistics
Matches: 162, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
41 2 0.01
42 157 0.97
43 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (42 bp):
TGCTCGAAAGACTTACTGATGACCCAAATGATTTAATCATCA
Found at i:1044895 original size:84 final size:84
Alignment explanation
Indices: 1044800--1045032 Score: 306
Period size: 84 Copynumber: 2.8 Consensus size: 84
1044790 TTTATTATCT
* ** *
1044800 TGCTCGAAAGACTCAAAAATGACTCAAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1 TGCTCGAAAGACTTACTAATGACCCAAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
* *
1044865 CCAAATGATTTAATCATCA
66 CCAAAGGACTTAATCATCA
* * * *
1044884 TGCTCGAAAGACTTACTAATAACCCGAAA-GACTTCATCATCATGCTTGAAAGACTTACTGATGG
1 TGCTCGAAAGACTTACTAATGACCC-AAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * *
1044948 CCCGAAGGACTTCATCGTCA
65 CCCAAAGGACTTAATCATCA
* * *
1044968 TGCTCGAAAGACTTACTGAGGACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1 TGCTCGAAAGACTTACTAATGACCCAAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1045033 ACTTACTGAT
Statistics
Matches: 127, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
83 2 0.02
84 122 0.96
85 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (84 bp):
TGCTCGAAAGACTTACTAATGACCCAAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
CCAAAGGACTTAATCATCA
Found at i:1044937 original size:22 final size:21
Alignment explanation
Indices: 1044839--1044981 Score: 75
Period size: 22 Copynumber: 6.8 Consensus size: 21
1044829 GATTTAATCA
1044839 TCATGCTCGAAAGACTT-A-C
1 TCATGCTCGAAAGACTTCATC
* * * *
1044858 TGATGGC-CCAAATGATTTAATC
1 TCAT-GCTCGAAA-GACTTCATC
1044880 ATCATGCTCGAAAGACTT-A-C
1 -TCATGCTCGAAAGACTTCATC
* * *
1044900 TAATAACCCGAAAGACTTCATC
1 TCAT-GCTCGAAAGACTTCATC
*
1044922 ATCATGCTTGAAAGACTT-A-C
1 -TCATGCTCGAAAGACTTCATC
* * *
1044942 TGATGGCCCGAAGGACTTCATC
1 TCAT-GCTCGAAAGACTTCATC
1044964 GTCATGCTCGAAAGACTT
1 -TCATGCTCGAAAGACTT
1044982 ACTGAGGACC
Statistics
Matches: 90, Mismatches: 20, Indels: 25
0.67 0.15 0.19
Matches are distributed among these distances:
19 13 0.14
20 29 0.32
21 5 0.06
22 30 0.33
23 13 0.14
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (21 bp):
TCATGCTCGAAAGACTTCATC
Found at i:1045038 original size:13 final size:13
Alignment explanation
Indices: 1045020--1045044 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1045010 TGCTCGAAAG
1045020 ACTTACTGATGGC
1 ACTTACTGATGGC
1045033 ACTTACTGATGG
1 ACTTACTGATGG
1045045 ATTTCTTCAT
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:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:1045114 original size:76 final size:78
Alignment explanation
Indices: 1045007--1045161 Score: 233
Period size: 77 Copynumber: 2.0 Consensus size: 78
1044997 GATTTAATCA
* * *
1045007 TCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTT-CTTCATTACTATTTGGTGAAGG
1 TCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTACTATTCGGTGAAGC
1045071 CTTACAAATTACC
66 CTTACAAATTACC
* * *
1045084 TCATGCTCGAAAGAC-TACTGATGGCACTTACTGATGGGTTTGCTTCACTATTCTTCGGTGAAGC
1 TCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTACTATTCGGTGAAGC
*
1045148 CTTATAAATTACC
66 CTTACAAATTACC
1045161 T
1 T
1045162 GAAAGACTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
76 25 0.36
77 45 0.64
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (78 bp):
TCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCACTACTATTCGGTGAAGC
CTTACAAATTACC
Found at i:1059425 original size:146 final size:144
Alignment explanation
Indices: 1059153--1059540 Score: 485
Period size: 146 Copynumber: 2.6 Consensus size: 144
1059143 TATATCACTG
* * * *
1059153 AAGTTGTTGGTATTTTTTGGCATGG-GCAATATTAATGGCATTTTCTGAAGATTATTAATGGCCA
1 AAGTTGTTGGCATTTTCTGGCATGGTGCATTATTAATGGCATTTTCTAAAGATTATTAATGGCCA
** **
1059217 GTTATTGGGAGTTTCGGGCTGAAGCATTATTAGACATTACATTTCACTGAAAAGTTACTGAAGAT
66 -TT-TTGACA-TTTCGGGCTGAAGC-TTATTAGACACAACATTTCACTGAAAAGTTACTGAAGAT
*
1059282 GATT-AATGGGGCACTGAA
127 AATTGAA-GGGGCACTGAA
*
1059300 AATTTGTTGGCATTTTCTGGCATGGTGCATTATTAATGGCATTTTCTAAAGATTATTAATGGCCC
1 AAGTTGTTGGCATTTTCTGGCATGGTGCATTATTAATGGCATTTTCTAAAGATTATTAATGG-CC
* * *
1059365 ATTTTGACATTTCGGGATGAAGCTTTATTAGACACAACATTTCATTGAAAAG-TAGTTGAAGATA
65 ATTTTGACATTTCGGGCTGAAGC-TTATTAGACACAACATTTCACTGAAAAGTTA-CTGAAGATA
*
1059429 ATTGAAGGGGCATTGAA
128 ATTGAAGGGGCACTGAA
* * * *
1059446 AAGTTGCTAGCATTTTCTAGCATGGTGCATTATTAATGGCATTTTATAAAGATTATTAATGGTCC
1 AAGTTGTTGGCATTTTCTGGCATGGTGCATTATTAATGGCATTTTCTAAAGATTATTAATGG-CC
* *
1059511 GTTTTGACATCTTCGAGCTGAAGCTTATTA
65 ATTTTGACAT-TTCGGGCTGAAGCTTATTA
1059541 AATTAGCTTA
Statistics
Matches: 212, Mismatches: 24, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
145 2 0.01
146 132 0.62
147 39 0.18
148 36 0.17
149 3 0.01
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (144 bp):
AAGTTGTTGGCATTTTCTGGCATGGTGCATTATTAATGGCATTTTCTAAAGATTATTAATGGCCA
TTTTGACATTTCGGGCTGAAGCTTATTAGACACAACATTTCACTGAAAAGTTACTGAAGATAATT
GAAGGGGCACTGAA
Found at i:1061928 original size:28 final size:28
Alignment explanation
Indices: 1061896--1061955 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
1061886 TATCAATAAG
1061896 ATATATTTAACTAAAATCAAATTCATAC
1 ATATATTTAACTAAAATCAAATTCATAC
* *
1061924 ATATATTTAACTAAACTTAAATTCATAC
1 ATATATTTAACTAAAATCAAATTCATAC
1061952 ATAT
1 ATAT
1061956 TTAAAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATATTTAACTAAAATCAAATTCATAC
Found at i:1071907 original size:11 final size:11
Alignment explanation
Indices: 1071893--1071921 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1071883 ATAGGCCCTT
1071893 AATATCTTCGG
1 AATATCTTCGG
1071904 AATATCTTCGG
1 AATATCTTCGG
1071915 AATATCT
1 AATATCT
1071922 CTCTCAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (11 bp):
AATATCTTCGG
Found at i:1071965 original size:18 final size:19
Alignment explanation
Indices: 1071942--1071978 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1071932 ATGCACTTAT
1071942 TTTTCAAAATCAAA-ATAG
1 TTTTCAAAATCAAAGATAG
1071960 TTTTCAAAATCAAAGATAG
1 TTTTCAAAATCAAAGATAG
1071979 ACTTTGGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
TTTTCAAAATCAAAGATAG
Found at i:1078179 original size:19 final size:19
Alignment explanation
Indices: 1078131--1078179 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
1078121 ATCGAAATAG
1078131 GGTACCGATACCATCAAAT
1 GGTACCGATACCATCAAAT
** *
1078150 GGTATTGATACCATCAGAT
1 GGTACCGATACCATCAAAT
*
1078169 GGTACCAATAC
1 GGTACCGATAC
1078180 TACTATATAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (19 bp):
GGTACCGATACCATCAAAT
Found at i:1084428 original size:173 final size:175
Alignment explanation
Indices: 1084139--1084486 Score: 682
Period size: 173 Copynumber: 2.0 Consensus size: 175
1084129 TTTAATATAA
1084139 ATAATGACGATGTGCCTTTTAAGGATTGTATTTATGTTCCTTTGTCAAGATTTCTAAATGATAGT
1 ATAATGACGATGTGCCTTTTAAGGATTGTATTTATGTTCCTTTGTCAAGATTTCTAAATGATAGT
1084204 TCTACCTCTCTTAAGTTCCCCAATTGTCTCTTTTTGCTCCTCATTATGTGGC-TTTTCACCCCTC
66 TCTACCTCTCTTAAGTTCCCCAATTGTCTCTTTTTGCTCCTCATTATGTGGCTTTTTCACCCCTC
1084268 CGGTAGTAAAGCTACCAATATGCGTGTTTATAATTA-TGGTGGTT
131 CGGTAGTAAAGCTACCAATATGCGTGTTTATAATTATTGGTGGTT
1084312 ATAATGACGATGTGCCTTTTAAGGATTGTATTTATGTTCCTTTGTCAAGATTTCTAAATGATAGT
1 ATAATGACGATGTGCCTTTTAAGGATTGTATTTATGTTCCTTTGTCAAGATTTCTAAATGATAGT
1084377 TCTACCTCTCTTAAGTTCCCCAATTGTCTCTTTTTGCTCCTCATTATGTGGCTTTTTCACCCCTC
66 TCTACCTCTCTTAAGTTCCCCAATTGTCTCTTTTTGCTCCTCATTATGTGGCTTTTTCACCCCTC
1084442 CGGTAGTAAAGCTACCAATATGCGTGTTTATAATTATTGGTGGTT
131 CGGTAGTAAAGCTACCAATATGCGTGTTTATAATTATTGGTGGTT
1084487 TTATCATATT
Statistics
Matches: 173, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
173 117 0.68
174 48 0.28
175 8 0.05
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.42
Consensus pattern (175 bp):
ATAATGACGATGTGCCTTTTAAGGATTGTATTTATGTTCCTTTGTCAAGATTTCTAAATGATAGT
TCTACCTCTCTTAAGTTCCCCAATTGTCTCTTTTTGCTCCTCATTATGTGGCTTTTTCACCCCTC
CGGTAGTAAAGCTACCAATATGCGTGTTTATAATTATTGGTGGTT
Found at i:1087574 original size:3 final size:3
Alignment explanation
Indices: 1087562--1087608 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
1087552 CCTGCACACT
* *
1087562 TAA T-A TAA TAA TAA TAA TAA -AT TAA TAA TAA TAA TAA T-T TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1087607 TA
1 TA
1087609 TTCTTTAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1087589 original size:17 final size:17
Alignment explanation
Indices: 1087567--1087608 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
1087557 ACACTTAATA
1087567 TAATAATAATAATAAAT
1 TAATAATAATAATAAAT
*
1087584 TAATAATAATAATAATT
1 TAATAATAATAATAAAT
1087601 TAATAATA
1 TAATAATA
1087609 TTCTTTAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAATAATAAAT
Found at i:1088299 original size:131 final size:132
Alignment explanation
Indices: 1087886--1088316 Score: 577
Period size: 134 Copynumber: 3.2 Consensus size: 132
1087876 TTTAGGACGA
* *
1087886 TTCTTCTCATTATGAACTCTTAATTGG-AAATGTCAA-CCCCCAAGTGAGGTGTCACTGATTCGA
1 TTCTTCTCATTATGAACTCTCAATTGGAAAAT-T-AATCCCTCAAGTGAGGTGTCACTGATTCGA
* *
1087949 AATAACCGTGAATCGAGTGATAGGTCAAACAAGCTCTTCTCATTATGAACTTTCTT-CCTTTGTC
64 AAT-GCCGTGAATCGAGTGATAGGTCAAA-AAGCTCTTCTCATTATGAAC-TTCTTCCCTCTGTC
*
1088013 AGATGAG
126 GGATGAG
* *
1088020 TTCTTCTTATTATGAACTCTCAATT-GAAAATTTCAATCCCTCAAGTGAGGTGTCACTGATTTGA
1 TTCTTCTCATTATGAACTCTCAATTGGAAAA-TT-AATCCCTCAAGTGAGGTGTCACTGATTCGA
** * *
1088084 AATGATGTGAATCGAGTGATAGGTCGAACAAGCTCTTGTCATTATGAACTTCTTCTCCCTCTGTC
64 AATGCCGTGAATCGAGTGATAGGTC-AAAAAGCTCTTCTCATTATGAACTTC-T-TCCCTCTGTC
1088149 GGATGAG
126 GGATGAG
* * **
1088156 TTCTTCTCATTATGAACTCTTC-ATTGGAAAATTGATCCCTCAAGCGAGGCATCA-TGATTCGAA
1 TTCTTCTCATTATGAACTC-TCAATTGGAAAATTAATCCCTCAAGTGAGGTGTCACTGATTCGAA
1088219 ATGCCGTGAATCGAGTGATAGGTCAAAAAGCTCTTCTCATTATGAACTTCTTCCCTCTGTCGGAT
65 ATGCCGTGAATCGAGTGATAGGTCAAAAAGCTCTTCTCATTATGAACTTCTTCCCTCTGTCGGAT
1088284 GAG
130 GAG
*
1088287 TTCTTCTCATTATGAACTCTCTATTGGAAA
1 TTCTTCTCATTATGAACTCTCAATTGGAAA
1088317 TGTTGAATGT
Statistics
Matches: 266, Mismatches: 21, Indels: 23
0.86 0.07 0.07
Matches are distributed among these distances:
130 2 0.01
131 44 0.17
132 1 0.00
133 28 0.11
134 99 0.37
135 49 0.18
136 36 0.14
137 7 0.03
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (132 bp):
TTCTTCTCATTATGAACTCTCAATTGGAAAATTAATCCCTCAAGTGAGGTGTCACTGATTCGAAA
TGCCGTGAATCGAGTGATAGGTCAAAAAGCTCTTCTCATTATGAACTTCTTCCCTCTGTCGGATG
AG
Found at i:1089222 original size:20 final size:20
Alignment explanation
Indices: 1089193--1089247 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1089183 AACCCTCATT
1089193 TTTC-TCTTTTCAGTTTTTCA
1 TTTCTTCTTTTCA-TTTTTCA
*
1089213 TTTCTTTTTTTCATTTTTCA
1 TTTCTTCTTTTCATTTTTCA
1089233 TTT-TTCATTTT-ATTT
1 TTTCTTC-TTTTCATTT
1089248 CATTTTCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
20 18 0.58
21 7 0.23
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTCTTCTTTTCATTTTTCA
Found at i:1089223 original size:14 final size:13
Alignment explanation
Indices: 1089188--1089260 Score: 64
Period size: 13 Copynumber: 5.6 Consensus size: 13
1089178 TCTCAAACCC
*
1089188 TCATTTTTCTCTTT
1 TCATTTTTC-ATTT
1089202 TCAGTTTTTCA-TT
1 TCA-TTTTTCATTT
*
1089215 TCTTTTTTTCATTTT
1 TC-ATTTTTCA-TTT
1089230 TCATTTTTCATTT
1 TCATTTTTCATTT
1089243 T-A--TTTCATTT
1 TCATTTTTCATTT
1089253 TCATTTTT
1 TCATTTTT
1089261 TCATCTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
10 9 0.18
11 1 0.02
12 1 0.02
13 18 0.37
14 10 0.20
15 10 0.20
ACGTcount: A:0.12, C:0.15, G:0.01, T:0.71
Consensus pattern (13 bp):
TCATTTTTCATTT
Found at i:1089231 original size:7 final size:7
Alignment explanation
Indices: 1089188--1089284 Score: 67
Period size: 7 Copynumber: 13.1 Consensus size: 7
1089178 TCTCAAACCC
1089188 TCATTTT
1 TCATTTT
1089195 TC-TCTTT
1 TCAT-TTT
1089202 TCAGTTTT
1 TCA-TTTT
1089210 TCATTTCT
1 TCATTT-T
1089218 T--TTTT
1 TCATTTT
1089223 TCATTTT
1 TCATTTT
1089230 TCATTTT
1 TCATTTT
1089237 TCATTTTATT
1 TCA--TT-TT
1089247 TCA-TTT
1 TCATTTT
1089253 TCATTTTT
1 TCA-TTTT
1089261 TCATCTTT
1 TCAT-TTT
*
1089269 TTATTTGT
1 TCATTT-T
*
1089277 TCCTTTT
1 TCATTTT
1089284 T
1 T
1089285 TTTCTTCAAG
Statistics
Matches: 74, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
5 2 0.03
6 9 0.12
7 30 0.41
8 25 0.34
9 3 0.04
10 5 0.07
ACGTcount: A:0.11, C:0.15, G:0.02, T:0.71
Consensus pattern (7 bp):
TCATTTT
Found at i:1089231 original size:28 final size:28
Alignment explanation
Indices: 1089191--1089274 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 28
1089181 CAAACCCTCA
*
1089191 TTTTTC-TCTTTTCAGTTTTTCA-TTTCTT
1 TTTTTCAT-TTTTCA-TTTTTCATTTTATT
1089219 TTTTTCATTTTTCATTTTTCATTTTATT
1 TTTTTCATTTTTCATTTTTCATTTTATT
*
1089247 TCATTTTCATTTTTTCATCTTTTTATTT
1 T--TTTTCA-TTTTTCAT-TTTTCATTT
1089275 GTTCCTTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.15
28 18 0.38
29 1 0.02
30 6 0.12
31 8 0.17
32 8 0.17
ACGTcount: A:0.12, C:0.14, G:0.01, T:0.73
Consensus pattern (28 bp):
TTTTTCATTTTTCATTTTTCATTTTATT
Found at i:1089260 original size:17 final size:17
Alignment explanation
Indices: 1089228--1089259 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1089218 TTTTTTCATT
1089228 TTTCATTTTTCATTTTA
1 TTTCATTTTTCATTTTA
1089245 TTTCA-TTTTCATTTT
1 TTTCATTTTTCATTTT
1089260 TTCATCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCATTTTTCATTTTA
Found at i:1089261 original size:24 final size:23
Alignment explanation
Indices: 1089199--1089284 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 23
1089189 CATTTTTCTC
1089199 TTTTCAGTTTTTCA--TTTC-TTT
1 TTTTCA-TTTTTCATTTTTCATTT
1089220 TTTTCATTTTTCATTTTTCATTT
1 TTTTCATTTTTCATTTTTCATTT
*
1089243 TATTTCA-TTTTCATTTTTTCATCT
1 T-TTTCATTTTTCA-TTTTTCATTT
*
1089267 TTTT-ATTTGTTCCTTTTT
1 TTTTCATTT-TTCATTTTT
1089285 TTTCTTCAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.12
21 6 0.11
22 5 0.09
23 20 0.36
24 18 0.32
ACGTcount: A:0.12, C:0.14, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTCATTTTTCATTTTTCATTT
Found at i:1100335 original size:15 final size:15
Alignment explanation
Indices: 1100311--1100344 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1100301 TAAAAACGTC
1100311 TTTTAAAAAAAT-AA
1 TTTTAAAAAAATCAA
1100325 TTTTAAGAAAAATCAA
1 TTTTAA-AAAAATCAA
1100341 TTTT
1 TTTT
1100345 TTAAGACAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 6 0.33
16 6 0.33
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (15 bp):
TTTTAAAAAAATCAA
Found at i:1102173 original size:3 final size:3
Alignment explanation
Indices: 1102165--1102216 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
1102155 CCTGCACACT
* *
1102165 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA T-T TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1102212 TAA TA
1 TAA TA
1102217 TTCTTTAACC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 1 0.02
3 43 0.98
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1106651 original size:13 final size:13
Alignment explanation
Indices: 1106633--1106657 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1106623 CTTAACTCTC
1106633 ACCTAACTTTCAT
1 ACCTAACTTTCAT
1106646 ACCTAACTTTCA
1 ACCTAACTTTCA
1106658 CCTAACTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (13 bp):
ACCTAACTTTCAT
Found at i:1106652 original size:24 final size:24
Alignment explanation
Indices: 1106619--1106664 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1106609 AAATGAGACA
*
1106619 CATACTTAACTCTCACCTAACTTT
1 CATACCTAACTCTCACCTAACTTT
*
1106643 CATACCTAACTTTCACCTAACT
1 CATACCTAACTCTCACCTAACT
1106665 AATTTGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (24 bp):
CATACCTAACTCTCACCTAACTTT
Found at i:1106662 original size:11 final size:11
Alignment explanation
Indices: 1106625--1106664 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1106615 GACACATACT
*
1106625 TAACTCTCACC
1 TAACTTTCACC
1106636 TAACTTTCATACC
1 TAACTTTC--ACC
1106649 TAACTTTCACC
1 TAACTTTCACC
1106660 TAACT
1 TAACT
1106665 AATTTGATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 15 0.58
13 11 0.42
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (11 bp):
TAACTTTCACC
Found at i:1110143 original size:24 final size:24
Alignment explanation
Indices: 1110079--1110143 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
1110069 ATTGTTGTAA
* *
1110079 TTCCAGCCTCGTCCACGATTGCGAC
1 TTCCA-CCTCGTCTATGATTGCGAC
1110104 TTCCACCTCGTCTATGATTGCGAC
1 TTCCACCTCGTCTATGATTGCGAC
*
1110128 TTCCACCTCGTTTATG
1 TTCCACCTCGTCTATG
1110144 GCTTTACCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
24 32 0.86
25 5 0.14
ACGTcount: A:0.15, C:0.35, G:0.17, T:0.32
Consensus pattern (24 bp):
TTCCACCTCGTCTATGATTGCGAC
Found at i:1117668 original size:7 final size:7
Alignment explanation
Indices: 1117659--1117695 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
1117649 GCAGCAGCAA
*
1117659 CAATCAA
1 CAATCAG
1117666 CAATCAG
1 CAATCAG
1117673 CAATCAG
1 CAATCAG
1117680 CAATCAG
1 CAATCAG
1117687 CAATCAG
1 CAATCAG
1117694 CA
1 CA
1117696 GAGAGACCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.46, C:0.30, G:0.11, T:0.14
Consensus pattern (7 bp):
CAATCAG
Found at i:1122277 original size:43 final size:42
Alignment explanation
Indices: 1122230--1122427 Score: 186
Period size: 42 Copynumber: 4.7 Consensus size: 42
1122220 AATAGGTGTG
*
1122230 GACATTTAGCGGCGTTTTTTGTATAAACGCCGCAACTGATTAT
1 GACATTTAGCGGC-TTTTTTGTATAAACGCCGCAACAGATTAT
* * *
1122273 GACATTTAGCGGCTTTTTTTGTTTAAATGCAGCAACAGATTAT
1 GACATTTAGCGGC-TTTTTTGTATAAACGCCGCAACAGATTAT
* * * *
1122316 GACATTTAGCGGCATTTTTGTTTAAACGTCGCAATA-AGTTAT
1 GACATTTAGCGGCTTTTTTGTATAAACGCCGCAACAGA-TTAT
* ** * *
1122358 GATATTTAGCAACTTGTTTGTATAAACGCCG-AACCAGGTTAT
1 GACATTTAGCGGCTTTTTTGTATAAACGCCGCAA-CAGATTAT
* * *
1122400 GATATTTAGTGG-TGTTTTTATATAAACG
1 GACATTTAGCGGCT-TTTTTGTATAAACG
1122428 GCAAATGTGT
Statistics
Matches: 127, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
41 4 0.03
42 72 0.57
43 51 0.40
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (42 bp):
GACATTTAGCGGCTTTTTTGTATAAACGCCGCAACAGATTAT
Found at i:1122358 original size:42 final size:42
Alignment explanation
Indices: 1122230--1122367 Score: 147
Period size: 43 Copynumber: 3.2 Consensus size: 42
1122220 AATAGGTGTG
* *
1122230 GACATTTAGCGGCGTTTTTTGTATAAACGCCGCAACTGA-TTAT
1 GACATTTAGCGGCGTTTTTTGTTTAAACG-CGCAA-TAAGTTAT
* * *
1122273 GACATTTAGCGGCTTTTTTTGTTTAAATGCAGCAA-CAGATTAT
1 GACATTTAGCGGCGTTTTTTGTTTAAACGC-GCAATAAG-TTAT
*
1122316 GACATTTAGCGGC-ATTTTTGTTTAAACGTCGCAATAAGTTAT
1 GACATTTAGCGGCGTTTTTTGTTTAAACG-CGCAATAAGTTAT
*
1122358 GATATTTAGC
1 GACATTTAGC
1122368 AACTTGTTTG
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
41 1 0.01
42 31 0.38
43 50 0.61
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (42 bp):
GACATTTAGCGGCGTTTTTTGTTTAAACGCGCAATAAGTTAT
Found at i:1122646 original size:27 final size:27
Alignment explanation
Indices: 1122610--1122678 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
1122600 AACCATTCAA
*
1122610 GTAATGTAGTTCAACATTAAGTCAAAT
1 GTAATATAGTTCAACATTAAGTCAAAT
*
1122637 GTAATATAGTTCAACATTAAGTGAAAT
1 GTAATATAGTTCAACATTAAGTCAAAT
*
1122664 GT-ACATAGTTCAACA
1 GTAATATAGTTCAACA
1122679 ACTATAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 12 0.31
27 27 0.69
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (27 bp):
GTAATATAGTTCAACATTAAGTCAAAT
Found at i:1124944 original size:12 final size:12
Alignment explanation
Indices: 1124914--1124948 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1124904 ATCTTTTTAT
1124914 TTATCTTGTTT-
1 TTATCTTGTTTC
*
1124925 TAATCTTGTTTC
1 TTATCTTGTTTC
1124937 TTATCTTGTTTC
1 TTATCTTGTTTC
1124949 CAGCACACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.11, C:0.14, G:0.09, T:0.66
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:1131072 original size:21 final size:21
Alignment explanation
Indices: 1131048--1131088 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1131038 TGGACATAGT
* *
1131048 GGTGGTTATGGTGAAGGTGGA
1 GGTGGTAATGATGAAGGTGGA
*
1131069 GGTGGTAATGATGGAGGTGG
1 GGTGGTAATGATGAAGGTGG
1131089 TAAGGATGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.54, T:0.27
Consensus pattern (21 bp):
GGTGGTAATGATGAAGGTGGA
Found at i:1131074 original size:15 final size:14
Alignment explanation
Indices: 1131056--1131103 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
1131046 GTGGTGGTTA
1131056 TGGTGAAGGTGGAGG
1 TGGT-AAGGTGGAGG
*
1131071 TGGTAATGATGGAGG
1 TGGTAA-GGTGGAGG
1131086 TGGTAAGGATGGAGG
1 TGGTAAGG-TGGAGG
1131101 TGG
1 TGG
1131104 AGATGGTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 3 0.10
15 26 0.90
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (14 bp):
TGGTAAGGTGGAGG
Found at i:1134187 original size:44 final size:44
Alignment explanation
Indices: 1134114--1134238 Score: 153
Period size: 44 Copynumber: 2.8 Consensus size: 44
1134104 AAAGGAACAA
**
1134114 CAAAGACGCAGTATGCCAGAACAACCGAGAACAGTAAATGCAAAC
1 CAAAGA-GCAGTATGCCAGAACAACCGAGAACAGTAAACACAAAC
* * ** *
1134159 CAAAGAGCAGTATGCCAGACCAATCGAGAACAAAAAACACAAAT
1 CAAAGAGCAGTATGCCAGAACAACCGAGAACAGTAAACACAAAC
**
1134203 C-AAGAGCAGTATGCCAGATTAACCGAGAACAGTAAA
1 CAAAGAGCAGTATGCCAGAACAACCGAGAACAGTAAA
1134239 GGAGCAATCT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 30 0.44
44 32 0.47
45 6 0.09
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.10
Consensus pattern (44 bp):
CAAAGAGCAGTATGCCAGAACAACCGAGAACAGTAAACACAAAC
Found at i:1153840 original size:20 final size:20
Alignment explanation
Indices: 1153815--1153852 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1153805 TTTGGTTCAC
1153815 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1153835 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1153853 GAAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:1154869 original size:21 final size:21
Alignment explanation
Indices: 1154843--1154914 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
1154833 ATGTTATGGA
1154843 AATGTGAACCTTGAACAAGTG
1 AATGTGAACCTTGAACAAGTG
** *
1154864 AATGTGAACAGTGAACTAGTG
1 AATGTGAACCTTGAACAAGTG
*
1154885 AATGTGAA-CTGTGAACCAGTG
1 AATGTGAACCT-TGAACAAGTG
1154906 AATGTGAAC
1 AATGTGAAC
1154915 ATACTCTATG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (21 bp):
AATGTGAACCTTGAACAAGTG
Found at i:1154873 original size:14 final size:15
Alignment explanation
Indices: 1154854--1154915 Score: 62
Period size: 14 Copynumber: 4.4 Consensus size: 15
1154844 ATGTGAACCT
1154854 TGAACAAGTGAA-TG
1 TGAACAAGTGAACTG
1154868 TGAAC-AGTGAACTAG
1 TGAACAAGTGAACT-G
*
1154883 TG-A-ATGTGAACTG
1 TGAACAAGTGAACTG
*
1154896 TGAACCAGTGAA-TG
1 TGAACAAGTGAACTG
1154910 TGAACA
1 TGAACA
1154916 TACTCTATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 9 0.23
14 22 0.56
15 8 0.21
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.23
Consensus pattern (15 bp):
TGAACAAGTGAACTG
Found at i:1155071 original size:21 final size:21
Alignment explanation
Indices: 1155046--1155095 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1155036 AGTCGAGGGT
*
1155046 TTATGTGGTCTTTCGAGATAA
1 TTATGTGGTCTTTCGAGACAA
*
1155067 TTATGTGGTCTTTCGGGACAA
1 TTATGTGGTCTTTCGAGACAA
1155088 TTATGTGG
1 TTATGTGG
1155096 CACTTCGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.10, G:0.28, T:0.42
Consensus pattern (21 bp):
TTATGTGGTCTTTCGAGACAA
Found at i:1155102 original size:21 final size:21
Alignment explanation
Indices: 1155065--1155170 Score: 56
Period size: 21 Copynumber: 4.9 Consensus size: 21
1155055 CTTTCGAGAT
*
1155065 AATTATGTGGTC-TTTCGGGAC
1 AATTATGTGG-CACTTCGGGAC
1155086 AATTATGTGGCACTTCGGTGTA-
1 AATTATGTGGCACTTCGG-G-AC
* * *
1155108 ACTCTATGTGGCACTTTAGTG-C
1 AAT-TATGTGGCAC-TTCGGGAC
* * **
1155130 AAACCTATTTGGGTCTTCGGGAC
1 -AA-TTATGTGGCACTTCGGGAC
1155153 AATTATGTGGCACTTCGG
1 AATTATGTGGCACTTCGG
1155171 TGCAAATTAC
Statistics
Matches: 61, Mismatches: 15, Indels: 18
0.65 0.16 0.19
Matches are distributed among these distances:
20 1 0.02
21 27 0.44
22 9 0.15
23 21 0.34
24 3 0.05
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (21 bp):
AATTATGTGGCACTTCGGGAC
Found at i:1155137 original size:23 final size:23
Alignment explanation
Indices: 1155089--1155137 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
1155079 TCGGGACAAT
* *
1155089 TATGTGGCACTTCGGTGTAACTC
1 TATGTGGCACTTCAGTGAAACTC
*
1155112 TATGTGGCACTTTAGTGCAAAC-C
1 TATGTGGCACTTCAGTG-AAACTC
1155135 TAT
1 TAT
1155138 TTGGGTCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (23 bp):
TATGTGGCACTTCAGTGAAACTC
Found at i:1156215 original size:18 final size:17
Alignment explanation
Indices: 1156160--1156215 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 17
1156150 ATGTTACTTT
*
1156160 ATTTAAGCATG-AGTTC
1 ATTTAAACATGCAGTTC
1156176 ATTTAAACATGCA-TTGC
1 ATTTAAACATGCAGTT-C
1156193 ATTTAAAGCAT-CTAGTTC
1 ATTTAAA-CATGC-AGTTC
1156211 ATTTA
1 ATTTA
1156216 GGGAAGTAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 12 0.35
17 10 0.29
18 10 0.29
19 2 0.06
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (17 bp):
ATTTAAACATGCAGTTC
Found at i:1156293 original size:17 final size:17
Alignment explanation
Indices: 1156272--1156332 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
1156262 ATTCATGCAT
1156272 CTAGTTCATTAATAAAG
1 CTAGTTCATTAATAAAG
* *
1156289 TTAGTTTATTAATTAAA-
1 CTAGTTCATTAA-TAAAG
* * *
1156306 CTAGTTCACTCATCAAG
1 CTAGTTCATTAATAAAG
1156323 CTAGTTCATT
1 CTAGTTCATT
1156333 TATTAAACTA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
16 3 0.09
17 27 0.79
18 4 0.12
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (17 bp):
CTAGTTCATTAATAAAG
Found at i:1156310 original size:34 final size:34
Alignment explanation
Indices: 1156272--1156342 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
1156262 ATTCATGCAT
* * *
1156272 CTAGTTCATTAATAAAGTTAGTTTATTAATTAAA
1 CTAGTTCACTAATAAAGCTAGTTCATTAATTAAA
* * *
1156306 CTAGTTCACTCATCAAGCTAGTTCATTTATTAAA
1 CTAGTTCACTAATAAAGCTAGTTCATTAATTAAA
1156340 CTA
1 CTA
1156343 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (34 bp):
CTAGTTCACTAATAAAGCTAGTTCATTAATTAAA
Found at i:1157472 original size:64 final size:63
Alignment explanation
Indices: 1157367--1157486 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 63
1157357 ATTGTTCAAG
* * * * *
1157367 GTGTATCGATGCACATGAAGTGTATCGATGCACTACTTTAAAATAAAAACATTGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTT-AAATAAAAACATCGAATGCCATCA
* * *
1157431 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAAT
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTTAAATAAAAACATCGAAT
1157487 ATGATTTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 15 0.31
64 33 0.69
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCACCTTAAATAAAAACATCGAATGCCATCA
Found at i:1158200 original size:23 final size:23
Alignment explanation
Indices: 1158174--1158259 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
1158164 TATGGCACTA
*
1158174 CGGTGCAATTCTACGAAGTACTT
1 CGGTGCAATTCTACGAGGTACTT
* * *
1158197 CGGTGCAATTCTATGTGGCACTT
1 CGGTGCAATTCTACGAGGTACTT
* *
1158220 CAGTGCAATTCTACGTGGTACTT
1 CGGTGCAATTCTACGAGGTACTT
* * *
1158243 CGATGCATTTATACGAG
1 CGGTGCAATTCTACGAG
1158260 CTGTGGTGAC
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (23 bp):
CGGTGCAATTCTACGAGGTACTT
Found at i:1158243 original size:46 final size:46
Alignment explanation
Indices: 1158136--1158249 Score: 124
Period size: 46 Copynumber: 2.5 Consensus size: 46
1158126 TTAAGGAATT
* * *
1158136 TTCTACGTGGTCCTTAGG-GACAATCTCATATGGCACTACGGTGCAA
1 TTCTACGTGGTACTTCGGTG-CAATCTCATATGGCACTACAGTGCAA
** * *
1158182 TTCTACGAAGTACTTCGGTGCAAT-TCTATGTGGCACTTCAGTGCAA
1 TTCTACGTGGTACTTCGGTGCAATCTC-ATATGGCACTACAGTGCAA
*
1158228 TTCTACGTGGTACTTCGATGCA
1 TTCTACGTGGTACTTCGGTGCA
1158250 TTTATACGAG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
45 2 0.04
46 53 0.95
47 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (46 bp):
TTCTACGTGGTACTTCGGTGCAATCTCATATGGCACTACAGTGCAA
Found at i:1158324 original size:21 final size:21
Alignment explanation
Indices: 1158300--1158343 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1158290 AGTACTCACA
1158300 TACCTTAGGTTCTCAGTATGG
1 TACCTTAGGTTCTCAGTATGG
1158321 TACCTTAGGTTCTCAGTATGG
1 TACCTTAGGTTCTCAGTATGG
1158342 TA
1 TA
1158344 TCATGAGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (21 bp):
TACCTTAGGTTCTCAGTATGG
Found at i:1164189 original size:52 final size:53
Alignment explanation
Indices: 1164111--1164215 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 53
1164101 GTTGCTTATT
1164111 GATCATTAGATGATAACTAAGCTTAAGGAAAGCTTAGATTATCTT-AAATCAA
1 GATCATTAGATGATAACTAAGCTTAAGGAAAGCTTAGATTATCTTAAAATCAA
1164163 GATCATTAGATGATAACTAAGCTTAAGGAAAGCTTAGATTATCTTAAAATCAA
1 GATCATTAGATGATAACTAAGCTTAAGGAAAGCTTAGATTATCTTAAAATCAA
1164216 AAGATGATGG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 45 0.87
53 7 0.13
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (53 bp):
GATCATTAGATGATAACTAAGCTTAAGGAAAGCTTAGATTATCTTAAAATCAA
Found at i:1164694 original size:65 final size:65
Alignment explanation
Indices: 1164616--1164738 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 65
1164606 CATTACTTTA
*
1164616 AAATAAAAACATCGAAT-GCCA-TGAGTGTATCGATGCATA-AGTATTGCATCGATGCACCCCCC
1 AAATAAAAACATCGAATAG-CATTGA-TGTATCGATGCATAGA-TAGTGCATCGATGCACCCCCC
1164678 CTT
63 CTT
* * *
1164681 AAATACAAACATCGAATAGGATTTATGTATCGATGCATAGATAGTGCATCGATGCACC
1 AAATAAAAACATCGAATAGCATTGATGTATCGATGCATAGATAGTGCATCGATGCACC
1164739 TGTCAAGGGA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
65 47 0.92
66 4 0.08
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (65 bp):
AAATAAAAACATCGAATAGCATTGATGTATCGATGCATAGATAGTGCATCGATGCACCCCCCCTT
Found at i:1165435 original size:23 final size:23
Alignment explanation
Indices: 1165377--1165437 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
1165367 CAATCTTATA
*
1165377 TGGCACTTCGGTACAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1165400 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1165423 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
1165438 TTTATACAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1165956 original size:20 final size:21
Alignment explanation
Indices: 1165919--1165958 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1165909 AAATTAAGTT
1165919 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1165940 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1165959 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1166211 original size:19 final size:19
Alignment explanation
Indices: 1166187--1166225 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1166177 TCGAATGCAT
1166187 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
* *
1166206 TCCATGCATCGATGCTCTC
1 TCCATGCACCGATGCACTC
1166225 T
1 T
1166226 GAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.15, T:0.28
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1166242 original size:65 final size:64
Alignment explanation
Indices: 1166173--1166316 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 64
1166163 GAATTAATTG
*** * *
1166173 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCTCTCTGAATA-TTTTCA
1 AACATCGAATGCATTCCATGCACCGATGCACAAGCCATGCATCGATGCAC-CAGAATATTTTTC-
1166237 A
64 A
** * **
1166238 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACCAGGCTATTTTTCA
1 AACATCGAATGCATTCCATGCACCGATGCACAAGCCATGCATCGATGCACCAGAATATTTTTCA
1166302 AACATCGAATGCATT
1 AACATCGAATGCATT
1166317 TCGCATCGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 20 0.29
65 48 0.71
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTCCATGCACCGATGCACAAGCCATGCATCGATGCACCAGAATATTTTTCA
Found at i:1172110 original size:20 final size:21
Alignment explanation
Indices: 1172081--1172136 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1172071 TTTGTGCTTC
*
1172081 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
1172101 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
1172123 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1172137 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:1174530 original size:20 final size:21
Alignment explanation
Indices: 1174493--1174532 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1174483 AAATTAAGTT
1174493 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1174514 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1174533 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1174925 original size:64 final size:64
Alignment explanation
Indices: 1174749--1174910 Score: 211
Period size: 64 Copynumber: 2.5 Consensus size: 64
1174739 AAATTAATTG
* * *
1174749 AACATCGAATGCATTCTATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTC-ATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* ** **
1174814 AACATCGAATGCATTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-A
1 AACATCGAATGCATTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCAA
1174877 AACATCGAATGCATTTCATGCATCGATGCACACT
1 AACATCGAATGCA-TTCATGCATCGATGCACACT
1174911 TGGTGCACCG
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 18 0.21
64 51 0.61
65 15 0.18
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1178231 original size:14 final size:14
Alignment explanation
Indices: 1178208--1178254 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
1178198 CATTTCATTA
*
1178208 AACCATTTTATCAT
1 AACCACTTTATCAT
*
1178222 AACCACTTTATCTT
1 AACCACTTTATCAT
1178236 CAAACCAC-TTATCAT
1 --AACCACTTTATCAT
1178251 AACC
1 AACC
1178255 TATAACCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 4 0.14
14 12 0.43
15 6 0.21
16 6 0.21
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (14 bp):
AACCACTTTATCAT
Found at i:1180490 original size:17 final size:17
Alignment explanation
Indices: 1180470--1180523 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1180460 ATTCATGCAT
1180470 CTAGTTCATTAATTAAA
1 CTAGTTCATTAATTAAA
* * * *
1180487 CTAGTTCACTCATCAAG
1 CTAGTTCATTAATTAAA
* *
1180504 CTATTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
1180521 CTA
1 CTA
1180524 ACTCTTAATT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.41
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1185868 original size:16 final size:16
Alignment explanation
Indices: 1185838--1185873 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 16
1185828 AAAATAAATT
1185838 TTTATGATTAATATTA
1 TTTATGATTAATATTA
1185854 TTTAT-ATT-A-ATTA
1 TTTATGATTAATATTA
1185867 TTTATGA
1 TTTATGA
1185874 CATTGGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 9 0.47
14 2 0.11
15 3 0.16
16 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTATGATTAATATTA
Found at i:1192431 original size:23 final size:23
Alignment explanation
Indices: 1192403--1192448 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1192393 GGTTGTTGTA
1192403 TACTCAAATTCTATATAAATATG
1 TACTCAAATTCTATATAAATATG
1192426 TACTCAAATTCTATATAAATATG
1 TACTCAAATTCTATATAAATATG
1192449 GCAAGGATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (23 bp):
TACTCAAATTCTATATAAATATG
Done.