Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005891.1 Hibiscus syriacus cultivar Beakdansim tig00013832_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: 189764
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:12948 original size:30 final size:29
Alignment explanation
Indices: 12914--13042 Score: 177
Period size: 30 Copynumber: 4.3 Consensus size: 29
12904 CAGGAGCCAA
**
12914 CTGAGGAGGGGTTCGACGAACTAGAGCCGC
1 CTGAGGAGGGGTT-GACGAACCGGAGCCGC
*
12944 CTGAGGAGGGGTTTGACGAGCCGGAGCCGC
1 CTGAGGAGGGG-TTGACGAACCGGAGCCGC
*
12974 CTGAGGAGGCGGTTGACGAGCCGGAGCCGC
1 CTGAGGAGG-GGTTGACGAACCGGAGCCGC
*
13004 CTGAGGATGTGGTTGACGAACCGGAGCCGC
1 CTGAGGA-GGGGTTGACGAACCGGAGCCGC
13034 CTGAGGAGG
1 CTGAGGAGG
13043 AGGCGGGGTA
Statistics
Matches: 90, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
29 1 0.01
30 84 0.93
31 5 0.06
ACGTcount: A:0.19, C:0.23, G:0.44, T:0.13
Consensus pattern (29 bp):
CTGAGGAGGGGTTGACGAACCGGAGCCGC
Found at i:16815 original size:15 final size:15
Alignment explanation
Indices: 16797--16847 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
16787 AAATTTTTTC
16797 AAATAAT-TAAATATA
1 AAATAATAT-AATATA
16812 AAATAAATATAATATA
1 AAAT-AATATAATATA
* *
16828 ATATAATATAATAAA
1 AAATAATATAATATA
16843 AAATA
1 AAATA
16848 GTTTTATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 18 0.58
16 12 0.39
17 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAATATAATATA
Found at i:16825 original size:5 final size:5
Alignment explanation
Indices: 16806--16840 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
16796 CAAATAATTA
*
16806 AATAT AAAAT AAATAT AATAT AATAT AATAT AATA
1 AATAT AATAT -AATAT AATAT AATAT AATAT AATA
16841 AAAAATAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:20376 original size:3 final size:3
Alignment explanation
Indices: 20368--20392 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20358 ACTTAATCTA
20368 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
20393 GGAGTTCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:22891 original size:16 final size:16
Alignment explanation
Indices: 22870--22908 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
22860 ATTATTTTAT
22870 TATGTTTCTTAATAGA
1 TATGTTTCTTAATAGA
22886 TATGTTTCTTAATAGA
1 TATGTTTCTTAATAGA
*
22902 AATGTTT
1 TATGTTT
22909 TTTTTATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (16 bp):
TATGTTTCTTAATAGA
Found at i:28399 original size:23 final size:23
Alignment explanation
Indices: 28356--28400 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28346 TCTATAATAA
* *
28356 TATGTTCTTATTTATTTTTATTT
1 TATGTTCTTATTAATTATTATTT
28379 TATGTTACTT-TTAATTATTATT
1 TATGTT-CTTATTAATTATTATT
28401 ACATTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (23 bp):
TATGTTCTTATTAATTATTATTT
Found at i:28574 original size:2 final size:2
Alignment explanation
Indices: 28567--28598 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28557 AAGGTAAGCA
28567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28599 CTTTTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30299 original size:23 final size:23
Alignment explanation
Indices: 30272--30315 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
30262 TATTTTATAA
*
30272 ATATTTTTAAATTATAATTTTTT
1 ATATTTATAAATTATAATTTTTT
*
30295 ATATTTATAATTTATAATTTT
1 ATATTTATAAATTATAATTTT
30316 ATTTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATATTTATAAATTATAATTTTTT
Found at i:30302 original size:16 final size:16
Alignment explanation
Indices: 30250--30307 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
30240 TGAAAATATT
30250 TAATTTCTTTAATATTTTA
1 TAATTT-TTT-ATA-TTTA
*
30269 TAAATATTTTTA-AATTA
1 T-AAT-TTTTTATATTTA
30286 TAATTTTTTATATTTA
1 TAATTTTTTATATTTA
30302 TAATTT
1 TAATTT
30308 ATAATTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 6 0.18
16 13 0.38
17 4 0.12
18 1 0.03
19 2 0.06
20 6 0.18
21 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTTTTTATATTTA
Found at i:30322 original size:21 final size:21
Alignment explanation
Indices: 30273--30324 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
30263 ATTTTATAAA
30273 TATTTTTAAA-TTATAATTTTT
1 TATTTTTAAATTTATAA-TTTT
*
30294 TATATTTATAATTTATAA-TTT
1 TATTTTTA-AATTTATAATTTT
30315 TATTTTTAAA
1 TATTTTTAAA
30325 ATTCTTATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.07
21 17 0.63
22 2 0.07
23 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTTTAAATTTATAATTTT
Found at i:30408 original size:19 final size:20
Alignment explanation
Indices: 30366--30408 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
30356 TTATGAATAT
30366 TTTAATTTTTTAGTATTTTA
1 TTTAATTTTTTAGTATTTTA
30386 -TTAATTTCTTTA-T-TTTTA
1 TTTAATTT-TTTAGTATTTTA
30404 TTTAA
1 TTTAA
30409 AAATTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTAATTTTTTAGTATTTTA
Found at i:35275 original size:60 final size:60
Alignment explanation
Indices: 35221--35334 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
35211 ATTTTATATT
* ** *
35221 AAAATTTCTCAAATATTTCAT-TTACATAAATTTAAAAGAAAAATAATAAAATTTTAAACA
1 AAAATTTCTCAAATATAT-ATAAAACATAAATTTAAAAGAAAAAGAATAAAATTTTAAACA
* * * *
35281 AAAATTTTTGAATTATATATAAAACATAAATTTAAAAGAAAAAGAATAATATTT
1 AAAATTTCTCAAATATATATAAAACATAAATTTAAAAGAAAAAGAATAAAATTT
35335 GAATTATATA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
59 2 0.04
60 43 0.96
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (60 bp):
AAAATTTCTCAAATATATATAAAACATAAATTTAAAAGAAAAAGAATAAAATTTTAAACA
Found at i:39625 original size:23 final size:23
Alignment explanation
Indices: 39594--39662 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
39584 CATCACAGCT
*
39594 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
39617 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
39640 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
39663 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:39849 original size:103 final size:103
Alignment explanation
Indices: 39681--39895 Score: 403
Period size: 103 Copynumber: 2.1 Consensus size: 103
39671 TGTCCATAAG
* *
39681 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
39746 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
*
39784 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
39849 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
39887 GACCACATA
1 GACCACATA
39896 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:40036 original size:24 final size:24
Alignment explanation
Indices: 40008--40060 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
39998 TGTAGTTCTT
*
40008 TCACATAGCTCATCGT-CATATAAA
1 TCACATAGCTCAT-ATACATATAAA
*
40032 TCACATATCTCATATACATATAAA
1 TCACATAGCTCATATACATATAAA
40056 -CACAT
1 TCACAT
40061 GGTTCACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.30
Consensus pattern (24 bp):
TCACATAGCTCATATACATATAAA
Found at i:44858 original size:23 final size:23
Alignment explanation
Indices: 44832--44900 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
44822 CACCATAGCT
*
44832 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
44855 CGTAGAATTGCACCGGAGTACCG
1 CGTAGAATTGCACCGAAGTGCCA
*
44878 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
44901 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:45087 original size:103 final size:103
Alignment explanation
Indices: 44919--45128 Score: 384
Period size: 103 Copynumber: 2.0 Consensus size: 103
44909 TGTCCATAAG
* *
44919 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
44984 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
*
45022 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
*
45087 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
45125 GACC
1 GACC
45129 GCGTAGACCC
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:51690 original size:202 final size:205
Alignment explanation
Indices: 51323--51737 Score: 658
Period size: 202 Copynumber: 2.0 Consensus size: 205
51313 ACTTGTCCCA
51323 TGTAAGACATGTCAAAGTGTATAAGCAGTGCTTGTACCTATCCTTGCTCATGCAGTTCAAAAGTT
1 TGTAAGACATGTCAAAGTGTATAAGCAGTGCTTGTACCTATCCTTGCTCATGCAGTTCAAAAGTT
51388 TTGAAATCGCCTTATGCCGTTGTCTGTTGATGAGTTCCTCATCAGATTAATTGACAAAACAAGAT
66 TTGAAATCG-C-TAT-CCG-TGTCTGTTGATGAGTTCCTCATCAGATTAATTGACAAAACAAGAT
51453 AGTAGTTTAATTTAATTCAATCAGAAACCTTAATTTGTACCATATGTTGCTCTGACTCTTCA-TT
127 AGTAGTTTAATTTAATTCAATCAGAAACCTTAATTTGTACCATATGTTGCTCTGACTCTTCATTT
51517 TGTCTTGAAGTACC
192 TGTCTTGAAGTACC
*
51531 TGTAAGACATGTCAAAGTGTATAAGCAGTTCTTGTACCTATCCTTGCTCATGCAGTTCAAAAGTT
1 TGTAAGACATGTCAAAGTGTATAAGCAGTGCTTGTACCTATCCTTGCTCATGCAGTTCAAAAG-T
* * ** * *
51596 TTTGAAATCG-TCT-C-TGTCTGTTGATGAGTTCCTCATCTGATTAATTGACACGATAAGTTAGT
65 TTTGAAATCGCTATCCGTGTCTGTTGATGAGTTCCTCATCAGATTAATTGACAAAACAAGATAGT
* * * *
51658 GGTTTAATTTAATTCGATCAGAAACCTTAATTTTTATCATATGTTGCTCTGACTCTTCATTTTGT
130 AGTTTAATTTAATTCAATCAGAAACCTTAATTTGTACCATATGTTGCTCTGACTCTTCATTTTGT
51723 CTTGAAGTACC
195 CTTGAAGTACC
51734 TGTA
1 TGTA
51738 TCCGTTGCAT
Statistics
Matches: 194, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
202 98 0.51
203 20 0.10
204 1 0.01
206 2 0.01
208 62 0.32
209 11 0.06
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (205 bp):
TGTAAGACATGTCAAAGTGTATAAGCAGTGCTTGTACCTATCCTTGCTCATGCAGTTCAAAAGTT
TTGAAATCGCTATCCGTGTCTGTTGATGAGTTCCTCATCAGATTAATTGACAAAACAAGATAGTA
GTTTAATTTAATTCAATCAGAAACCTTAATTTGTACCATATGTTGCTCTGACTCTTCATTTTGTC
TTGAAGTACC
Found at i:51949 original size:12 final size:12
Alignment explanation
Indices: 51932--51956 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51922 ACAAAGCACC
51932 ATTTGGTGCCTA
1 ATTTGGTGCCTA
51944 ATTTGGTGCCTA
1 ATTTGGTGCCTA
51956 A
1 A
51957 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:56886 original size:65 final size:65
Alignment explanation
Indices: 56782--56913 Score: 248
Period size: 65 Copynumber: 2.0 Consensus size: 65
56772 GCTGTACATG
56782 AGACCATGGTCAAGGTTTGTATAATTTGTGTTTC-TTTTTTCTAGATGAGTCGTGTGGTATTGGA
1 AGACCATGGTCAAGGTTTGTATAATTTGTGTTTCTTTTTTTCTAGAT-AGTCGTGTGGTATTGGA
56846 A
65 A
56847 AGACCATGGTCAAGGTTTGTATAATTTGTGTTTCTTTTTTTCTAGATAGTCGTGTGGTATTGGAA
1 AGACCATGGTCAAGGTTTGTATAATTTGTGTTTCTTTTTTTCTAGATAGTCGTGTGGTATTGGAA
56912 AG
1 AG
56914 TATAGCGTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
65 54 0.82
66 12 0.18
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (65 bp):
AGACCATGGTCAAGGTTTGTATAATTTGTGTTTCTTTTTTTCTAGATAGTCGTGTGGTATTGGAA
Found at i:59996 original size:103 final size:104
Alignment explanation
Indices: 59817--60030 Score: 403
Period size: 103 Copynumber: 2.1 Consensus size: 104
59807 TGGGGGATTC
*
59817 TATTGTTGGCTGTCACCTTAGAGAAAGTTCTTCCTGGTTTTCTATTTGCTTGTAGTTTATCTATT
1 TATTGTTGGCTGTCACCTTAGAGAAAGTTCTTCCTGGTTTTCTATTTGCTTGTAGTTTATCTAAT
59882 GTATAACTATGATGCC-TTTCTTTTCACGTATCCTTGAG
66 GTATAACTATGATGCCTTTTCTTTTCACGTATCCTTGAG
59920 TATTGTTGGCTGTCACCTTAGAGAAAGTTCTTCCTGGTTTTCTATTTGCTTGTAGTTTATCTAAT
1 TATTGTTGGCTGTCACCTTAGAGAAAGTTCTTCCTGGTTTTCTATTTGCTTGTAGTTTATCTAAT
59985 GTATAACTATGATGCCTTTTCTTTTCACGTATCCTTGAG
66 GTATAACTATGATGCCTTTTCTTTTCACGTATCCTTGAG
60024 TCATTGT
1 T-ATTGT
60031 ACGGGGCATT
Statistics
Matches: 108, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
103 80 0.74
104 23 0.21
105 5 0.05
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (104 bp):
TATTGTTGGCTGTCACCTTAGAGAAAGTTCTTCCTGGTTTTCTATTTGCTTGTAGTTTATCTAAT
GTATAACTATGATGCCTTTTCTTTTCACGTATCCTTGAG
Found at i:76418 original size:21 final size:21
Alignment explanation
Indices: 76394--76434 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
76384 CGATTAACAA
76394 TACGTCTTAACGTAAAATGAT
1 TACGTCTTAACGTAAAATGAT
76415 TACGTCTTAACGTAAAATGA
1 TACGTCTTAACGTAAAATGA
76435 ACTAAGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (21 bp):
TACGTCTTAACGTAAAATGAT
Found at i:76534 original size:17 final size:17
Alignment explanation
Indices: 76499--76549 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
76489 TAATAACATA
*
76499 TAAATATATATTTTA-AT
1 TAAATA-ATATTTAATAT
76516 TAAATAATATTTAATAT
1 TAAATAATATTTAATAT
*
76533 TATATAA-ATTTGAATAT
1 TAAATAATATTT-AATAT
76550 ATTGATGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 11 0.37
17 19 0.63
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
TAAATAATATTTAATAT
Found at i:78923 original size:38 final size:38
Alignment explanation
Indices: 78863--79014 Score: 130
Period size: 38 Copynumber: 3.9 Consensus size: 38
78853 TAGGAAAACG
* *
78863 TGTTTTAAAAAATTATAATATATATTTTCCAAAAATTA
1 TGTTTTAAAAAACTATAATATATATTTTCCAAAAATAA
* *
78901 TGTTTTCAAAAACTATATTATATATATGTTTTCAAAAAATAA
1 TGTTTTAAAAAACTATA--ATATATA--TTTTCCAAAAATAA
** *
78943 T-TTTTAAGAAAACTAT-ATATTATATGTTTTTAAAAA-CA
1 TGTTTTAA-AAAACTATAATA-TATAT-TTTCCAAAAATAA
* * *
78981 TGTTTTCAAAAATTATAATATATATTTTTCAAAA
1 TGTTTTAAAAAACTATAATATATATTTTCCAAAA
79015 CTATGTATAT
Statistics
Matches: 94, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
37 8 0.09
38 30 0.32
39 19 0.20
40 11 0.12
41 5 0.05
42 21 0.22
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (38 bp):
TGTTTTAAAAAACTATAATATATATTTTCCAAAAATAA
Found at i:79055 original size:26 final size:26
Alignment explanation
Indices: 78983--79055 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
78973 TAAAAACATG
78983 TTTTCAAAA--ATTATA-ATATATAT
1 TTTTCAAAACTATTATATATATATAT
79006 TTTTCAAAACTATGTATAT-TATATAT
1 TTTTCAAAACTAT-TATATATATATAT
* *
79032 TTTT-GAAATTATTATATATGATAT
1 TTTTCAAAACTATTATATAT-ATAT
79056 CATATATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
23 9 0.21
24 5 0.12
25 9 0.21
26 19 0.45
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (26 bp):
TTTTCAAAACTATTATATATATATAT
Found at i:81220 original size:15 final size:16
Alignment explanation
Indices: 81200--81239 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
81190 TTTATTTCAA
*
81200 AATGATT-AAGCGCTG
1 AATGATTCAAACGCTG
*
81215 AATGATTCAAATGCTG
1 AATGATTCAAACGCTG
81231 AATGATTCA
1 AATGATTCA
81240 GAGGCTCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (16 bp):
AATGATTCAAACGCTG
Found at i:82180 original size:107 final size:107
Alignment explanation
Indices: 82054--82264 Score: 413
Period size: 107 Copynumber: 2.0 Consensus size: 107
82044 ATGTATTGTT
*
82054 TTTTTTTTTTTGGGGGTGGGGGAGTTGTGGTGGATACGAAACCATAGAATTTCATTTTATGAATG
1 TTTTTTTTTTCGGGGGTGGGGGAGTTGTGGTGGATACGAAACCATAGAATTTCATTTTATGAATG
82119 CCAATGACAATAACATTCCATGTAAAGGAACGATGACTATTC
66 CCAATGACAATAACATTCCATGTAAAGGAACGATGACTATTC
82161 TTTTTTTTTTCGGGGGTGGGGGAGTTGTGGTGGATACGAAACCATAGAATTTCATTTTATGAATG
1 TTTTTTTTTTCGGGGGTGGGGGAGTTGTGGTGGATACGAAACCATAGAATTTCATTTTATGAATG
82226 CCAATGACAATAACATTCCATGTAAAGGAACGATGACTA
66 CCAATGACAATAACATTCCATGTAAAGGAACGATGACTA
82265 GGATCTGTAG
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (107 bp):
TTTTTTTTTTCGGGGGTGGGGGAGTTGTGGTGGATACGAAACCATAGAATTTCATTTTATGAATG
CCAATGACAATAACATTCCATGTAAAGGAACGATGACTATTC
Found at i:85059 original size:20 final size:20
Alignment explanation
Indices: 85031--85069 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
85021 CCAATATATA
*
85031 TAAAAACTTCCATTTTTATC
1 TAAAAACTTCCAATTTTATC
*
85051 TAAAGACTTCCAATTTTAT
1 TAAAAACTTCCAATTTTAT
85070 ACATAGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.44
Consensus pattern (20 bp):
TAAAAACTTCCAATTTTATC
Found at i:90906 original size:21 final size:21
Alignment explanation
Indices: 90881--90928 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
90871 CCTAATATTG
*
90881 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTACAA
90902 CAATGTCAAAATTAGGTACAA
1 CAATGTCAAAATTAGGTACAA
*
90923 TAATGT
1 CAATGT
90929 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTACAA
Found at i:95509 original size:21 final size:21
Alignment explanation
Indices: 95484--95531 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
95474 CCTAATATTG
95484 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
95505 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
95526 TAATGT
1 CAATGT
95532 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:97121 original size:9 final size:9
Alignment explanation
Indices: 97107--97153 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
97097 CCGGGTAAAA
*
97107 AATATTAAT
1 AATATTATT
97116 AATATTATT
1 AATATTATT
97125 AA-ATTATT
1 AATATTATT
*
97133 ATTATTATT
1 AATATTATT
*
97142 ATTATTATT
1 AATATTATT
97151 AAT
1 AAT
97154 TTACATGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 7 0.21
9 27 0.79
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
AATATTATT
Found at i:97124 original size:3 final size:3
Alignment explanation
Indices: 97118--97151 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
97108 ATATTAATAA
*
97118 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
97152 ATTTACATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:97209 original size:23 final size:22
Alignment explanation
Indices: 97190--97247 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
97180 TAGAGCCCAT
97190 TACAAAGCTCAACAGAAGCCCGA
1 TACAAA-CTCAACAGAAGCCCGA
* *
97213 TCCATACTCAACAGAAGCCCGA
1 TACAAACTCAACAGAAGCCCGA
* *
97235 TCCATACTCAACA
1 TACAAACTCAACA
97248 AAAGTCCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.40, C:0.34, G:0.12, T:0.14
Consensus pattern (22 bp):
TACAAACTCAACAGAAGCCCGA
Found at i:97223 original size:22 final size:22
Alignment explanation
Indices: 97197--97247 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
97187 CATTACAAAG
97197 CTCAACAGAAGCCCGATCCATA
1 CTCAACAGAAGCCCGATCCATA
97219 CTCAACAGAAGCCCGATCCATA
1 CTCAACAGAAGCCCGATCCATA
97241 CTCAACA
1 CTCAACA
97248 AAAGTCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.37, G:0.12, T:0.14
Consensus pattern (22 bp):
CTCAACAGAAGCCCGATCCATA
Found at i:100792 original size:24 final size:25
Alignment explanation
Indices: 100743--100793 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
100733 AATAATGAAA
* *
100743 AATATAATTTTTTAATACTAATATT
1 AATATAATTTTATAATAATAATATT
100768 AATAT-ATTTTATAATTAATAA-ATT
1 AATATAATTTTATAA-TAATAATATT
100792 AA
1 AA
100794 AAATATTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
AATATAATTTTATAATAATAATATT
Found at i:100851 original size:21 final size:21
Alignment explanation
Indices: 100825--100867 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
100815 TTGTACATTT
100825 TGGTAGGAGTAAAATGGTTCA
1 TGGTAGGAGTAAAATGGTTCA
100846 TGGTAGGAGTAAAATGGTTCA
1 TGGTAGGAGTAAAATGGTTCA
100867 T
1 T
100868 CTATTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.33, T:0.30
Consensus pattern (21 bp):
TGGTAGGAGTAAAATGGTTCA
Found at i:101366 original size:2 final size:2
Alignment explanation
Indices: 101361--101389 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
101351 AAATCAATTT
101361 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
101390 GTGAATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:103155 original size:49 final size:49
Alignment explanation
Indices: 103102--103226 Score: 137
Period size: 49 Copynumber: 2.6 Consensus size: 49
103092 TTTACCTGTA
*
103102 TGACCTACCCTGAAGAGCAGC-GAAGCAGA-CCCTATTTCTTTTCTCGACC
1 TGACCTACCCTGAAGAGCAGCGGAA-CAAATCCCT-TTTCTTTTCTCGACC
** * *
103151 TGACCTATTCTGAAGAGTAGCGGAACAAATCCCTTTTCTTTTCTCGATC
1 TGACCTACCCTGAAGAGCAGCGGAACAAATCCCTTTTCTTTTCTCGACC
* * * *
103200 TAACTTACCTTGAAGAGCAACGGAACA
1 TGACCTACCCTGAAGAGCAGCGGAACA
103227 TATCAAATCT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
49 55 0.89
50 7 0.11
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (49 bp):
TGACCTACCCTGAAGAGCAGCGGAACAAATCCCTTTTCTTTTCTCGACC
Found at i:105484 original size:14 final size:16
Alignment explanation
Indices: 105445--105490 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
105435 TAATTCTATT
105445 TTATTCATAATATTTAA
1 TTATT-ATAATATTTAA
*
105462 TTATTATAATA-TTAC
1 TTATTATAATATTTAA
105477 TT-TTATAA-ATTTAA
1 TTATTATAATATTTAA
105491 AAAAATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 1 0.04
14 9 0.35
15 5 0.19
16 6 0.23
17 5 0.19
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATTATAATATTTAA
Found at i:105513 original size:20 final size:20
Alignment explanation
Indices: 105483--105535 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
105473 TTACTTTTAT
105483 AAATT-TAAAAAAATCAAAA
1 AAATTATAAAAAAATCAAAA
**
105502 AAATTATAAAAAAATTTAAA
1 AAATTATAAAAAAATCAAAA
105522 AAATTATAAAAAAA
1 AAATTATAAAAAAA
105536 ATTAATATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATTATAAAAAAATCAAAA
Found at i:105522 original size:8 final size:10
Alignment explanation
Indices: 105490--105534 Score: 58
Period size: 9 Copynumber: 4.6 Consensus size: 10
105480 TATAAATTTA
*
105490 AAAAAATCA-
1 AAAAAATTAT
105499 AAAAAATTAT
1 AAAAAATTAT
105509 AAAAAAATT-T
1 -AAAAAATTAT
105519 AAAAAATTAT
1 AAAAAATTAT
105529 AAAAAA
1 AAAAAA
105535 AATTAATATG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
9 16 0.50
10 8 0.25
11 8 0.25
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:105539 original size:12 final size:11
Alignment explanation
Indices: 105498--105535 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
105488 TAAAAAAATC
105498 AAAAAAATTAT
1 AAAAAAATTAT
105509 AAAAAAATT-T
1 AAAAAAATTAT
105519 -AAAAAATTAT
1 AAAAAAATTAT
105529 AAAAAAA
1 AAAAAAA
105536 ATTAATATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 8 0.32
10 2 0.08
11 15 0.60
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAAAATTAT
Found at i:107969 original size:62 final size:62
Alignment explanation
Indices: 107845--107976 Score: 142
Period size: 62 Copynumber: 2.1 Consensus size: 62
107835 TCACATTATT
* * * * ** *
107845 ACATTCATTAAGTTTTTTTACCTCTCATGAGGATTTTTCCCAAATACATGAATTGCATTACC
1 ACATTCATTAAGATTTCTAACCTCTCATGAGGACTTTTCCCAAATACATGAATCACAATACC
* *
107907 ACATTCATTTAGATTTCTAACCTCTCATGAGGACCTTTT-CTAAACT-CATGAATCACAATACC
1 ACATTCATTAAGATTTCTAACCTCTCATGAGGA-CTTTTCCCAAA-TACATGAATCACAATACC
*
107969 ATATTCAT
1 ACATTCAT
107977 GAAAGTATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
62 53 0.91
63 5 0.09
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (62 bp):
ACATTCATTAAGATTTCTAACCTCTCATGAGGACTTTTCCCAAATACATGAATCACAATACC
Found at i:110509 original size:242 final size:242
Alignment explanation
Indices: 110084--110564 Score: 881
Period size: 242 Copynumber: 2.0 Consensus size: 242
110074 GGCAACGTTC
110084 ATTTATTGAGATCGATAACGAAGCTTCCACTTATGCTTGGGTGGTCGTTATTGGTCTTGGAAAAT
1 ATTTATTGAGATCGATAACGAAGCTTCCACTTATGCTTGGGTGGTCGTTATTGGTCTTGGAAAAT
*
110149 CAACATCTTTTTTTAAAATTTTACATACATAATGGATTTTAAATAAATAAAAATTAAAACTCAAA
66 CAACATCTTTTTTTAAAATTTAACATACATAATGGATTTTAAATAAATAAAAATTAAAACTCAAA
*
110214 AATCCCAAATTTAAAATATAGGGTAATCGACTATGTACCAATTTTAGGCGTTGTGGGGGTGTTAA
131 AATCCCAAATTTAAAATATAAGGTAATCGACTATGTACCAATTTTAGGCGTTGTGGGGGTGTTAA
* *
110279 TCATTTCCCACGCGTAACTGATTCCCGAGCCTGATTTCTGATTTCTG
196 TCATTTCCCACACGTAACTGACTCCCGAGCCTGATTTCTGATTTCTG
*
110326 ATTTATTGAGATCGATAACGAAGCTTCCACTTATGCTTGGGTGGTCGTTATTGGTCTTGGTAAAT
1 ATTTATTGAGATCGATAACGAAGCTTCCACTTATGCTTGGGTGGTCGTTATTGGTCTTGGAAAAT
*
110391 CAACATCTTTTTTTTAAATTTAACATACATAATGGATTTTAAATAAATAAAAATTAAAACTCAAA
66 CAACATCTTTTTTTAAAATTTAACATACATAATGGATTTTAAATAAATAAAAATTAAAACTCAAA
*
110456 CATCCCAAATTTAAAATATAAGGTAATCGACTATGTACCAATTTTAGGCGTTGTGGGGGTGTTAA
131 AATCCCAAATTTAAAATATAAGGTAATCGACTATGTACCAATTTTAGGCGTTGTGGGGGTGTTAA
* *
110521 TTATTTCCCACACGTAACTGACTCTCGAGCCTGATTTCTGATTT
196 TCATTTCCCACACGTAACTGACTCCCGAGCCTGATTTCTGATTT
110565 TGCAAACCAA
Statistics
Matches: 230, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
242 230 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (242 bp):
ATTTATTGAGATCGATAACGAAGCTTCCACTTATGCTTGGGTGGTCGTTATTGGTCTTGGAAAAT
CAACATCTTTTTTTAAAATTTAACATACATAATGGATTTTAAATAAATAAAAATTAAAACTCAAA
AATCCCAAATTTAAAATATAAGGTAATCGACTATGTACCAATTTTAGGCGTTGTGGGGGTGTTAA
TCATTTCCCACACGTAACTGACTCCCGAGCCTGATTTCTGATTTCTG
Found at i:111755 original size:28 final size:28
Alignment explanation
Indices: 111720--111787 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
111710 TTGGACTAAA
111720 TGAAGTTAAAAGTGCATATTTGAAAATT
1 TGAAGTTAAAAGTGCATATTTGAAAATT
111748 TGAAGTTAAAAGTGCATATTTGAAAATT
1 TGAAGTTAAAAGTGCATATTTGAAAATT
111776 TGAAGTTAAAAG
1 TGAAGTTAAAAG
111788 CAACGACTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (28 bp):
TGAAGTTAAAAGTGCATATTTGAAAATT
Found at i:112567 original size:24 final size:24
Alignment explanation
Indices: 112540--112646 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
112530 AAACGGAGAT
*
112540 ATCAGAAATCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAA
* * *
112564 ATCAGATATCAAAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAA
* * * * * *
112588 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAA
**
112612 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAA
112636 ATCAGAAATCA
1 ATCAGAAATCA
112647 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAA
Found at i:112646 original size:48 final size:48
Alignment explanation
Indices: 112540--112648 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
112530 AAACGGAGAT
* * *
112540 ATCAGAAATCAAAACATAATTCAAATCAGATATCAAAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAAATCAGATATCAAAACAGAATCCAA
* * * * * * *
112588 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAAATCAGATATCAAAACAGAATCCAA
112636 ATCAGAAATCAGA
1 ATCAGAAATCAGA
112649 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAAATCAGATATCAAAACAGAATCCAA
Found at i:114844 original size:29 final size:29
Alignment explanation
Indices: 114772--114848 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
114762 ATTTAATTCC
114772 CACCAAAATCGAATTATTTACCAAAATAG
1 CACCAAAATCGAATTATTTACCAAAATAG
* *
114801 CACCAAAATCAAATTATTTACCAAAATAT
1 CACCAAAATCGAATTATTTACCAAAATAG
***
114830 CACCAGTTTCGAATTATTT
1 CACCAAAATCGAATTATTT
114849 CCGTGCGACG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (29 bp):
CACCAAAATCGAATTATTTACCAAAATAG
Found at i:116733 original size:2 final size:2
Alignment explanation
Indices: 116726--116756 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
116716 CTTTTAATAC
116726 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 A
116757 CCCCCATCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:116944 original size:24 final size:24
Alignment explanation
Indices: 116917--117023 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
116907 AAACGGAGAT
*
116917 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
116941 ATCAGATATTAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
116965 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
116989 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
117013 ATCAGAAATCA
1 ATCAGAAATCA
117024 GATAAAATAT
Statistics
Matches: 61, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.48, C:0.16, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:117023 original size:48 final size:48
Alignment explanation
Indices: 116917--117025 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
116907 AAACGGAGAT
* * * * *
116917 ATCAGAAATCAAAACATAATTCAGATCAGATATTAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
116965 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
117013 ATCAGAAATCAGA
1 ATCAGAAATCAGA
117026 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:119663 original size:29 final size:29
Alignment explanation
Indices: 119601--119801 Score: 235
Period size: 29 Copynumber: 6.9 Consensus size: 29
119591 AATTTTACAC
* *
119601 AAATAGCACCAAAA-CAGAATTTAATTCCCA
1 AAATAGCACCAAAATC-GAA-TTATTTACCA
* *
119631 GAATAGCACCAAAACCGAATTAATTT-CCA
1 AAATAGCACCAAAATCGAATT-ATTTACCA
* * *
119660 GAATTGCACCAAAAACCGAATTATTTACCA
1 AAATAGCACC-AAAATCGAATTATTTACCA
*
119690 AAATAGCACCAAAATCGAATTATTTACTA
1 AAATAGCACCAAAATCGAATTATTTACCA
*
119719 AAATAGCACCAAAATCGAATGATTTACCA
1 AAATAGCACCAAAATCGAATTATTTACCA
* ***
119748 AAATATCACCAGTTTCGAATTATTTACCA
1 AAATAGCACCAAAATCGAATTATTTACCA
119777 AAATAGCACCAAAATCGAATTATTT
1 AAATAGCACCAAAATCGAATTATTT
119802 CCGTGCGACG
Statistics
Matches: 149, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
29 107 0.72
30 41 0.28
31 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (29 bp):
AAATAGCACCAAAATCGAATTATTTACCA
Found at i:120874 original size:19 final size:19
Alignment explanation
Indices: 120852--120903 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
120842 ATTATACAGA
120852 AAAATAATAGTTAATTTAT
1 AAAATAATAGTTAATTTAT
120871 AAAATAATAGTTAATTTAT
1 AAAATAATAGTTAATTTAT
*
120890 AAAGTAATAGTTAA
1 AAAATAATAGTTAA
120904 CTCATGTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (19 bp):
AAAATAATAGTTAATTTAT
Found at i:122430 original size:20 final size:20
Alignment explanation
Indices: 122366--122438 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
122356 TCTAATATGT
* *
122366 GTATCGATACC-TGGCGGGG
1 GTATCGATACCATGGTGAGG
* *
122385 GTATCGGTACCATAGCAT-AGGG
1 GTATCGATACCAT-G-GTGA-GG
122407 GTATCGATACCATGGTGAGG
1 GTATCGATACCATGGTGAGG
122427 GTATCGATACCA
1 GTATCGATACCA
122439 AGCTACATCA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
19 10 0.23
20 16 0.37
21 3 0.07
22 14 0.33
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (20 bp):
GTATCGATACCATGGTGAGG
Found at i:122456 original size:95 final size:94
Alignment explanation
Indices: 122290--122511 Score: 236
Period size: 95 Copynumber: 2.3 Consensus size: 94
122280 GATTCAACCA
* ** *
122290 GTATCGGTATCCA-AGCAATGTGGTATCGATACCATGGTAAGGGTATCGATACCATTAAACATCG
1 GTATCGGTA-CCATAGCAA-GGGGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCA
* * *** *
122354 AATCTAATATGT-G-TATCGATACCTGGCGGGG
64 AAGCTAAT-T-TCGATATCGATACATAAAGAGG
* **
122385 GTATCGGTACCATAGCATAGGGGTATCGATACCATGGTGAGGGTATCGATACCAAGCTACATCAA
1 GTATCGGTACCATAGCA-AGGGGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAA
122450 AGCTAATTTCGATATCGATACATAAAGAGG
65 AGCTAATTTCGATATCGATACATAAAGAGG
*
122480 GTATCGATACCATAAGC-AGGGGTATCGATACC
1 GTATCGGTACCAT-AGCAAGGGGTATCGATACC
122512 TAAGGGCCAG
Statistics
Matches: 108, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
93 1 0.01
94 20 0.19
95 83 0.77
96 4 0.04
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (94 bp):
GTATCGGTACCATAGCAAGGGGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAA
GCTAATTTCGATATCGATACATAAAGAGG
Found at i:122504 original size:21 final size:21
Alignment explanation
Indices: 122462--122515 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
122452 CTAATTTCGA
122462 TATCGATA-CATAA-AGAGGG
1 TATCGATACCATAAGAGAGGG
122481 TATCGATACCATAAGCAG-GGG
1 TATCGATACCATAAG-AGAGGG
122502 TATCGATACC-TAAG
1 TATCGATACCATAAG
122516 GGCCAGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.25
20 9 0.28
21 13 0.41
22 2 0.06
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (21 bp):
TATCGATACCATAAGAGAGGG
Found at i:123019 original size:34 final size:34
Alignment explanation
Indices: 122955--123019 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
122945 TTATAGCTGA
* * * *
122955 AATGTATATGGGTACATTGTCAGCATAAAAGAAT
1 AATGCATATGGGTACATTATCAACAGAAAAGAAT
*
122989 AATGCATATGGGTGCATTATCAACAGAAAAG
1 AATGCATATGGGTACATTATCAACAGAAAAG
123020 TATACTAGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.26
Consensus pattern (34 bp):
AATGCATATGGGTACATTATCAACAGAAAAGAAT
Found at i:123054 original size:45 final size:45
Alignment explanation
Indices: 122989--123289 Score: 394
Period size: 45 Copynumber: 6.7 Consensus size: 45
122979 ATAAAAGAAT
*
122989 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTAGAGTTGA
* * *
123034 AATGCATATGGGTGTC-TTATCAACAGAAAAATATGCTAGAGTTGA
1 AATGCATATGGGTG-CATTATCAACATAAAAGTATACTAGAGTTGA
*
123079 TAATGCATATGGGTACATTATCAACATAAAAGTATA-TATG-GTTGA
1 -AATGCATATGGGTGCATTATCAACATAAAAGTATACTA-GAGTTGA
* * *
123124 AATGTATATGGGTACATTATCAACATAAAAGTATACTATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTAGAGTTGA
*
123169 AATGCATATGGGTGCATTATCAACATAAAAGTATATTATG-GTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTA-GAGTTGA
*** * * *
123214 AATATGTATGGGTACATTATCAACATAAAAGTATAATATAGTTGA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTAGAGTTGA
*
123259 AATACATATGGGTGCATTATCAACATAAAAG
1 AATGCATATGGGTGCATTATCAACATAAAAG
123290 ATGTTAGAAT
Statistics
Matches: 227, Mismatches: 21, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
44 34 0.15
45 162 0.71
46 31 0.14
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATACTAGAGTTGA
Found at i:123209 original size:90 final size:89
Alignment explanation
Indices: 122989--123289 Score: 435
Period size: 90 Copynumber: 3.3 Consensus size: 89
122979 ATAAAAGAAT
* * *
122989 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTA-GAGTTGAAATGCATATGGGTGTC-TT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATA-TATG-GTTGAAATGTATATGGGT-ACATT
* * * *
123052 ATCAACAGAAAAATATGCTAGAGTTGA
63 ATCAACATAAAAGTATACTATAGTTGA
*
123079 TAATGCATATGGGTACATTATCAACATAAAAGTATATATGGTTGAAATGTATATGGGTACATTAT
1 -AATGCATATGGGTGCATTATCAACATAAAAGTATATATGGTTGAAATGTATATGGGTACATTAT
123144 CAACATAAAAGTATACTATAGTTGA
65 CAACATAAAAGTATACTATAGTTGA
* *
123169 AATGCATATGGGTGCATTATCAACATAAAAGTATATTATGGTTGAAATATGTATGGGTACATTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATA-TATGGTTGAAATGTATATGGGTACATTAT
*
123234 CAACATAAAAGTATAATATAGTTGA
65 CAACATAAAAGTATACTATAGTTGA
*
123259 AATACATATGGGTGCATTATCAACATAAAAG
1 AATGCATATGGGTGCATTATCAACATAAAAG
123290 ATGTTAGAAT
Statistics
Matches: 194, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
89 35 0.18
90 125 0.64
91 34 0.18
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (89 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATATATGGTTGAAATGTATATGGGTACATTATC
AACATAAAAGTATACTATAGTTGA
Found at i:123258 original size:135 final size:134
Alignment explanation
Indices: 122989--123289 Score: 437
Period size: 135 Copynumber: 2.2 Consensus size: 134
122979 ATAAAAGAAT
*
122989 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGTCTTAT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTAGAGTTGAAATGCATATGGGTGTCTTAT
* * *
123054 CAACAGAAAAATATGCTAGAGTTGATAATGCATATGGGTACATTATCAACATAAAAGTATATATG
66 CAACAGAAAAATATACTAGAGTTGAAAATG-ATATGGGTACATTATCAACATAAAAGTATATATA
123119 GTTGA
130 GTTGA
* * *
123124 AATGTATATGGGTACATTATCAACATAAAAGTATACTATAGTTGAAATGCATATGGGTG-CATTA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATACTAGAGTTGAAATGCATATGGGTGTC-TTA
* * *
123188 TCAACATAAAAGTATATTATG-GTTGAAATATG-TATGGGTACATTATCAACATAAAAGTATAAT
65 TCAACAGAAAAATATACTA-GAGTTGAAA-ATGATATGGGTACATTATCAACATAAAAGTAT-AT
123251 ATAGTTGA
127 ATAGTTGA
*
123259 AATACATATGGGTGCATTATCAACATAAAAG
1 AATGCATATGGGTGCATTATCAACATAAAAG
123290 ATGTTAGAAT
Statistics
Matches: 149, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
134 29 0.19
135 116 0.78
136 4 0.03
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.31
Consensus pattern (134 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATACTAGAGTTGAAATGCATATGGGTGTCTTAT
CAACAGAAAAATATACTAGAGTTGAAAATGATATGGGTACATTATCAACATAAAAGTATATATAG
TTGA
Found at i:123323 original size:90 final size:90
Alignment explanation
Indices: 122989--123332 Score: 380
Period size: 90 Copynumber: 3.8 Consensus size: 90
122979 ATAAAAGAAT
* * * * *
122989 AATGCATATGGGTGCATTATCAACAGAAAAGTATACTA-GAGTTGAAATGCATATGGGTGTCTTA
1 AATGCATATGGGTGCATTATCAACATAAAAGTATATTATGAGTTAAAATGTATAT-GGTGTATTA
* * * *
123053 TCAACAGAAAAATATGCTAGAGTTGA
65 TCAACATAAAAGTATACTATAGTTGA
* *
123079 TAATGCATATGGGTACATTATCAACATAAAAGTATA-TATG-GTTGAAATGTATATGG-GTACAT
1 -AATGCATATGGGTGCATTATCAACATAAAAGTATATTATGAGTTAAAATGTATATGGTGT--AT
123141 TATCAACATAAAAGTATACTATAGTTGA
63 TATCAACATAAAAGTATACTATAGTTGA
* **
123169 AATGCATATGGGTGCATTATCAACATAAAAGTATATTATG-GTTGAAATATGTAT-GGGTACATT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATATTATGAGTT-AAA-ATGTATATGGTGTATT
*
123232 ATCAACATAAAAGTATAATATAGTTGA
64 ATCAACATAAAAGTATACTATAGTTGA
* * * *
123259 AATACATATGGGTGCATTATCAACATAAAAG-ATGTTA-GAATTTAAAATGTATAATGATGTATT
1 AATGCATATGGGTGCATTATCAACATAAAAGTATATTATG-AGTTAAAATGTAT-ATGGTGTATT
*
123322 ATAAACATAAA
64 ATCAACATAAA
123333 TGGATGTTAC
Statistics
Matches: 220, Mismatches: 22, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
88 9 0.04
89 44 0.20
90 123 0.56
91 38 0.17
92 6 0.03
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.32
Consensus pattern (90 bp):
AATGCATATGGGTGCATTATCAACATAAAAGTATATTATGAGTTAAAATGTATATGGTGTATTAT
CAACATAAAAGTATACTATAGTTGA
Found at i:123323 original size:135 final size:134
Alignment explanation
Indices: 122993--123332 Score: 366
Period size: 135 Copynumber: 2.5 Consensus size: 134
122983 AAGAATAATG
* * * * * *
122993 CATATGGGTGCATTATCAACAGAAAAGTATACTAGAGTTGAAATGCATATGGGTGTC-TTATCAA
1 CATATGGGTACATTATCAACATAAAAGTATACTAAAGTTAAAATGCATATGGATG-CATTATAAA
* * ** * *
123057 CAGAAAAATATGCTA-GAGTTGATA-ATGCATATGGGTACATTATCAACATAAAAGTATATATGG
65 CATAAAAGTATATTATG-GTTGAAATATG--TATGGGTACATTATCAACATAAAAGTATATATAG
*
123120 TTGAAATG
127 TTGAAATA
* * * * *
123128 TATATGGGTACATTATCAACATAAAAGTATACTATAGTTGAAATGCATATGGGTGCATTATCAAC
1 CATATGGGTACATTATCAACATAAAAGTATACTAAAGTTAAAATGCATATGGATGCATTATAAAC
123193 ATAAAAGTATATTATGGTTGAAATATGTATGGGTACATTATCAACATAAAAGTATAATATAGTTG
66 ATAAAAGTATATTATGGTTGAAATATGTATGGGTACATTATCAACATAAAAGTAT-ATATAGTTG
123258 AAATA
130 AAATA
* ** * * *
123263 CATATGGGTGCATTATCAACATAAAAG-ATGTTAGAATTTAAAATGTATAAT-GATGTATTATAA
1 CATATGGGTACATTATCAACATAAAAGTATACTA-AAGTTAAAATGCAT-ATGGATGCATTATAA
123326 ACATAAA
64 ACATAAA
123333 TGGATGTTAC
Statistics
Matches: 177, Mismatches: 22, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
134 33 0.19
135 138 0.78
136 6 0.03
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.32
Consensus pattern (134 bp):
CATATGGGTACATTATCAACATAAAAGTATACTAAAGTTAAAATGCATATGGATGCATTATAAAC
ATAAAAGTATATTATGGTTGAAATATGTATGGGTACATTATCAACATAAAAGTATATATAGTTGA
AATA
Found at i:141458 original size:17 final size:17
Alignment explanation
Indices: 141436--141470 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
141426 TCAACAAGTG
141436 GGGGAGGTAAAGATGGA
1 GGGGAGGTAAAGATGGA
141453 GGGGAGGTAAAGATGGA
1 GGGGAGGTAAAGATGGA
141470 G
1 G
141471 ACAAATAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.54, T:0.11
Consensus pattern (17 bp):
GGGGAGGTAAAGATGGA
Found at i:141507 original size:10 final size:10
Alignment explanation
Indices: 141492--141525 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
141482 AAAAGAGATA
*
141492 ATATATATAT
1 ATATATATGT
141502 ATATATATGT
1 ATATATATGT
*
141512 ATGTATATGT
1 ATATATATGT
141522 ATAT
1 ATAT
141526 GGTACTGGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (10 bp):
ATATATATGT
Found at i:143389 original size:26 final size:26
Alignment explanation
Indices: 143333--143389 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
143323 ATTGTTAGAT
143333 TAAAAAATATATATATATAAAAAAGA
1 TAAAAAATATATATATATAAAAAAGA
*
143359 AAAAAAATAT-TA-ATATAATAAAAAGA
1 TAAAAAATATATATATAT-A-AAAAAGA
143385 TAAAA
1 TAAAA
143390 CAGATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 4 0.15
25 3 0.11
26 20 0.74
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (26 bp):
TAAAAAATATATATATATAAAAAAGA
Found at i:143399 original size:26 final size:28
Alignment explanation
Indices: 143334--143399 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 28
143324 TTGTTAGATT
*
143334 AAAAA-ATATATATATATAAAAAAGAAA
1 AAAAAGATAAATATATATAAAAAAGAAA
* * *
143361 AAAAATATTAATATA-AT-AAAAAGATA
1 AAAAAGATAAATATATATAAAAAAGAAA
*
143387 AAACAGATAAATA
1 AAAAAGATAAATA
143400 AACGTTAGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 18 0.56
27 7 0.22
28 7 0.22
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.23
Consensus pattern (28 bp):
AAAAAGATAAATATATATAAAAAAGAAA
Found at i:143429 original size:13 final size:14
Alignment explanation
Indices: 143411--143440 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
143401 ACGTTAGTAA
143411 AAAATAAAA-AAAT
1 AAAATAAAATAAAT
143424 AAAATAAAATAAAT
1 AAAATAAAATAAAT
143438 AAA
1 AAA
143441 CCAATCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:145150 original size:105 final size:105
Alignment explanation
Indices: 144847--146170 Score: 1889
Period size: 106 Copynumber: 12.7 Consensus size: 105
144837 CATTGTTCCA
* * *
144847 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGGTTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT-GTTGTTGACAA
* * * *
144911 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * ** *
144953 AGTCCAACATCCTTCGTTGTGAAGTTGAAATTGATTCTG-AA-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
145013 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
145053 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
145118 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
145158 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAAAT-TTGTTGACAACC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
* *
145222 AGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
145262 AGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTGTTGACAAC
145327 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
145368 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTGTTGACAAC
* *
145433 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
145474 AGTCCACTATCATTCGCTGTGAAGTTGAAATTGACTCT-AGAATTGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAATTG-TTGTTGACAA
* *
145538 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTAGTCTGA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
145580 AGTCCAATATCCTTCGTTGCGAAGTTGAAATTGG----GAAGTT--G----T-TTATTGAAAACC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
145634 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
145674 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTTTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATTGTTGTTGACAAC
*
145739 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
145780 AGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTGTTGACAAC
145844 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
145885 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTTTTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA--ATTGTTGTTGACAA
* *
145950 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCAGG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** * *
145992 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTATGAAATTATTGTTGACAAGC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
146057 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
146097 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAAAT-TTGTTGACAACC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
146161 AGCGGTCCCT
66 AGCGGTCCCT
146171 CATACGTTGT
Statistics
Matches: 1103, Mismatches: 89, Indels: 54
0.89 0.07 0.04
Matches are distributed among these distances:
94 81 0.07
96 1 0.00
98 5 0.00
100 84 0.08
101 1 0.00
102 10 0.01
103 1 0.00
104 125 0.11
105 297 0.27
106 401 0.36
107 96 0.09
108 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:149971 original size:26 final size:26
Alignment explanation
Indices: 149915--149971 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
149905 ATTGTTAGAT
149915 TAAAAAATATATATATATAAAAAAGA
1 TAAAAAATATATATATATAAAAAAGA
*
149941 AAAAAAATAT-TA-ATATAATAAAAAGA
1 TAAAAAATATATATATAT-A-AAAAAGA
149967 TAAAA
1 TAAAA
149972 CAGATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 4 0.15
25 3 0.11
26 20 0.74
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (26 bp):
TAAAAAATATATATATATAAAAAAGA
Found at i:149981 original size:26 final size:28
Alignment explanation
Indices: 149916--149981 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 28
149906 TTGTTAGATT
*
149916 AAAAA-ATATATATATATAAAAAAGAAA
1 AAAAAGATAAATATATATAAAAAAGAAA
* * *
149943 AAAAATATTAATATA-AT-AAAAAGATA
1 AAAAAGATAAATATATATAAAAAAGAAA
*
149969 AAACAGATAAATA
1 AAAAAGATAAATA
149982 AACGTTAGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 18 0.56
27 7 0.22
28 7 0.22
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.23
Consensus pattern (28 bp):
AAAAAGATAAATATATATAAAAAAGAAA
Found at i:150011 original size:13 final size:14
Alignment explanation
Indices: 149993--150022 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
149983 ACGTTAGTAA
149993 AAAATAAAA-AAAT
1 AAAATAAAATAAAT
150006 AAAATAAAATAAAT
1 AAAATAAAATAAAT
150020 AAA
1 AAA
150023 CCAATCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:157458 original size:23 final size:23
Alignment explanation
Indices: 157430--157475 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
157420 TCGCCCGGAG
* *
157430 TTATTTTGTTATATATATATATA
1 TTATTTTATTATACATATATATA
*
157453 TTATTTTATTATACATATGTATA
1 TTATTTTATTATACATATATATA
157476 CATATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (23 bp):
TTATTTTATTATACATATATATA
Found at i:157614 original size:37 final size:36
Alignment explanation
Indices: 157515--157805 Score: 196
Period size: 37 Copynumber: 8.1 Consensus size: 36
157505 TGTGAAGATG
* *
157515 TTTTTGACAAAATATAT--TATATAATTTTCAAAAAAGGA
1 TTTTTGAAAAAATATATAATATATAATTTT---AAAA-CA
* ** * * *
157553 TTTTCGAAAATTTATATATTATATAGTTTTTGAAAATA
1 TTTTTGAAAAAATATATAATATATA-ATTTT-AAAACA
157591 TTTTT-AAAAAATATATAATATATAATTTTGAAAACA
1 TTTTTGAAAAAATATATAATATATAATTTT-AAAACA
* *
157627 --TTT------ATATGCT-ATATA-ATTTTTAAAACA
1 TTTTTGAAAAAATAT-ATAATATATAATTTTAAAACA
** *
157654 -TTTTGAAAACTTATATAATAAATAGATTTTAAAAGCA
1 TTTTTGAAAAAATATATAATATATA-ATTTTAAAA-CA
* * * *
157691 TTTTTGAAAAATTATATAATATATAGTTTAAAAATA
1 TTTTTGAAAAAATATATAATATATAATTTTAAAACA
157727 TTTTTGAAAAAATATATAATATATAATTTTAAAAACA
1 TTTTTGAAAAAATATATAATATATAATTTT-AAAACA
** *
157764 TTTTTGAAAACTTATATAATATTTAATTTTTAAAACA
1 TTTTTGAAAAAATATATAATATATAA-TTTTAAAACA
157801 TTTTT
1 TTTTT
157806 TAATATTATA
Statistics
Matches: 204, Mismatches: 31, Indels: 37
0.75 0.11 0.14
Matches are distributed among these distances:
27 6 0.03
28 8 0.04
29 9 0.04
30 1 0.00
33 1 0.00
34 10 0.05
35 1 0.00
36 46 0.23
37 64 0.31
38 44 0.22
39 4 0.02
40 6 0.03
41 4 0.02
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (36 bp):
TTTTTGAAAAAATATATAATATATAATTTTAAAACA
Found at i:157624 original size:25 final size:27
Alignment explanation
Indices: 157590--157654 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
157580 TTTTGAAAAT
157590 ATTTTTAAAA-A-ATATATAATATATA
1 ATTTTTAAAACATATATATAATATATA
* * **
157615 ATTTTGAAAACATTTATATGCTATATA
1 ATTTTTAAAACATATATATAATATATA
157642 ATTTTTAAAACAT
1 ATTTTTAAAACAT
157655 TTTGAAAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 9 0.27
26 1 0.03
27 23 0.70
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (27 bp):
ATTTTTAAAACATATATATAATATATA
Found at i:157806 original size:38 final size:37
Alignment explanation
Indices: 157616--157805 Score: 224
Period size: 37 Copynumber: 5.1 Consensus size: 37
157606 TAATATATAA
**
157616 TTTTGAAAACATTTATATGCTATATAATTTTTAAAACA-
1 TTTTGAAAAC--TTATATAATATATAATTTTTAAAACAT
*
157654 TTTTGAAAACTTATATAATAAATAGA-TTTTAAAAGCAT
1 TTTTGAAAACTTATATAATATATA-ATTTTTAAAA-CAT
* * * *
157692 TTTTGAAAAATTATATAATATAT-AGTTTAAAAATAT
1 TTTTGAAAACTTATATAATATATAATTTTTAAAACAT
** *
157728 TTTTGAAAAAATATATAATATATAATTTTAAAAACAT
1 TTTTGAAAACTTATATAATATATAATTTTTAAAACAT
*
157765 TTTTGAAAACTTATATAATATTTAATTTTTAAAACAT
1 TTTTGAAAACTTATATAATATATAATTTTTAAAACAT
157802 TTTT
1 TTTT
157806 TAATATTATA
Statistics
Matches: 133, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
36 44 0.33
37 58 0.44
38 31 0.23
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTTGAAAACTTATATAATATATAATTTTTAAAACAT
Found at i:157809 original size:26 final size:27
Alignment explanation
Indices: 157763--157827 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
157753 TTTTAAAAAC
157763 ATTTTTGAAAACTTATATAATATT-TA-
1 ATTTTT-AAAACTTATATAATATTATAT
* *
157789 ATTTTTAAAACATTTTTTAATATTATAT
1 ATTTTTAAAAC-TTATATAATATTATAT
157817 AGTTTTTAAAA
1 A-TTTTTAAAA
157828 AACCTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 5 0.15
26 16 0.48
27 2 0.06
28 1 0.03
29 9 0.27
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (27 bp):
ATTTTTAAAACTTATATAATATTATAT
Found at i:157849 original size:33 final size:34
Alignment explanation
Indices: 157801--157864 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
157791 TTTTAAAACA
* *
157801 TTTTTTAATATTATATAG-TTTTTAAAAAACCTT
1 TTTTTTAAAAGTATATAGTTTTTTAAAAAACCTT
157834 TTTTTTAAAAGTATATAGTTTTTTAAAAAAC
1 TTTTTTAAAAGTATATAGTTTTTTAAAAAAC
157865 AATTTTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (34 bp):
TTTTTTAAAAGTATATAGTTTTTTAAAAAACCTT
Found at i:157890 original size:40 final size:37
Alignment explanation
Indices: 157845--157938 Score: 127
Period size: 39 Copynumber: 2.5 Consensus size: 37
157835 TTTTTAAAAG
*
157845 TATATAGTTTTTTAAAAAACAATTTTGAAATTTTATAT
1 TATATAGTTTTTTAAAAAAC-ATTTTGAAAATTTATAT
*
157883 ATAATATA-TGTTTTTAAAAAACATTTTTAAAATTTATAT
1 -T-ATATAGT-TTTTTAAAAAACATTTTGAAAATTTATAT
157922 TATATAGTTTTTTAAAA
1 TATATAGTTTTTTAAAA
157939 TATATTTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
37 14 0.28
38 2 0.04
39 17 0.34
40 17 0.34
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (37 bp):
TATATAGTTTTTTAAAAAACATTTTGAAAATTTATAT
Found at i:157950 original size:4 final size:4
Alignment explanation
Indices: 157941--157991 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
157931 TTTTAAAATA
* *
157941 TATT TATT TATT TA-- TATT TATT TATT AATAT TATT T-GT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TAT-T TATT TATT TATT TATT
157987 TATT T
1 TATT T
157992 CTCTTTTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 2 0.05
3 2 0.05
4 32 0.82
5 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:157958 original size:14 final size:14
Alignment explanation
Indices: 157939--157991 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
157929 TTTTTTAAAA
157939 TATATTTATTTATT
1 TATATTTATTTATT
157953 TATATTTATTTATT
1 TATATTTATTTATT
* *
157967 AATA-TTATTTGTT
1 TATATTTATTTATT
*
157980 ATTTATTTATTT
1 -TATATTTATTT
157992 CTCTTTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 8 0.24
14 19 0.58
15 6 0.18
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TATATTTATTTATT
Found at i:164750 original size:20 final size:20
Alignment explanation
Indices: 164725--164773 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
164715 TTATTTGATA
164725 ATAAATATTTAAATAGTTCT
1 ATAAATATTTAAATAGTTCT
164745 ATAAATATTTAAATAGTTCT
1 ATAAATATTTAAATAGTTCT
164765 ATAAATATT
1 ATAAATATT
164774 GTGTTCGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (20 bp):
ATAAATATTTAAATAGTTCT
Found at i:165954 original size:17 final size:18
Alignment explanation
Indices: 165915--165961 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
165905 TGTTTATGAG
*
165915 GGAATTGGAATCTGTGAA
1 GGAATTGAAATCTGTGAA
*
165933 GGAATTGAAATCTGT-CA
1 GGAATTGAAATCTGTGAA
165950 GGAATTGAAATC
1 GGAATTGAAATC
165962 CAATTACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (18 bp):
GGAATTGAAATCTGTGAA
Found at i:166000 original size:44 final size:44
Alignment explanation
Indices: 165950--166033 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
165940 AAATCTGTCA
*
165950 GGAATTGAAATCCAATTACATATTCTGTTTGGTTGGCAGAAAAT
1 GGAATTGAAATCCAATTACATATTCTGTTTGGTTCGCAGAAAAT
* *
165994 GGAATTGGAATCCAATTTCATATTCTGTTTGGTTCGCAGA
1 GGAATTGAAATCCAATTACATATTCTGTTTGGTTCGCAGA
166034 CATGTCAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (44 bp):
GGAATTGAAATCCAATTACATATTCTGTTTGGTTCGCAGAAAAT
Found at i:166608 original size:33 final size:33
Alignment explanation
Indices: 166531--166643 Score: 155
Period size: 28 Copynumber: 3.5 Consensus size: 33
166521 CCTAAACTCG
*
166531 AACCCGACTAGACCCGAATATCACACTTAAAAA
1 AACCCGACTCGACCCGAATATCACACTTAAAAA
166564 AACCC-A----ACCCGAATATCACACTTAAAAA
1 AACCCGACTCGACCCGAATATCACACTTAAAAA
*
166592 AACCCGACTCGACCCGAACATCACACTTAAAAAA
1 AACCCGACTCGACCCGAATATCACACTT-AAAAA
*
166626 AACCCGACCCGACCCGAA
1 AACCCGACTCGACCCGAA
166644 CAAAATAAAG
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
28 27 0.38
29 1 0.01
32 1 0.01
33 21 0.29
34 22 0.31
ACGTcount: A:0.44, C:0.35, G:0.09, T:0.12
Consensus pattern (33 bp):
AACCCGACTCGACCCGAATATCACACTTAAAAA
Found at i:170409 original size:6 final size:6
Alignment explanation
Indices: 170400--170477 Score: 68
Period size: 6 Copynumber: 13.2 Consensus size: 6
170390 CACATATACC
* ** * * * * *
170400 ATCATT ATCATC ATCAAC ATTATT ATCCTT ATCCTT ATCACT ATCACT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
*
170448 ATCACT ATCATT ATCATT -TCATT ATCATT A
1 ATCATT ATCATT ATCATT ATCATT ATCATT A
170478 ATCCATTTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
5 5 0.08
6 56 0.92
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (6 bp):
ATCATT
Found at i:170731 original size:24 final size:24
Alignment explanation
Indices: 170685--170734 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
170675 CAGCTCGTAT
*
170685 AAATTGCACCGAAGTGCTGCATAG
1 AAATTGCACCGAAGTGCTACATAG
*
170709 AAATTGCATCGAAGTG-TCACATAG
1 AAATTGCACCGAAGTGCT-ACATAG
170733 AA
1 AA
170735 TGTCCCGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (24 bp):
AAATTGCACCGAAGTGCTACATAG
Found at i:170758 original size:19 final size:20
Alignment explanation
Indices: 170728--170788 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
170718 CGAAGTGTCA
170728 CATAGAATGTCCCGAAGGAC
1 CATAGAATGTCCCGAAGGAC
*
170748 CATAG-ATGTCCTGAAGGAC
1 CATAGAATGTCCCGAAGGAC
* *
170767 CTTGTAGAATGTCTCGAAGGAC
1 C--ATAGAATGTCCCGAAGGAC
170789 TACGTAGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 14 0.41
20 5 0.15
21 3 0.09
22 12 0.35
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (20 bp):
CATAGAATGTCCCGAAGGAC
Found at i:170795 original size:22 final size:20
Alignment explanation
Indices: 170730--170803 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 20
170720 AAGTGTCACA
*
170730 TAGAATGTCCCGAAGGAC-CA
1 TAGAATGT-CCGAAGGACTCG
*
170750 TAG-ATGTCCTGAAGGACCTTG
1 TAGAATGTCC-GAAGGA-CTCG
170771 TAGAATGTCTCGAAGGACTACG
1 TAGAATGTC-CGAAGGACT-CG
170793 TAGAATTGTCC
1 TAGAA-TGTCC
170804 TGAATGACCG
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
18 2 0.05
19 10 0.23
20 4 0.09
21 5 0.11
22 18 0.41
23 5 0.11
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (20 bp):
TAGAATGTCCGAAGGACTCG
Found at i:170820 original size:45 final size:41
Alignment explanation
Indices: 170728--170820 Score: 96
Period size: 45 Copynumber: 2.2 Consensus size: 41
170718 CGAAGTGTCA
*
170728 CATAGAATGTCCCGAAGGACCATAGATGTCCTGAAGGACCT
1 CATAGAATGTCCCGAAGGACCATAGATGTCCTGAAGGACCG
** * * *
170769 TGTAGAATGTCTCGAAGGACTACGTAGAATTGTCCTGAATGACCG
1 CATAGAATGTCCCGAAGGAC--CATAG-A-TGTCCTGAAGGACCG
170814 CATAGAA
1 CATAGAA
170821 CCATTGACTC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
41 17 0.43
43 4 0.10
44 1 0.03
45 18 0.45
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (41 bp):
CATAGAATGTCCCGAAGGACCATAGATGTCCTGAAGGACCG
Found at i:172310 original size:21 final size:21
Alignment explanation
Indices: 172284--172325 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
172274 ATTTTAATTT
172284 TATGAAGGAGTACCGATACCC
1 TATGAAGGAGTACCGATACCC
*
172305 TATGAAGGGGTACCGATACCC
1 TATGAAGGAGTACCGATACCC
172326 CCTATCGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (21 bp):
TATGAAGGAGTACCGATACCC
Found at i:173683 original size:3 final size:3
Alignment explanation
Indices: 173662--173702 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
173652 TGAGGAAAGG
* *
173662 GAA G-A GAA GAA AAA CAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
173703 TGAGAAGGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:175342 original size:21 final size:21
Alignment explanation
Indices: 175316--175355 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
175306 TACCAATTGG
175316 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
175337 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
175356 CATTAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:175665 original size:17 final size:17
Alignment explanation
Indices: 175643--175695 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
175633 GATTGCTCGG
175643 ATGGTATCTATACCCCT
1 ATGGTATCTATACCCCT
* *
175660 ATGGTATCGATACCCCCC
1 ATGGTATCTATA-CCCCT
*
175678 AGGGGTATCTATACCCCT
1 A-TGGTATCTATACCCCT
175696 GGCTACAACG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 11 0.38
18 9 0.31
19 9 0.31
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (17 bp):
ATGGTATCTATACCCCT
Found at i:177410 original size:22 final size:21
Alignment explanation
Indices: 177378--177423 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 21
177368 ACAGTAAAAT
177378 ACAGTATGAACAATACCGTGA
1 ACAGTATGAACAATACCGTGA
177399 ACAGTAATGAACAATACCGTGA
1 ACAGT-ATGAACAATACCGTGA
177421 ACA
1 ACA
177424 TTGCCCTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (21 bp):
ACAGTATGAACAATACCGTGA
Found at i:177508 original size:21 final size:22
Alignment explanation
Indices: 177470--177512 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
177460 AATTCTTGAG
*
177470 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGATTACCCTGCTACA
177492 GGGAACCGA-TACCCTGCTACA
1 GGGAACCGATTACCCTGCTACA
177513 TTACTGCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.26, C:0.35, G:0.23, T:0.16
Consensus pattern (22 bp):
GGGAACCGATTACCCTGCTACA
Found at i:178387 original size:30 final size:30
Alignment explanation
Indices: 178353--178415 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
178343 TTATATCGCG
* *
178353 TAGACATATTATTTTCATACCTTTATCACA
1 TAGACATATCATTTCCATACCTTTATCACA
178383 TAGACATATCATTTCCATACCTTTATCACA
1 TAGACATATCATTTCCATACCTTTATCACA
178413 TAG
1 TAG
178416 CTCATATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (30 bp):
TAGACATATCATTTCCATACCTTTATCACA
Found at i:181302 original size:21 final size:21
Alignment explanation
Indices: 181269--181311 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
181259 GATATGTAAA
181269 TCGCATTGCGATTTTCTGAAT
1 TCGCATTGCGATTTTCTGAAT
* *
181290 TCGCGTTGTGATTTTCTGAAT
1 TCGCATTGCGATTTTCTGAAT
181311 T
1 T
181312 AAACGCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (21 bp):
TCGCATTGCGATTTTCTGAAT
Found at i:181355 original size:20 final size:20
Alignment explanation
Indices: 181326--181370 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
181316 GCGAATCTAT
* *
181326 AATTCGCAACACATAAGTCA
1 AATTCACAACACAAAAGTCA
* *
181346 AATTCACAACATAAAAGTTA
1 AATTCACAACACAAAAGTCA
181366 AATTC
1 AATTC
181371 GCAAAGCGCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (20 bp):
AATTCACAACACAAAAGTCA
Found at i:181552 original size:22 final size:22
Alignment explanation
Indices: 181526--181572 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
181516 CTATGGCGAC
181526 ATCTGTCCCCATCTCCGACAAA
1 ATCTGTCCCCATCTCCGACAAA
*
181548 ATCTGTCCCCATCTCCGACGAA
1 ATCTGTCCCCATCTCCGACAAA
181570 ATC
1 ATC
181573 CGTCTATCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.40, G:0.11, T:0.23
Consensus pattern (22 bp):
ATCTGTCCCCATCTCCGACAAA
Found at i:183575 original size:20 final size:20
Alignment explanation
Indices: 183552--183660 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
183542 AAAATTTGTA
183552 TTGCGAATTAGAAAATCGAG
1 TTGCGAATTAGAAAATCGAG
* * *
183572 TTGCGAA-AACAAAATTCGCG
1 TTGCGAATTAGAAAA-TCGAG
* *
183592 TTACAAATTCAG--AATCGAG
1 TTGCGAATT-AGAAAATCGAG
* *
183611 TTGCGAATTTA-AAATTCAGTG
1 TTGCGAA-TTAGAAAATC-GAG
* *
183632 TTGCGAATTTGAAAATCGCG
1 TTGCGAATTAGAAAATCGAG
183652 TTGCGAATT
1 TTGCGAATT
183661 TGGAAATCTC
Statistics
Matches: 66, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
19 15 0.23
20 36 0.55
21 14 0.21
22 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (20 bp):
TTGCGAATTAGAAAATCGAG
Found at i:183586 original size:40 final size:40
Alignment explanation
Indices: 183531--183658 Score: 125
Period size: 40 Copynumber: 3.2 Consensus size: 40
183521 ACTAAAACCT
* *
183531 GTTGCGAAATTAAAATTTGTATTGCGAATTAGAAAATCGA
1 GTTGCGAAATTAAAATTAGTGTTGCGAATTAGAAAATCGA
** * * * *
183571 GTTGCGAAAACAAAATTCGCGTTACAAATTCAG--AATCGA
1 GTTGCGAAATTAAAATTAGTGTTGCGAATT-AGAAAATCGA
* * *
183610 GTTGCGAATTTAAAATTCAGTGTTGCGAATTTGAAAATCGC
1 GTTGCGAAATTAAAATT-AGTGTTGCGAATTAGAAAATCGA
183651 GTTGCGAA
1 GTTGCGAA
183659 TTTGGAAATC
Statistics
Matches: 68, Mismatches: 16, Indels: 7
0.75 0.18 0.08
Matches are distributed among these distances:
39 21 0.31
40 32 0.47
41 15 0.22
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTAGTGTTGCGAATTAGAAAATCGA
Found at i:183661 original size:20 final size:20
Alignment explanation
Indices: 183604--183782 Score: 109
Period size: 20 Copynumber: 8.9 Consensus size: 20
183594 ACAAATTCAG
*
183604 AATCGAGTTGCGAATTT-AA
1 AATCGCGTTGCGAATTTGAA
*
183623 AATTCAGTGTTGCGAATTTGAA
1 AA-TC-GCGTTGCGAATTTGAA
*
183645 AATCGCGTTGCGAATTTGGA
1 AATCGCGTTGCGAATTTGAA
*
183665 AATCTCGTTGCG-ATTT-ACA
1 AATCGCGTTGCGAATTTGA-A
* *
183684 GATTCACGTTGCG-ATTT-ACA
1 -AATCGCGTTGCGAATTTGA-A
*
183704 AATTCGCGTTTGCGAATTTGGA
1 AA-TCGCG-TTGCGAATTTGAA
* * * * *
183726 AGTTGAGTTGCGAAATTGGA
1 AATCGCGTTGCGAATTTGAA
** *
183746 GTTCGCGTTGCAAATTTG-A
1 AATCGCGTTGCGAATTTGAA
*
183765 GATCGCGTTGCGAATTTG
1 AATCGCGTTGCGAATTTG
183783 TTGGTCATTT
Statistics
Matches: 129, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
19 25 0.19
20 72 0.56
21 22 0.17
22 10 0.08
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (20 bp):
AATCGCGTTGCGAATTTGAA
Found at i:183736 original size:61 final size:61
Alignment explanation
Indices: 183604--183782 Score: 158
Period size: 61 Copynumber: 3.0 Consensus size: 61
183594 ACAAATTCAG
*
183604 AATC-GAGTTGCGAATTTAAAATTCAGTGTTGCGAATTTGAAAATCGCGTTGCGAATTTGGA
1 AATCTGAGTTGCG-ATTTAAAATTCAGCGTTGCGAATTTGAAAATCGCGTTGCGAATTTGGA
* *
183665 AATCT-CGTTGCGATTTACAGATTCA-CGTTGCG-ATTT-ACAAATTCGCGTTTGCGAATTTGGA
1 AATCTGAGTTGCGATTTA-AAATTCAGCGTTGCGAATTTGA-AAA-TCGCG-TTGCGAATTTGGA
* * ** * * *
183726 AGT-TGAGTTGCGAAATTGGAGTTC-GCGTTGCAAATTTG-AGATCGCGTTGCGAATTTG
1 AATCTGAGTTGCG-ATTTAAAATTCAGCGTTGCGAATTTGAAAATCGCGTTGCGAATTTG
183783 TTGGTCATTT
Statistics
Matches: 96, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
58 1 0.01
59 18 0.19
60 22 0.23
61 48 0.50
62 7 0.07
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (61 bp):
AATCTGAGTTGCGATTTAAAATTCAGCGTTGCGAATTTGAAAATCGCGTTGCGAATTTGGA
Found at i:183760 original size:19 final size:19
Alignment explanation
Indices: 183732--183780 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
183722 TGGAAGTTGA
*
183732 GTTGCGAAATTGGAGTTCGC
1 GTTGC-AAATTGGAGATCGC
*
183752 GTTGCAAATTTGAGATCGC
1 GTTGCAAATTGGAGATCGC
*
183771 GTTGCGAATT
1 GTTGCAAATT
183781 TGTTGGTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (19 bp):
GTTGCAAATTGGAGATCGC
Found at i:189496 original size:10 final size:10
Alignment explanation
Indices: 189475--189511 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
189465 ATGCACGATG
189475 ATAAAAACCTC
1 ATAAAAA-CTC
189486 ATAAAAACTC
1 ATAAAAACTC
189496 ATAAAAACTC
1 ATAAAAACTC
189506 ATAAAA
1 ATAAAA
189512 GATAATAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 19 0.73
11 7 0.27
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (10 bp):
ATAAAAACTC
Done.