Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009233.1 Hibiscus syriacus cultivar Beakdansim tig00112852_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: 663203
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 3 of 3
Found at i:534971 original size:33 final size:33
Alignment explanation
Indices: 534929--534999 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
534919 AATACTAACT
*
534929 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
534962 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
534995 TGAAA
1 TGAAA
535000 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:535233 original size:22 final size:22
Alignment explanation
Indices: 535181--535235 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
535171 TGGTTGTGAG
**
535181 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
535203 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
535225 GGATTTCTTCG
1 GGATTTCTTCG
535236 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:535407 original size:20 final size:20
Alignment explanation
Indices: 535382--535474 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
535372 CTTTAAATAT
535382 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
535402 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
535422 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
535442 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
535462 CGCGTTGCGATTT
1 CGCGTTGCGATTT
535475 TGATATTCGC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 65 0.98
21 1 0.02
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:535483 original size:20 final size:20
Alignment explanation
Indices: 535442--535618 Score: 94
Period size: 20 Copynumber: 8.8 Consensus size: 20
535432 TTTACGGATA
*
535442 CGCGTTGCGATTTATG-TGTT
1 CGCGTTGCGATTT-TGATATT
535462 CGCGTTGCGATTTTGATATT
1 CGCGTTGCGATTTTGATATT
* *
535482 CGCGTTGCGATTTTGGAAAAT
1 CGCGTTGCGATTTT-GATATT
** *
535503 CGCAATGCGAATTTG-TACTAT
1 CGCGTTGCGATTTTGATA-T-T
* * * *
535524 CGCATTGCGATTTTCAAGAAT
1 CGCGTTGCGATTTT-GATATT
* *
535545 CGCGTTGCGATTTTGGAAACT
1 CGCGTTGCGATTTT-GATATT
** * **
535566 -GATTTGCGATTCTGGGGA-T
1 CGCGTTGCGATT-TTGATATT
*
535585 CGCGTTGCGATTTTTAT-TT
1 CGCGTTGCGATTTTGATATT
535604 CGCGTTGCGATTTTG
1 CGCGTTGCGATTTTG
535619 TTGGTCATTT
Statistics
Matches: 118, Mismatches: 30, Indels: 19
0.71 0.18 0.11
Matches are distributed among these distances:
19 20 0.17
20 51 0.43
21 46 0.39
23 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (20 bp):
CGCGTTGCGATTTTGATATT
Found at i:535511 original size:21 final size:21
Alignment explanation
Indices: 535461--535563 Score: 84
Period size: 21 Copynumber: 5.0 Consensus size: 21
535451 ATTTATGTGT
* * *
535461 TCGCGTTGCGATTTT-GATAT
1 TCGCATTGCGATTTTGGAAAA
*
535481 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
535502 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
535523 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
535544 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
535564 CTGATTTGCG
Statistics
Matches: 65, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
20 16 0.25
21 47 0.72
22 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:535554 original size:42 final size:41
Alignment explanation
Indices: 535461--535618 Score: 112
Period size: 42 Copynumber: 3.9 Consensus size: 41
535451 ATTTATGTGT
* *
535461 TCGCGTTGCGATTTTGATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
535502 TCGCAATGCGAATTTG-TACTATCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGATA-T-TCGCATTGCGATTTTGCAA-AA
* * * ***
535544 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
535584 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
535619 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 20
0.70 0.15 0.16
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 26 0.29
42 29 0.33
43 1 0.01
44 1 0.01
ACGTcount: A:0.19, C:0.16, G:0.26, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:537759 original size:181 final size:180
Alignment explanation
Indices: 537435--537781 Score: 405
Period size: 181 Copynumber: 1.9 Consensus size: 180
537425 TCCTCTGTTC
* * * * * *
537435 CCACCAATTCACTCTTCTCCTGGGCATTTTGATAAACATCTGGCCTGCCAGACGACGATTGTTTT
1 CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACACCCGGCCTGCCAGACAACGATTGTTCT
* * *
537500 ATAAACTCTGACTCCCTGGCATTGGTTCGTGGGGTAACTGAAAACCCAGATGGGATATCACCTGA
66 ATAAACTCAGACTCACTGGCATTGGTTCGTGGAGTAACTGAAAACCCAGATGGGATATCACCTGA
* * * * *
537565 GGTTACTTTAACAGCTCCAAAAATTTCATTTATTTCATTTCGCTCCTTTT
131 GGTAACATTAACAGATCCAAAAATATCAGTTATTTCATTTCGCTCCTTTT
* * *
537615 CCACCAATTCACTCCTCTGCTGGGCATTTTGACAAACACCCCGGCCTTCTAGACAACGATTGTTC
1 CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACA-CCCGGCCTGCCAGACAACGATTGTTC
* * * * * *
537680 TATAAACTCA-AGCTCACTGGC-TGTGTTTCGTGGAGTTATTGAAAACCCAGATTTGG-TTTCAT
65 TATAAACTCAGA-CTCACTGGCAT-TGGTTCGTGGAGTAACTGAAAACCCAGA-TGGGATATCAC
*
537742 CTG-GAGTAACATTAACAGATCCTAAAATATCAGTTATTTC
127 CTGAG-GTAACATTAACAGATCCAAAAATATCAGTTATTTC
537782 CTGGAAGAGT
Statistics
Matches: 138, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
180 38 0.28
181 97 0.70
182 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (180 bp):
CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACACCCGGCCTGCCAGACAACGATTGTTCT
ATAAACTCAGACTCACTGGCATTGGTTCGTGGAGTAACTGAAAACCCAGATGGGATATCACCTGA
GGTAACATTAACAGATCCAAAAATATCAGTTATTTCATTTCGCTCCTTTT
Found at i:543006 original size:23 final size:23
Alignment explanation
Indices: 542980--543027 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
542970 ATAAAGTACA
*
542980 ATAACATACTAGGTAGCACTTAT
1 ATAACATAATAGGTAGCACTTAT
** *
543003 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCACTTAT
543026 AT
1 AT
543028 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCACTTAT
Found at i:543430 original size:25 final size:25
Alignment explanation
Indices: 543373--543438 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
543363 CACTCAAAAG
*
543373 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*** *
543398 ACAAACATACTTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
543423 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
543439 TTAATGATAA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:544692 original size:25 final size:25
Alignment explanation
Indices: 544664--544711 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
544654 ACGGAGCTTC
*
544664 CTTAGGGTTCAAGGGGGCTCGGTTT
1 CTTAGGGATCAAGGGGGCTCGGTTT
544689 CTTAGGGATCAAGGGGGCTCGGT
1 CTTAGGGATCAAGGGGGCTCGGT
544712 CATTGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.15, C:0.17, G:0.42, T:0.27
Consensus pattern (25 bp):
CTTAGGGATCAAGGGGGCTCGGTTT
Found at i:554493 original size:15 final size:16
Alignment explanation
Indices: 554465--554496 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
554455 AAAATCTTTC
554465 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
554481 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
554496 T
1 T
554497 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:555271 original size:16 final size:16
Alignment explanation
Indices: 555247--555280 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
555237 TATCGCCGAC
*
555247 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
555263 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
555279 CG
1 CG
555281 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:556450 original size:179 final size:180
Alignment explanation
Indices: 556128--556472 Score: 428
Period size: 179 Copynumber: 1.9 Consensus size: 180
556118 TCCTCTGTTC
* * * * * *
556128 CCACCAATTCACTCTTCTCCTGGGCATTTTGATAAACATCTGGCCTGCCAGACGACGATTGTTTT
1 CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACACCCGGCCTGCCAGACAACGATTGTTCT
* *
556193 ATAAACTCAGACTCCCCGGCATTGGTTCGTGGGGTAACTGAAAACCCAGATGGGATTTCACCTGA
66 ATAAACTCAGACTCACCGGCATTGGTTCGTGGAGTAACTGAAAACCCAGATGGGATTTCACCTGA
* * *
556258 GGCTACTTTAACAGCTCC-AAAATTTCAGTTATTTCATTTCGCTCCTTTT
131 GGCTACATTAACAGATCCTAAAATATCAGTTATTTCATTTCGCTCCTTTT
* * *
556307 CCACCAATTCACTCCTCTGCTGGGCATTTTGACAAACACCCGGCCTTCTAGACAACGATTGTTCT
1 CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACACCCGGCCTGCCAGACAACGATTGTTCT
* * * * ** * *
556372 ATAAACTCA-AGCTCACTGGC-TGTGTTTCGTGGAGTTATTGAAAACCCAGATTTGTTTTCATCT
66 ATAAACTCAGA-CTCACCGGCAT-TGGTTCGTGGAGTAACTGAAAACCCAGATGGGATTTCACCT
*
556435 G-GAGTTACATTAACAGATCCTAAAATATCAGTTATTTC
129 GAG-GCTACATTAACAGATCCTAAAATATCAGTTATTTC
556473 CTGGAAGAGT
Statistics
Matches: 139, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
178 3 0.02
179 120 0.86
180 16 0.12
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (180 bp):
CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACACCCGGCCTGCCAGACAACGATTGTTCT
ATAAACTCAGACTCACCGGCATTGGTTCGTGGAGTAACTGAAAACCCAGATGGGATTTCACCTGA
GGCTACATTAACAGATCCTAAAATATCAGTTATTTCATTTCGCTCCTTTT
Found at i:563990 original size:3 final size:3
Alignment explanation
Indices: 563982--564034 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
563972 ATTTGTAAAT
* **
563982 TAA TAA TAA TAA TAG TAA TAA TAA T-A TAA CGA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
564029 TAA TAA
1 TAA TAA
564035 CGATAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:564254 original size:43 final size:42
Alignment explanation
Indices: 564189--564471 Score: 178
Period size: 43 Copynumber: 6.5 Consensus size: 42
564179 TGTTGGGGAC
* * * *
564189 GACACTGCTCATACGTGGTGAAGAGTTTGGGTCGTCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTTT-GGTCATCTAAAGGT
*
564232 GACACGGCTCCTACGTGATGAAGAGTTATTGGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAG-T-TTGGTCATCTAAAGGT
* * * ** * *
564276 GATAACACAGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGT
1 G---ACACGGCTCCTACGTGATGAAGA-GTTTGGTCATCTAAAGGT
* * * *
564322 GACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCT---GAT
1 GACACGGCTCCTACGTGATGAAGAG-TTTGGTCATCTAAAGGT
* *
564362 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
1 GACACGGCTCCTACGTGATGAAGAGTT-TGGTCATCTAAAGGT
* * * * ** * *
564405 GATAACATGGTTCCTACGTGACGAGGACGGCTGGTTATCT-ATGGTT
1 G---ACACGGCTCCTACGTGATGAAGA-GTTTGGTCATCTAAAGG-T
564451 GACACGGCTCCTACGTGATGA
1 GACACGGCTCCTACGTGATGA
564472 GGAGATCTGG
Statistics
Matches: 186, Mismatches: 38, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
39 1 0.01
40 32 0.17
42 1 0.01
43 71 0.38
44 14 0.08
45 5 0.03
46 40 0.22
47 21 0.11
48 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (42 bp):
GACACGGCTCCTACGTGATGAAGAGTTTGGTCATCTAAAGGT
Found at i:564492 original size:129 final size:130
Alignment explanation
Indices: 564231--564511 Score: 438
Period size: 129 Copynumber: 2.2 Consensus size: 130
564221 CGTCTAAAGG
*
564231 TGACACGGCTCCTACGTGATGAAGAGTTATTGGCCATCTAAAGGTGATAACACAGTTCCTACGTG
1 TGACACGGCTCCTACGTGATGAAGAGTTACTGGCCATCTAAAGGTGATAACACAGTTCCTACGTG
* *
564296 ATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGA
66 ACGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCGGA
* **
564361 TGACACGGCTCATACGTGATGAAGAGTT-CTGGCCATCTAAAGGTGATAACATGGTTCCTACGTG
1 TGACACGGCTCCTACGTGATGAAGAGTTACTGGCCATCTAAAGGTGATAACACAGTTCCTACGTG
* * * *
564425 ACGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGA
66 ACGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCGGA
* * *
564490 TGACGCGGTTCCTACATGATGA
1 TGACACGGCTCCTACGTGATGA
564512 GGACGGCTGG
Statistics
Matches: 137, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
129 110 0.80
130 27 0.20
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (130 bp):
TGACACGGCTCCTACGTGATGAAGAGTTACTGGCCATCTAAAGGTGATAACACAGTTCCTACGTG
ACGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCGGA
Found at i:564590 original size:28 final size:28
Alignment explanation
Indices: 564540--564593 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
564530 AGGAGTTATG
* *
564540 GTTTCAAGAGAAACCAAATCAAAGATTT
1 GTTTCAAAAGAAACCAAACCAAAGATTT
564568 GTTTCAAAAGAAA-CAAACCCAAAGAT
1 GTTTCAAAAGAAACCAAA-CCAAAGAT
564594 GATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (28 bp):
GTTTCAAAAGAAACCAAACCAAAGATTT
Found at i:564951 original size:15 final size:15
Alignment explanation
Indices: 564931--564968 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
564921 ATCTTGCTTT
564931 AAGAGAAAATGTTTC
1 AAGAGAAAATGTTTC
564946 AAGAGAAAATGTTTC
1 AAGAGAAAATGTTTC
*
564961 AAGTGAAA
1 AAGAGAAA
564969 CGACTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (15 bp):
AAGAGAAAATGTTTC
Found at i:565191 original size:62 final size:63
Alignment explanation
Indices: 565125--565324 Score: 202
Period size: 62 Copynumber: 3.2 Consensus size: 63
565115 AAGGTTGGTA
* *
565125 TTTTCAAAAGAAGTTGTC-TCGAGAGTCAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA-TT
1 TTTTCAAAAGAAATTGTCTTAGAGAGTCAAAATTTTGTTTCAAA-GAAACAAACTCAAAGATTT
* *
565187 TTTTCAAAAGAAATTGTCTTTA-ATAGAT-AAAATTTTGTTTC-----AACATACTCAAAGATTT
1 TTTTCAAAAGAAATTGTC-TTAGAGAG-TCAAAATTTTGTTTCAAAGAAACAAACTCAAAGA-TT
565245 T
63 T
* * * *
565246 TGTTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATT
1 T-TTTCAAAAGAAATTGTCTT-AGAGAGTCAAAATTTTGTTT-CAAAGAAACAAACTCAAAGATT
565311 T
63 T
565312 TTTTCAAAAGAAA
1 TTTTCAAAAGAAA
565325 CAATCTCAAA
Statistics
Matches: 112, Mismatches: 11, Indels: 27
0.75 0.07 0.18
Matches are distributed among these distances:
57 13 0.12
59 5 0.04
60 15 0.13
61 15 0.13
62 18 0.16
63 16 0.14
64 2 0.02
65 11 0.10
66 4 0.04
67 13 0.12
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (63 bp):
TTTTCAAAAGAAATTGTCTTAGAGAGTCAAAATTTTGTTTCAAAGAAACAAACTCAAAGATTT
Found at i:565340 original size:27 final size:28
Alignment explanation
Indices: 565275--565343 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
565265 TTAAGAGAGA
*
565275 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
565303 CAAAGATTTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
565331 CAAAGATTTTTTT
1 CAAAGATTTTTTT
565344 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:565490 original size:25 final size:25
Alignment explanation
Indices: 565443--565554 Score: 89
Period size: 29 Copynumber: 4.1 Consensus size: 25
565433 CAAAACTTTG
* *
565443 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
565469 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
565496 TATTCAAAAGGAACCAACTCCAAGATTTT
1 T-TTCAAAA-GAAACAACTCAAAGA--TT
* *
565525 TATTTAAAAGGAACAAACTCAAAGATT
1 T-TTCAAAAGAAAC-AACTCAAAGATT
565552 TTT
1 TTT
565555 ATAAGAGAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
25 8 0.11
26 14 0.20
27 8 0.11
28 10 0.14
29 31 0.44
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.29
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:565520 original size:29 final size:29
Alignment explanation
Indices: 565458--565556 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 29
565448 AAATAAATAG
*
565458 ACTCAAAG--ATTT-TTCAAAA-GAAACA
1 ACTCAAAGATATTTATTCAAAAGGAACCA
565483 ACTCAAAGATATTTATTCAAAAGGAACCA
1 ACTCAAAGATATTTATTCAAAAGGAACCA
* * * *
565512 ACTCCAAGATTTTTATTTAAAAGGAACAA
1 ACTCAAAGATATTTATTCAAAAGGAACCA
*
565541 ACTCAAAGATTTTTAT
1 ACTCAAAGATATTTAT
565557 AAGAGAAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
25 8 0.12
27 4 0.06
28 7 0.11
29 45 0.70
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29
Consensus pattern (29 bp):
ACTCAAAGATATTTATTCAAAAGGAACCA
Found at i:566213 original size:4 final size:4
Alignment explanation
Indices: 566197--566242 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
566187 ATACAAATTT
*
566197 TATG TAT- TATG TATG TATG --TG TATT TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
566242 T
1 T
566243 TTTCTCGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 32 0.86
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:566226 original size:18 final size:17
Alignment explanation
Indices: 566199--566234 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
566189 ACAAATTTTA
566199 TGTATTATGTATGTATG
1 TGTATTATGTATGTATG
566216 TGTATTTATGTATGTATG
1 TGTA-TTATGTATGTATG
566234 T
1 T
566235 ATGTATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (17 bp):
TGTATTATGTATGTATG
Found at i:574168 original size:3 final size:3
Alignment explanation
Indices: 574160--574212 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
574150 ATTTGTAAAT
* **
574160 TAA TAA TAA TAA TAG TAA TAA TAA T-A TAA CGA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
574207 TAA TAA
1 TAA TAA
574213 CGATAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:580521 original size:47 final size:47
Alignment explanation
Indices: 580418--580522 Score: 130
Period size: 42 Copynumber: 2.3 Consensus size: 47
580408 ATGTGAAACA
* * *
580418 AATTTTTCGATTCGGTTCAGTTCTGTAATACTATTTTTGATAAACTG
1 AATTTTTCGATTCGGTTCAGTTCGGTAATACGATTTTTGATAAACCG
* *
580465 -A-TTTT---TTCGGTTCGGTTCGGTAATGCGATTTTTGATAAACCG
1 AATTTTTCGATTCGGTTCAGTTCGGTAATACGATTTTTGATAAACCG
580507 AATTTTTCGATTCGGT
1 AATTTTTCGATTCGGT
580523 AATGAGTTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
42 32 0.67
43 1 0.02
44 4 0.08
45 4 0.08
46 1 0.02
47 6 0.12
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (47 bp):
AATTTTTCGATTCGGTTCAGTTCGGTAATACGATTTTTGATAAACCG
Found at i:585133 original size:21 final size:22
Alignment explanation
Indices: 585092--585134 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
585082 CATTATTTTA
* *
585092 TTGTTGCATGTTGATGACATGC
1 TTGTTGCAGGTTCATGACATGC
585114 TTGTTGCAGGTTCA-GACATGC
1 TTGTTGCAGGTTCATGACATGC
585135 AAGAGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.37
Consensus pattern (22 bp):
TTGTTGCAGGTTCATGACATGC
Found at i:586780 original size:15 final size:15
Alignment explanation
Indices: 586760--586789 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
586750 ATATCAACAC
586760 CATTTTGCATACATT
1 CATTTTGCATACATT
*
586775 CATTTTTCATACATT
1 CATTTTGCATACATT
586790 ACTCATAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.50
Consensus pattern (15 bp):
CATTTTGCATACATT
Found at i:594481 original size:18 final size:18
Alignment explanation
Indices: 594458--594494 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
594448 TCCAAGTTTA
594458 TCTTTTCAAAATTCAATT
1 TCTTTTCAAAATTCAATT
**
594476 TCTTTTTGAAATTCAATT
1 TCTTTTCAAAATTCAATT
594494 T
1 T
594495 ATTCTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.03, T:0.54
Consensus pattern (18 bp):
TCTTTTCAAAATTCAATT
Found at i:595222 original size:122 final size:121
Alignment explanation
Indices: 595016--595451 Score: 678
Period size: 122 Copynumber: 3.6 Consensus size: 121
595006 TTCCAGAGAA
* * *
595016 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAAAAGAAGTTCATAATGAGAAGAACTTATTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
595081 ACCTTTGCATGACTCTATCACAGAAGGAGATAGATCATCATCAACTTTTCCAGAGAA-
66 ACCTTTGTATGACTCTATCACAGAAGGAGATAGATCATCATCAACATTGCC-G-GAAG
* *
595138 AGTTCATAATGAGAAGAACTTATCTTAAGAGGAATAAGAAGTTCATAATGAGAA-AAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAA-CTTGTTC
*
595202 AACCTTTGTATGACTCTATCACAGAAGGAGATAGATCATCATCAACGTTGCCGGAAGG
65 AACCTTTGTATGACTCTATCACAGAAGGAGATAGATCATCATCAACATTGCCGGAA-G
* *
595260 AGTTCATAATGAAAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAGCTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
595325 ACCTTTGTATGACTCTCTCACAGAAGGAGATAGATCAGCATCAACATTGCCGGAAGG
66 ACCTTTGTATGACTCTATCACAGAAGGAGATAGATCATCATCAACATTGCCGGAA-G
* *
595382 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAATAACTTGTTCG
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCA
595447 ACCTT
66 ACCTT
595452 AGCTTGATTC
Statistics
Matches: 293, Mismatches: 17, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
120 3 0.01
121 3 0.01
122 286 0.98
123 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.25
Consensus pattern (121 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTGTATGACTCTATCACAGAAGGAGATAGATCATCATCAACATTGCCGGAAG
Found at i:595803 original size:16 final size:16
Alignment explanation
Indices: 595754--595795 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
595744 GTTCATAATG
*
595754 AGAAGAACTCAACTGA
1 AGAAGAACTCATCTGA
*
595770 AGAAGAATTCATCTGA
1 AGAAGAACTCATCTGA
595786 AGAAGAACTC
1 AGAAGAACTC
595796 GTCCGAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.17
Consensus pattern (16 bp):
AGAAGAACTCATCTGA
Found at i:596353 original size:17 final size:16
Alignment explanation
Indices: 596330--596368 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
596320 TATTTTCCAA
* *
596330 AAAATAAGTTAAATAG
1 AAAATAAATAAAATAG
596346 ATAAATAAATAAAATAG
1 A-AAATAAATAAAATAG
596363 AAAATA
1 AAAATA
596369 TGATAGTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (16 bp):
AAAATAAATAAAATAG
Found at i:600879 original size:180 final size:180
Alignment explanation
Indices: 600556--600901 Score: 430
Period size: 180 Copynumber: 1.9 Consensus size: 180
600546 TCCTCTGTTC
* * * * * *
600556 CCACCAATTCACTCTTCTCCTGGGCATTTTGATAAACATCTGGCCTGCCAGACGACGATTGTTTT
1 CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACACCCGGCCTGCCAGACAACGATTGTTCT
* * * * * *
600621 ATAAACCCAGATTCCCTGGCATTGGTTCGTGGGGTAACTGAAAACCCAGATGGGATTTCACCTGA
66 ATAAACCAAGACTCACTGGCATTGGTTCGTGGAGTAACTGAAAACCCAGATCGGATTTCACCGGA
* * *
600686 GGTTACTTTAACAGCTCCAAAAATTTCAGTTATTTCATTTCGCTCCTTTT
131 GGTTACATTAACAGATCCAAAAATATCAGTTATTTCATTTCGCTCCTTTT
* * *
600736 CCACCAATTCACTCCTCTGCTGGGCATTTTGACAAACACCCGGCCTTCTAGACAACGATTGTTCT
1 CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACACCCGGCCTGCCAGACAACGATTGTTCT
* * *
600801 ATAAACTCAAG-CTCACTGGC-TGTGTTTCGTGGAGTTATTGAAAACCCAGATTCGG-TTTCATC
66 ATAAAC-CAAGACTCACTGGCAT-TGGTTCGTGGAGTAACTGAAAACCCAGA-TCGGATTTCA-C
*
600863 CGGA-GTTACATTAACAGATCCTAAAATATCAGTTATTTC
127 CGGAGGTTACATTAACAGATCCAAAAATATCAGTTATTTC
600902 CTGGAAGAGT
Statistics
Matches: 140, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
179 1 0.01
180 129 0.92
181 10 0.07
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (180 bp):
CCACCAATTCACTCCTCTCCTGGGCATTTTGACAAACACCCGGCCTGCCAGACAACGATTGTTCT
ATAAACCAAGACTCACTGGCATTGGTTCGTGGAGTAACTGAAAACCCAGATCGGATTTCACCGGA
GGTTACATTAACAGATCCAAAAATATCAGTTATTTCATTTCGCTCCTTTT
Found at i:604707 original size:225 final size:225
Alignment explanation
Indices: 604316--604736 Score: 779
Period size: 225 Copynumber: 1.9 Consensus size: 225
604306 ATTTGTTAGA
604316 TGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATGTTTACCAAATGCAGAATCTTTAGGCT
1 TGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATGTTTACCAAATGCAGAATCTTTAGGCT
604381 CGTATAATCTTCGAATATTTGGATGCCCTCTGCAGATAGCTCGAGATCCTTGCAGTGTCTAATAG
66 CGTATAATCTTCGAATATTTGGATGCCCTCTGCAGATAGCTCGAGATCCTTGCAGTGTCTAATAG
*
604446 AAAGACTTTCAAGAGAAGTGAGATGTCGGAACACAGGAAAGAGTGACCTCAATCCATTGCAATTC
131 AAAGACTTTCAAGAGAAGTGAGATGTCGGAACACAGGAAAGAGTGACCTCAATCCACTGCAATTC
604511 TGTATATGCAACAATTTCAAGTGAACATGG
196 TGTATATGCAACAATTTCAAGTGAACATGG
* * * *
604541 TGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATGTTTACCAGATGGAGATTCTTTCGGCT
1 TGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATGTTTACCAAATGCAGAATCTTTAGGCT
*
604606 CGTATAATCTTCGAATATTTGGATGCCCTCTGCAGATAGCTCGAGCTCCTTGCAGTGTCTAATAG
66 CGTATAATCTTCGAATATTTGGATGCCCTCTGCAGATAGCTCGAGATCCTTGCAGTGTCTAATAG
*
604671 AAAGACTTTCAAGAGAAGTGAGATGTTGGAACACAGGAAAGAGTGACCTCAATCCACTGCAATTC
131 AAAGACTTTCAAGAGAAGTGAGATGTCGGAACACAGGAAAGAGTGACCTCAATCCACTGCAATTC
604736 T
196 T
604737 CGATTTCTAG
Statistics
Matches: 189, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
225 189 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (225 bp):
TGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATGTTTACCAAATGCAGAATCTTTAGGCT
CGTATAATCTTCGAATATTTGGATGCCCTCTGCAGATAGCTCGAGATCCTTGCAGTGTCTAATAG
AAAGACTTTCAAGAGAAGTGAGATGTCGGAACACAGGAAAGAGTGACCTCAATCCACTGCAATTC
TGTATATGCAACAATTTCAAGTGAACATGG
Found at i:607489 original size:21 final size:23
Alignment explanation
Indices: 607465--607508 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
607455 CATACATAGC
607465 ATCTTTCA-GCTTT-GCTAGCCA
1 ATCTTTCACGCTTTCGCTAGCCA
*
607486 ATCTTTGACGCTTTCGCTAGCCA
1 ATCTTTCACGCTTTCGCTAGCCA
607509 CGGACTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (23 bp):
ATCTTTCACGCTTTCGCTAGCCA
Found at i:608175 original size:35 final size:36
Alignment explanation
Indices: 608129--608217 Score: 135
Period size: 35 Copynumber: 2.5 Consensus size: 36
608119 GATGATATAT
* *
608129 CAAAACGATATCATTTTAGATACTTG-AAAAACCAC
1 CAAAACGATATCATTTTAGATAATTGAAAAAAACAC
*
608164 CAAAACGATATCATTTTAGATAATTGAAAAAAATAC
1 CAAAACGATATCATTTTAGATAATTGAAAAAAACAC
*
608200 CAAAACGATATCGTTTTA
1 CAAAACGATATCATTTTA
608218 AATTTCTGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 25 0.51
36 24 0.49
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (36 bp):
CAAAACGATATCATTTTAGATAATTGAAAAAAACAC
Found at i:610369 original size:42 final size:42
Alignment explanation
Indices: 610323--610414 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
610313 TTTTTGATTT
**
610323 GGTTCGGTTCTG-TAATGCAATTTTTGATAAATTGAATTTTTC
1 GGTTCGGTTC-GATAATGCAATTTTTGATAAACCGAATTTTTC
*
610365 GGTTCGGTTCGATAATGCGATTTTTGATAAACCGAATTTTTC
1 GGTTCGGTTCGATAATGCAATTTTTGATAAACCGAATTTTTC
610407 GGTTCGGT
1 GGTTCGGT
610415 AATGAGTTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 1 0.02
42 45 0.98
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (42 bp):
GGTTCGGTTCGATAATGCAATTTTTGATAAACCGAATTTTTC
Found at i:615071 original size:13 final size:13
Alignment explanation
Indices: 615036--615073 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
615026 ATGATTAGTT
*
615036 TATAAAATTGTAA
1 TATAAAATTTTAA
615049 TATAAAATTTTAA
1 TATAAAATTTTAA
615062 -ATAATAATTTTA
1 TATAA-AATTTTA
615074 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
TATAAAATTTTAA
Found at i:624926 original size:123 final size:123
Alignment explanation
Indices: 624722--624970 Score: 462
Period size: 123 Copynumber: 2.0 Consensus size: 123
624712 AATTTCCCAC
* *
624722 TTTGTTGGCTTTCTCTATCTGTATTTCACACGCAAGGCTCACCATTAACATGCTTTAATATTAAG
1 TTTGTTGACTTTCGCTATCTGTATTTCACACGCAAGGCTCACCATTAACATGCTTTAATATTAAG
624787 CTAATGACTCATCAAACTCCCTTAAAATTGTTTACATACTGAAAGCTTAAGCATGTTG
66 CTAATGACTCATCAAACTCCCTTAAAATTGTTTACATACTGAAAGCTTAAGCATGTTG
* *
624845 TTTGTTGACTTTCGCTATCTGTATTTCACACGCAAGGCTCACCATTAACATTCTTTCATATTAAG
1 TTTGTTGACTTTCGCTATCTGTATTTCACACGCAAGGCTCACCATTAACATGCTTTAATATTAAG
624910 CTAATGACTCATCAAACTCCCTTAAAATTGTTTACATACTGAAAGCTTAAGCATGTTG
66 CTAATGACTCATCAAACTCCCTTAAAATTGTTTACATACTGAAAGCTTAAGCATGTTG
624968 TTT
1 TTT
624971 ACTAACATGG
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 122 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (123 bp):
TTTGTTGACTTTCGCTATCTGTATTTCACACGCAAGGCTCACCATTAACATGCTTTAATATTAAG
CTAATGACTCATCAAACTCCCTTAAAATTGTTTACATACTGAAAGCTTAAGCATGTTG
Found at i:625666 original size:16 final size:16
Alignment explanation
Indices: 625632--625675 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
625622 TTTAATACTT
* *
625632 TAATAATATTATTATTA
1 TAATAA-ATAATTAATA
625649 TAATAAATAATTAATA
1 TAATAAATAATTAATA
*
625665 TAATTAATAAT
1 TAATAAATAAT
625676 ATTTTATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATAAATAATTAATA
Found at i:625695 original size:37 final size:37
Alignment explanation
Indices: 625631--625703 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
625621 TTTTAATACT
*
625631 TTAATAATATTATTATTATAATAAATAATTAATATAA
1 TTAATAATATTATTATTATAATAAATAAATAATATAA
* *
625668 TTAATAATATT-TTATTATATTTTAATAAATAATATA
1 TTAATAATATTATTATTATA-ATAAATAAATAATATA
625704 TAAAATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 8 0.25
37 24 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
TTAATAATATTATTATTATAATAAATAAATAATATAA
Found at i:625716 original size:41 final size:43
Alignment explanation
Indices: 625638--625725 Score: 119
Period size: 41 Copynumber: 2.1 Consensus size: 43
625628 ACTTTAATAA
*
625638 TATTATTATTATAATAAATAATTAATATAATTAATAAT-ATTT
1 TATTATTATTATAATAAATAATTAATAAAATTAATAATAATTT
* *
625680 TATTA-TATTTTAATAAATAA-TATATAAAATTTATAATAATTT
1 TATTATTATTATAATAAATAATTA-ATAAAATTAATAATAATTT
625722 TATT
1 TATT
625726 TATAAAATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
40 2 0.05
41 26 0.63
42 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (43 bp):
TATTATTATTATAATAAATAATTAATAAAATTAATAATAATTT
Found at i:625810 original size:24 final size:26
Alignment explanation
Indices: 625773--625836 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
625763 CATTAAATAA
*
625773 ATTAATCTAATATTTAA-AAATATAATT
1 ATTAAT-T-ATATTTAATAAATAAAATT
*
625800 ATT-ATTTTA-TTAATAAATAAAATT
1 ATTAATTATATTTAATAAATAAAATT
625824 ATTAATTATATTT
1 ATTAATTATATTT
625837 GATGTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 4 0.13
24 14 0.45
25 6 0.19
26 4 0.13
27 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTAATTATATTTAATAAATAAAATT
Found at i:625932 original size:14 final size:14
Alignment explanation
Indices: 625913--625947 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
625903 ATGATATCCT
625913 AAAATATTTTTAAA
1 AAAATATTTTTAAA
*
625927 AAAATATTTTTCAA
1 AAAATATTTTTAAA
625941 AAAATAT
1 AAAATAT
625948 AATTTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATATTTTTAAA
Found at i:626510 original size:2 final size:2
Alignment explanation
Indices: 626503--626538 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
626493 TGCAATTTGA
626503 AT AT 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 AT AT
626539 TTAAATCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:630223 original size:18 final size:19
Alignment explanation
Indices: 630181--630224 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
630171 TTTAGTTCAC
* *
630181 GGAATATAAGATTATCAGT
1 GGAATAAAAGATTACCAGT
630200 GAGAATAAAAGATTACCAG-
1 G-GAATAAAAGATTACCAGT
630219 GGAATA
1 GGAATA
630225 GGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 2 0.09
20 15 0.68
ACGTcount: A:0.48, C:0.07, G:0.23, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGT
Found at i:630406 original size:38 final size:37
Alignment explanation
Indices: 630370--630441 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
630360 TTACAAATTG
630370 TAAAAATATTTATAT-ATTTTCTTTAAAAAATTAAAT
1 TAAAAATATTTATATAATTTTCTTTAAAAAATTAAAT
* * * *
630406 TCATAATATTTATATAATTTTGTTTACAAAATTAAA
1 TAAAAATATTTATATAATTTTCTTTAAAAAATTAAA
630442 AATAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 13 0.42
37 18 0.58
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
TAAAAATATTTATATAATTTTCTTTAAAAAATTAAAT
Found at i:633188 original size:14 final size:15
Alignment explanation
Indices: 633169--633202 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
633159 TTTAACTATG
*
633169 TATATTTTTC-AATT
1 TATATTATTCAAATT
633183 TATATTATTCAAATT
1 TATATTATTCAAATT
633198 TATAT
1 TATAT
633203 AACAACACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
TATATTATTCAAATT
Found at i:637133 original size:2 final size:2
Alignment explanation
Indices: 637128--637153 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
637118 TCTCTCTCTC
637128 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
637154 AAACCTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:644152 original size:22 final size:22
Alignment explanation
Indices: 644124--644190 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
644114 AACGGTCAAC
*
644124 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCA
*
644146 GGTCAACGGTCGGGTCGGGTAA
1 GGTCAACGGTCGGGTCGGGTCA
644168 GGTCAACGGTCGGGTCGGGTCA
1 GGTCAACGGTCGGGTCGGGTCA
644190 G
1 G
644191 ACCGGTCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.13, C:0.21, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCA
Found at i:644203 original size:9 final size:9
Alignment explanation
Indices: 644185--644283 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
644175 GGTCGGGTCG
*
644185 GGTCAGACC
1 GGTCAAACC
644194 GGTCAAACC
1 GGTCAAACC
* *
644203 GATTCAGACC
1 G-GTCAAACC
644213 GGTCAAACC
1 GGTCAAACC
*
644222 GGTTCGAACC
1 GG-TCAAACC
*
644232 GGTTGAAACC
1 GG-TCAAACC
644242 GGTCAAACC
1 GGTCAAACC
644251 GGTCAGAACC
1 GGTCA-AACC
*
644261 GGTTGAAAACC
1 GG-T-CAAACC
*
644272 GGTTAAACC
1 GGTCAAACC
644281 GGT
1 GGT
644284 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:644242 original size:29 final size:31
Alignment explanation
Indices: 644210--644284 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
644200 ACCGATTCAG
644210 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
644239 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
644269 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
644285 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:644262 original size:19 final size:19
Alignment explanation
Indices: 644185--644283 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
644175 GGTCGGGTCG
644185 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
644203 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
*
644222 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
644242 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
644261 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
644281 GGT
1 GGT
644284 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.06
19 39 0.58
20 16 0.24
21 8 0.12
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:651383 original size:7 final size:7
Alignment explanation
Indices: 651371--651401 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
651361 GTCAAAGAAA
651371 GTCAACG
1 GTCAACG
651378 GTCAACG
1 GTCAACG
651385 GTCAACG
1 GTCAACG
651392 GTCAACG
1 GTCAACG
651399 GTC
1 GTC
651402 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:651408 original size:5 final size:5
Alignment explanation
Indices: 651398--651455 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
651388 AACGGTCAAC
* *
651398 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
651447 GGTCG GGTC
1 GGTCG GGTC
651456 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:651419 original size:22 final size:22
Alignment explanation
Indices: 651391--651455 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
651381 AACGGTCAAC
651391 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
651413 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
651435 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
651456 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:651470 original size:9 final size:9
Alignment explanation
Indices: 651452--651549 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
651442 GGTCGGGTCG
*
651452 GGTCAGACC
1 GGTCAAACC
651461 GGTCAAACC
1 GGTCAAACC
*
651470 GATTC-AACC
1 G-GTCAAACC
651479 GGTCAAACC
1 GGTCAAACC
*
651488 GGTTCGAACC
1 GG-TCAAACC
*
651498 GGTTGAAACC
1 GG-TCAAACC
651508 GGTCAAACC
1 GGTCAAACC
651517 GGTCAGAACC
1 GGTCA-AACC
*
651527 GGTTGAAAACC
1 GG-T-CAAACC
*
651538 GGTTAAACC
1 GGTCAAACC
651547 GGT
1 GGT
651550 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
8 2 0.03
9 39 0.53
10 25 0.34
11 7 0.09
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:651499 original size:10 final size:10
Alignment explanation
Indices: 651466--651530 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 10
651456 AGACCGGTCA
*
651466 AACCGATTC-
1 AACCGGTTCG
*
651475 AACCGG-TCA
1 AACCGGTTCG
651484 AACCGGTTCG
1 AACCGGTTCG
651494 AACCGGTT-G
1 AACCGGTTCG
*
651503 AAACCGG-TCA
1 -AACCGGTTCG
651513 AACCGG-TCAG
1 AACCGGTTC-G
651523 AACCGGTT
1 AACCGGTT
651531 GAAAACCGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
8 2 0.04
9 21 0.46
10 22 0.48
11 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (10 bp):
AACCGGTTCG
Found at i:651510 original size:29 final size:31
Alignment explanation
Indices: 651475--651550 Score: 122
Period size: 29 Copynumber: 2.5 Consensus size: 31
651465 AAACCGATTC
651475 AACCGGTCAAACCGGTTC-GAACCGGTTG-A
1 AACCGGTCAAACCGGTTCAGAACCGGTTGAA
651504 AACCGGTCAAACCGG-TCAGAACCGGTTGAA
1 AACCGGTCAAACCGGTTCAGAACCGGTTGAA
*
651534 AACCGGTTAAACCGGTT
1 AACCGGTCAAACCGGTT
651551 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 2 0.05
29 25 0.58
30 15 0.35
31 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (31 bp):
AACCGGTCAAACCGGTTCAGAACCGGTTGAA
Found at i:653089 original size:2 final size:2
Alignment explanation
Indices: 653082--653107 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
653072 ACTTGCTATG
653082 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
653108 TAATAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.