Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002010.1 Hibiscus syriacus cultivar Beakdansim tig00004109_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: 121478
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:933 original size:55 final size:55
Alignment explanation
Indices: 870--1011 Score: 212
Period size: 55 Copynumber: 2.6 Consensus size: 55
860 CAACTTCAAA
* * * *
870 CTTCATTCATCGGATGTCTTTCTTCATGGATCGATCTTCAATCAGTTTCGAATTT
1 CTTCATTCATCGGATGTCCTTCTTCATGAATCGATCTTCAATCAGGTTCAAATTT
* * *
925 CTTCATTCATCTGATGTCCATCTTCATGAATCGTTCTTCAATCAGGTTCAAATTT
1 CTTCATTCATCGGATGTCCTTCTTCATGAATCGATCTTCAATCAGGTTCAAATTT
*
980 CTTCATTCATCGAATGTCCTTCTTCATGAATC
1 CTTCATTCATCGGATGTCCTTCTTCATGAATC
1012 ACTTGAATGT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 77 1.00
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (55 bp):
CTTCATTCATCGGATGTCCTTCTTCATGAATCGATCTTCAATCAGGTTCAAATTT
Found at i:7525 original size:17 final size:19
Alignment explanation
Indices: 7493--7528 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
7483 TTAATCCGAG
7493 AATGATATAGAAAAATAAT
1 AATGATATAGAAAAATAAT
7512 AATGA-ATA-AAAAATAAT
1 AATGATATAGAAAAATAAT
7529 TATAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (19 bp):
AATGATATAGAAAAATAAT
Found at i:7794 original size:16 final size:16
Alignment explanation
Indices: 7773--7809 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
7763 GACCACTCAT
7773 TTGGTGATCGAGTACG
1 TTGGTGATCGAGTACG
* *
7789 TTGGTGCTCGAGTTCG
1 TTGGTGATCGAGTACG
7805 TTGGT
1 TTGGT
7810 CTTCTGTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.14, G:0.38, T:0.38
Consensus pattern (16 bp):
TTGGTGATCGAGTACG
Found at i:16255 original size:5 final size:5
Alignment explanation
Indices: 16245--16270 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16235 TGACTTAGAA
16245 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
16271 AATAATAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:33279 original size:22 final size:23
Alignment explanation
Indices: 33254--33296 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
33244 CCGTTTATCC
*
33254 ACCTTCTAG-AGCTGCTGACTGG
1 ACCTTCTAGAAGCTGATGACTGG
33276 ACCTTCTAGAAGCTGATGACT
1 ACCTTCTAGAAGCTGATGACT
33297 CACTGCCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (23 bp):
ACCTTCTAGAAGCTGATGACTGG
Found at i:37266 original size:13 final size:13
Alignment explanation
Indices: 37248--37272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37238 ATGGGGTACA
37248 TAAAAATTAAAAT
1 TAAAAATTAAAAT
37261 TAAAAATTAAAA
1 TAAAAATTAAAA
37273 AAAATCAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAAAATTAAAAT
Found at i:37282 original size:17 final size:16
Alignment explanation
Indices: 37256--37302 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
37246 CATAAAAATT
*
37256 AAAATTAAAAATTAAAA
1 AAAATCAAAAA-TAAAA
37273 AAAATCAAAAATAAAA
1 AAAATCAAAAATAAAA
**
37289 CTAATC-AAAATAAA
1 AAAATCAAAAATAAA
37303 TATGGGTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 8 0.30
16 9 0.33
17 10 0.37
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATCAAAAATAAAA
Found at i:43707 original size:28 final size:28
Alignment explanation
Indices: 43667--43737 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
43657 TCTTAAGGAG
*
43667 TGGTCTTTTGGGACATATATGTTATATA
1 TGGTCCTTTGGGACATATATGTTATATA
* *
43695 TGGTCCTTTGGGACATATGTGTTATATG
1 TGGTCCTTTGGGACATATATGTTATATA
*
43723 TGGTCCTTCGGGACA
1 TGGTCCTTTGGGACA
43738 AATCCTACGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.41
Consensus pattern (28 bp):
TGGTCCTTTGGGACATATATGTTATATA
Found at i:47913 original size:28 final size:28
Alignment explanation
Indices: 47881--47953 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
47871 GTTCTTAAGG
* *
47881 TGTGGTCCTTTGGGACATATGTGTTATA
1 TGTGGTCCTTCGGGACATATATGTTATA
* *
47909 TGTGGTCATTCGGGGCATATATGTTATA
1 TGTGGTCCTTCGGGACATATATGTTATA
47937 TGTGGTCCTTCGGGACA
1 TGTGGTCCTTCGGGACA
47954 AATCCTACGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.18, C:0.14, G:0.30, T:0.38
Consensus pattern (28 bp):
TGTGGTCCTTCGGGACATATATGTTATA
Found at i:56872 original size:29 final size:30
Alignment explanation
Indices: 56810--56882 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
56800 AAAAAGTTAT
* * *
56810 GTAAAATTG-ATTACTTGAAAATTATTTTAC
1 GTAAAA-TGAATTACCTAAAAATTATTTTAA
56840 GTAAAATGAATTACCTAAAAATTA-TTTAA
1 GTAAAATGAATTACCTAAAAATTATTTTAA
56869 GTAAAATGAATTAC
1 GTAAAATGAATTAC
56883 ATTTTTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 20 0.51
30 19 0.49
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37
Consensus pattern (30 bp):
GTAAAATGAATTACCTAAAAATTATTTTAA
Found at i:57239 original size:16 final size:16
Alignment explanation
Indices: 57218--57281 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
57208 ATAAATATAG
57218 TATTAA-AATATAATAT
1 TATTAATAAT-TAATAT
57234 TATTAA-AATT-ATAT
1 TATTAATAATTAATAT
57248 TA-TAATAATATTAAATAT
1 TATTAAT-A-ATT-AATAT
57266 T-TTAATAATTAATAT
1 TATTAATAATTAATAT
57281 T
1 T
57282 TTTATTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
13 3 0.07
14 6 0.14
15 8 0.19
16 15 0.36
17 1 0.02
18 9 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTAATAATTAATAT
Found at i:57263 original size:50 final size:48
Alignment explanation
Indices: 57168--57320 Score: 117
Period size: 50 Copynumber: 3.1 Consensus size: 48
57158 AATAATAAAT
* *
57168 TATTAAACATTATATATTATTATAA-TATATCTA-AGTACATA-TAAATATA
1 TATTAAA-ATTA-ATATTATTAAAATTATAT-TATAATA-ATATTAAATATA
57217 GTATTAAAATATAATATTATTAAAATTATATTATAATAATATTAAATAT-
1 -TATTAAAAT-TAATATTATTAAAATTATATTATAATAATATTAAATATA
*
57266 T-TTAATAATTAATATTTTTATTAAAATGATA--ATAA-AATATTAAAT-TAA
1 TATTAA-AATTAATA---TTATTAAAATTATATTATAATAATATTAAATAT-A
57314 TATTAAA
1 TATTAAA
57321 TAAATAAAAT
Statistics
Matches: 89, Mismatches: 3, Indels: 24
0.77 0.03 0.21
Matches are distributed among these distances:
46 1 0.01
47 19 0.21
48 10 0.11
49 22 0.25
50 37 0.42
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (48 bp):
TATTAAAATTAATATTATTAAAATTATATTATAATAATATTAAATATA
Found at i:57320 original size:19 final size:19
Alignment explanation
Indices: 57284--57334 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
57274 TTAATATTTT
*
57284 TATTAAAATGATAATAAAA
1 TATTAAAATAATAATAAAA
* *
57303 TATTAAATTAAT-ATTAAA
1 TATTAAAATAATAATAAAA
*
57321 TAAATAAAATAATA
1 T-ATTAAAATAATA
57335 TATTTTTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
TATTAAAATAATAATAAAA
Found at i:57721 original size:19 final size:20
Alignment explanation
Indices: 57684--57721 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
57674 TTTATAAATA
**
57684 TAAAAATAATAAATTTAATT
1 TAAAAATAATAAAACTAATT
57704 TAAAAAT-ATAAAACTAAT
1 TAAAAATAATAAAACTAAT
57722 AAATTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAATAATAAAACTAATT
Found at i:57743 original size:28 final size:28
Alignment explanation
Indices: 57669--57736 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
57659 AAAAATACTG
* *
57669 TTTAGTTTATAAATATAAAAATAATAAA
1 TTTAATTTAAAAATATAAAAATAATAAA
*
57697 TTTAATTTAAAAATATAAAACTAATAAA
1 TTTAATTTAAAAATATAAAAATAATAAA
*
57725 TTTATTTTAAAA
1 TTTAATTTAAAA
57737 TTTTAAATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
TTTAATTTAAAAATATAAAAATAATAAA
Found at i:65241 original size:21 final size:19
Alignment explanation
Indices: 65216--65255 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
65206 GTAATACTTT
65216 TAAATAAATTTTAATATAAAA
1 TAAAT-AATTTTAA-ATAAAA
*
65237 TAAATATTTTTAAATAAAA
1 TAAATAATTTTAAATAAAA
65256 ATAACAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAATAATTTTAAATAAAA
Found at i:65273 original size:26 final size:25
Alignment explanation
Indices: 65231--65302 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
65221 AAATTTTAAT
65231 ATAAAAT-AAATATTTTTAAATAAAA
1 ATAAAATAAAATA-TTTTAAATAAAA
* *
65256 ATAACAATAAAATATTTTAAATTAAG
1 ATAA-AATAAAATATTTTAAATAAAA
*
65282 TTAATAATAAAATATATTTAA
1 ATAA-AATAAAATAT-TTTAA
65303 TAAGTTAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
25 4 0.10
26 26 0.65
27 10 0.25
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (25 bp):
ATAAAATAAAATATTTTAAATAAAA
Found at i:65319 original size:26 final size:26
Alignment explanation
Indices: 65264--65338 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
65254 AAATAACAAT
*
65264 AAAATAT-TTTAAATTAAGTTAATA-AT
1 AAAATATATTT-AA-TAAGTTAATATAA
65290 AAAATATATTTAATAAGTTAATATAA
1 AAAATATATTTAATAAGTTAATATAA
*
65316 AAAATA-ATTT-TTAAGTTAATATA
1 AAAATATATTTAATAAGTTAATATA
65339 TATATATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
24 12 0.27
25 14 0.31
26 16 0.36
27 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
AAAATATATTTAATAAGTTAATATAA
Found at i:65330 original size:24 final size:26
Alignment explanation
Indices: 65276--65356 Score: 89
Period size: 25 Copynumber: 3.2 Consensus size: 26
65266 AATATTTTAA
*
65276 ATTAAGTTAATA-ATAAAATATATTT
1 ATTAAGTTAATATAAAAAATATATTT
*
65301 AATAAGTTAATATAAAAAATA-ATTT
1 ATTAAGTTAATATAAAAAATATATTT
* *
65326 -TTAAGTTAATAT-ATATATATATTAT
1 ATTAAGTTAATATAAAAAATATATT-T
65351 ATTAAG
1 ATTAAG
65357 AATTTAAGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
23 5 0.11
24 14 0.30
25 16 0.34
26 12 0.26
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (26 bp):
ATTAAGTTAATATAAAAAATATATTT
Found at i:65993 original size:24 final size:25
Alignment explanation
Indices: 65942--65995 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
65932 ATACTTTTAA
* * *
65942 TAAATTAAAATAAATTATATATTAT
1 TAAATGAAAATAAATAAAATATTAT
*
65967 TAAATGAAAATAAA-AAAATATTTT
1 TAAATGAAAATAAATAAAATATTAT
65991 TAAAT
1 TAAAT
65996 TAAGTTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
TAAATGAAAATAAATAAAATATTAT
Found at i:66372 original size:39 final size:38
Alignment explanation
Indices: 66306--66411 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 38
66296 ATTTTTAAAA
*
66306 AATTTAGAACGTTAATGTGAAACAATTTAAGAAATTAAG
1 AATTTAGAATGTT-ATGTGAAACAATTTAAGAAATTAAG
*
66345 AATTTAGAATGTTATGGTGACAA-AATTTAAGAAATTAGG
1 AATTTAGAATGTTAT-GTGA-AACAATTTAAGAAATTAAG
* * * *
66384 ATTTTTGAATGTTAGAGTGAAATAATTT
1 AATTTAGAATGTTA-TGTGAAACAATTT
66412 GAGGATTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
38 4 0.07
39 52 0.90
40 2 0.03
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.36
Consensus pattern (38 bp):
AATTTAGAATGTTATGTGAAACAATTTAAGAAATTAAG
Found at i:66832 original size:31 final size:31
Alignment explanation
Indices: 66797--66864 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
66787 GGGTGACCAC
66797 ATCTTAATTAAATAAAAACGAAAGTGATCAT
1 ATCTTAATTAAATAAAAACGAAAGTGATCAT
* *
66828 ATCTTAATTGAATAAAAACGTAAGTGATCAT
1 ATCTTAATTAAATAAAAACGAAAGTGATCAT
66859 ATCTTA
1 ATCTTA
66865 TGTATTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACGAAAGTGATCAT
Found at i:67347 original size:24 final size:25
Alignment explanation
Indices: 67320--67379 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 25
67310 GTCGAGTTTT
*
67320 TAAATTATTATTTAAATTTA-ATTA
1 TAAATTATTATATAAATTTATATTA
*
67344 TAAA-TATT-TATAATTTTATATTA
1 TAAATTATTATATAAATTTATATTA
*
67367 TTAATTGATTATA
1 TAAATT-ATTATA
67380 ATTTAAACGA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 8 0.28
23 11 0.38
24 5 0.17
25 3 0.10
26 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TAAATTATTATATAAATTTATATTA
Found at i:73367 original size:15 final size:14
Alignment explanation
Indices: 73348--73397 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
73338 TATATTATAA
73348 TTATTTAATAATTT
1 TTATTTAATAATTT
* *
73362 ATTATTTTATTAAATT
1 -TTA-TTTAATAATTT
73378 TTATTGTAATAATTT
1 TTATT-TAATAATTT
73393 TTATT
1 TTATT
73398 ACTTTTTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 18 0.62
16 9 0.31
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
TTATTTAATAATTT
Found at i:75617 original size:19 final size:19
Alignment explanation
Indices: 75595--75634 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
75585 TGTTTACAAA
* *
75595 TAATTGTAAAGTTTTTATT
1 TAATTATAAACTTTTTATT
*
75614 TAATTATGAACTTTTTATT
1 TAATTATAAACTTTTTATT
75633 TA
1 TA
75635 TTTTTTTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (19 bp):
TAATTATAAACTTTTTATT
Found at i:85049 original size:21 final size:21
Alignment explanation
Indices: 85023--85062 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
85013 CCCCCTTTGA
*
85023 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
85044 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
85063 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:90405 original size:59 final size:59
Alignment explanation
Indices: 90307--90442 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 59
90297 AGCATACTAG
* * * * * *
90307 ATATTCGGGAATACACTAAAGGATACCTAGAGTATATGGTGGGCACGACCTTATGTGTC
1 ATATTCGGGATTGCACTAAAGGATACCTAGAGCAGATGGTGGACACGACCATATGTGTC
* *
90366 ATATTCGGGATTGTACTTAAGGATACCTAGTA-CAGATGGTGGACACGACCATATGTGTC
1 ATATTCGGGATTGCACTAAAGGATACCTAG-AGCAGATGGTGGACACGACCATATGTGTC
*
90425 ATACTCGGGATTGCACTA
1 ATATTCGGGATTGCACTA
90443 CGGTGCAGGT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 64 0.98
60 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (59 bp):
ATATTCGGGATTGCACTAAAGGATACCTAGAGCAGATGGTGGACACGACCATATGTGTC
Found at i:90635 original size:46 final size:45
Alignment explanation
Indices: 90531--90669 Score: 188
Period size: 45 Copynumber: 3.1 Consensus size: 45
90521 GAATAATGAC
* * *
90531 AAGTGTATTGGTAAAATAAACTTACGAGCTTATGGAATAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGT
* * * * *
90576 CAGTATATGGGTAAAATAAGCTTAAGAGCTTATGTGGTTAAATGAT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATG-GGATAAATGGT
*
90622 AAGTATTTTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGT
1 AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGT
90667 AAG
1 AAG
90670 AAATTTTATA
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 41 0.52
46 38 0.48
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (45 bp):
AAGTATATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGT
Found at i:90676 original size:46 final size:45
Alignment explanation
Indices: 90538--90669 Score: 183
Period size: 46 Copynumber: 2.9 Consensus size: 45
90528 GACAAGTGTA
* * * *
90538 TTGGTAAAATAAACTTACGAGCTTATGGAATAAATGGTCAGTATA
1 TTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATT
* * * *
90583 TGGGTAAAATAAGCTTAAGAGCTTATGTGGTTAAATGATAAGTATT
1 TTGGTAAAATAAGCTTACGAGCTTATG-GGATAAATGGTAAGTATT
90629 TTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 TTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
90670 AAATTTTATA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
45 36 0.49
46 38 0.51
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (45 bp):
TTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATT
Found at i:92955 original size:29 final size:29
Alignment explanation
Indices: 92906--93013 Score: 171
Period size: 29 Copynumber: 3.7 Consensus size: 29
92896 TTGGCCGTAG
* **
92906 GTCGCCATGCCTTCCGGGCGACCTACTAC
1 GTCGCCATGGCTTCCCAGCGACCTACTAC
*
92935 GTTGCCATGGCTTCCCAGCGACCTACTAC
1 GTCGCCATGGCTTCCCAGCGACCTACTAC
92964 GTCGCCATGGCTTCCCAGCGACCTACTAC
1 GTCGCCATGGCTTCCCAGCGACCTACTAC
*
92993 GTCGCCATGGCTTCCCGGCGA
1 GTCGCCATGGCTTCCCAGCGA
93014 GCTGCACAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 73 1.00
ACGTcount: A:0.15, C:0.40, G:0.24, T:0.21
Consensus pattern (29 bp):
GTCGCCATGGCTTCCCAGCGACCTACTAC
Found at i:93289 original size:23 final size:22
Alignment explanation
Indices: 93263--93309 Score: 85
Period size: 23 Copynumber: 2.1 Consensus size: 22
93253 CGTGAATTCA
93263 GCTGCATTATTGCAGCACTTATT
1 GCTGCATTATTGCAGCA-TTATT
93286 GCTGCATTATTGCAGCATTATT
1 GCTGCATTATTGCAGCATTATT
93308 GC
1 GC
93310 AGTCCTTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (22 bp):
GCTGCATTATTGCAGCATTATT
Found at i:93297 original size:11 final size:11
Alignment explanation
Indices: 93266--93311 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
93256 GAATTCAGCT
93266 GCATTATTGCA
1 GCATTATTGCA
*
93277 GCACTTATTGCT
1 GCA-TTATTGCA
93289 GCATTATTGCA
1 GCATTATTGCA
93300 GCATTATTGCA
1 GCATTATTGCA
93311 G
1 G
93312 TCCTTCAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (11 bp):
GCATTATTGCA
Found at i:93466 original size:23 final size:23
Alignment explanation
Indices: 93428--93489 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
93418 AAAGAAAGTG
*
93428 AGAAGAGAGCAAGGGAAAAGAGGA
1 AGAAGA-AGAAAGGGAAAAGAGGA
*
93452 AGAAGAATAAAGGGAAAAGAGGA
1 AGAAGAAGAAAGGGAAAAGAGGA
*
93475 ATAAGAAGAAAGGGA
1 AGAAGAAGAAAGGGA
93490 TAGCACAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 28 0.82
24 6 0.18
ACGTcount: A:0.58, C:0.02, G:0.37, T:0.03
Consensus pattern (23 bp):
AGAAGAAGAAAGGGAAAAGAGGA
Found at i:93585 original size:39 final size:39
Alignment explanation
Indices: 93542--93650 Score: 143
Period size: 39 Copynumber: 2.8 Consensus size: 39
93532 TTATTATTTT
** *
93542 AAATTATTAGTTTGTTAGTTTA-TGGTTTAAGGTAAAACA
1 AAATT-TTAGTTAATTAGTTTAGTAGTTTAAGGTAAAACA
93581 AAATTTTAGTTAATTAG-TTAGTTAGTTTAAGGTAAAACA
1 AAATTTTAGTTAATTAGTTTAG-TAGTTTAAGGTAAAACA
93620 AAATTTTAGTTAATTAGTTT-GTCAGTTTAAG
1 AAATTTTAGTTAATTAGTTTAGT-AGTTTAAG
93651 TTTTTATTAT
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
37 3 0.05
38 11 0.17
39 47 0.75
40 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.17, T:0.44
Consensus pattern (39 bp):
AAATTTTAGTTAATTAGTTTAGTAGTTTAAGGTAAAACA
Found at i:93652 original size:22 final size:23
Alignment explanation
Indices: 93627--93675 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
93617 ACAAAATTTT
93627 AGTTAATTAGT-TTGTCAGTTTA
1 AGTTAATTAGTATTGTCAGTTTA
* * *
93649 AGTT-TTTATTATTGTTAGTTTA
1 AGTTAATTAGTATTGTCAGTTTA
93671 AGTTA
1 AGTTA
93676 TATCATACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.55
Consensus pattern (23 bp):
AGTTAATTAGTATTGTCAGTTTA
Found at i:93773 original size:28 final size:27
Alignment explanation
Indices: 93734--93786 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
93724 ATATTAAAAA
93734 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
93762 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
93787 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:93792 original size:27 final size:29
Alignment explanation
Indices: 93733--93797 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
93723 TATATTAAAA
93733 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
93762 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
93788 AAATAGTTAA
1 AAATAATTAA
93798 GTTATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:94034 original size:21 final size:21
Alignment explanation
Indices: 94008--94047 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
93998 GATAATGAGT
94008 TTGTTAGTTTAAATTATATTA
1 TTGTTAGTTTAAATTATATTA
*
94029 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAATTATAT
94048 CATATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAATTATATTA
Found at i:94283 original size:29 final size:30
Alignment explanation
Indices: 94234--94353 Score: 127
Period size: 30 Copynumber: 4.3 Consensus size: 30
94224 TAATTAATTT
* *
94234 TTTAGTAG-TAAA-TTATAATTAAA-AATCG
1 TTTATTAGTTAAAGTTAT-ATTAAAGAATAG
*
94262 TTTATTAGTTTAAGTTATATTAAAGAATAG
1 TTTATTAGTTAAAGTTATATTAAAGAATAG
94292 TTTATTAGTTAAAGTTATATTAAAG---A-
1 TTTATTAGTTAAAGTTATATTAAAGAATAG
94318 ---A-TAGTTAAAGTTATATTAAAGAATAG
1 TTTATTAGTTAAAGTTATATTAAAGAATAG
94344 TTTATTAGTT
1 TTTATTAGTT
94354 GTTTAAGGGA
Statistics
Matches: 77, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
22 20 0.26
23 1 0.01
25 1 0.01
27 1 0.01
28 7 0.09
29 10 0.13
30 37 0.48
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.44
Consensus pattern (30 bp):
TTTATTAGTTAAAGTTATATTAAAGAATAG
Found at i:94292 original size:22 final size:22
Alignment explanation
Indices: 94267--94347 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
94257 AATCGTTTAT
94267 TAGTTTAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
94289 TAGTTTATTAGTTAAAGTTATATTAAAGAA
1 TAG-----T--TTA-AGTTATATTAAAGAA
*
94319 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
94341 TAGTTTA
1 TAGTTTA
94348 TTAGTTGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
22 24 0.49
23 2 0.04
25 1 0.02
27 1 0.02
29 3 0.06
30 18 0.37
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:94297 original size:15 final size:16
Alignment explanation
Indices: 94274--94324 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
94264 TATTAGTTTA
94274 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
***
94290 AGTT-TATTAGTTAA-
1 AGTTATATTAAAGAAT
94304 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
94320 AGTTA
1 AGTTA
94325 AAGTTATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:94316 original size:11 final size:11
Alignment explanation
Indices: 94300--94338 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
94290 AGTTTATTAG
94300 TTAAAGTTATA
1 TTAAAGTTATA
*
94311 TTAAAG-AATA
1 TTAAAGTTATA
94321 GTTAAAGTTATA
1 -TTAAAGTTATA
94333 TTAAAG
1 TTAAAG
94339 AATAGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (11 bp):
TTAAAGTTATA
Found at i:98294 original size:28 final size:30
Alignment explanation
Indices: 98246--98308 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
98236 ATTTTTTATA
98246 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
98276 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
98304 TAATA
1 TAATA
98309 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:98315 original size:28 final size:28
Alignment explanation
Indices: 98250--98315 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
98240 TTTATATAAT
98250 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
98278 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
98306 ATAATTTATA
1 ATAATATATA
98316 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:98318 original size:21 final size:21
Alignment explanation
Indices: 98285--98333 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
98275 CTAATATAAT
98285 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
98306 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
98327 ATTAACT
1 A-TAACT
98334 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:98777 original size:23 final size:23
Alignment explanation
Indices: 98747--98790 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
98737 GCTTGGCTGT
98747 AATCTCCCAGCTATGGATGCAGG
1 AATCTCCCAGCTATGGATGCAGG
98770 AATCTCCCAGCTATGGATGCA
1 AATCTCCCAGCTATGGATGCA
98791 ACGCATGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
AATCTCCCAGCTATGGATGCAGG
Found at i:98886 original size:29 final size:29
Alignment explanation
Indices: 98833--98915 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 29
98823 TCGCCAGCTT
* * * *
98833 GGTCGCCGGGACTGCTTGGCAACCTACAA
1 GGTCGCTGGGAGTGCATGGCGACCTACAA
* ***
98862 GGTCGCTGGGAGTGCATGGTGACCTTGTA
1 GGTCGCTGGGAGTGCATGGCGACCTACAA
98891 GGTCGCTGGGAGTGCATGGCGACCT
1 GGTCGCTGGGAGTGCATGGCGACCT
98916 GTGTTGGGGG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.16, C:0.24, G:0.39, T:0.22
Consensus pattern (29 bp):
GGTCGCTGGGAGTGCATGGCGACCTACAA
Found at i:102890 original size:18 final size:19
Alignment explanation
Indices: 102867--102902 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
102857 AAGATTTGTA
102867 ATTATT-TATTTTAATAGT
1 ATTATTATATTTTAATAGT
*
102885 ATTATTATTTTTTAATAG
1 ATTATTATATTTTAATAG
102903 AAACCACTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
ATTATTATATTTTAATAGT
Found at i:103441 original size:23 final size:23
Alignment explanation
Indices: 103355--103441 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
103345 TCACAAAGGT
* *
103355 AGAGATAAACGTG-ACACAAAGGT
1 AGAGATAAACGTGCA-ACATAGGC
* *
103378 ATAGATAAGCGTGCAACATAGGC
1 AGAGATAAACGTGCAACATAGGC
103401 AGAGATAAACGTGCAACATAGGC
1 AGAGATAAACGTGCAACATAGGC
*
103424 AGAGATAAACGTGTAACA
1 AGAGATAAACGTGCAACA
103442 CAAACAAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
23 55 0.98
24 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (23 bp):
AGAGATAAACGTGCAACATAGGC
Found at i:103479 original size:12 final size:13
Alignment explanation
Indices: 103462--103490 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
103452 TATTCTTATT
103462 AAAAAATAAA-AG
1 AAAAAATAAAGAG
103474 AAAAAATAAAGAG
1 AAAAAATAAAGAG
103487 AAAA
1 AAAA
103491 GAGAACCGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (13 bp):
AAAAAATAAAGAG
Found at i:111193 original size:2 final size:2
Alignment explanation
Indices: 111186--111270 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
111176 ATTTCTCCTC
111186 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
111228 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
111270 C
1 C
111271 GTTTGTCTGT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:113717 original size:18 final size:19
Alignment explanation
Indices: 113682--113718 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
113672 CACGGAATGT
113682 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
113702 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
113719 TTATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:114253 original size:635 final size:633
Alignment explanation
Indices: 113093--114241 Score: 1918
Period size: 637 Copynumber: 1.8 Consensus size: 633
113083 AAGATTATCA
*
113093 GGGAATGTTGTATTTGTGTTGGTTGGTTTAGCAGGAATGTAAGATTACCGTGTTTGGTTAAAGGA
1 GGGAATGTTGTATTTGTGTTGGTTGGTTTAACAGGAATGTAAGATTACCGTGTTTGGTTAAAGGA
*
113158 ATAAAAGATTATTGGAATATATATTTGACCAAATTGTCCTTATTATATTTGTATAATATTACAAA
66 ATAAAAGATTATTGGAATATATATTTGACCAAATTATCCTTATTATATTTGTATAATATTACAAA
113223 TTGTAAAATATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTTTACA
131 TTGTAAAATATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTTTACA
*
113288 AAATTAAAAATATAAAAAAGGTTTAATGAAAGGGTAAAAAAAATTTTAACCCCTGAACTTCATAT
196 AAATTAAAAATATAAAAAAGGTTTAATGAAAGGGTAAAAAAAATTTTAACCCCTGAACCTCATAT
* *
113353 AAAATTTTAATTATAGATTTTTTTATAAATCTAAAATAATTTAAAGATAAATTTTAAATTTAACT
261 AAAATTTTAATTATAGATTTTTTTATAAATCTAAAATAATTTAAAGAAAAATTTTAAATTTAACC
* * *
113418 TTCGTAGAATTTTTATTATCCAATGACAGAAGAATGATATTTTAAAAAAATAAAAATTTAAGGGC
326 TTCGTAGAATTTTTATTATCCAATAACAGAAGAATGATATTTTAAAAAAACAAAAATTTAAAGGC
* * * *
113483 ATTTTAGTCCAAAACGCCGGTAATGTTACAATACCTAATGGAATGGAGGTAATGACATTTCCAAT
391 ATTTTAGTCCAAAACGCCGGTAATGTTACAATACATAAGGGAATGGAAGTAATGACATTCCCAAT
* * *
113548 AATATACCCAAAAAAATCTACTATCGGTAATAAAACATTATCGGGAGTGAGATTTTCGACCAACC
456 AATATACCCAAAAAAATCTACTATCGGTAATAAAACATTACCGGGAATGAGA-TTTCCACCAACC
113613 AAACATGGGAATGTGGGATTACAATCCTTGAACCAAACACCCTTAGGGTGCGTTTGGTTCACGGA
520 AAACATGGGAATGTGGGATTACAATCCTTGAACCAAACACCCTTAGGGTGCGTTTGGTTCACGGA
113678 ATGTAAGATTACCAGTGGGAATAAAAGATTACCAGGGAATATTATTACT
585 ATGTAAGATTACCAGTGGGAATAAAAGATTACCAGGGAATATTATTACT
*
113727 GGGAATGTTGTATTTTGTGTTTGGTTGGTTTAACAGGAATGTAAGATTATCGTGTTTGGTTAAAG
1 GGGAATGTTGTA-TTTGTG-TTGGTTGGTTTAACAGGAATGTAAGATTACCGTGTTTGGTTAAAG
* *
113792 GAAT-AAAGATTATTGGAATGTATATTTGACCAAATTATCTTTATTATATTTGTATAATATTACA
64 GAATAAAAGATTATTGGAATATATATTTGACCAAATTATCCTTATTATATTTGTATAATATTACA
113856 AATTGTAAAATATTTATATA-TTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTTTT
129 AATTGTAAAATATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAA-TTTTTTT
113920 ACAAAATTAAAAATATAAAAAA-GTTTAATGAAAGGGTAAAAAAAATTTTAA-CCCTGAACCTCA
193 ACAAAATTAAAAATATAAAAAAGGTTTAATGAAAGGGTAAAAAAAATTTTAACCCCTGAACCTCA
*
113983 TATAAAA-TTTAATTATAGATTTTTTTTGTAAATCTAAAATAATTTAAAGAAAAATTTGT-AATT
258 TATAAAATTTTAATTATAGA-TTTTTTTATAAATCTAAAATAATTTAAAGAAAAATTT-TAAATT
*
114046 TAACCTTCGTAGAATTTTTATTATTCAATAACAGAAGAATGATACTTTTGGAAAAAAAACAAAAA
321 TAACCTTCGTAGAATTTTTATTATCCAATAACAGAAGAATGATA-TTTT---AAAAAAACAAAAA
114111 TTTAAAGGCATTTTAGTCCAAAACGCCGGTAATGTTACAATACATAAGGGAA-GGAAAGTAATGA
382 TTTAAAGGCATTTTAGTCCAAAACGCCGGTAATGTTACAATACATAAGGGAATGG-AAGTAATGA
** * **
114175 CATTCCCGGTAATATACCCCAAAAAATCTACTATTTGTAATAAAACATTACCGGGAATGAG-TTT
446 CATTCCCAATAATATACCCAAAAAAATCTACTATCGGTAATAAAACATTACCGGGAATGAGATTT
114239 CCA
511 CCA
114242 GTTACCAAAC
Statistics
Matches: 480, Mismatches: 25, Indels: 19
0.92 0.05 0.04
Matches are distributed among these distances:
632 12 0.03
633 98 0.20
634 82 0.17
635 117 0.24
636 49 0.10
637 122 0.25
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (633 bp):
GGGAATGTTGTATTTGTGTTGGTTGGTTTAACAGGAATGTAAGATTACCGTGTTTGGTTAAAGGA
ATAAAAGATTATTGGAATATATATTTGACCAAATTATCCTTATTATATTTGTATAATATTACAAA
TTGTAAAATATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTTTACA
AAATTAAAAATATAAAAAAGGTTTAATGAAAGGGTAAAAAAAATTTTAACCCCTGAACCTCATAT
AAAATTTTAATTATAGATTTTTTTATAAATCTAAAATAATTTAAAGAAAAATTTTAAATTTAACC
TTCGTAGAATTTTTATTATCCAATAACAGAAGAATGATATTTTAAAAAAACAAAAATTTAAAGGC
ATTTTAGTCCAAAACGCCGGTAATGTTACAATACATAAGGGAATGGAAGTAATGACATTCCCAAT
AATATACCCAAAAAAATCTACTATCGGTAATAAAACATTACCGGGAATGAGATTTCCACCAACCA
AACATGGGAATGTGGGATTACAATCCTTGAACCAAACACCCTTAGGGTGCGTTTGGTTCACGGAA
TGTAAGATTACCAGTGGGAATAAAAGATTACCAGGGAATATTATTACT
Found at i:120638 original size:20 final size:22
Alignment explanation
Indices: 120599--120638 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
120589 AATCCTTATC
*
120599 TATTGTAAATGTTCTCATTTAA
1 TATTGTAAATGATCTCATTTAA
120621 TATTGTAAAT-AT-TCATTT
1 TATTGTAAATGATCTCATTT
120639 GTCATTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (22 bp):
TATTGTAAATGATCTCATTTAA
Done.