Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008215.1 Hibiscus syriacus cultivar Beakdansim tig00110841_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: 76829
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:2040 original size:282 final size:283
Alignment explanation
Indices: 1519--2071 Score: 990
Period size: 285 Copynumber: 2.0 Consensus size: 283
1509 GATATGTTCA
*
1519 CCAAGCCAGTTACGACAGACAAGTTCATGCTTTGCTTGGACTTGTTGATGTTTCGAGTTATTAAA
1 CCAAGCCAGTTACGACAGACAAGTTCATGCTTTGCTTGAACTTGTTGATGTTTCGAGTTATTAAA
1584 GAAGTAAGGTAACCCAACCCACATTGAATGTTTCCTAAGGGGCAGGATATTCGCCAAGGTGGAGA
66 GAAGTAAGGTAACCCAACCCACATTGAATGTTTCCTAAGGGGCAGGATATTC-CCAAGGTGGAGA
1649 TTTGTTAGTATGACTCATAAATATACTGAGAAAGTCTCGTAGTGGGGGTTACGATTATGTGGGTT
130 TTTGTTAGTATGACTCATAAATATACTGAGAAAGTCTCGTAGTGGGGGTTACGATTATGTGGGTT
1714 AGGGTGCGGGGACTAAGGAACCGCGTATGGTATAAGGTTATTTTTATAAATATGTATCAGGGTTT
195 AGGGTGCGGGGACTAAGGAACCGCGTATGGTATAAGGTTATTTTT-TAAATATGTATCAGGGTTT
1779 ATTTATTATAAATAAATAAGGTAAC
259 ATTTATTATAAATAAATAAGGTAAC
* *
1804 CCAAGCCAGTTACGATAGACAAGTTCATGCTTTGCTTGAACTTG-TGAATGTTTCGAGTTGTTAA
1 CCAAGCCAGTTACGACAGACAAGTTCATGCTTTGCTTGAACTTGTTG-ATGTTTCGAGTTATTAA
1868 AGAAGTAAGGTAACCCAACCCACATTGAATGTTTCCTAAGGGGCA-GATATT-CCAAGGTGGAGA
65 AGAAGTAAGGTAACCCAACCCACATTGAATGTTTCCTAAGGGGCAGGATATTCCCAAGGTGGAGA
1931 -TTGTTAGGTATGACTCATAAATATACTGAGAAAGTCTCGTAGTGGGGGTTACGATTATGTGGGT
130 TTTGTTA-GTATGACTCATAAATATACTGAGAAAGTCTCGTAGTGGGGGTTACGATTATGTGGGT
*
1995 TGGGGTGCGGGGACTAAGGAACCGCGGTATGGTATAAGG-TATTTTTTAAATATGTATCAGGGTT
194 TAGGGTGCGGGGACTAAGGAACCGC-GTATGGTATAAGGTTATTTTTTAAATATGTATCAGGGTT
2059 TATTTATTATAAA
258 TATTTATTATAAA
2072 AGTAGATGTA
Statistics
Matches: 261, Mismatches: 4, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
281 37 0.14
282 100 0.38
283 13 0.05
284 8 0.03
285 103 0.39
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.31
Consensus pattern (283 bp):
CCAAGCCAGTTACGACAGACAAGTTCATGCTTTGCTTGAACTTGTTGATGTTTCGAGTTATTAAA
GAAGTAAGGTAACCCAACCCACATTGAATGTTTCCTAAGGGGCAGGATATTCCCAAGGTGGAGAT
TTGTTAGTATGACTCATAAATATACTGAGAAAGTCTCGTAGTGGGGGTTACGATTATGTGGGTTA
GGGTGCGGGGACTAAGGAACCGCGTATGGTATAAGGTTATTTTTTAAATATGTATCAGGGTTTAT
TTATTATAAATAAATAAGGTAAC
Found at i:4426 original size:2 final size:2
Alignment explanation
Indices: 4421--4461 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
4411 TTTTAATTTA
*
4421 AT AT AT AT AT AT AT AT A- AT AT AT AT AT TT 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 AT AT AT
4462 GGGATAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5150 original size:12 final size:12
Alignment explanation
Indices: 5133--5159 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5123 TTAATTGCGA
5133 AAATTGAAATTT
1 AAATTGAAATTT
5145 AAATTGAAATTT
1 AAATTGAAATTT
5157 AAA
1 AAA
5160 AAATTTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATTGAAATTT
Found at i:6368 original size:15 final size:15
Alignment explanation
Indices: 6350--6378 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6340 GACCACTACA
6350 TCCCGAAGGACTATG
1 TCCCGAAGGACTATG
6365 TCCCGAAGGACTAT
1 TCCCGAAGGACTAT
6379 TATACCCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.21
Consensus pattern (15 bp):
TCCCGAAGGACTATG
Found at i:6549 original size:29 final size:29
Alignment explanation
Indices: 6462--6564 Score: 165
Period size: 29 Copynumber: 3.6 Consensus size: 29
6452 TTTTATATGT
*
6462 TCATGTA-CTCATGTAATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
6490 TCATGTAGTTCATGTCA-TTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
6518 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
6547 TCATGTTGCTCATGTCAT
1 TCATGTAGCTCATGTCAT
6565 GTTCATATCA
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
28 34 0.49
29 35 0.51
ACGTcount: A:0.18, C:0.19, G:0.17, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:8720 original size:3 final size:3
Alignment explanation
Indices: 8714--8749 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
8704 AGTAAAAACA
8714 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAAT AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AAT A
8750 TATTTAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:8735 original size:13 final size:13
Alignment explanation
Indices: 8717--8749 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
8707 AAAAACAAAT
8717 AATAATAATAATA
1 AATAATAATAATA
8730 AATAATAATAATA
1 AATAATAATAATA
8743 AATAATA
1 AATAATA
8750 TATTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:8749 original size:16 final size:16
Alignment explanation
Indices: 8713--8743 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
8703 AAGTAAAAAC
8713 AAATAATAATAATAAT
1 AAATAATAATAATAAT
8729 AAATAATAATAATAA
1 AAATAATAATAATAA
8744 ATAATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:9387 original size:121 final size:121
Alignment explanation
Indices: 9068--9770 Score: 922
Period size: 121 Copynumber: 5.8 Consensus size: 121
9058 AAAATCTTAA
* *
9068 GCACGGTATCCTTCTTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
* * * * * *
9133 AATTGAATATCATTCGTTGTGAAGTTGAAATCCAATCTAGAGATG-AATGCTGCTTGTGG
66 AATTGGATATCCTTCGTCGTGAAGTTGAAATCC-A---AGGGTTGCATTGCTGCTTGTGG
*
9192 G-ACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
* *
9256 AATTGTATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTACTTGTGG
66 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGG
* ** * *
9312 GCACGATATCCTTCGTCGTGAAGTTGAAATCATTAATGGCTCATTCATTGCAAAGTTGAGCTTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
* * * * *
9377 AATTGGATATCC-TCGTTGTGAAGTT-AAATCCATCTAGAGATGGA-TGCTTCTTGTGG
66 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCA---AGGGTTGCATTGCTGCTTGTGG
*
9433 GCACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
* * *
9498 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTACATTGCTTCTTGTAG
66 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGG
* *
9554 GCACGATATCCTTCGTCGTGAAGCTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
* * *
9619 AATTGGATATCCTTTGT-GTGAAGTTGAAAT-CAAGGGTT-TATTACTGCTTGT-G
66 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGG
* ** ** * *
9671 GCACGATATCCTTCTTCGTGAAGTTGAAATTAT-GATAACTCCTTCGTTGTGAAGTTGAGCTTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
* *
9735 AATTGGATATCATTCGTCATGAAGTTGAAATCCAAG
66 AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAG
9771 TATTGTTCAC
Statistics
Matches: 518, Mismatches: 51, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
116 43 0.08
117 42 0.08
118 14 0.03
119 20 0.04
120 43 0.08
121 239 0.46
122 19 0.04
123 97 0.19
124 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (121 bp):
GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
AATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTGG
Found at i:9501 original size:242 final size:243
Alignment explanation
Indices: 9068--9770 Score: 1019
Period size: 242 Copynumber: 2.9 Consensus size: 243
9058 AAAATCTTAA
* *
9068 GCACGGTATCCTTCTTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
* *
9133 AATTGAATATCATTCGTTGTGAAGTTGAAATCCAATCTAGAGATGAATGCTGCTTGTGGG-ACGA
66 AATTGGATATC-CTCGTTGTGAAGTTGAAATCC-ATCTAGAGATGAATGCTGCTTGTGGGCACGA
*
9197 TATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTGAATTGT
129 TATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTGAATTGG
* *
9262 ATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTACTTGTGG
194 ATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTACATTGCTACTTGTAG
* ** * *
9312 GCACGATATCCTTCGTCGTGAAGTTGAAATCATTAATGGCTCATTCATTGCAAAGTTGAGCTTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
* *
9377 AATTGGATATCCTCGTTGTGAAGTT-AAATCCATCTAGAGATGGATGCTTCTTGTGGGCACGATA
66 AATTGGATATCCTCGTTGTGAAGTTGAAATCCATCTAGAGATGAATGCTGCTTGTGGGCACGATA
9441 TCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTGAATTGGAT
131 TCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTGAATTGGAT
*
9506 ATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTACATTGCTTCTTGTAG
196 ATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTACATTGCTACTTGTAG
* *
9554 GCACGATATCCTTCGTCGTGAAGCTGAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTG
1 GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
* * * * * *
9619 AATTGGATATCCT-TTGTGTGAAGTTGAAAT-CA---AGGGTTTATTACTGCTTGT-GGCACGAT
66 AATTGGATATCCTCGT-TGTGAAGTTGAAATCCATCTAGAGATGAATGCTGCTTGTGGGCACGAT
* * ** ** * *
9678 ATCCTTCTTCGTGAAGTTGAAATTAT-GATAACTCCTTCGTTGTGAAGTTGAGCTTTGAATTGGA
130 ATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTGAATTGGA
* *
9742 TATCATTCGTCATGAAGTTGAAATCCAAG
195 TATCCTTCGTCGTGAAGTTGAAATCCAAG
9771 TATTGTTCAC
Statistics
Matches: 416, Mismatches: 40, Indels: 13
0.89 0.09 0.03
Matches are distributed among these distances:
237 61 0.15
238 30 0.07
239 12 0.03
241 25 0.06
242 203 0.49
243 17 0.04
244 68 0.16
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (243 bp):
GCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTG
AATTGGATATCCTCGTTGTGAAGTTGAAATCCATCTAGAGATGAATGCTGCTTGTGGGCACGATA
TCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGCGAAGTTGAGCTTTGAATTGGAT
ATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTACATTGCTACTTGTAG
Found at i:9800 original size:58 final size:64
Alignment explanation
Indices: 9729--9888 Score: 215
Period size: 58 Copynumber: 2.6 Consensus size: 64
9719 GTGAAGTTGA
* * * *
9729 GCTTTGAATTGGATATCATTCGTCATGAAGTTGAAATCCAAG-T-A-T-TG-TTCACCAAA-TG
1 GCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTTGAGTAAGTTTCACCAAATTG
*
9787 GCTTTGAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAAGTTTGAGTAAGTTTCACCAAATTG
1 GCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAAG-TTGAGTAAGTTTCACCAAATTG
*
9852 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAAT
1 GCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAAT
9889 TGACTCTGAA
Statistics
Matches: 88, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
58 38 0.43
60 1 0.01
61 1 0.01
62 1 0.01
63 1 0.01
64 9 0.10
65 37 0.42
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (64 bp):
GCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTTGAGTAAGTTTCACCAAATTG
Found at i:10022 original size:64 final size:64
Alignment explanation
Indices: 9864--10102 Score: 388
Period size: 64 Copynumber: 3.7 Consensus size: 64
9854 TTTGAGTTGG
* *
9864 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAATTGGAAAGTTGTTTGTGTGAGTCTA
1 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGT-TGAGTCCA
* * * * *
9929 ATATCCTTCGCTGGGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTATTGAGTCCA
1 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAGTCCA
*
9993 ATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAGTCCA
1 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAGTCCA
*
10057 ATATCTTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAA
1 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAA
10103 TTATTTGTTG
Statistics
Matches: 160, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 110 0.69
65 50 0.31
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (64 bp):
ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAGTCCA
Found at i:10022 original size:129 final size:128
Alignment explanation
Indices: 9864--10099 Score: 400
Period size: 129 Copynumber: 1.8 Consensus size: 128
9854 TTTGAGTTGG
* * *
9864 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAATTGGAAAGTTGTTTGTGTGAGTCTA
1 ATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGT-TGAGTCCA
9929 ATATCCTTCGCTGGGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTATTGAGTCCA
65 ATATCCTTCGCTGGGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTATTGAGTCCA
9993 ATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAGTCCAA
1 ATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAGTCCAA
* * * *
10058 TATCTTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTG
66 TATCCTTCGCTGGGAAGTTGAAATTGACTCTAAATGAAACTG
10100 GAATTATTTG
Statistics
Matches: 100, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
128 46 0.46
129 54 0.54
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (128 bp):
ATATCCTTCGATGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAGTCCAA
TATCCTTCGCTGGGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTGTTTATTGAGTCCA
Found at i:10772 original size:33 final size:31
Alignment explanation
Indices: 10695--10770 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
10685 ACTGAATTCC
*
10695 CAAAGATGCCCCAATATTCGATGTTGAATAT
1 CAAAGATGCCCCAACATTCGATGTTGAATAT
* * *
10726 CAAAAAATGCCCCAACATTTGATGTTGAATCTT
1 C-AAAGATGCCCCAACATTCGATGTTGAAT-AT
10759 CAAAGATGCCCC
1 CAAAGATGCCCC
10771 CATTGTCCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
31 1 0.03
32 35 0.92
33 2 0.05
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (31 bp):
CAAAGATGCCCCAACATTCGATGTTGAATAT
Found at i:14602 original size:16 final size:17
Alignment explanation
Indices: 14581--14618 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
14571 CTGTCTTTTT
14581 AAAAACAATTTTAAGA-
1 AAAAACAATTTTAAGAC
*
14597 AAAAACATTTTTAAGAC
1 AAAAACAATTTTAAGAC
14614 AAAAA
1 AAAAA
14619 ACTGGTATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (17 bp):
AAAAACAATTTTAAGAC
Found at i:14861 original size:29 final size:29
Alignment explanation
Indices: 14827--14891 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
14817 TGAAAACATT
* *
14827 AACTTAAAGGATTAAAATAACAA-AATAGA
1 AACTTAAAGGACTAAAATAA-AATAACAGA
*
14856 AACTTAAATGACTAAAATAAAATAACAGA
1 AACTTAAAGGACTAAAATAAAATAACAGA
14885 AACTTAA
1 AACTTAA
14892 GTATCAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 2 0.06
29 30 0.94
ACGTcount: A:0.62, C:0.09, G:0.08, T:0.22
Consensus pattern (29 bp):
AACTTAAAGGACTAAAATAAAATAACAGA
Found at i:15324 original size:22 final size:22
Alignment explanation
Indices: 15299--15350 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
15289 GTCATTGTAG
15299 GCCACTACCGTCACGCCACCGC
1 GCCACTACCGTCACGCCACCGC
15321 GCCACTACCGTCACGCCACCGC
1 GCCACTACCGTCACGCCACCGC
15343 GCCACTAC
1 GCCACTAC
15351 TTCCGCCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.54, G:0.17, T:0.10
Consensus pattern (22 bp):
GCCACTACCGTCACGCCACCGC
Found at i:15680 original size:3 final size:3
Alignment explanation
Indices: 15672--15754 Score: 152
Period size: 3 Copynumber: 28.3 Consensus size: 3
15662 AAAAGAAGGA
15672 AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15718 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
15755 TGCTACTGGA
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.05
3 74 0.95
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16182 original size:3 final size:3
Alignment explanation
Indices: 16176--16209 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
16166 AGTAAAAATA
16176 AAT AAT AAT AAT AAAT AAT AAAT AAT AAT AAT AA
1 AAT AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AA
16210 CATAATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:16183 original size:17 final size:16
Alignment explanation
Indices: 16163--16216 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
16153 AACACTTATT
16163 ATAAGTAAAAATAAATA
1 ATAA-TAAAAATAAATA
16180 ATAATAATAAAT-AATAA
1 ATAATAA-AAATAAAT-A
*
16197 ATAATAATAATAACATA
1 ATAATAAAAATAA-ATA
16214 ATA
1 ATA
16217 TATTTAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 9 0.28
17 21 0.66
18 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (16 bp):
ATAATAAAAATAAATA
Found at i:16185 original size:10 final size:10
Alignment explanation
Indices: 16172--16206 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
16162 TATAAGTAAA
16172 AATAAATAAT
1 AATAAATAAT
16182 AAT-AATAAAT
1 AATAAAT-AAT
16192 AATAAATAAT
1 AATAAATAAT
16202 AATAA
1 AATAA
16207 TAACATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAAATAAT
Found at i:16190 original size:13 final size:13
Alignment explanation
Indices: 16172--16209 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
16162 TATAAGTAAA
16172 AATAAATAATAAT
1 AATAAATAATAAT
16185 AATAAATAATAAAT
1 AATAAATAAT-AAT
16199 AAT-AATAATAA
1 AATAAATAATAA
16210 CATAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 2 0.08
13 16 0.67
14 6 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAAATAATAAT
Found at i:16195 original size:20 final size:20
Alignment explanation
Indices: 16163--16216 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 20
16153 AACACTTATT
16163 ATAAGTAAA-AATAAATAATA
1 ATAA-TAAATAATAAATAATA
16183 ATAATAAATAATAAATAATA
1 ATAATAAATAATAAATAATA
16203 ATAATAACATAATA
1 ATAATAA-ATAATA
16217 TATTTAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.12
20 22 0.69
21 6 0.19
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (20 bp):
ATAATAAATAATAAATAATA
Found at i:17011 original size:2 final size:2
Alignment explanation
Indices: 17004--17032 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16994 ATGTAAGGTC
17004 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
17033 GCTTTCCTAG
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:18475 original size:18 final size:20
Alignment explanation
Indices: 18434--18475 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
18424 AAATTTTAAA
*
18434 TTTTTATATAATTTAGTTAT
1 TTTTTATATAATTTAGTTAC
*
18454 TTTTTAT-TAA-TTATTTAC
1 TTTTTATATAATTTAGTTAC
18472 TTTT
1 TTTT
18476 ACCTTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 10 0.50
19 3 0.15
20 7 0.35
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTATATAATTTAGTTAC
Found at i:19107 original size:13 final size:13
Alignment explanation
Indices: 19091--19115 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19081 TCCCAAAACC
19091 CTTCACTTGAAAT
1 CTTCACTTGAAAT
19104 CTTCACTTGAAA
1 CTTCACTTGAAA
19116 ACAAACTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (13 bp):
CTTCACTTGAAAT
Found at i:19668 original size:27 final size:27
Alignment explanation
Indices: 19626--19689 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
19616 TTAATGTTAT
*
19626 TTATATAATAATTATTATTATTATA-A
1 TTATATAATAATTATTATTAATATATA
19652 TTATAATAATAATTATTATTAATATATA
1 TTAT-ATAATAATTATTATTAATATATA
*
19680 TTATTTAATA
1 TTATATAATA
19690 TTACAAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 4 0.12
27 25 0.74
28 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTATATAATAATTATTATTAATATATA
Found at i:20153 original size:18 final size:19
Alignment explanation
Indices: 20112--20147 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20102 GGAGAGACAG
20112 AAACAGAGCAAAAACAACA
1 AAACAGAGCAAAAACAACA
*
20131 AAACAGAG-AACAACAAC
1 AAACAGAGCAAAAACAAC
20148 CCAACAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.22, G:0.11, T:0.00
Consensus pattern (19 bp):
AAACAGAGCAAAAACAACA
Found at i:25078 original size:15 final size:15
Alignment explanation
Indices: 25058--25089 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
25048 ATCAATACCT
25058 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
25073 TTTTGCATACATTCA
1 TTTTGCATACATGCA
25088 TT
1 TT
25090 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:32427 original size:4 final size:4
Alignment explanation
Indices: 32418--32464 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
32408 TTGAAGAGAA
32418 AAAG AAAG -AA- AAAG AAA- AAA- AAAG AAAAG AAA- AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG
32462 AAA
1 AAA
32465 AAGGAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
3 13 0.34
4 21 0.55
5 4 0.11
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:32445 original size:15 final size:15
Alignment explanation
Indices: 32414--32466 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
32404 ATGCTTGAAG
*
32414 AGAAAAAGAAAGAAAA
1 AGAAAAAAAAAG-AAA
32430 AGAAAAAAAAAGAAA
1 AGAAAAAAAAAGAAA
32445 AGAAAAAAGAAAG-AA
1 AGAAAAAA-AAAGAAA
32460 AGAAAAA
1 AGAAAAA
32467 GGAAAAAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
15 20 0.57
16 15 0.43
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAGAAA
Found at i:32471 original size:15 final size:15
Alignment explanation
Indices: 32414--32476 Score: 76
Period size: 16 Copynumber: 4.1 Consensus size: 15
32404 ATGCTTGAAG
32414 AGAAAAAGAAAGAAAA
1 AGAAAAAGAAAG-AAA
*
32430 AGAAAAAAAAAGAAA
1 AGAAAAAGAAAGAAA
32445 AGAAAAAAGAAAG-AA
1 AG-AAAAAGAAAGAAA
32460 AGAAAAAGGAAA-AAA
1 AGAAAAA-GAAAGAAA
32475 AG
1 AG
32477 GGGGTCAAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 5 0.12
15 17 0.40
16 20 0.48
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAAGAAA
Found at i:32475 original size:10 final size:10
Alignment explanation
Indices: 32414--32473 Score: 68
Period size: 10 Copynumber: 5.7 Consensus size: 10
32404 ATGCTTGAAG
32414 AGAAAAAGAA
1 AGAAAAAGAA
32424 AGAAAAAGAA
1 AGAAAAAGAA
*
32434 AAAAAAAGAAA
1 AGAAAAAG-AA
32445 AGAAAAAAGAA
1 AG-AAAAAGAA
32456 AGAAAGAA-AA
1 AGAAA-AAGAA
32466 AGGAAAAA
1 A-GAAAAA
32474 AAGGGGGTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 25 0.57
11 13 0.30
12 6 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:33884 original size:83 final size:83
Alignment explanation
Indices: 33745--34055 Score: 435
Period size: 83 Copynumber: 3.6 Consensus size: 83
33735 AACAAATGCC
*
33745 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAATCAATC
**
33810 ATTGAATTTGGAAGAATA
66 ATTGAATTTGGAAGAGGA
* *
33828 ATGTGCTCATAGCATCTTCTAGAAGTGTTCCTTGAGTTATCTGATCTGATTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAATCAATC
33893 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
*
33911 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTTGGTATGAACCA-C
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTA--AA--ATC
*
33975 AGAACCAGTTATTGAATTTGGAAGAGGA
62 ---A--A-TCATTGAATTTGGAAGAGGA
* * *
34003 ATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTTGATTTG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTG
34056 ATATAAAACC
Statistics
Matches: 205, Mismatches: 13, Indels: 11
0.90 0.06 0.05
Matches are distributed among these distances:
83 131 0.64
85 2 0.01
86 1 0.00
87 1 0.00
89 1 0.00
91 1 0.00
92 68 0.33
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTAAAATCAATC
ATTGAATTTGGAAGAGGA
Found at i:34055 original size:175 final size:166
Alignment explanation
Indices: 33745--34055 Score: 444
Period size: 175 Copynumber: 1.8 Consensus size: 166
33735 AACAAATGCC
33745 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
* *
33810 ATTGAATTTGGAAGAATAATGTGCTCATAGCATCTTCTAGAAGTGTTCCTTGAGTTATCTGATCT
66 ATTGAATTTGGAAGAAGAATGTGCTAATAGCATCTTCTAGAAGTGTTCCTTGAGTTATCTGATCT
33875 GATTTGGTAAAATCAATCATTGAATTTGGAAGAGGA
131 GATTTGGTAAAATCAATCATTGAATTTGGAAGAGGA
*
33911 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTTGGTATGAACCA-C
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA--AA--ATC
* * * *
33975 AGAACCAGTTATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
62 ---A--A-TCATTGAATTTGGAAGAAGAATGTGCTAATAGCATCTTCTAGAAGTGTTCCTTGAGT
* *
34040 TCTCTGATTTGATTTG
121 TATCTGATCTGATTTG
34056 ATATAAAACC
Statistics
Matches: 126, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
166 55 0.44
168 2 0.02
169 1 0.01
170 1 0.01
172 1 0.01
174 1 0.01
175 65 0.52
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (166 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
ATTGAATTTGGAAGAAGAATGTGCTAATAGCATCTTCTAGAAGTGTTCCTTGAGTTATCTGATCT
GATTTGGTAAAATCAATCATTGAATTTGGAAGAGGA
Found at i:34070 original size:92 final size:92
Alignment explanation
Indices: 33893--34070 Score: 286
Period size: 92 Copynumber: 1.9 Consensus size: 92
33883 AAAATCAATC
*
33893 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
* * *
33958 GTTTTGGTATGAACCACAGAACCAGTT
66 GATTTGATATAAACCACAGAACCAGTT
* *
33985 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTT
1 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
34050 GATTTGATATAAAACC-CAGAA
66 GATTTGATAT-AAACCACAGAA
34071 ACAATCATTG
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 75 0.95
93 4 0.05
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (92 bp):
ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GATTTGATATAAACCACAGAACCAGTT
Found at i:34497 original size:52 final size:52
Alignment explanation
Indices: 34433--34537 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
34423 TATCGATATC
34433 TGTGAAAACATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAAACATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
*
34485 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAAACATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
34537 T
1 T
34538 TAACATGTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.32
Consensus pattern (52 bp):
TGTGAAAACATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
Found at i:35519 original size:112 final size:112
Alignment explanation
Indices: 34834--35718 Score: 1387
Period size: 113 Copynumber: 7.8 Consensus size: 112
34824 GCAAAGATTT
*
34834 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAGTTCATAATAAGAAGAACTCATCTGAAG
* ** * * *
34899 AAGGAAGAAGAAGTTCATAATGAGAAAAATTTGTTTAACCTTTTGTTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
* * * *** *
34947 GAATTCATCA-TGTGATGGATTAAAATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATTACT
1 AAATCCATCACT-TGATGGATCAGCTTTTCCAGAG-A-AGTTCATAATAAGAAGAACTCA-T-C-
* * ** *
35010 TGAAGGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTC
60 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
35063 AAATCCATCACTTGATGGATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATAAGAAGAACTCATCTGAAG
** * *
35128 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAACTTATGCTC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
*
35176 AAATCCATCACTTGATGGATCGGCTTTTCCAGAAGAAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATAAGAAGAACTCATCTGAAG
35241 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
* *
35289 AAATCCATCACTTGATGTATCAGCTTTTCCAGAAGAAGTTCATAATAAGAAAAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAG-AGAAGTTCATAATAAGAAGAACTCATCTGAAG
35354 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
65 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
35402 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGA
*
35467 AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGATC
66 AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
35514 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGA
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGA
35579 AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
* * *
35626 AAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAGTTCATAATAAGAAGAACTCATCTGAAG
35691 AAGGAAGAAGAAGTTCATAATGAGAAGA
65 AAGGAAGAAGAAGTTCATAATGAGAAGA
35719 ACTCATCTGA
Statistics
Matches: 724, Mismatches: 39, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
112 224 0.31
113 402 0.56
114 2 0.00
115 2 0.00
116 91 0.13
117 2 0.00
118 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (112 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAGTTCATAATAAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
Found at i:35716 original size:40 final size:39
Alignment explanation
Indices: 35661--35789 Score: 184
Period size: 36 Copynumber: 3.5 Consensus size: 39
35651 TTTCCAGAGA
35661 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAG
35701 AAGTTCATAATGAGAAGAACTCATCTGAAG-A-AA-AAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAG
*
35737 AATTTCATAATGAGAAGAACTCATCTG-A-AAGAAG-A-
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAG
35772 AA-TTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
35790 TTTGTTCAAC
Statistics
Matches: 85, Mismatches: 1, Indels: 12
0.87 0.01 0.12
Matches are distributed among these distances:
34 16 0.19
35 4 0.05
36 32 0.38
37 2 0.02
39 1 0.01
40 30 0.35
ACGTcount: A:0.50, C:0.10, G:0.20, T:0.20
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAG
Found at i:35718 original size:17 final size:16
Alignment explanation
Indices: 35696--35791 Score: 61
Period size: 17 Copynumber: 5.6 Consensus size: 16
35686 TGAAGAAGGA
35696 AGAAGAAGTTCATAATG
1 AGAAGAA-TTCATAATG
*
35713 AGAAGAACTCATCTGAA-G
1 AGAAGAATTCA--T-AATG
*
35731 AAAAAGAATTTCATAATG
1 -AGAAGAA-TTCATAATG
* *
35749 AGAAGAACTCAT-CTG
1 AGAAGAATTCATAATG
35764 AAAGAAGAAATTCATAATG
1 --AGAAG-AATTCATAATG
35783 AGAAGAATT
1 AGAAGAATT
35792 TGTTCAACCT
Statistics
Matches: 61, Mismatches: 8, Indels: 21
0.68 0.09 0.23
Matches are distributed among these distances:
15 2 0.03
16 11 0.18
17 25 0.41
18 10 0.16
19 10 0.16
20 3 0.05
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.22
Consensus pattern (16 bp):
AGAAGAATTCATAATG
Found at i:35855 original size:182 final size:185
Alignment explanation
Indices: 35546--35896 Score: 518
Period size: 182 Copynumber: 1.9 Consensus size: 185
35536 GCTTTTCCAG
*
35546 AGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTG
1 AGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * *
35611 TTCAACCTTTTGCTCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGA
66 TTCAACCTTTTGCTCAAATCCATCACTCAATGGATCAACCTTTACAGAGAAAGTTCATAATGAGA
*
35676 AGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAA
131 AGAACTCATCTGAAGAA-G-AG-A-AAGTTCATAATAAGAAGAACTCATCTGAAGAAAA
* * *
35735 AGAATTTCATAATGAGAAGAACTCATCTG-A-AA-GAAG-A-AA-TTCATAATGAGAAGAATTTG
1 AGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * *
35794 TTCAACC-TTTGTTCAAATTCATCACTTAATGGATCAACCTTTACAGAGAAAGTTCATAATGAGA
66 TTCAACCTTTTGCTCAAATCCATCACTCAATGGATCAACCTTTACAGAGAAAGTTCATAATGAGA
35858 AGAACTCATCTGAAGAAGAGAAAGTTCATAATAAGAAGA
131 AGAACTCATCTGAAGAAGAGAAAGTTCATAATAAGAAGA
35897 GCTTATTCAA
Statistics
Matches: 151, Mismatches: 11, Indels: 11
0.87 0.06 0.06
Matches are distributed among these distances:
178 17 0.11
179 1 0.01
180 2 0.01
181 1 0.01
182 68 0.45
183 25 0.17
184 2 0.01
185 1 0.01
186 4 0.03
187 2 0.01
188 1 0.01
189 27 0.18
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.25
Consensus pattern (185 bp):
AGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTTTGCTCAAATCCATCACTCAATGGATCAACCTTTACAGAGAAAGTTCATAATGAGA
AGAACTCATCTGAAGAAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAAA
Found at i:36198 original size:14 final size:13
Alignment explanation
Indices: 36137--36199 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
36127 CATTTTAATG
*
36137 TTATTTATATAATAA
1 TTATTAATAT-AT-A
*
36152 TTATTATTATA-A
1 TTATTAATATATA
36164 TTA-TAATA-ATTA
1 TTATTAATATA-TA
36176 TTATTAATATATA
1 TTATTAATATATA
36189 TTATTTAATAT
1 TTA-TTAATAT
36200 TACAAAACCC
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
10 1 0.03
11 4 0.10
12 8 0.20
13 10 0.25
14 9 0.22
15 8 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTAATATATA
Found at i:36664 original size:18 final size:19
Alignment explanation
Indices: 36623--36658 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
36613 GGAGAGACAG
36623 AAACAGAGCAAAAACAACA
1 AAACAGAGCAAAAACAACA
*
36642 AAACAGAG-AACAACAAC
1 AAACAGAGCAAAAACAAC
36659 CCAACAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.22, G:0.11, T:0.00
Consensus pattern (19 bp):
AAACAGAGCAAAAACAACA
Found at i:48624 original size:29 final size:28
Alignment explanation
Indices: 48586--48643 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
48576 TTAGATGTTA
* *
48586 TATCATTTATACCATTAAATTTTTAATTT
1 TATCAATTATACCACTAAATTTTT-ATTT
* *
48615 TATCAATTATAGCACTGAATTTTTATTT
1 TATCAATTATACCACTAAATTTTTATTT
48643 T
1 T
48644 CGTTTTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.53
Consensus pattern (28 bp):
TATCAATTATACCACTAAATTTTTATTT
Found at i:53279 original size:36 final size:36
Alignment explanation
Indices: 53239--53369 Score: 190
Period size: 36 Copynumber: 3.6 Consensus size: 36
53229 ATCCATTATT
*
53239 AGCTTTGATACATTTGTGTATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
* * * *
53275 AGCTTTGGTATATTCATATATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
53311 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGATACATTCGTGTATCAATGTTATCATATC
* * *
53347 AGCTTTGGTATATTTGTGTATCA
1 AGCTTTGATACATTCGTGTATCA
53370 GTGTCCAGCA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 83 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (36 bp):
AGCTTTGATACATTCGTGTATCAATGTTATCATATC
Found at i:53997 original size:14 final size:14
Alignment explanation
Indices: 53978--54010 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53968 TAGAACTATT
53978 TTAGTTTA-TTTTA
1 TTAGTTTAGTTTTA
53991 CTTAGTTTAGTTTTA
1 -TTAGTTTAGTTTTA
54006 TTAGT
1 TTAGT
54011 ATCTATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.64
Consensus pattern (14 bp):
TTAGTTTAGTTTTA
Found at i:61591 original size:18 final size:18
Alignment explanation
Indices: 61568--61672 Score: 174
Period size: 18 Copynumber: 5.8 Consensus size: 18
61558 ATTCTTAAGG
*
61568 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
*
61586 AGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACAT
61604 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
61622 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
61640 AGTGGTCCTTCGGGATAA
1 AGTGGTCCTTCGGGACAT
61658 AGTGGTCCTTCGGGA
1 AGTGGTCCTTCGGGA
61673 TAAGTGTTAA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 82 1.00
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:61627 original size:54 final size:54
Alignment explanation
Indices: 61568--61672 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
61558 ATTCTTAAGG
61568 AGTGGTCCTTCAGGACATAGTGGTCCTTCGGGACAAAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCAGGACATAGTGGTCCTTCGGGACAAAGTGGTCCTTCGGGACAT
* *
61622 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGATAAAGTGGTCCTTCGGGA
1 AGTGGTCCTTCAGGACATAGTGGTCCTTCGGGACAAAGTGGTCCTTCGGGA
61673 TAAGTGTTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.27
Consensus pattern (54 bp):
AGTGGTCCTTCAGGACATAGTGGTCCTTCGGGACAAAGTGGTCCTTCGGGACAT
Found at i:63560 original size:18 final size:18
Alignment explanation
Indices: 63537--63580 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
63527 TATGACTCAA
63537 AGAGGAAGGGGTAGAGGT
1 AGAGGAAGGGGTAGAGGT
63555 AGAGGAAGGGGTAGAGGT
1 AGAGGAAGGGGTAGAGGT
63573 AGAGGAAG
1 AGAGGAAG
63581 AAGTCAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.55, T:0.09
Consensus pattern (18 bp):
AGAGGAAGGGGTAGAGGT
Found at i:66369 original size:19 final size:22
Alignment explanation
Indices: 66339--66396 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 22
66329 AGAATGTTCG
*
66339 AATGGTACCGATACCCCC-TA-
1 AATGGTATCGATACCCCCATAC
*
66359 TA-GGTATCGATACCCCCATAC
1 AATGGTATCGATACCCCCATAC
66380 AATGGTATCGATACCCC
1 AATGGTATCGATACCCC
66397 TCAGATGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 14 0.44
20 3 0.09
21 1 0.03
22 14 0.44
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (22 bp):
AATGGTATCGATACCCCCATAC
Found at i:74193 original size:24 final size:23
Alignment explanation
Indices: 74146--74202 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 23
74136 TTTGAATGCT
74146 TTTGGATTTTTTATTTGAGTTTG
1 TTTGGATTTTTTATTTGAGTTTG
74169 TTTGGATTGTTTTACTTTGAG-TTG
1 TTTGGATT-TTTTA-TTTGAGTTTG
74193 TTTGGATTTT
1 TTTGGATTTT
74203 GGATGTTCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 10 0.31
24 16 0.50
25 6 0.19
ACGTcount: A:0.12, C:0.02, G:0.23, T:0.63
Consensus pattern (23 bp):
TTTGGATTTTTTATTTGAGTTTG
Found at i:74538 original size:27 final size:25
Alignment explanation
Indices: 74496--74562 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 25
74486 TAACAAAAAG
74496 GGGGAGAAGTGTTTAAAGTGTTTTAAA
1 GGGGAGAAGTG-TTAAAGTG-TTTAAA
*
74523 GGGGAAAAAGTGTTAAAGTGTTTAAA
1 GGGG-AGAAGTGTTAAAGTGTTTAAA
74549 GGGGAGAAGTGTTA
1 GGGGAGAAGTGTTA
74563 GAGTAAGGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 9 0.24
26 10 0.27
27 12 0.32
28 6 0.16
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (25 bp):
GGGGAGAAGTGTTAAAGTGTTTAAA
Found at i:75039 original size:20 final size:21
Alignment explanation
Indices: 74994--75046 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
74984 TAACCCTATA
74994 GGTATCGATACCCCCATGCAAT
1 GGTATCGATACCCCCATG-AAT
75016 GGTATCGATACCCCTCA-G-AT
1 GGTATCGATACCCC-CATGAAT
*
75036 GGTACCGATAC
1 GGTATCGATAC
75047 TCTAAGGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 12 0.41
22 15 0.52
23 2 0.07
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (21 bp):
GGTATCGATACCCCCATGAAT
Found at i:75118 original size:21 final size:21
Alignment explanation
Indices: 75088--75142 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
75078 TTACACTACA
*
75088 GGTACCGATACCCTATAAAGG
1 GGTACTGATACCCTATAAAGG
75109 GGTACTGATACCCTATAAAGG
1 GGTACTGATACCCTATAAAGG
75130 GGTACTGATACCC
1 GGTACTGATACCC
75143 CCACGCTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (21 bp):
GGTACTGATACCCTATAAAGG
Done.