Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004816.1 Hibiscus syriacus cultivar Beakdansim tig00010851_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: 48390
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1980 original size:44 final size:45
Alignment explanation
Indices: 1893--1982 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 45
1883 TATTGTAGCA
*
1893 AGAAATGATAAACGTTGAGGCATTTTTTGAAGGCCCATATCATCC
1 AGAAATGATAAACGTTGAGGCATTTCTTGAAGGCCCATATCATCC
* *
1938 AGAAATGATAAATGTTGGGGCA-TTCTTGAAGGCCCATATCATCC
1 AGAAATGATAAACGTTGAGGCATTTCTTGAAGGCCCATATCATCC
1982 A
1 A
1983 AGAATACAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 22 0.52
45 20 0.48
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (45 bp):
AGAAATGATAAACGTTGAGGCATTTCTTGAAGGCCCATATCATCC
Found at i:3448 original size:42 final size:44
Alignment explanation
Indices: 3389--3537 Score: 155
Period size: 42 Copynumber: 3.5 Consensus size: 44
3379 GAAGCTTCAA
* * *
3389 CTTGACTCTCTCGTGAAGAGGAGAC-ATCTTTCAATAT-TCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATATTTCAATATGTCATT
* * *
3431 CTTGACTTTCTCATGAAGA-AAGTCAATATTTCAATATTGTTATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATATTTCAATA-TGTCATT
* * * *
3475 CTTGACTTTCT--TGAAGAGGAGTCAATTTTTTAGTGTTGTCATT
1 CTTGACTTTCTCGTGAAGAGGAGTCAATATTTCAAT-ATGTCATT
3518 CTTGACTTTCTCGTGAAGAG
1 CTTGACTTTCTCGTGAAGAG
3538 AAGAAGATCT
Statistics
Matches: 88, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
41 3 0.03
42 33 0.38
43 30 0.34
44 15 0.17
45 7 0.08
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (44 bp):
CTTGACTTTCTCGTGAAGAGGAGTCAATATTTCAATATGTCATT
Found at i:4790 original size:133 final size:132
Alignment explanation
Indices: 4475--4837 Score: 444
Period size: 131 Copynumber: 2.8 Consensus size: 132
4465 CAATCTTCCT
* * * * ** *
4475 TGAAGAACAGTGGAATGAATCAACGTTTCCATATCTGATTTACCCTGAAGAAGTATCAGAGTATA
1 TGAAGAATAGTGGAATGAATAAACATTTCCATATCTGATTTACCCTGAAGAAGTAGCAGAACAAA
* * * ** * * *
4540 TCCCTTTTTTCCATATTTGATATTCCCTGAGGAGCTCTGGAAAAATATGCCTCGATATACTATTC
66 TCCCCTTTTTCCATATTTGATCTTCCCTGAGGAACAATAGAAAAATATGCCTCGATATAATATTA
*
4605 CC
131 AC
* * *
4607 T-AA-ATATAGTGGAATGAATAAACATTTCTAGATCTGATTTACCCTAAAGAAGTAGCAGAACAA
1 TGAAGA-ATAGTGGAATGAATAAACATTTCCATATCTGATTTACCCTGAAGAAGTAGCAGAACAA
*
4670 ATCCCCTTTTTCCATATTTGATCTTCCAC-GAGGAACAATAGAACAAATATGCCTCGATTTAATA
65 ATCCCCTTTTTCCATATTTGATCTTCC-CTGAGGAACAATAGAA-AAATATGCCTCGATATAATA
4734 TTAAC
128 TTAAC
* * * *
4739 TGAAGAATAGTGGAATGAATAAACATTTCCATATCTGATTTACTCTGAAGAAGCAGCGGATCAAA
1 TGAAGAATAGTGGAATGAATAAACATTTCCATATCTGATTTACCCTGAAGAAGTAGCAGAACAAA
* *
4804 TTCCCTTTTTCCATATTTGATCTTCCTTGAGGAA
66 TCCCCTTTTTCCATATTTGATCTTCCCTGAGGAA
4838 TAGTGGAACA
Statistics
Matches: 196, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
130 1 0.01
131 85 0.43
132 24 0.12
133 85 0.43
134 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (132 bp):
TGAAGAATAGTGGAATGAATAAACATTTCCATATCTGATTTACCCTGAAGAAGTAGCAGAACAAA
TCCCCTTTTTCCATATTTGATCTTCCCTGAGGAACAATAGAAAAATATGCCTCGATATAATATTA
AC
Found at i:4850 original size:133 final size:132
Alignment explanation
Indices: 4409--4900 Score: 494
Period size: 133 Copynumber: 3.7 Consensus size: 132
4399 GGAGCATATC
* * * *
4409 CCCTTTTTCTAGATTTGATATTCCTTGAGGAACAGTGGAACAAATCTACCGT-GATTCAATCTTC
1 CCCTTTTTCCATATTTGATATTCCTTGAGGAACAGTGGAACAAATATACC-TCGATTCAATATTC
* * * *
4473 CTTGAAGAACAGTGGAATGAATCAACGTTTCCATATCTGATTTACCCTGAAGAAGTATCAGAGT-
65 C-TGAAGAATAGTGGAATGAATAAACATTTCCATATCTGATTTACCCTGAAGAAGTAGCAGA-TC
*
4537 ATA-T
128 AAATT
* * ** * *
4541 CCCTTTTTTCCATATTTGATATTCCCTGAGGAGCTCTGGAA-AAATATGCCTCGATAT-ACTATT
1 CCC-TTTTTCCATATTTGATATTCCTTGAGGAACAGTGGAACAAATATACCTCGAT-TCAATATT
* * * *
4604 CCCT-AA-ATATAGTGGAATGAATAAACATTTCTAGATCTGATTTACCCTAAAGAAGTAGCAGAA
64 -CCTGAAGA-ATAGTGGAATGAATAAACATTTCCATATCTGATTTACCCTGAAGAAGTAGCAGAT
*
4667 CAAATC
127 CAAATT
* ** * * * * *
4673 CCCTTTTTCCATATTTGATCTTCCACGAGGAACAATAGAACAAATATGCCTCGATTTAATATTAA
1 CCCTTTTTCCATATTTGATATTCCTTGAGGAACAGTGGAACAAATATACCTCGATTCAATATT-C
* * *
4738 CTGAAGAATAGTGGAATGAATAAACATTTCCATATCTGATTTACTCTGAAGAAGCAGCGGATCAA
65 CTGAAGAATAGTGGAATGAATAAACATTTCCATATCTGATTTACCCTGAAGAAGTAGCAGATCAA
4803 ATT
130 ATT
* * * *
4806 CCCTTTTTCCATATTTGATCTTCCTTGAGGAATAGTGGAACAAATCTATCTCGATTCAATATTCC
1 CCCTTTTTCCATATTTGATATTCCTTGAGGAACAGTGGAACAAATATACCTCGATTCAATATTCC
** * * *
4871 ATGAAGAGCAATGGAATGAATCAACGTTTC
66 -TGAAGAATAGTGGAATGAATAAACATTTC
4901 AGATGATCTA
Statistics
Matches: 295, Mismatches: 53, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
130 1 0.00
131 83 0.28
132 43 0.15
133 167 0.57
134 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (132 bp):
CCCTTTTTCCATATTTGATATTCCTTGAGGAACAGTGGAACAAATATACCTCGATTCAATATTCC
TGAAGAATAGTGGAATGAATAAACATTTCCATATCTGATTTACCCTGAAGAAGTAGCAGATCAAA
TT
Found at i:6284 original size:107 final size:107
Alignment explanation
Indices: 6053--6303 Score: 267
Period size: 107 Copynumber: 2.3 Consensus size: 107
6043 GCTTTTTAGT
* * * *
6053 CCCTATAAGTTAGTCGTGTTTTTGTATTTTAGTCACCTGAGATGACAAGATTGCTATTTACCCTA
1 CCCTAT-AGTTAG-CGTGTTTTTGCACTTTAGTCACCTGAGAGGACAAAATTGCTATTTACCCTA
* * *
6118 TTTCAGGTGTGTTATACATTTATTGAGTTATTTTCTGTTTAGTCC
64 TTTCA-GTGCGTTATACATTTATTGAGTTATTTGCTGTTTAGTAC
* * * * *
6163 CCCTAT-GTTTAGCGTGTTTTTGCACTTTGGTCACGTGTGAGGACCAAAATTGTTATTTACCCTT
1 CCCTATAG-TTAGCGTGTTTTTGCACTTTAGTCACCTGAGAGGA-CAAAATTGCTATTTACCCTA
* * *
6227 TTTTA-TGCGTTATACATTTATTGGGTTATTTGCTTTTTA-TAC
64 TTTCAGTGCGTTATACATTTATTGAGTTATTTGCTGTTTAGTAC
*
6269 CCCTATAGTTGAGCGTGTTTTTACA-TTCTAGTCAC
1 CCCTATAGTT-AGCGTGTTTTTGCACTT-TAGTCAC
6304 ATGTAGTGAT
Statistics
Matches: 119, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
106 12 0.10
107 50 0.42
108 26 0.22
109 25 0.21
110 6 0.05
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (107 bp):
CCCTATAGTTAGCGTGTTTTTGCACTTTAGTCACCTGAGAGGACAAAATTGCTATTTACCCTATT
TCAGTGCGTTATACATTTATTGAGTTATTTGCTGTTTAGTAC
Found at i:7194 original size:12 final size:13
Alignment explanation
Indices: 7171--7207 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
7161 GCTTGATGTA
7171 TGTTTGTATTTTT
1 TGTTTGTATTTTT
7184 TGTTT-TA-TTTT
1 TGTTTGTATTTTT
*
7195 TGTATGTATTTTT
1 TGTTTGTATTTTT
7208 AATTGGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 8 0.38
12 4 0.19
13 9 0.43
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.76
Consensus pattern (13 bp):
TGTTTGTATTTTT
Found at i:8670 original size:22 final size:22
Alignment explanation
Indices: 8651--8696 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
8641 AACATGATTA
8651 ATGGCTTCCAAAATGTTGATGAG
1 ATGG-TTCCAAAATGTTGATGAG
*
8674 TTTGGTTCCAAAATGTTGATGAG
1 -ATGGTTCCAAAATGTTGATGAG
8697 TTTGGGTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.35
Consensus pattern (22 bp):
ATGGTTCCAAAATGTTGATGAG
Found at i:8682 original size:23 final size:23
Alignment explanation
Indices: 8656--8701 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
8646 GATTAATGGC
8656 TTCCAAAATGTTGATGAGTTTGG
1 TTCCAAAATGTTGATGAGTTTGG
8679 TTCCAAAATGTTGATGAGTTTGG
1 TTCCAAAATGTTGATGAGTTTGG
8702 GTCGATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (23 bp):
TTCCAAAATGTTGATGAGTTTGG
Found at i:11597 original size:178 final size:178
Alignment explanation
Indices: 11291--11639 Score: 635
Period size: 178 Copynumber: 2.0 Consensus size: 178
11281 TCTTTGAAAC
11291 TTCTTAGGAGTTGTACATCACGTACACAATACTTCCAAATACATAGAGGTTTGAATAATCAACTG
1 TTCTTAGGAGTTGTACATCACGTACACAATACTTCCAAATACATAGAGGTTTGAATAATCAACTG
* *
11356 GTTTACCAGTCCACATCTCCATTGGTGTCTTTAGCTCTATTGCAGTTGATGGAGCTTGATTCACC
66 GTTTACCAGTCCACATCTCCATTGGTGTCTTCAGCTCTATTGCAGTTGATGGAGCTCGATTCACC
*
11421 AAATAACAGGCGATATTGACTGCTTCTGGCCAGAATGATTTGAATAAT
131 AAATAACAGGCGATATTGACTGCTTCTGGCCAAAATGATTTGAATAAT
* *
11469 TTCTTGGGAGTTGTACATCACGTACACAATACTTCCAAATACATGGAGGTTTGAATAATCAACTG
1 TTCTTAGGAGTTGTACATCACGTACACAATACTTCCAAATACATAGAGGTTTGAATAATCAACTG
11534 GTTTACCAGTCCACATCTCCATTGGTGTCTTCAGCTCTATTGCAGTTGATGGAGCTCGATTCACC
66 GTTTACCAGTCCACATCTCCATTGGTGTCTTCAGCTCTATTGCAGTTGATGGAGCTCGATTCACC
* *
11599 AAATAACAGGTGGTATTGACTGCTTCTGGCCAAAATGATTT
131 AAATAACAGGCGATATTGACTGCTTCTGGCCAAAATGATTT
11640 TTCTAGGCCT
Statistics
Matches: 164, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
178 164 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (178 bp):
TTCTTAGGAGTTGTACATCACGTACACAATACTTCCAAATACATAGAGGTTTGAATAATCAACTG
GTTTACCAGTCCACATCTCCATTGGTGTCTTCAGCTCTATTGCAGTTGATGGAGCTCGATTCACC
AAATAACAGGCGATATTGACTGCTTCTGGCCAAAATGATTTGAATAAT
Found at i:18673 original size:14 final size:14
Alignment explanation
Indices: 18637--18663 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18627 ATTTATTTTT
18637 TAATTATATTTATA
1 TAATTATATTTATA
18651 TAATTATATTTAT
1 TAATTATATTTAT
18664 TATTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:21689 original size:37 final size:37
Alignment explanation
Indices: 21640--21751 Score: 172
Period size: 37 Copynumber: 3.0 Consensus size: 37
21630 AACATAACGT
*
21640 TAGAATTTTACTAGGGA-TCAAACTCCTAAAAATAGGA
1 TAGAATTCTACTA-GGATTCAAACTCCTAAAAATAGGA
* *
21677 TAGAGTTCTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAATTCTACTAGGATTCAAACTCCTAAAAATAGGA
*
21714 TAGAATTCTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAATTCTACTAGGATTCAAACTCCTAAAAATAGGA
21751 T
1 T
21752 CCACAAGCAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 3 0.04
37 65 0.96
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (37 bp):
TAGAATTCTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:22249 original size:2 final size:2
Alignment explanation
Indices: 22244--22283 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
22234 TTTAGATTAC
22244 AT AT 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 AT AT
22284 TTTTTATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22320 original size:12 final size:12
Alignment explanation
Indices: 22244--22321 Score: 76
Period size: 12 Copynumber: 6.9 Consensus size: 12
22234 TTTAGATTAC
*
22244 ATATATATATAT
1 ATATATATTTAT
*
22256 ATATATATATAT
1 ATATATATTTAT
*
22268 ATATATATATAT
1 ATATATATTTAT
*
22280 ATAT-TTTTTAT
1 ATATATATTTAT
*
22291 -TATCTATTT-T
1 ATATATATTTAT
22301 AT-TA-ATTTAT
1 ATATATATTTAT
22311 ATATATATTTA
1 ATATATATTTA
22322 CTATTTTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
9 4 0.07
10 8 0.14
11 12 0.21
12 33 0.58
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATATATTTAT
Found at i:22330 original size:43 final size:40
Alignment explanation
Indices: 22267--22389 Score: 144
Period size: 41 Copynumber: 3.0 Consensus size: 40
22257 TATATATATA
* *
22267 TATATATATATATATATTTTTTATTATCTATTTTATTAATT
1 TATATATATATTTATATTTTTTATTAT-TATTTTATTTATT
*
22308 TATATATATATTTACTATTTTTTA-T-GT-TTTTATTTATT
1 TATATATATATTTA-TATTTTTTATTATTATTTTATTTATT
*
22346 ATATATATACTATTTTTACTTTTTTATTATTATTTTATTTATT
1 -TATATATA-TATTTATA-TTTTTTATTATTATTTTATTTATT
22389 T
1 T
22390 GTTTTATTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
38 10 0.14
39 11 0.16
40 12 0.17
41 15 0.21
42 11 0.16
43 11 0.16
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (40 bp):
TATATATATATTTATATTTTTTATTATTATTTTATTTATT
Found at i:22351 original size:39 final size:40
Alignment explanation
Indices: 22267--22388 Score: 144
Period size: 39 Copynumber: 3.0 Consensus size: 40
22257 TATATATATA
* *
22267 TATATATATATATATA-TTTTTTATTATCTATTTTATTAAT
1 TATATATATATATTTACTTTTTTATTAT-TATTTTATTTAT
*
22307 T-TATATATATATTTACTATTTT-TTATGT-TTTTATTTAT
1 TATATATATATATTTACTTTTTTATTAT-TATTTTATTTAT
22345 TATATATATACTATTTTTACTTTTTTATTATTATTTTATTTAT
1 TATATATATA-TA--TTTACTTTTTTATTATTATTTTATTTAT
22388 T
1 T
22389 TGTTTTATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
38 10 0.14
39 26 0.37
40 8 0.11
42 11 0.16
43 15 0.21
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (40 bp):
TATATATATATATTTACTTTTTTATTATTATTTTATTTAT
Found at i:22357 original size:33 final size:32
Alignment explanation
Indices: 22305--22378 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
22295 TATTTTATTA
*
22305 ATTTATATATATATTTACTATTTTTTA-TGTTTTT
1 ATTTAT-TATATATATACTA-TTTTTACT-TTTTT
22339 ATTTATTATATATATACTATTTTTACTTTTTT
1 ATTTATTATATATATACTATTTTTACTTTTTT
22371 A-TTATTAT
1 ATTTATTAT
22379 TTTATTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 7 0.18
32 12 0.32
33 13 0.34
34 6 0.16
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.66
Consensus pattern (32 bp):
ATTTATTATATATATACTATTTTTACTTTTTT
Found at i:22369 original size:31 final size:33
Alignment explanation
Indices: 22305--22378 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 33
22295 TATTTTATTA
* *
22305 ATTTATATATATATTTACTATTTTTTATGTTTTT
1 ATTTAT-TATATATATACTATTTTTTATCTTTTT
22339 ATTTATTATATATATACTA-TTTTTA-CTTTTT
1 ATTTATTATATATATACTATTTTTTATCTTTTT
22370 -TATTATTAT
1 AT-TTATTAT
22379 TTTATTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 1 0.03
31 12 0.32
32 6 0.16
33 12 0.32
34 6 0.16
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.66
Consensus pattern (33 bp):
ATTTATTATATATATACTATTTTTTATCTTTTT
Found at i:22408 original size:39 final size:39
Alignment explanation
Indices: 22277--22409 Score: 103
Period size: 40 Copynumber: 3.3 Consensus size: 39
22267 TATATATATA
*
22277 TATATATTTTTTATTATCTATTTTATTAATTTATATATATATT
1 TATATATTTTTTATTAT-TATTTTATTTATTTAT-T-T-TATT
* * * **
22320 TA-CTATTTTTTATGT-TTTTATTTATTATATATATACTATT
1 TATATATTTTTTAT-TATTAT-TTTATT-TATTTATTTTATT
*
22360 T-T-TACTTTTTTATTATTATTTTATTTATTTGTTTTATT
1 TATATA-TTTTTTATTATTATTTTATTTATTTATTTTATT
22398 TATATATTTTTT
1 TATATATTTTTT
22410 CCTTTTTCTT
Statistics
Matches: 71, Mismatches: 11, Indels: 20
0.70 0.11 0.20
Matches are distributed among these distances:
38 10 0.14
39 16 0.23
40 18 0.25
41 2 0.03
42 17 0.24
43 8 0.11
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (39 bp):
TATATATTTTTTATTATTATTTTATTTATTTATTTTATT
Found at i:22441 original size:2 final size:2
Alignment explanation
Indices: 22436--22482 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
22426 TTATATTTTC
22436 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
22478 TA TA T
1 TA TA T
22483 TTATTTTACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25637 original size:12 final size:13
Alignment explanation
Indices: 25608--25663 Score: 64
Period size: 13 Copynumber: 4.4 Consensus size: 13
25598 AGATCCAATA
25608 AGAACAAAA-AAAG
1 AGAA-AAAACAAAG
25621 AGAAAAAACAAAG
1 AGAAAAAACAAAG
25634 -G-AAAAACAAAG
1 AGAAAAAACAAAG
*
25645 AGAAAATAAAAAAG
1 AGAAAA-AACAAAG
25659 AGAAA
1 AGAAA
25664 TAAAAATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
11 10 0.26
12 6 0.16
13 11 0.29
14 11 0.29
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (13 bp):
AGAAAAAACAAAG
Found at i:25638 original size:10 final size:12
Alignment explanation
Indices: 25613--25650 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
25603 CAATAAGAAC
25613 AAAA-AAAGAGAA
1 AAAACAAAGAG-A
25625 AAAACAAAG-GA
1 AAAACAAAGAGA
25636 AAAACAAAGAGA
1 AAAACAAAGAGA
25648 AAA
1 AAA
25651 TAAAAAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.42
12 10 0.42
13 4 0.17
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAACAAAGAGA
Found at i:25668 original size:12 final size:12
Alignment explanation
Indices: 25615--25669 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
25605 ATAAGAACAA
*
25615 AAAAAGAGAAAA
1 AAAAAGAGAAAT
25627 AACAAAG-GAAA-
1 AA-AAAGAGAAAT
25638 AACAAAGAGAAAAT
1 AA-AAAGAG-AAAT
25652 AAAAAAGAGAAAT
1 -AAAAAGAGAAAT
25665 AAAAA
1 AAAAA
25670 TCAAGGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
11 7 0.18
12 12 0.32
13 11 0.29
14 6 0.16
15 2 0.05
ACGTcount: A:0.78, C:0.04, G:0.15, T:0.04
Consensus pattern (12 bp):
AAAAAGAGAAAT
Found at i:32327 original size:2 final size:2
Alignment explanation
Indices: 32322--32350 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
32312 AAAATAGTAA
32322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32351 AATTAATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32776 original size:37 final size:37
Alignment explanation
Indices: 32735--32842 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
32725 TTTTGGATCT
* *
32735 TATTTTTAGGAGTTTGAATCATAATAGAACTGTATCC
1 TATTTTTAGGAGTTTGAATCATAATAAAACTCTATCC
* *
32772 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCC
1 TATTTTTAGGAGTTTGAATCATAATAAAACTCTATCC
* *
32809 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAATAAAACTCTA
32843 ACGTTATGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAATAAAACTCTATCC
Found at i:33461 original size:85 final size:83
Alignment explanation
Indices: 33394--33568 Score: 242
Period size: 83 Copynumber: 2.1 Consensus size: 83
33384 GCTGTAAGTT
* * *
33394 TGATTTGCCTCTGAGTTGAATGTAATCGAACTCAAAGGTCTTTCATGACAGATAACCCTTCTAGC
1 TGATGTGCCTCTGAGCTGAACGTAATCGAACTCAAAGGTCTTTCATGACAGATAACCCTTCTAGC
33459 CTTGAGTTATGCTACAAA
66 CTTGAGTTATGCTACAAA
* * * * * * ** *
33477 TGATGTGTCTTTGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGTTGACAGATGACCCTTCTAGC
1 TGATGTGCCTCTGAGCTGAACGTAATCGAACTCAAAGGTCTTTCATGACAGATAACCCTTCTAGC
33542 CTTGAGTTATGCTACAAA
66 CTTGAGTTATGCTACAAA
33560 TGATGTGCC
1 TGATGTGCC
33569 CTTGAAGCTG
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (83 bp):
TGATGTGCCTCTGAGCTGAACGTAATCGAACTCAAAGGTCTTTCATGACAGATAACCCTTCTAGC
CTTGAGTTATGCTACAAA
Found at i:33707 original size:34 final size:35
Alignment explanation
Indices: 33605--33759 Score: 251
Period size: 34 Copynumber: 4.4 Consensus size: 35
33595 AAGGTATTGG
*
33605 GTTTCAAGAGAAACATTTTCAAAGGGTTTTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAA-GG--TTTTTTTTGT
33643 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
*
33678 GTTTAAAGAGAAACAATTTCAAAGG-TTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
33712 GTTTCAAGAGAAACAATTTCAAAGG-TTTTTTTGT
1 GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
33746 GTTTCAAGAGAAAC
1 GTTTCAAGAGAAAC
33760 TGTCTCAAGG
Statistics
Matches: 114, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
34 56 0.49
35 34 0.30
37 2 0.02
38 22 0.19
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.41
Consensus pattern (35 bp):
GTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTGT
Found at i:33721 original size:69 final size:70
Alignment explanation
Indices: 33605--33759 Score: 251
Period size: 69 Copynumber: 2.2 Consensus size: 70
33595 AAGGTATTGG
*
33605 GTTTCAAGAGAAACATTTTCAAAGGGTTTTTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTT
1 GTTTCAAGAGAAACAATTTCAAAGGG--TTTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGG-T
33670 TTTTTTGT
63 TTTTTTGT
*
33678 GTTTAAAGAGAAACAATTTCAAA-GG-TTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
1 GTTTCAAGAGAAACAATTTCAAAGGGTTTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
33741 TTTGT
66 TTTGT
33746 GTTTCAAGAGAAAC
1 GTTTCAAGAGAAAC
33760 TGTCTCAAGG
Statistics
Matches: 79, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
68 22 0.28
69 34 0.43
72 2 0.03
73 21 0.27
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.41
Consensus pattern (70 bp):
GTTTCAAGAGAAACAATTTCAAAGGGTTTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTTT
TTTGT
Found at i:33793 original size:37 final size:37
Alignment explanation
Indices: 33745--33907 Score: 159
Period size: 37 Copynumber: 4.6 Consensus size: 37
33735 GGTTTTTTTG
* *
33745 TGTTTCAAGAGAAACTGTCTCAAGGGAGGCAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
33782 TGTTTCAAGAGAAACATAT-TC-A-A-AG-----ATTGG
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT-T
*
33812 CGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
*
33848 TGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAATTT
*
33885 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
33908 AACTCGTTTT
Statistics
Matches: 104, Mismatches: 8, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
29 5 0.05
30 16 0.15
31 1 0.01
32 1 0.01
33 2 0.02
34 2 0.02
35 1 0.01
36 31 0.30
37 41 0.39
38 4 0.04
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:33863 original size:36 final size:37
Alignment explanation
Indices: 33813--33907 Score: 149
Period size: 36 Copynumber: 2.6 Consensus size: 37
33803 AAAGATTGGC
33813 GTTTCAA-GAGAAACTGTCTCAAGAGAGACAA-AATTT
1 GTTTCAAGGA-AAACTGTCTCAAGAGAGACAAGAATTT
*
33849 GTTTCAAGGAAAACTGTCTCAAGAGAGACAAGATTTT
1 GTTTCAAGGAAAACTGTCTCAAGAGAGACAAGAATTT
*
33886 GTTTCAAGGGAAACTGTCTCAA
1 GTTTCAAGGAAAACTGTCTCAA
33908 AACTCGTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
36 28 0.51
37 27 0.49
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (37 bp):
GTTTCAAGGAAAACTGTCTCAAGAGAGACAAGAATTT
Found at i:34022 original size:37 final size:37
Alignment explanation
Indices: 33972--34043 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
33962 TCAAGGTTTA
* *
33972 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAAAGAAACTATCTCAAGAGAGACAAAATTT
34009 TGTTTCAAAAGAAACTATCTCAAGAGAGACAAAAT
1 TGTTTCAAAAGAAACTATCTCAAGAGAGACAAAAT
34044 AAATTTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (37 bp):
TGTTTCAAAAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:34064 original size:102 final size:102
Alignment explanation
Indices: 33945--34189 Score: 339
Period size: 102 Copynumber: 2.4 Consensus size: 102
33935 ATATTTTGTG
* * *
33945 TTTCAAGGGAAACGTTTTCAAGGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
1 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* *
34010 GTTTCAAAAGAAACTATCTCAAGAGAGAC-AAAATAAA
66 GTTTCAAAAGAAACTACCCCAAGAGAGACAAAAAT-AA
* *
34047 TTTCAAATGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
** * * **
34112 GTTTCAAGGGAAACTACCCCAAGCGAGATAAAAATTT
66 GTTTCAAAAGAAACTACCCCAAGAGAGACAAAAATAA
* *
34149 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGGGAAA
1 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAA
34190 TAAAATTTTG
Statistics
Matches: 126, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
102 121 0.96
103 5 0.04
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (102 bp):
TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
GTTTCAAAAGAAACTACCCCAAGAGAGACAAAAATAA
Found at i:34156 original size:36 final size:37
Alignment explanation
Indices: 34074--34160 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
34064 TCAATGTTTA
* ** * * *
34074 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAAATT
*
34111 TGTTTCAAGGGAAACTACCCCAAGCGAGATAAAAATT
1 TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAAATT
34148 T-TTTCAAGGGAAA
1 TGTTTCAAGGGAAA
34161 TGTTTTCAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 12 0.28
37 31 0.72
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAAATT
Found at i:34164 original size:87 final size:89
Alignment explanation
Indices: 34072--34290 Score: 248
Period size: 87 Copynumber: 2.4 Consensus size: 89
34062 TTTCAATGTT
*
34072 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCG
1 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGAAAACTACCCCAAGCG
*
34137 AGATAAAAATT-TTTTCAAGGGAAA
66 AGAT-AAAATTCATTTCAAGGGAAA
* *** * * * * * *
34161 TGT-TTTCAATG-TTTA-TGTTTCAAGGGAAATAAAATTTTGTTTCAAGGAAAACTATCTCAATC
1 TATGTTTCAA-GAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGAAAACTACCCCAAGC
34223 GAGATAAAATTCATTTCAAGGGAAA
65 GAGATAAAATTCATTTCAAGGGAAA
34248 TGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 ----TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
34291 AGTTCCAAAA
Statistics
Matches: 102, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
86 6 0.06
87 57 0.56
88 7 0.07
89 3 0.03
91 3 0.03
92 7 0.07
93 19 0.19
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (89 bp):
TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGAAAACTACCCCAAGCG
AGATAAAATTCATTTCAAGGGAAA
Found at i:34704 original size:106 final size:106
Alignment explanation
Indices: 34567--34841 Score: 424
Period size: 106 Copynumber: 2.6 Consensus size: 106
34557 CTAGAACAAA
* * * * * *
34567 GAAATTGTTTGTTGACAGCTAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCC
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
*
34632 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGG
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGG
**
34673 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAGTCC
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
* *
34738 AATATCCTTCGCTGTGAAGTTGAAATTGGTTCTAAAATTGG
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGG
* * *
34779 GAAATTGTTTGTTGACAACCAGTCGTACCTTCGTTGTGGAGTTGAACTTGTGTTGTCTCGAGT
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
34842 GGCATGATAT
Statistics
Matches: 153, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 153 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (106 bp):
GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
AATATCCTTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGG
Found at i:35473 original size:32 final size:33
Alignment explanation
Indices: 35437--35527 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
35427 ATTCCCAAAG
* *
35437 ATGCCCCAATATTCGATGTTGAATCT-AAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTAAAAAAA
*
35469 ATGCCCCAACATTTGATGTTAAATCTAAAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTAAAAAAA
*
35502 ATGCACCAACATTTGATGTTGAATCT
1 ATGCCCCAACATTTGATGTTGAATCT
35528 TCAAAGATGC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 23 0.43
33 30 0.57
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (33 bp):
ATGCCCCAACATTTGATGTTGAATCTAAAAAAA
Found at i:36580 original size:69 final size:69
Alignment explanation
Indices: 36465--36602 Score: 197
Period size: 69 Copynumber: 2.0 Consensus size: 69
36455 TGTCTCTCTC
* * * *
36465 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAGTAGTTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAATGATTCAATAGTTCAGAAATGATTGTGCTTGATCAAAC
36530 TCAT
66 TCAT
* * *
36534 TTGATGCTCTATGATCTTCGAGTGAAATGTTTCAAT-GATTCGGAAATGATTGTGCTTGATCAAA
1 TTGATGCTCCATGATCTTCGAGTGAAATGATTCAATAG-TTCAGAAATGATTGTGCTTGATCAAA
36598 CTCAT
65 CTCAT
36603 AGTTTGAATC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 1 0.02
69 60 0.98
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCGAGTGAAATGATTCAATAGTTCAGAAATGATTGTGCTTGATCAAAC
TCAT
Found at i:36703 original size:13 final size:14
Alignment explanation
Indices: 36674--36723 Score: 70
Period size: 13 Copynumber: 3.8 Consensus size: 14
36664 TTTTTCTTCA
36674 ATTTTC-CTTTGTT
1 ATTTTCTCTTTGTT
36687 -TTTTCTCTTT-TT
1 ATTTTCTCTTTGTT
36699 ATTTTCTCTTTGTT
1 ATTTTCTCTTTGTT
*
36713 TTTTTCTCTTT
1 ATTTTCTCTTT
36724 TTCTCTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
14 12 0.36
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (14 bp):
ATTTTCTCTTTGTT
Found at i:36713 original size:26 final size:26
Alignment explanation
Indices: 36674--36725 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 26
36664 TTTTTCTTCA
36674 ATTTTCCTTTG-TTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTTCTCTTTTT
36699 ATTTTCTCTTTGTTTTTTTCTCTTTTT
1 ATTTTC-CTTTGTTTTTTTCTCTTTTT
36726 CTCTTTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (26 bp):
ATTTTCCTTTGTTTTTTTCTCTTTTT
Found at i:39941 original size:18 final size:19
Alignment explanation
Indices: 39915--39958 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
39905 TAAAGAAACG
*
39915 AAAAGAAAAGAAAA-AAAT
1 AAAAAAAAAGAAAAGAAAT
* *
39933 AAAAAAAAATAAAAGACAT
1 AAAAAAAAAGAAAAGAAAT
39952 AAAAAAA
1 AAAAAAA
39959 TAAAATCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (19 bp):
AAAAAAAAAGAAAAGAAAT
Found at i:40604 original size:37 final size:37
Alignment explanation
Indices: 40554--40665 Score: 172
Period size: 37 Copynumber: 3.0 Consensus size: 37
40544 ATGCTTCTGG
*
40554 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
40591 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
40628 ATCATATTTTTAGGAGTTTGAATCCA-AGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAAT-CATAGTAAAACTCT
40665 A
1 A
40666 ATGTTATGTT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 67 0.99
38 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:42174 original size:18 final size:17
Alignment explanation
Indices: 42151--42209 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 17
42141 TTTAAGTTAT
42151 CTTATGTATGCATATTTA
1 CTTATGT-TGCATATTTA
*
42169 CTTATGTTTCATATTTA
1 CTTATGTTGCATATTTA
* **
42186 TCCTAAACTTGCATATTTA
1 --CTTATGTTGCATATTTA
42205 CTTAT
1 CTTAT
42210 ATGTTATTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
17 12 0.38
18 7 0.22
19 13 0.41
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (17 bp):
CTTATGTTGCATATTTA
Found at i:42183 original size:17 final size:18
Alignment explanation
Indices: 42151--42185 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42141 TTTAAGTTAT
42151 CTTATGTATGCATATTTA
1 CTTATGTATGCATATTTA
*
42169 CTTATGT-TTCATATTTA
1 CTTATGTATGCATATTTA
42186 TCCTAAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (18 bp):
CTTATGTATGCATATTTA
Found at i:45321 original size:3 final size:3
Alignment explanation
Indices: 45313--45376 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
45303 AATATTTATT
* *
45313 TAA TAA TAA TAA TAA TGTA TAA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45359 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
45377 AAGCAAACTG
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
3 54 0.96
4 2 0.04
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:45677 original size:74 final size:74
Alignment explanation
Indices: 45551--45729 Score: 286
Period size: 74 Copynumber: 2.4 Consensus size: 74
45541 GAAGTCTTAT
* * *
45551 CATCTTGCACTATAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
45616 TTTTGAAAA
66 TTTTGAAAA
* * **
45625 CATCCTGCACTGTAGGGCTTATGGATGACCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
45690 TTTTGAAAA
66 TTTTGAAAA
*
45699 CATCATGCATTGTAGGTCTTACAGATGACCC
1 CATCATGCACTGTAGGTCTTACAGATGACCC
45730 GAAAGTTTTG
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 94 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (74 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
TTTTGAAAA
Found at i:45746 original size:45 final size:45
Alignment explanation
Indices: 45680--46127 Score: 675
Period size: 45 Copynumber: 10.0 Consensus size: 45
45670 TCAAAAAGCT
* * *
45680 CCCGAAGGCTTTTTGAAAACATCATGCATTGTAGGTCTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * *
45727 CCCGAAAGTTTTGAAAACATCATGCATTGTAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
45772 CCCGAAAGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
45817 CCCGAAGGCTTTG-AAACATCATGCACTGAAGGGCTTATAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * *
45861 CCCGAAGATTTTGATAACATCATGCACTGAAGGGCTTACAGATAA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * *
45906 CCCGAAGGCTTTG-AAACATCATGCACTAAAGGGCTTACAGAAGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
45950 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
45995 CCCGAAGGTTTTGATAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
46040 CCCAAAGGTTTTGAAAACATCATGCAATGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
46085 CCCGAAGGTTTTGAAAACATCATGCACTAAAAGGCTTACAGAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
46128 ATGAGAAATA
Statistics
Matches: 370, Mismatches: 29, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
44 81 0.22
45 282 0.76
47 7 0.02
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.23
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:45880 original size:89 final size:89
Alignment explanation
Indices: 45690--46127 Score: 653
Period size: 89 Copynumber: 4.9 Consensus size: 89
45680 CCCGAAGGCT
* * * * *
45690 TTTTGAAAACATCATGCATTGTAGGTCTTACAGATGACCCGAAAGTTTTGAAAACATCATGCATT
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG-AAACATCATGCACT
*
45755 GTAGGGCTTACAGATGACCCGAA-A
65 GAAGGGCTTACAGATGACCCGAAGA
*
45779 GTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAACATCATGCACT
1 -TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAACATCATGCACT
*
45844 GAAGGGCTTATAGATGACCCGAAGA
65 GAAGGGCTTACAGATGACCCGAAGA
* * * *
45869 TTTTGATAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGCTTTGAAACATCATGCACTA
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAACATCATGCACTG
* *
45934 AAGGGCTTACAGAAGACCCGAAGG
66 AAGGGCTTACAGATGACCCGAAGA
*
45958 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGATAACATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGA-AACATCATGCACT
* *
46023 GAAGGGCTTACAGATGACCCAAAGG
65 GAAGGGCTTACAGATGACCCGAAGA
*
46048 TTTTGAAAACATCATGCAATGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTG-AAACATCATGCACT
* *
46113 AAAAGGCTTACAGAT
65 GAAGGGCTTACAGAT
46128 ATGAGAAATA
Statistics
Matches: 320, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
89 164 0.51
90 155 0.48
91 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (89 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAACATCATGCACTG
AAGGGCTTACAGATGACCCGAAGA
Found at i:45968 original size:134 final size:135
Alignment explanation
Indices: 45680--46127 Score: 686
Period size: 134 Copynumber: 3.3 Consensus size: 135
45670 TCAAAAAGCT
* * * *
45680 CCCGAAGGCTTTTTGAAAACATCATGCATTGTAGGTCTTACAGATGACCCGAA-AGTTTTGAAAA
1 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGA-TTTTGATAA
* * *
45744 CATCATGCATTGTAGGGCTTACAGATGACCCGAAAGTTTTGAAAACATCATGCACTGAAGGGCTT
63 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTT
45809 ACAGATGA
128 ACAGATGA
*
45817 CCCGAAGGCTTTG-AAACATCATGCACTGAAGGGCTTATAGATGACCCGAAGATTTTGATAACAT
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGATTTTGATAACAT
* * *
45881 CATGCACTGAAGGGCTTACAGATAACCCGAAGGCTTTG-AAACATCATGCACTAAAGGGCTTACA
66 CATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACA
*
45945 GAAGA
131 GATGA
*
45950 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGATAACAT
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGATTTTGATAACAT
* *
46015 CATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCAATGAAGGGCTTACA
66 CATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACA
46080 GATGA
131 GATGA
* * *
46085 CCCGAAGGTTTTGAAAACATCATGCACTAAAAGGCTTACAGAT
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
46128 ATGAGAAATA
Statistics
Matches: 285, Mismatches: 23, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
133 42 0.15
134 161 0.56
135 73 0.26
137 9 0.03
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.23
Consensus pattern (135 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGATTTTGATAACAT
CATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACA
GATGA
Found at i:46814 original size:22 final size:20
Alignment explanation
Indices: 46789--46843 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
46779 AATAAAGCTT
46789 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTG--AAGAGAATCTA
*
46811 TCATCTTTGGAGAGAATCTA
1 TCATCTTTGAAGAGAATCTA
46831 TCATC-TTGAAGAG
1 TCATCTTTGAAGAG
46844 TGTAGATGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 7 0.23
20 15 0.48
22 9 0.29
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (20 bp):
TCATCTTTGAAGAGAATCTA
Done.