Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000245.1 Hibiscus syriacus cultivar Beakdansim tig00000431_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: 78780
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:687 original size:95 final size:93
Alignment explanation
Indices: 555--750 Score: 281
Period size: 95 Copynumber: 2.1 Consensus size: 93
545 TCCTGTATAG
** *
555 ATATTAT-ATCACCTTTATCAGGCTAGTTGAATATTATCCAT-AAGTTGGAGGCATTTAACCAAT
1 ATATTATAATCACCTTTATCAGGCTACCTGAATATTATCCATAAAGTCGG-GGCATTTAACCAAT
618 TGCTCTAGAGGGACAACTCAAGCTTTATTGT
65 TGCTCTAGAGGG-CAACTCAAGCTTTA-TGT
* *
649 ATATTATAATTACCTTTATCAGGCTACCTGAATCTTATCCATAAAGTCGGGGCATTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTACCTGAATATTATCCATAAAGTCGGGGCATTTAACCAATT
* *
714 GCTTTAGAGGGCATCTCAAGCTTTATGT
66 GCTCTAGAGGGCAACTCAAGCTTTATGT
742 ATA-TATAAT
1 ATATTATAAT
751 ATAATCTGGG
Statistics
Matches: 93, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
92 6 0.06
93 6 0.06
94 20 0.22
95 55 0.59
96 6 0.06
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (93 bp):
ATATTATAATCACCTTTATCAGGCTACCTGAATATTATCCATAAAGTCGGGGCATTTAACCAATT
GCTCTAGAGGGCAACTCAAGCTTTATGT
Found at i:3365 original size:16 final size:15
Alignment explanation
Indices: 3328--3367 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3318 TTATGTATGG
* *
3328 AAATTAATAAAATAA
1 AAATAAATAAAAGAA
3343 AAATAAATAAAAGAA
1 AAATAAATAAAAGAA
3358 ATAATAAATA
1 A-AATAAATA
3368 TATATACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAATAAATAAAAGAA
Found at i:4321 original size:12 final size:12
Alignment explanation
Indices: 4304--4329 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4294 CAGCTAGGGT
4304 TTCAAACCCTAG
1 TTCAAACCCTAG
4316 TTCAAACCCTAG
1 TTCAAACCCTAG
4328 TT
1 TT
4330 GGCTCGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (12 bp):
TTCAAACCCTAG
Found at i:4346 original size:23 final size:23
Alignment explanation
Indices: 4316--4362 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
4306 CAAACCCTAG
4316 TTCAAACCCTAGTTGGCTCGGGT
1 TTCAAACCCTAGTTGGCTCGGGT
4339 TTCAAACCCTAGTTGGCTCGGGT
1 TTCAAACCCTAGTTGGCTCGGGT
4362 T
1 T
4363 ACGTCTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.32
Consensus pattern (23 bp):
TTCAAACCCTAGTTGGCTCGGGT
Found at i:6152 original size:19 final size:19
Alignment explanation
Indices: 6106--6146 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
6096 GATTGTCCTC
6106 ACTTCAATACAGATTTACA
1 ACTTCAATACAGATTTACA
6125 ACTTCAATACAGATTTACA
1 ACTTCAATACAGATTTACA
6144 ACT
1 ACT
6147 GTAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (19 bp):
ACTTCAATACAGATTTACA
Found at i:6672 original size:60 final size:59
Alignment explanation
Indices: 6563--6681 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 59
6553 CATTTGACAC
* * * * *
6563 GATGCCTTCAAGTTCCAGGGGAGGCATTCAACTGCGAGCTTCTTTGACCTCAATGTCGA
1 GATGCCTTCAAGTTCAAGGGGAGGCATTCAACTACCAGCTTCTTCGACCTAAATGTCGA
*
6622 GATGCCTTCAAGTTCAAGGGGAAGGCATTCAACTACCAGCTTGTTCGACCTAAATGTCGA
1 GATGCCTTCAAGTTCAAGGGG-AGGCATTCAACTACCAGCTTCTTCGACCTAAATGTCGA
6682 CATCGTGGAG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
59 20 0.38
60 33 0.62
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (59 bp):
GATGCCTTCAAGTTCAAGGGGAGGCATTCAACTACCAGCTTCTTCGACCTAAATGTCGA
Found at i:8999 original size:17 final size:17
Alignment explanation
Indices: 8977--9011 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
8967 AGAAAACGAT
8977 ACAACTCAAA-AATAAAA
1 ACAACT-AAATAATAAAA
8994 ACAACTAAATAATAAAA
1 ACAACTAAATAATAAAA
9011 A
1 A
9012 TAATTCAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (17 bp):
ACAACTAAATAATAAAA
Found at i:9014 original size:23 final size:24
Alignment explanation
Indices: 8984--9037 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
8974 GATACAACTC
8984 AAAAATAA-AAACAACTAAATAAT
1 AAAAATAATAAACAACTAAATAAT
*
9007 AAAAATAATTCAAACAATTAAATAAT
1 AAAAATAA-T-AAACAACTAAATAAT
9033 AAAAA
1 AAAAA
9038 CATTAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
26 19 0.70
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (24 bp):
AAAAATAATAAACAACTAAATAAT
Found at i:9597 original size:21 final size:21
Alignment explanation
Indices: 9571--9632 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
9561 GAAATGGTTG
*
9571 TGGTACCATCTAAAACGGCTT
1 TGGTACCATCTGAAACGGCTT
* *
9592 TGGTACCATCTGAAACGACAT
1 TGGTACCATCTGAAACGGCTT
* *
9613 CGGTACCATCTGAAATGGCT
1 TGGTACCATCTGAAACGGCT
9633 GCAGAATGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (21 bp):
TGGTACCATCTGAAACGGCTT
Found at i:10253 original size:20 final size:20
Alignment explanation
Indices: 10228--10265 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10218 ATATTCTAAT
*
10228 TATATAATGATAATTAAAAG
1 TATATAATAATAATTAAAAG
*
10248 TATATAATAATATTTAAA
1 TATATAATAATAATTAAA
10266 TACATACCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
TATATAATAATAATTAAAAG
Found at i:11320 original size:10 final size:11
Alignment explanation
Indices: 11280--11323 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
11270 AGAAACGTGT
*
11280 TAGATAAAAAA
1 TAGAAAAAAAA
* *
11291 TTGAAAATAAA
1 TAGAAAAAAAA
11302 TAGAAAAAAAA
1 TAGAAAAAAAA
11313 TA-AAAAAAAA
1 TAGAAAAAAAA
11323 T
1 T
11324 GACCGAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (11 bp):
TAGAAAAAAAA
Found at i:11565 original size:3 final size:3
Alignment explanation
Indices: 11537--11600 Score: 89
Period size: 3 Copynumber: 21.7 Consensus size: 3
11527 AAAAAGGGTA
11537 AAT AA- AAT AAAT AA- AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
11581 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
11601 ACAGTAAGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.11
3 45 0.79
4 6 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:11902 original size:17 final size:18
Alignment explanation
Indices: 11865--11929 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 18
11855 AAATGTTTTA
* *
11865 AAAAAATAATAATAAATT
1 AAAAAATAATAACAAAAT
11883 AAAAAATAA-AACAAAAT
1 AAAAAATAATAACAAAAT
* *
11900 AAAACAT-ATAA-AATAT
1 AAAAAATAATAACAAAAT
11916 AATAATAATAATAA
1 AA-AA-AATAATAA
11930 TAATAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 7 0.18
17 16 0.42
18 11 0.29
19 4 0.11
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAATAATAACAAAAT
Found at i:11922 original size:3 final size:3
Alignment explanation
Indices: 11914--11966 Score: 72
Period size: 3 Copynumber: 17.0 Consensus size: 3
11904 CATATAAAAT
11914 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATGA AGT- ATA TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A A-TA ATA -ATA ATA
11961 ATA ATA
1 ATA ATA
11967 GTAAGTAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.02
3 39 0.85
4 5 0.11
5 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12378 original size:37 final size:37
Alignment explanation
Indices: 12328--12436 Score: 200
Period size: 37 Copynumber: 2.9 Consensus size: 37
12318 CTTATGGATT
12328 CTATTTTTAGGAGTTTGAATCATAGTAAAACTCTATC
1 CTATTTTTAGGAGTTTGAATCATAGTAAAACTCTATC
*
12365 CTATTTTTAGGAGTTTGAATCATAGTAAAACTCGATC
1 CTATTTTTAGGAGTTTGAATCATAGTAAAACTCTATC
*
12402 CTATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 CTATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
12437 ACGTTATGTT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (37 bp):
CTATTTTTAGGAGTTTGAATCATAGTAAAACTCTATC
Found at i:13735 original size:110 final size:110
Alignment explanation
Indices: 13549--13938 Score: 663
Period size: 110 Copynumber: 3.5 Consensus size: 110
13539 TTCAATATTT
* *
13549 TTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAATCAGTCGCC
1 TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCC
* * *
13614 CCTTAGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCA
66 CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
* *
13659 TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTGTTTGTTGACAGTCATTCGCC
1 TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCC
13724 CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
66 CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
** * * *
13769 TTCATTGTGAAATTAAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGATAGTCAGTCGCC
1 TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCC
*
13834 CCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
66 CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
13879 TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAG
1 TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAG
13939 CTTGTCTCGA
Statistics
Matches: 260, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 260 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (110 bp):
TTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAGTCAGTCGCC
CCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCC
Found at i:15660 original size:11 final size:12
Alignment explanation
Indices: 15639--15672 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
15629 TTTATTTTAT
15639 CTTTGTTTTTTC
1 CTTTGTTTTTTC
15651 CTTTGTTTTTTC
1 CTTTGTTTTTTC
15663 TCTTT-TTTTT
1 -CTTTGTTTTT
15673 GTTCTGATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (12 bp):
CTTTGTTTTTTC
Found at i:15677 original size:14 final size:13
Alignment explanation
Indices: 15614--15677 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 13
15604 TTTTTCTTGG
*
15614 TTTTTGTTTCTCT
1 TTTTTTTTTCTCT
*
15627 TTTTTATTTTATCT
1 TTTTT-TTTTCTCT
*
15641 TTGTTTTTTC-CT
1 TTTTTTTTTCTCT
*
15653 TTGTTTTTTCTCT
1 TTTTTTTTTCTCT
15666 TTTTTTTGTTCT
1 TTTTTTT-TTCT
15678 GATTGGATCT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
12 12 0.28
13 17 0.40
14 14 0.33
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.78
Consensus pattern (13 bp):
TTTTTTTTTCTCT
Found at i:18686 original size:22 final size:23
Alignment explanation
Indices: 18641--18687 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
18631 AGTGAAGATA
* *
18641 AAAATGAATACAATAAGAAAAAT
1 AAAATGAAGACAAAAAGAAAAAT
*
18664 AAAATGAAGA-AAAAAGAATAAT
1 AAAATGAAGACAAAAAGAAAAAT
18686 AA
1 AA
18688 TGATAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (23 bp):
AAAATGAAGACAAAAAGAAAAAT
Found at i:18808 original size:25 final size:24
Alignment explanation
Indices: 18767--18813 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
18757 AAGAATATAA
18767 AAAAATAAAGATAAGGAATAAAAAT
1 AAAAATAAAGATAAGGAA-AAAAAT
*
18792 AAAAATGAA-ATAGAGGAAAAAA
1 AAAAATAAAGATA-AGGAAAAAA
18814 GGGTAAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (24 bp):
AAAAATAAAGATAAGGAAAAAAAT
Found at i:19147 original size:18 final size:18
Alignment explanation
Indices: 19111--19160 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
19101 ATAAAATGTT
*
19111 TTAAAAAATAATAATAAA
1 TTAAAAAATAATAAAAAA
19129 TTAAAAAATAA-AACAAAA
1 TTAAAAAATAATAA-AAAA
*
19147 -TAAAACAT-ATAAAA
1 TTAAAAAATAATAAAA
19161 TATAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 3 0.11
17 11 0.39
18 14 0.50
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (18 bp):
TTAAAAAATAATAAAAAA
Found at i:19150 original size:17 final size:18
Alignment explanation
Indices: 19112--19177 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
19102 TAAAATGTTT
* *
19112 TAAAAAATAATAATAAAT
1 TAAAAAATAATAACAAAA
19130 TAAAAAATAA-AACAAAA
1 TAAAAAATAATAACAAAA
* *
19147 TAAAACAT-ATAA-AATA
1 TAAAAAATAATAACAAAA
19163 TAATAATAATAATAA
1 TAA-AA-AATAATAA
19178 TAATGAAGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 7 0.18
17 16 0.41
18 12 0.31
19 4 0.10
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAAAATAATAACAAAA
Found at i:19228 original size:17 final size:20
Alignment explanation
Indices: 19193--19229 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
19183 AAGTATATAT
19193 AATAATAATAGTAAGAAAAA
1 AATAATAATAGTAAGAAAAA
19213 AATAA-AATA-TAA-AAAAA
1 AATAATAATAGTAAGAAAAA
19230 TTGAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 4 0.24
20 5 0.29
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (20 bp):
AATAATAATAGTAAGAAAAA
Found at i:22070 original size:11 final size:11
Alignment explanation
Indices: 22056--22082 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
22046 AAAAAGAAAG
22056 AAAAATAATAA
1 AAAAATAATAA
22067 AAAAATAATAA
1 AAAAATAATAA
22078 AAAAA
1 AAAAA
22083 GGTAAAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:23910 original size:35 final size:35
Alignment explanation
Indices: 23871--23943 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
23861 ATAAGTTAAC
*
23871 CCCTAAATTCTATCAGTTCAACGTCACTGAATGAG
1 CCCTAAATTCTATCAATTCAACGTCACTGAATGAG
* **
23906 CCCTAAATTCTATCAATTCCACGTCACTGCGTGAG
1 CCCTAAATTCTATCAATTCAACGTCACTGAATGAG
23941 CCC
1 CCC
23944 AATAGGGAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.27
Consensus pattern (35 bp):
CCCTAAATTCTATCAATTCAACGTCACTGAATGAG
Found at i:35614 original size:26 final size:27
Alignment explanation
Indices: 35578--35648 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
35568 CCCCTTGAGT
35578 TTTAAAATGACCGAAATAC-CTCGAGC
1 TTTAAAATGACCGAAATACTCTCGAGC
*
35604 TTTAAAATGACCGAAATACTCTCGAGT
1 TTTAAAATGACCGAAATACTCTCGAGC
** *
35631 TTTGGAATGACCTAAATA
1 TTTAAAATGACCGAAATA
35649 TCGTCATTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 19 0.47
27 21 0.52
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (27 bp):
TTTAAAATGACCGAAATACTCTCGAGC
Found at i:35639 original size:27 final size:26
Alignment explanation
Indices: 35574--35648 Score: 105
Period size: 26 Copynumber: 2.8 Consensus size: 26
35564 TTACCCCCTT
35574 GAGTTTTAAAATGACCGAAATACCTC
1 GAGTTTTAAAATGACCGAAATACCTC
*
35600 GAGCTTTAAAATGACCGAAATACTCTC
1 GAGTTTTAAAATGACCGAAATAC-CTC
** *
35627 GAGTTTTGGAATGACCTAAATA
1 GAGTTTTAAAATGACCGAAATA
35649 TCGTCATTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 22 0.51
27 21 0.49
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (26 bp):
GAGTTTTAAAATGACCGAAATACCTC
Found at i:36626 original size:39 final size:38
Alignment explanation
Indices: 36576--36698 Score: 131
Period size: 39 Copynumber: 3.2 Consensus size: 38
36566 AAGACCTTAA
* ** *
36576 TTACCGTAGGCTCCTCTGCTTCATGCACATGGTAAGTCC
1 TTACCGAAGGCTCCTCTGCTTTGTACACA-GGTAAGTCC
* * *
36615 TTACCGAAGGCTCCTTTGCTTTGTATACAGGATAAGCCC
1 TTACCGAAGGCTCCTCTGCTTTGTACACAGG-TAAGTCC
*
36654 TTACC-ACAGGCTCTTCTGCTTTGTACACAGGGTAAGTCC
1 TTACCGA-AGGCTCCTCTGCTTTGTACACA-GGTAAGTCC
36693 TTACCG
1 TTACCG
36699 CGAGCCCTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
38 3 0.04
39 64 0.93
40 2 0.03
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.31
Consensus pattern (38 bp):
TTACCGAAGGCTCCTCTGCTTTGTACACAGGTAAGTCC
Found at i:41539 original size:19 final size:19
Alignment explanation
Indices: 41496--41577 Score: 85
Period size: 19 Copynumber: 4.2 Consensus size: 19
41486 AATCAGATTG
41496 CCCAGGGGGTACAGATTCACC
1 CCCAGGGGGTACAGATT--CC
41517 CCCAGGGGG-AGCAGATTCC
1 CCCAGGGGGTA-CAGATTCC
*
41536 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATT-CC
* * *
41556 CCCACGGGGTACCGAGTCC
1 CCCAGGGGGTACAGATTCC
41575 CCC
1 CCC
41578 TGTCTAACGG
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
19 21 0.38
20 19 0.35
21 15 0.27
ACGTcount: A:0.18, C:0.39, G:0.30, T:0.12
Consensus pattern (19 bp):
CCCAGGGGGTACAGATTCC
Found at i:41565 original size:20 final size:20
Alignment explanation
Indices: 41496--41577 Score: 96
Period size: 20 Copynumber: 4.1 Consensus size: 20
41486 AATCAGATTG
41496 CCCAGGGGGTACAGATTCACC
1 CCCAGGGGGTACAGATTC-CC
41517 CCCAGGGGG-AGCAGATT-CC
1 CCCAGGGGGTA-CAGATTCCC
*
41536 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
* * *
41556 CCCACGGGGTACCGAGTCCC
1 CCCAGGGGGTACAGATTCCC
41576 CC
1 CC
41578 TGTCTAACGG
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
19 16 0.29
20 24 0.44
21 15 0.27
ACGTcount: A:0.18, C:0.39, G:0.30, T:0.12
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:44988 original size:21 final size:21
Alignment explanation
Indices: 44955--45007 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
44945 CCTAGGGGGT
44955 ACAGATT-CCCCCCAGGGAGA
1 ACAGATTCCCCCCCAGGGAGA
* *
44975 ACAGATTCCCCCCCAGGGGGT
1 ACAGATTCCCCCCCAGGGAGA
*
44996 ACCGATTCCCCC
1 ACAGATTCCCCC
45008 TGTCTAACGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.23, C:0.42, G:0.23, T:0.13
Consensus pattern (21 bp):
ACAGATTCCCCCCCAGGGAGA
Found at i:45394 original size:34 final size:34
Alignment explanation
Indices: 45355--45436 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
45345 TTTTGTAAAG
* *
45355 GGGAAAGGTTCTAGCTAATCCTGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAATCCCGTATAAAAGCTA
45389 GGGAAAGGTTCTAGCTAATCCCGTATAAAAGCTA
1 GGGAAAGGTTCTAGCTAATCCCGTATAAAAGCTA
*
45423 GGGAAAAGTTCTAG
1 GGGAAAGGTTCTAG
45437 TTTAGCCCGG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (34 bp):
GGGAAAGGTTCTAGCTAATCCCGTATAAAAGCTA
Found at i:46645 original size:20 final size:20
Alignment explanation
Indices: 46622--46690 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
46612 TTTATGGTTT
*
46622 TTATTGTTTTAGACTTAATA
1 TTATGGTTTTAGACTTAATA
** ** *
46642 TTATGGTTTGTTTA-TGGATT
1 TTATGGTTT-TAGACTTAATA
*
46662 TTATTGTTTTAGACTTAATA
1 TTATGGTTTTAGACTTAATA
46682 TTATGGTTT
1 TTATGGTTT
46691 GTATATGGAT
Statistics
Matches: 34, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.23, C:0.03, G:0.16, T:0.58
Consensus pattern (20 bp):
TTATGGTTTTAGACTTAATA
Found at i:46651 original size:40 final size:40
Alignment explanation
Indices: 46596--46929 Score: 270
Period size: 40 Copynumber: 8.7 Consensus size: 40
46586 ATTTGACATT
* *
46596 TTAATATTATTGTTTGTTTATGGTTTTTATTGTTTTAGAC
1 TTAATATTATGGTTTGTTTATGGATTTTATTGTTTTAGAC
46636 TTAATATTATGGTTTGTTTATGGATTTTATTGTTTTAGAC
1 TTAATATTATGGTTTGTTTATGGATTTTATTGTTTTAGAC
* * ** *
46676 TTAATATTATGGTTTGTATATGGATTCTCGAAAGATGTTA-AC
1 TTAATATTATGGTTTGTTTATGGATT-T-TATTG-TTTTAGAC
** * * *
46718 --AATGCT-TGATTT-TTT-T--A--ATATTGTTCTAGAC
1 TTAATATTATGGTTTGTTTATGGATTTTATTGTTTTAGAC
* * * *
46749 TTAATATTATGGTTTG---A--G-TCTTA-AGATTTGACAC
1 TTAATATTATGGTTTGTTTATGGATTTTATTG-TTTTAGAC
* * *
46783 TTTAATATTATTGTTTGTTTATGGACTTTATTTTTTTAGAC
1 -TTAATATTATGGTTTGTTTATGGATTTTATTGTTTTAGAC
* * * * *
46824 TTAATATTATGGTTTGTATATGGATTTTATTATTCTAAAG
1 TTAATATTATGGTTTGTTTATGGATTTTATTGTTTTAGAC
*
46864 TTAATATTGTGGTTTGTTTATGGATTTTATTGTTTTAGAC
1 TTAATATTATGGTTTGTTTATGGATTTTATTGTTTTAGAC
*
46904 TTAATATTTTGGTTTGTTTATGGATT
1 TTAATATTATGGTTTGTTTATGGATT
46930 CTCTATGAAA
Statistics
Matches: 227, Mismatches: 46, Indels: 42
0.72 0.15 0.13
Matches are distributed among these distances:
30 3 0.01
31 4 0.02
33 5 0.02
34 12 0.05
35 16 0.07
37 1 0.00
38 3 0.01
39 5 0.02
40 160 0.70
41 10 0.04
42 4 0.02
43 4 0.02
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.54
Consensus pattern (40 bp):
TTAATATTATGGTTTGTTTATGGATTTTATTGTTTTAGAC
Found at i:46836 original size:188 final size:191
Alignment explanation
Indices: 46514--46889 Score: 605
Period size: 188 Copynumber: 2.0 Consensus size: 191
46504 TTAATCTTAG
*
46514 AAGATGTTAACAATGTTTGATTTTTGTTGTTTAATATTGTTCTAGACTTAATATTATGGTTTGAG
1 AAGATGTTAACAATGCTTGA--TTTGTTGTTTAATATTGTTCTAGACTTAATATTATGGTTTGAG
* **
46579 TCTTAAGATTTGACATTTTAATATTATTGTTTGTTTATGGTTTTTATTGTTTTAGACTTAATATT
64 TCTTAAGATTTGACACTTTAATATTATTGTTTGTTTATGGACTTTATTGTTTTAGACTTAATATT
* * * *
46644 ATGGTTTGTTTATGGATTTTATTGTTTTAGACTTAATATTATGGTTTGTATATGGATTCTCGA
129 ATGGTTTGTATATGGATTTTATTATTCTAAACTTAATATTATGGTTTGTATATGGATTCTCGA
46707 AAGATGTTAACAATGCTTGA-TT-TT-TTTAATATTGTTCTAGACTTAATATTATGGTTTGAGTC
1 AAGATGTTAACAATGCTTGATTTGTTGTTTAATATTGTTCTAGACTTAATATTATGGTTTGAGTC
*
46769 TTAAGATTTGACACTTTAATATTATTGTTTGTTTATGGACTTTATTTTTTTAGACTTAATATTAT
66 TTAAGATTTGACACTTTAATATTATTGTTTGTTTATGGACTTTATTGTTTTAGACTTAATATTAT
* * *
46834 GGTTTGTATATGGATTTTATTATTCTAAAGTTAATATTGTGGTTTGTTTATGGATT
131 GGTTTGTATATGGATTTTATTATTCTAAACTTAATATTATGGTTTGTATATGGATT
46890 TTATTGTTTT
Statistics
Matches: 171, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
188 148 0.87
189 2 0.01
190 2 0.01
193 19 0.11
ACGTcount: A:0.26, C:0.05, G:0.16, T:0.53
Consensus pattern (191 bp):
AAGATGTTAACAATGCTTGATTTGTTGTTTAATATTGTTCTAGACTTAATATTATGGTTTGAGTC
TTAAGATTTGACACTTTAATATTATTGTTTGTTTATGGACTTTATTGTTTTAGACTTAATATTAT
GGTTTGTATATGGATTTTATTATTCTAAACTTAATATTATGGTTTGTATATGGATTCTCGA
Found at i:46991 original size:19 final size:20
Alignment explanation
Indices: 46947--46995 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
46937 AAATATTGAC
* *
46947 TTTATTTATAATTTTTTACA
1 TTTATTTATAATTTTTAAAA
*
46967 TCTATTTATAA-TTTTAAAA
1 TTTATTTATAATTTTTAAAA
46986 TTTATTTATA
1 TTTATTTATA
46996 TGTCGCACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATTTATAATTTTTAAAA
Found at i:51797 original size:29 final size:29
Alignment explanation
Indices: 51765--51823 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
51755 ATATTTCTTT
*
51765 AGGTCATGAGTTGTAGATTTATTAGAAGC
1 AGGTCATGAGTTGTAGATTCATTAGAAGC
51794 AGGTCATGAGTTGTAGATTCATTAGAAGC
1 AGGTCATGAGTTGTAGATTCATTAGAAGC
51823 A
1 A
51824 CTTTTCTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.27, T:0.32
Consensus pattern (29 bp):
AGGTCATGAGTTGTAGATTCATTAGAAGC
Found at i:54705 original size:3 final size:3
Alignment explanation
Indices: 54699--54781 Score: 100
Period size: 3 Copynumber: 28.0 Consensus size: 3
54689 TTGGTTTTTT
*
54699 TTA TTA TTA -TA TTTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
54744 TTA TTA TTA -AA ATA TTA TTTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
54782 CAGATACAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.07
3 60 0.86
4 5 0.07
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:57055 original size:25 final size:23
Alignment explanation
Indices: 56999--57068 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 23
56989 CATATTTATT
56999 TAATATTTAATT-CTTTTATTTCA
1 TAATATTT-ATTACTTTTATTTCA
* *
57022 AAATTTTTATTACTTATTATTTTCA
1 TAATATTTATTACTT-TTA-TTTCA
*
57047 TAATATTTATTATATTTTATTT
1 TAATATTTATTA-CTTTTATTT
57069 TATTTTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 3 0.08
23 9 0.24
24 6 0.16
25 18 0.47
26 2 0.05
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (23 bp):
TAATATTTATTACTTTTATTTCA
Found at i:58603 original size:8 final size:7
Alignment explanation
Indices: 58579--58620 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
58569 TTTTCATACA
58579 TGCA-TT
1 TGCATTT
58585 TGCATTT
1 TGCATTT
58592 TGCATCTT
1 TGCAT-TT
58600 TGCATTT
1 TGCATTT
* *
58607 TTCATTG
1 TGCATTT
58614 TGCATTT
1 TGCATTT
58621 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:58603 original size:15 final size:14
Alignment explanation
Indices: 58579--58620 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
58569 TTTTCATACA
58579 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
58592 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
58607 TTCATTGTGCATTT
1 TGCATTTTGCATTT
58621 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:58696 original size:12 final size:12
Alignment explanation
Indices: 58679--58724 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
58669 ACATTCATAT
58679 ATTTGCATTTAC
1 ATTTGCATTTAC
58691 ATTTGCATTTTTAC
1 ATTTGCA--TTTAC
* *
58705 GTTTGTATTTAC
1 ATTTGCATTTAC
58717 ATTTGCAT
1 ATTTGCAT
58725 ATTTCCATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 18 0.64
14 10 0.36
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.54
Consensus pattern (12 bp):
ATTTGCATTTAC
Found at i:58699 original size:26 final size:26
Alignment explanation
Indices: 58670--58724 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
58660 TTTATTGTTA
*
58670 CATTCATATATTTGCATTTACATTTG
1 CATTCATACATTTGCATTTACATTTG
** * *
58696 CATTTTTACGTTTGTATTTACATTTG
1 CATTCATACATTTGCATTTACATTTG
58722 CAT
1 CAT
58725 ATTTCCATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.53
Consensus pattern (26 bp):
CATTCATACATTTGCATTTACATTTG
Found at i:58703 original size:14 final size:14
Alignment explanation
Indices: 58685--58728 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
58675 ATATATTTGC
58685 ATTTACATTTGCAT
1 ATTTACATTTGCAT
* *
58699 TTTTACGTTTG--T
1 ATTTACATTTGCAT
58711 ATTTACATTTGCAT
1 ATTTACATTTGCAT
58725 ATTT
1 ATTT
58729 CCATAATTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
12 10 0.42
14 14 0.58
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:60808 original size:2 final size:2
Alignment explanation
Indices: 60801--60832 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
60791 TTATCCTTTA
60801 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
60833 CCTTTGTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61147 original size:25 final size:27
Alignment explanation
Indices: 61119--61171 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 27
61109 TATTATACTC
*
61119 ATCCAGCAAAGAAA-GAAAAAA-AAAA
1 ATCCAACAAAGAAAGGAAAAAAGAAAA
61144 ATCCAACAAAGAAAGGAAAAAAGAAAA
1 ATCCAACAAAGAAAGGAAAAAAGAAAA
61171 A
1 A
61172 AGAGGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 13 0.52
26 7 0.28
27 5 0.20
ACGTcount: A:0.72, C:0.11, G:0.13, T:0.04
Consensus pattern (27 bp):
ATCCAACAAAGAAAGGAAAAAAGAAAA
Found at i:61183 original size:18 final size:18
Alignment explanation
Indices: 61155--61230 Score: 82
Period size: 18 Copynumber: 4.0 Consensus size: 18
61145 TCCAACAAAG
*
61155 AAAGG-AAAAAAGAAAAA
1 AAAGGAAAAAAAAAAAAA
*
61172 AGAGGAAAAAAAAAAAAA
1 AAAGGAAAAAAAAAAAAA
61190 AAAGGAAAGAAATAAAAAAAAA
1 AAAGG--A-AAA-AAAAAAAAA
61212 AAAGGAAAAAAAGAAAAAA
1 AAAGGAAAAAAA-AAAAAA
61231 TTGAATCAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
17 4 0.08
18 18 0.36
19 9 0.18
20 2 0.04
21 3 0.06
22 14 0.28
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (18 bp):
AAAGGAAAAAAAAAAAAA
Found at i:61871 original size:32 final size:32
Alignment explanation
Indices: 61835--61896 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
61825 GTCAGACACA
*
61835 AGAAGTATCTCTACCAGATGAGCATAACAACG
1 AGAAGTATCTCTACAAGATGAGCATAACAACG
61867 AGAAGTATCTCTACAAGATGAGCATAACAA
1 AGAAGTATCTCTACAAGATGAGCATAACAA
61897 TCATTTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Found at i:66003 original size:22 final size:22
Alignment explanation
Indices: 65977--66053 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
65967 ATCTACACTC
65977 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
65999 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
66021 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
66043 TTCAAAGATGA
1 TTCAAAGATGA
66054 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:66855 original size:76 final size:76
Alignment explanation
Indices: 66729--66960 Score: 410
Period size: 76 Copynumber: 3.1 Consensus size: 76
66719 CTATTTCCCA
66729 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
66794 AGCCTTAGGGT
66 AGCCTTAGGGT
66805 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
66870 AGCTTTAGGGT
66 AGCCTTAGGGT
** *
66881 CATCTGTAAGTCCTACAGTGTTTGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
66946 AACCTTCGGGT
66 AGCCTTAGGGT
66957 CATC
1 CATC
66961 AGCATTTCCA
Statistics
Matches: 149, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 149 1.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:67113 original size:113 final size:113
Alignment explanation
Indices: 66958--67833 Score: 1089
Period size: 113 Copynumber: 7.8 Consensus size: 113
66948 CCTTCGGGTC
* * *
66958 ATCAGCATTTCCAGA-AGAA-TTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCA
1 ATCAACATTTCCAGAGA-AAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAAGAAGAAGTTCA
* *
67021 TAATAAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGG
65 TAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGG
* * * *
67070 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAATAACTTATCTGAAGAAGGAAGAAGAAGTTCAC
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAAGAAGAAGTTCAT
** * * * *
67135 AATGAGAAGAGTTTGTTTAACCTTTTGCTCAAATTCATCACTCGATGG
66 AATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGG
* * *
67183 ATCAGCATTACCAGAG-AAGTTCATAATGAGAAAAACTTATCTGAAGAAGGAAA-AAGAAGTTCA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAA-GAAAGAAGAAGTTCA
* *
67246 TAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGG
65 TAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGG
* * ** *
67295 ATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCTGAAGAA-AGAAGAAGAAATTC
1 ATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAAGA-AAGAAGAAGTTC
* * * *
67358 ATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATTA-TTCGATGG
64 ATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTT-GATGG
*
67408 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAA-AAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAAGAAGAAGTTCAT
* ** *
67472 AATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGG
66 AATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGG
* * * *
67520 ATCAGCATTACCAGAGAAAGTTCATAATGTGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAAGAAGAAGTTCAT
* * *
67585 AATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATACATCATTTGATGG
66 AATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGG
* * ** *
67633 ATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCTGAAGAA-ATAAGAAGAAATTC
1 ATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAGAAGA-AAGAAGAAGTTC
* * * *
67696 ATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCA-TTCGATTG
64 ATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTT-GATGG
*
67746 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCT---GAAG-AAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAAGAAGAAGTTCAT
* * *
67807 AATGAAAAGAGCTTGTTCAATCTTTTG
66 AATGAGAAGAACTTGTTCAACCTTTTG
67834 CATAACTCTA
Statistics
Matches: 662, Mismatches: 86, Indels: 35
0.85 0.11 0.04
Matches are distributed among these distances:
109 35 0.05
110 3 0.00
111 2 0.00
112 215 0.32
113 405 0.61
114 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (113 bp):
ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGG
Found at i:67351 original size:225 final size:226
Alignment explanation
Indices: 66958--67834 Score: 1130
Period size: 225 Copynumber: 3.9 Consensus size: 226
66948 CCTTCGGGTC
*
66958 ATCAGCATTTCCAGA-AGAA-TTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCA
1 ATCAACATTTCCAGAGA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCA
* * * *
67021 TAATAAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCACTTGATGGATCAACTTTTCCAGAG
65 TAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTCGATGGATCAACATTTCCAGAG
* * * *
67086 AAAGTTCATAATGAGAATAACTTATCTGAAGAAGGAAGAAGAAGTTCACAATGAGAAGAGTTTGT
130 AAAGTTCATAATGAGAAGAACTTATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGT
* * *
67151 TTAACCTTTTGCTCAAATTCATCACTCGATGG
195 TCAACCTTTTGCTTAAATTCATCATTCGATGG
* * * * *
67183 ATCAGCATTACCAGAG-AAGTTCATAATGAGAAAAACTTATCTGAAGAAGGAAA-AAGAAGTTCA
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAAGAAGAAATTCA
* * * *
67246 TAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAG-G
65 TAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTCGATGGATCAACATTTCCAGAG
* ** * **
67310 TAGAGTTCATAATGAGAAGAACTCGTCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTG
130 -AAAGTTCATAATGAGAAGAACTTATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTG
* * * *
67375 TTCAACTTTTTGTTTGAATTCATTATTCGATGG
194 TTCAACCTTTTGCTTAAATTCATCATTCGATGG
* * *
67408 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAA-AAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCAT
* ** * *
67472 AATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGCATTACCAGAGA
66 AATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTCGATGGATCAACATTTCCAGAGA
* *
67537 AAGTTCATAATGTGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
131 AAGTTCATAATGAGAAGAACTTATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
* * *
67602 CAACCTTTTGTTTAAATACATCATTTGATGG
196 CAACCTTTTGCTTAAATTCATCATTCGATGG
* * *
67633 ATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCTGAAGAA-ATAAGAAGAAATTC
1 ATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA-AAGAAGAAATTC
* * * * * *
67696 ATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTCGATTGATCAACTTTTCCAGA
64 ATAATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTCGATGGATCAACATTTCCAGA
*
67761 GAAAGTTCATAATGAGAAGAACTTATCT---G-AAGAAGAAGAAGTTCATAATGAAAAGAGCTTG
129 GAAAGTTCATAATGAGAAGAACTTATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTG
*
67822 TTCAATCTTTTGC
194 TTCAACCTTTTGC
67835 ATAACTCTAT
Statistics
Matches: 573, Mismatches: 70, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
222 41 0.07
223 1 0.00
224 7 0.01
225 394 0.69
226 130 0.23
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (226 bp):
ATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCAT
AATGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTCGATGGATCAACATTTCCAGAGA
AAGTTCATAATGAGAAGAACTTATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
CAACCTTTTGCTTAAATTCATCATTCGATGG
Found at i:67593 original size:338 final size:336
Alignment explanation
Indices: 66977--67834 Score: 1463
Period size: 338 Copynumber: 2.5 Consensus size: 336
66967 TCCAGAAGAA
* *
66977 TTCATAATGAGAAGAACTCATCTGAAG-AAGAAAGAAGAAATTCATAATAAGAAGAATTTGTTCA
1 TTCATAATGAGAAGAACTCGTCTGAAGAAAG-AAGAAGAAATTCATAATGAGAAGAATTTGTTCA
* * *
67041 ACCTTTTGTTTAAATTCATCACTT-GATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAATA
65 ACTTTTTGTTTGAATTCATCA-TTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGA
* * *
67105 ACTTATCTGAAGAAGGAAGAAGAAGTTCACAATGAGAAGAGTTTGTTTAACCTTTTGCTCAAATT
129 ACTTATCTGAAGAA--AAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATT
67170 CATCACTCGATGGATCAGCATTACCAGAGAAGTTCATAATGAGAAAAACTTATCTGAAGAAGGAA
192 CATCACTCGATGGATCAGCATTACCAGAGAAGTTCATAATGAGAAAAACTTATCTGAAGAAGGAA
*
67235 AAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGGATCAA
257 AAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATACATCATTTGATGGATCAA
67300 CATTGCCAGGTAGAG
322 CATTGCCAGGTAGAG
67315 TTCATAATGAGAAGAACTCGTCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
1 TTCATAATGAGAAGAACTCGTCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
*
67380 CTTTTTGTTTGAATTCATTATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAC
66 CTTTTTGTTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAC
* *
67445 TTATCTGAAGAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCAT
131 TTATCTGAAG-AAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATTCAT
* * *
67510 CACTCGATGGATCAGCATTACCAGAGAAAGTTCATAATGTGAAGAACTTATCTGAAGAAGGAAGA
195 CACTCGATGGATCAGCATTACCAGAG-AAGTTCATAATGAGAAAAACTTATCTGAAGAAGGAAAA
67575 AGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATACATCATTTGATGGATCAACA
259 AGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATACATCATTTGATGGATCAACA
67640 TTGCCAGGTAGAG
324 TTGCCAGGTAGAG
*
67653 TTCATAATGAGAAGAACTCGTCTGAAGAAATAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
1 TTCATAATGAGAAGAACTCGTCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
*
67718 CTTTTTGTTTGAATTCATCATTCGATTGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAC
66 CTTTTTGTTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAC
* *
67783 TTATCTGAAG--AAGAAGAAGTTCATAATGAAAAGAGCTTGTTCAATCTTTTGC
131 TTATCTGAAGAAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
67835 ATAACTCTAT
Statistics
Matches: 495, Mismatches: 21, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
335 39 0.08
337 75 0.15
338 376 0.76
339 5 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (336 bp):
TTCATAATGAGAAGAACTCGTCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
CTTTTTGTTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAAC
TTATCTGAAGAAAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATTCATC
ACTCGATGGATCAGCATTACCAGAGAAGTTCATAATGAGAAAAACTTATCTGAAGAAGGAAAAAG
AAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTAAATACATCATTTGATGGATCAACATT
GCCAGGTAGAG
Found at i:67967 original size:120 final size:120
Alignment explanation
Indices: 67746--67978 Score: 303
Period size: 120 Copynumber: 1.9 Consensus size: 120
67736 CATTCGATTG
* * * *
67746 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGTTCATAATG
1 ATCAACATTTCCAGAGAAAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAAGG
* *
67811 AAAAGAGCTTGTTCAATCTTTTGCATAACTCTATCACAGAAGGAGATATATCATC
66 AAAAGAACTTGTTCAATCTTTTGCATAACTCTATCACAAAAGGAGATATATCATC
*
67866 ATCAACATTTCCAGA-AGGAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAAG
1 ATCAACATTTCCAGAGA-AAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAAG
** * *
67930 GAGGAGAATTTGTTCAA-CTTTTTGC-TAGATTAC-ATCACAAAAGGAGATA
65 GAAAAGAACTTGTTCAATC-TTTTGCATA-ACT-CTATCACAAAAGGAGATA
67979 AATTGTCATC
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
119 4 0.04
120 93 0.95
121 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (120 bp):
ATCAACATTTCCAGAGAAAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAAGG
AAAAGAACTTGTTCAATCTTTTGCATAACTCTATCACAAAAGGAGATATATCATC
Found at i:68184 original size:3 final size:3
Alignment explanation
Indices: 68176--68254 Score: 92
Period size: 3 Copynumber: 27.0 Consensus size: 3
68166 ATTTGGTTTT
* *
68176 TTA TTA TTA TTA -TA TTTA TTA TTA TTA TTA CTA TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
68221 TTA TTA TTA TTA -AA ATA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
68255 CAGATACAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
2 5 0.08
3 58 0.89
4 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:69619 original size:2 final size:2
Alignment explanation
Indices: 69612--69641 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
69602 ATATCAGTCT
69612 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
69642 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:69646 original size:2 final size:2
Alignment explanation
Indices: 69641--69684 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
69631 ACACACACAC
69641 AT 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 AT
69683 AT
1 AT
69685 TTGTTTAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75993 original size:3 final size:3
Alignment explanation
Indices: 75987--76064 Score: 108
Period size: 3 Copynumber: 26.7 Consensus size: 3
75977 TTTTTATCCA
*
75987 TAT TAT TAT TAT TAT TAT TAT TA- TAT TA- TAG TAT TAT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
*
76031 TAT TAT TA- TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
76065 AATATATTAA
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
2 6 0.09
3 59 0.87
4 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:78184 original size:6 final size:7
Alignment explanation
Indices: 78163--78187 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
78153 CGTCTCTATT
78163 AATTAAA
1 AATTAAA
78170 AATTAAA
1 AATTAAA
78177 AATTAAA
1 AATTAAA
78184 AATT
1 AATT
78188 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Done.