Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000299.1 Hibiscus syriacus cultivar Beakdansim tig00000550_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: 47876
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:675 original size:19 final size:17
Alignment explanation
Indices: 651--698 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 17
641 CGCAACGAGA
651 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCG-AA-G
670 AAAATCGCAA--CG-AG
1 AAAATCGCAATGCGAAG
684 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
699 TTTTCATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.42
15 1 0.04
16 2 0.08
17 2 0.08
19 10 0.38
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (17 bp):
AAAATCGCAATGCGAAG
Found at i:688 original size:14 final size:14
Alignment explanation
Indices: 639--693 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 14
629 GAAACTGACT
639 ATCGCAACGAGAAAA
1 ATCGCAACGAG-AAA
654 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
673 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
687 ATCGCAA
1 ATCGCAA
694 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.31
15 8 0.23
17 4 0.11
19 11 0.31
20 1 0.03
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:742 original size:20 final size:20
Alignment explanation
Indices: 717--802 Score: 93
Period size: 20 Copynumber: 4.3 Consensus size: 20
707 TCGCATTGCG
*
717 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* **
737 ATTTTCGCGTTGCGATTTTCC
1 ATTTTCGAGTTGCGA-TAGCC
*
758 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* *
777 ATTTTCGCGTTGCGATAGAC
1 ATTTTCGAGTTGCGATAGCC
797 ATTTTC
1 ATTTTC
803 CGCGTTGCGT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
19 4 0.08
20 45 0.85
21 4 0.08
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:750 original size:34 final size:37
Alignment explanation
Indices: 705--792 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 37
695 GCGATTTTCA
* *
705 TTTCGCATTGCGATTTT-C-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCCTTCAATTGCGATAGCCAT
739 TTTCGCGTTGCGATTTTCCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCC--TTC-AATTGCGATAGCCAT
779 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
793 AGACATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 16 0.35
35 1 0.02
38 1 0.02
40 28 0.61
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (37 bp):
TTTCGCGTTGCGATTTTCCTTCAATTGCGATAGCCAT
Found at i:808 original size:21 final size:20
Alignment explanation
Indices: 725--811 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
715 CGATTTTCTA
*
725 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGACATTTTCGC
*** *
745 GTTGCGATTTTCCA-TTTCGA
1 GTTGCGA-TAGACATTTTCGC
* *
765 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGACATTTTCGC
785 GTTGCGATAGACATTTTCCGC
1 GTTGCGATAGACATTTT-CGC
806 GTTGCG
1 GTTGCG
812 TTTCCCCATT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.07
20 38 0.69
21 13 0.24
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGACATTTTCGC
Found at i:1122 original size:20 final size:21
Alignment explanation
Indices: 1078--1129 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1068 ATAGTCAGTA
*
1078 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1099 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1119 TCGCATTGCGA
1 TCGCATTGCGA
1130 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:4299 original size:19 final size:19
Alignment explanation
Indices: 4277--4341 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
4267 GGAAATTACT
4277 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4296 ATCGCAAT--G--A-GAAA
1 ATCGCAATGCGAAATGAAA
4310 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4329 ATCGCAACGCGAA
1 ATCGCAATGCGAA
4342 TTTAATTTCG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 12 0.30
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 24 0.60
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4311 original size:14 final size:14
Alignment explanation
Indices: 4292--4323 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4282 AATGCGAAAT
4292 GAAAATCGCAATGA
1 GAAAATCGCAATGA
*
4306 GAAAATCGCAATGC
1 GAAAATCGCAATGA
4320 GAAA
1 GAAA
4324 TGAAAATCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAATGA
Found at i:4388 original size:33 final size:33
Alignment explanation
Indices: 4337--4427 Score: 137
Period size: 33 Copynumber: 2.7 Consensus size: 33
4327 AAATCGCAAC
* *
4337 GCGAATTTAATTTCGCGTTGCGATTCTCTCATT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
4370 GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
* *
4403 GCAATTTTCATTTTCGCATTGCGAT
1 GCGATTTTCA-TTTCGCGTTGCGAT
4428 AGTACTTTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 40 0.75
34 13 0.25
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCATT
Found at i:4552 original size:14 final size:15
Alignment explanation
Indices: 4533--4569 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
4523 CATCAATTAA
4533 ACAAATCAA-CTTTT
1 ACAAATCAACCTTTT
4547 ACAAAT-AACCTTTT
1 ACAAATCAACCTTTT
4561 ACAAATCAA
1 ACAAATCAA
4570 TTAAACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
ACAAATCAACCTTTT
Found at i:5988 original size:21 final size:21
Alignment explanation
Indices: 5922--5988 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5912 GTGAATCGGG
5922 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAATGGTGGGAGGGGA
* * * ** * *
5942 CCTCTTTAACGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
5964 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
5985 CTCT
1 CTCT
5989 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.18, G:0.36, T:0.27
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Found at i:6007 original size:42 final size:42
Alignment explanation
Indices: 5953--6128 Score: 190
Period size: 42 Copynumber: 4.2 Consensus size: 42
5943 CTCTTTAACG
* *
5953 ATGACAGTGGCCTCTTGAATGGTGGGAGGGGACTCTCGAGGA
1 ATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
* * * * * * *
5995 ATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGGG
1 ATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
* *
6037 ATGACAGTGGCCTCTTGAACAGTGGGAGGGGACTCTCGAGGA
1 ATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
* * * * * * *
6079 ATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGGG
1 ATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
6121 ATGACAGG
1 ATGACAGG
6129 CGAGTCGGTC
Statistics
Matches: 106, Mismatches: 28, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 106 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.22
Consensus pattern (42 bp):
ATGACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
Found at i:6063 original size:84 final size:84
Alignment explanation
Indices: 5952--6127 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
5942 CCTCTTTAAC
**
5952 GATGACAGTGGCCTCTTGAATGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACAGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
6017 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
6036 GATGACAGTGGCCTCTTGAACAGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACAGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
6101 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
6120 GATGACAG
1 GATGACAG
6128 GCGAGTCGGT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACAGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:6515 original size:78 final size:79
Alignment explanation
Indices: 6365--6517 Score: 238
Period size: 78 Copynumber: 1.9 Consensus size: 79
6355 AAGACAAAAC
6365 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGACAGCAACCGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAAT--A-AGTTTAGCAGAATTGACAGCAACCGAA
6430 TAAATTTACTTCAACCA
63 TAAATTTACTTCAACCA
* *
6447 AAAGACAAATACTAACTTCACAGTGTTAATA-AAT-AGTTTAGCAGTATTGGCAGCAACCGAATA
1 AAAGACAAATACTAACTTCACAGTGTTAA-AGAATAAGTTTAGCAGAATTGACAGCAACCGAATA
6510 AATTTACT
65 AATTTACT
6518 AAGCAATATA
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
78 35 0.51
82 32 0.47
83 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (79 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAGTTTAGCAGAATTGACAGCAACCGAATAA
ATTTACTTCAACCA
Found at i:8277 original size:33 final size:33
Alignment explanation
Indices: 8223--8310 Score: 117
Period size: 33 Copynumber: 2.6 Consensus size: 33
8213 ACGAGATAAT
*
8223 GAGAATCACAACGCGGAAATGACTA-C-TGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGTG--ACGA
*
8257 GAGAATCGCAAGGCGAAATGACTATCGTGACGA
1 GAGAATCGCAACGCGAAATGACTATCGTGACGA
8290 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
8311 AAATCGCAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
33 34 0.69
34 13 0.27
35 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGTGACGA
Found at i:8353 original size:18 final size:19
Alignment explanation
Indices: 8293--8356 Score: 112
Period size: 19 Copynumber: 3.4 Consensus size: 19
8283 GTGACGAGAG
*
8293 AATCGCAACGCGAAATGAA
1 AATCGCAACACGAAATGAA
8312 AATCGCAACACGAAATGAA
1 AATCGCAACACGAAATGAA
8331 AATCGCAACACGAAATG-A
1 AATCGCAACACGAAATGAA
8349 AATCGCAA
1 AATCGCAA
8357 TGCGATTTTG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 9 0.20
19 35 0.80
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (19 bp):
AATCGCAACACGAAATGAA
Found at i:8391 original size:18 final size:19
Alignment explanation
Indices: 8357--8400 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
8347 GAAATCGCAA
*
8357 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
8376 TGCGATTTT-ATTTCGCGT
1 TGCGATTTTGATTTCGCGT
8394 TGCGATT
1 TGCGATT
8401 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:8979 original size:20 final size:20
Alignment explanation
Indices: 8951--9003 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
8941 GCGCTATGTA
*
8951 AATCGCGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
8971 AATCACGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
* *
8991 TATCTCGTTGCGA
1 AATCACGTTGCGA
9004 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCACGTTGCGAAAGTCAG
Found at i:13214 original size:20 final size:20
Alignment explanation
Indices: 13177--13214 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13167 CTTTCCTCGT
*
13177 ACAACATAAACTATAAGAGC
1 ACAACATAAACTAGAAGAGC
13197 ACAACA-AAACTTAGAAGA
1 ACAACATAAAC-TAGAAGA
13215 TAATCATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.58, C:0.18, G:0.11, T:0.13
Consensus pattern (20 bp):
ACAACATAAACTAGAAGAGC
Found at i:14156 original size:2 final size:2
Alignment explanation
Indices: 14149--14213 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
14139 CTGCTCAGGC
14149 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
*
14191 TA TA TA TA TA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
14214 CAGAAAACAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17171 original size:21 final size:21
Alignment explanation
Indices: 17147--17215 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
17137 ACATCTCCGT
* *
17147 AGGGTTATATTTCTAGCCCTC
1 AGGGTTACATTCCTAGCCCTC
*
17168 AGGGTTACATTCCTAGCCCGCC
1 AGGGTTACATTCCTAGCCC-TC
* *
17190 A-GGTTACATGCCTAGCCCAC
1 AGGGTTACATTCCTAGCCCTC
17210 AGGGTT
1 AGGGTT
17216 TTATAACACC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.28
Consensus pattern (21 bp):
AGGGTTACATTCCTAGCCCTC
Found at i:17771 original size:34 final size:34
Alignment explanation
Indices: 17724--17796 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
17714 TTAAATGTTT
* *
17724 TTAATATACAAATTAAAGTATTCGAAATTTAAAA
1 TTAAAATAAAAATTAAAGTATTCGAAATTTAAAA
** *
17758 TTAAAATAAAAATTATGGTATTCGAAATTTAACA
1 TTAAAATAAAAATTAAAGTATTCGAAATTTAAAA
17792 TTAAA
1 TTAAA
17797 TTCAACTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (34 bp):
TTAAAATAAAAATTAAAGTATTCGAAATTTAAAA
Found at i:18001 original size:70 final size:69
Alignment explanation
Indices: 17917--18146 Score: 233
Period size: 70 Copynumber: 3.4 Consensus size: 69
17907 TATACATTAA
*
17917 AACCAACTTATCACTTCACATTTATTCGTAAGAACATATCGATGCTCATTCCATACAATTTCAAT
1 AACCAACTTATCACTTCACATTTATTCGTAA-AACATATCGATGATCATTCCATACAATTTCAAT
17982 GTCAC
65 GTCAC
* ** * ** * * *
17987 AACCAACTTTTCACTTCACATTTATTC----AATTTATCCAT-AAAAGTT-TATCCAGTTT--AT
1 AACCAACTTATCACTTCACATTTATTCGTAAAACATATCGATGATCA-TTCCATACAATTTCAAT
* *
18044 TTAAAC
65 GT-CAC
* *
18050 ATCCAACTTATCACTTCACATTTATTCGTAAAAACATGTCGATGATCATTCCATACAATTTCAAT
1 AACCAACTTATCACTTCACATTTATTCGT-AAAACATATCGATGATCATTCCATACAATTTCAAT
18115 GTCAC
65 GTCAC
*
18120 AACCAACTTATCACTTCAAATTTATTC
1 AACCAACTTATCACTTCACATTTATTC
18147 AATTTATCCA
Statistics
Matches: 122, Mismatches: 27, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
62 3 0.02
63 27 0.22
64 8 0.07
65 10 0.08
68 9 0.07
69 9 0.07
70 53 0.43
71 3 0.02
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (69 bp):
AACCAACTTATCACTTCACATTTATTCGTAAAACATATCGATGATCATTCCATACAATTTCAATG
TCAC
Found at i:18157 original size:133 final size:133
Alignment explanation
Indices: 17917--18209 Score: 469
Period size: 133 Copynumber: 2.2 Consensus size: 133
17907 TATACATTAA
* *
17917 AACCAACTTATCACTTCACATTTATTCGTAAGAACATATCGATGCTCATTCCATACAATTTCAAT
1 AACCAACTTATCACTTCACATTTATTCGTAAAAACATATCGATGATCATTCCATACAATTTCAAT
* * * * *
17982 GTCACAACCAACTTTTCACTTCACATTTATTCAATTTATCCATAAAAGTTTATCCAGTTTATTTA
66 GTCACAACCAACTTATCACTTCAAATTTATTCAATTTATCCATAAAAGTTTATCCAATATATTCA
18047 AAC
131 AAC
* *
18050 ATCCAACTTATCACTTCACATTTATTCGTAAAAACATGTCGATGATCATTCCATACAATTTCAAT
1 AACCAACTTATCACTTCACATTTATTCGTAAAAACATATCGATGATCATTCCATACAATTTCAAT
* * *
18115 GTCACAACCAACTTATCACTTCAAATTTATTCAATTTATCCATAACATTTTATCTAATATATTCA
66 GTCACAACCAACTTATCACTTCAAATTTATTCAATTTATCCATAAAAGTTTATCCAATATATTCA
18180 AAC
131 AAC
*
18183 AACCAACTGATCACTTCACATTTATTC
1 AACCAACTTATCACTTCACATTTATTC
18210 AATTTATCCA
Statistics
Matches: 146, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
133 146 1.00
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (133 bp):
AACCAACTTATCACTTCACATTTATTCGTAAAAACATATCGATGATCATTCCATACAATTTCAAT
GTCACAACCAACTTATCACTTCAAATTTATTCAATTTATCCATAAAAGTTTATCCAATATATTCA
AAC
Found at i:18217 original size:63 final size:63
Alignment explanation
Indices: 18118--18245 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
18108 TTTCAATGTC
* *
18118 ACAACCAACTTATCACTTCAAATTTATTCAATTTATCCATAACATTTTATCTAATATATTCAA
1 ACAACCAACTGATCACTTCAAATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
* *
18181 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAA
1 ACAACCAACTGATCACTTCAAATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
18244 AC
1 AC
18246 TTCACATAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.38
Consensus pattern (63 bp):
ACAACCAACTGATCACTTCAAATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
Found at i:18719 original size:117 final size:117
Alignment explanation
Indices: 18489--19054 Score: 825
Period size: 117 Copynumber: 4.9 Consensus size: 117
18479 AGAAATAATA
* * * *
18489 GGTATTGACATGAATAGT--TCCCGGGGGACATGAGTGACATAATAGGGCAATAATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * *
18552 TCTGACAAAACAATCGAAGGAGCGCCCTCGGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* * *
18604 GGTACTGACATGAATAGTGCCCCCAAGGGACATGAGTGGCATAATAGGGCAATAATAACATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
*
18669 TCTGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* *
18721 GGTACTGACATGAATAGTGCCCCCGAGGGACATAAGTGACATAATAGGGCAATGATAATATATTC
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* *
18786 TCTGACAAAATAATGAAAGGCACGCCCCCGGGAACGCGCTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* *
18838 GGTACTGACATGAATAGTGCCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATATTA
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* * * * *
18903 TCTGATAAAATAATGGAAGACGCGCCCCCAGGAACACACTTTCACCACTTTG
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
* * * * *
18955 GGTACTGACATGAATAGT-ACCCCGAGAGACATGAGTGACATAATAGGACAATGATAACATCTTA
1 GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
* **
19019 TCTGATAAAATAATGGAAGGCGC-CCCCTAGGAACGC
66 TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGC
19055 ACCTTCACGT
Statistics
Matches: 412, Mismatches: 37, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
115 28 0.07
116 63 0.15
117 321 0.78
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.21
Consensus pattern (117 bp):
GGTACTGACATGAATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTC
TCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCTTTCACCACTTTG
Found at i:18845 original size:234 final size:232
Alignment explanation
Indices: 18387--19039 Score: 853
Period size: 234 Copynumber: 2.8 Consensus size: 232
18377 AGTTCCTCGG
** *
18387 GGGACATGTTTGACATAATAGGGCAA-AGATAACATATTCTCTGACAAAATAATGAAAGGCGCAC
1 GGGACATGAGTGACATAATAGGGCAATA-ATAACATATTCTCTGACAAAATAATGGAAGGCGCAC
* * * * * *
18451 CCCCGGGAATGCGCTTTCAACTCCCCTAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGG
65 CCCCGGGAACGCGCTTTC-A--CCACT------T--TGGGTACTGACATGAATAGTCCCCGAGGG
* * *
18516 ACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAACAATCGAAGG-AGCGCCCT
119 ACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT-GAAGGCAGCGCCCC
18580 CGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCAA
183 CGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCAA
*
18630 GGGACATGAGTGGCATAATAGGGCAATAATAACATATTCTCTGACAAAATAATGGAAGGCGCACC
1 GGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATGGAAGGCGCACC
*
18695 CCCGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACATAAGTGA
66 CCCGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGT--CCCCGAGGGACATGAGTGA
*
18760 CATAATAGGGCAATGATAATATATTCTCTGACAAAATAATGAAAGGCA-CGCCCCCGGGAACGCG
129 CATAATAGGGCAATGATAACATATTCTCTGACAAAATAATG-AAGGCAGCGCCCCCGGGAACGCG
*
18824 CTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGA
193 CTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCAA
* * * * * *
18864 GGGATATGAGTGACATAATAGGGCAATGATAACATATTATCTGATAAAATAATGGAAGACGCGCC
1 GGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATGGAAGGCGCACC
* * * *
18929 CCCAGGAACACACTTTCACCACTTTGGGTACTGACATGAATAGTACCCCGAGAGACATGAGTGAC
66 CCCGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGT-CCCCGAGGGACATGAGTGAC
* * * *
18994 ATAATAGGACAATGATAACATCTTATCTGATAAAATAATGGAAGGC
130 ATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT-GAAGGC
19040 GCCCCCTAGG
Statistics
Matches: 370, Mismatches: 34, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
232 18 0.05
233 58 0.16
234 212 0.57
235 1 0.00
240 4 0.01
242 1 0.00
243 75 0.20
244 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (232 bp):
GGGACATGAGTGACATAATAGGGCAATAATAACATATTCTCTGACAAAATAATGGAAGGCGCACC
CCCGGGAACGCGCTTTCACCACTTTGGGTACTGACATGAATAGTCCCCGAGGGACATGAGTGACA
TAATAGGGCAATGATAACATATTCTCTGACAAAATAATGAAGGCAGCGCCCCCGGGAACGCGCTT
TCACCACTTTGGGTACTGACATGAATAGTGCCCCCAA
Found at i:19594 original size:16 final size:16
Alignment explanation
Indices: 19573--19607 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
19563 TTGCATATCA
19573 AGCTGATCAAGTTGAT
1 AGCTGATCAAGTTGAT
19589 AGCTGATCAAGTTGAT
1 AGCTGATCAAGTTGAT
19605 AGC
1 AGC
19608 CCGACACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (16 bp):
AGCTGATCAAGTTGAT
Found at i:22944 original size:31 final size:31
Alignment explanation
Indices: 22906--23030 Score: 171
Period size: 31 Copynumber: 4.0 Consensus size: 31
22896 AGGGTCGAGG
22906 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
22937 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
22968 GTTTACCTATGTCCTTCTGGACATATGGGCT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * * *
22999 GATTACTTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
23030 G
1 G
23031 ATCCTTCGGG
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
31 82 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:26776 original size:31 final size:31
Alignment explanation
Indices: 26738--26870 Score: 230
Period size: 31 Copynumber: 4.3 Consensus size: 31
26728 AGGGTCGAGG
26738 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
26769 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
26800 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
26831 GTTTACCTATGTTCTTCTGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
26862 GATTACCTA
1 GTTTACCTA
26871 GGATTTTCAG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 99 1.00
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.41
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:26889 original size:31 final size:31
Alignment explanation
Indices: 26738--26893 Score: 206
Period size: 31 Copynumber: 5.0 Consensus size: 31
26728 AGGGTCGAGG
* *
26738 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGATATATGGACT
* *
26769 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGATATATGGACT
*
26800 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCAGGATATATGGACT
*
26831 GTTTACCTATGTTCTTCTGGATATATGGACT
1 GTTTACCTATGTTCTTCAGGATATATGGACT
* * * *
26862 GATTACCTAGGATT-TTCAGAATCTATGGACT
1 GTTTACCTATG-TTCTTCAGGATATATGGACT
26893 G
1 G
26894 GTCATTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 115 0.98
32 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCAGGATATATGGACT
Found at i:28451 original size:26 final size:27
Alignment explanation
Indices: 28394--28445 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28384 ATTAATATTC
*
28394 TATTTAAATGAATGTTTTTGTTTCTAA
1 TATTTAAATGAATGTGTTTGTTTCTAA
28421 TATTTAAATGTAAT-TGTTT-TTTCTA
1 TATTTAAATG-AATGTGTTTGTTTCTA
28446 TAATTTCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 14 0.61
28 3 0.13
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.58
Consensus pattern (27 bp):
TATTTAAATGAATGTGTTTGTTTCTAA
Found at i:28568 original size:21 final size:21
Alignment explanation
Indices: 28542--28583 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28532 AATAATTAAT
*
28542 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
28563 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
28584 TAATAATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:29262 original size:60 final size:61
Alignment explanation
Indices: 29184--29300 Score: 139
Period size: 61 Copynumber: 1.9 Consensus size: 61
29174 AAAAATACCA
* * * * *
29184 GCGTGGCATCCGACTCAGCA-GAACTCATATAAAGCGCGTCTCCGGGGATGCGCCTTACAC
1 GCGTGGCATCCGACTCAGCATAAACCCAGATAAAGCGCATCCCCGGGGATGCGCCTTACAC
* * *
29244 GCGTGGCATTCC-AGTCAGCATAAACCCAGGTAAAGTGCATCCCCGGGGATGCGCCTT
1 GCGTGGCA-TCCGACTCAGCATAAACCCAGATAAAGCGCATCCCCGGGGATGCGCCTT
29301 TGTGCCACCT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
60 15 0.32
61 32 0.68
ACGTcount: A:0.23, C:0.31, G:0.27, T:0.19
Consensus pattern (61 bp):
GCGTGGCATCCGACTCAGCATAAACCCAGATAAAGCGCATCCCCGGGGATGCGCCTTACAC
Found at i:29448 original size:5 final size:5
Alignment explanation
Indices: 29438--29755 Score: 636
Period size: 5 Copynumber: 63.6 Consensus size: 5
29428 GAGGTGAAAC
29438 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
29488 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
29538 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
29588 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
29638 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
29688 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
1 ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT ATTGT
29738 ATTGT ATTGT ATTGT ATT
1 ATTGT ATTGT ATTGT ATT
29756 ATATGCAAAA
Statistics
Matches: 313, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 313 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
ATTGT
Found at i:33153 original size:13 final size:13
Alignment explanation
Indices: 33121--33162 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
33111 AAACTCTAGT
* *
33121 TTAGGGTTTATAAT
1 TTAGGATTT-TAAG
33135 TTAGGATTTTAAG
1 TTAGGATTTTAAG
33148 TTAGGATTTTAAG
1 TTAGGATTTTAAG
33161 TT
1 TT
33163 TGGGGTAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (13 bp):
TTAGGATTTTAAG
Found at i:33839 original size:3 final size:3
Alignment explanation
Indices: 33831--33876 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
33821 ATATATTCCA
*
33831 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
33877 GTCGTTGTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:34787 original size:29 final size:29
Alignment explanation
Indices: 34745--34801 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
34735 ATGGTTTTGG
*
34745 GTAGGTCGCCAGGGCATCCCAGCGACATT
1 GTAGGTCACCAGGGCATCCCAGCGACATT
34774 GTAGGTCACCAGGGCATCCCAGCGACAT
1 GTAGGTCACCAGGGCATCCCAGCGACAT
34802 CCATGCTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.32, G:0.30, T:0.16
Consensus pattern (29 bp):
GTAGGTCACCAGGGCATCCCAGCGACATT
Found at i:34917 original size:23 final size:23
Alignment explanation
Indices: 34889--34946 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
34879 AATTCAACTG
34889 CATTATTGCAGCACTTATTGTTA
1 CATTATTGCAGCACTTATTGTTA
* *
34912 CATTATGGCAGCACTTATTGTTG
1 CATTATTGCAGCACTTATTGTTA
*
34935 CATAATTGCAGC
1 CATTATTGCAGC
34947 CCTTCAGCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (23 bp):
CATTATTGCAGCACTTATTGTTA
Found at i:35153 original size:8 final size:9
Alignment explanation
Indices: 35123--35160 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
35113 GAGGTAAGTT
35123 TTTTAATTA
1 TTTTAATTA
35132 TTTTAATTA
1 TTTTAATTA
*
35141 GTTT-ATTA
1 TTTTAATTA
35149 TTTTAAATTA
1 TTTT-AATTA
35159 TT
1 TT
35161 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:35214 original size:4 final size:4
Alignment explanation
Indices: 35197--35226 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
35187 AAACAATATT
*
35197 TTAG TTAA TTAG TTAG TTAG TTAG TTAG TT
1 TTAG TTAG TTAG TTAG TTAG TTAG TTAG TT
35227 TAAGGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (4 bp):
TTAG
Found at i:35245 original size:47 final size:49
Alignment explanation
Indices: 35154--35265 Score: 167
Period size: 47 Copynumber: 2.3 Consensus size: 49
35144 TATTATTTTA
* *
35154 AATTA-TTAGTTTGTTAGTTTATGGTTTAAGGTAAAACAATATTTTAGTT
1 AATTAGTTAGTTAGTTAGTTTA-GGTTTAAGGTAAAACAAAATTTTAGTT
35203 AATTAGTTAGTTAGTTAG-TTA-GTTTAAGGTAAAACAAAATTTTAGTT
1 AATTAGTTAGTTAGTTAGTTTAGGTTTAAGGTAAAACAAAATTTTAGTT
*
35250 AATTAGTTTGTTAGTT
1 AATTAGTTAGTTAGTT
35266 TAAGTTATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
47 40 0.68
49 8 0.14
50 11 0.19
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (49 bp):
AATTAGTTAGTTAGTTAGTTTAGGTTTAAGGTAAAACAAAATTTTAGTT
Found at i:35396 original size:28 final size:27
Alignment explanation
Indices: 35357--35409 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
35347 ATATTAAAAA
35357 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
35385 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
35410 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:35415 original size:27 final size:29
Alignment explanation
Indices: 35356--35420 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
35346 TATATTAAAA
35356 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
35385 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
35411 AAATAGTTAA
1 AAATAATTAA
35421 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:35651 original size:21 final size:21
Alignment explanation
Indices: 35626--35665 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
35616 GTTAATTAGT
35626 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
35647 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
35666 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:35939 original size:28 final size:29
Alignment explanation
Indices: 35850--35945 Score: 101
Period size: 28 Copynumber: 3.3 Consensus size: 29
35840 TAATTAATTT
* *
35850 TTTAGTAG-TAAA-TTATAATTAAAAATCG
1 TTTATTAGTTAAAGTTAT-ATTAAAAATAG
* *
35878 TTTATTAGTTTAAGTTATATTAAAGAATAT
1 TTTATTAGTTAAAGTTATATTAAA-AATAG
35908 TTTATTAGTTAAAG-T-TATTAAATAATAG
1 TTTATTAGTTAAAGTTATATTAAA-AATAG
35936 TTTATTAGTT
1 TTTATTAGTT
35946 GTTTAAGGGA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
28 28 0.48
29 10 0.17
30 20 0.34
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (29 bp):
TTTATTAGTTAAAGTTATATTAAAAATAG
Found at i:38266 original size:11 final size:12
Alignment explanation
Indices: 38239--38271 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
38229 TATTATAATT
38239 TCATTAGTAGTAA
1 TCATTAGTAG-AA
38252 TCATTAGTA-AA
1 TCATTAGTAGAA
38263 TCATTAGTA
1 TCATTAGTA
38272 TTAAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (12 bp):
TCATTAGTAGAA
Found at i:38303 original size:17 final size:17
Alignment explanation
Indices: 38259--38313 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
38249 TAATCATTAG
* *
38259 TAAATCATTAGTATTAAA
1 TAAATCATTATTAAT-AA
* *
38277 TAATTAATTATTAATAA
1 TAAATCATTATTAATAA
38294 TAAATCATTATTAATAA
1 TAAATCATTATTAATAA
38311 TAA
1 TAA
38314 TTACAAAACA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
17 20 0.65
18 11 0.35
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAATCATTATTAATAA
Found at i:38523 original size:3 final size:3
Alignment explanation
Indices: 38515--38641 Score: 64
Period size: 3 Copynumber: 43.7 Consensus size: 3
38505 TTACTATTAA
* * * *
38515 ATT ATT ATT ATA ATG ATT ATT ATT A-A ATC ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * * *
38562 ATT A-A ATC ATT ATT ATA ATG ATT ATT ACT A-A ATC ATT ATT ATA ATG
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
38608 ATT ATT ACT A-A ATC ATT ATT ATA ATA ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
38642 CAAATCATTA
Statistics
Matches: 95, Mismatches: 25, Indels: 8
0.74 0.20 0.06
Matches are distributed among these distances:
2 4 0.04
3 91 0.96
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (3 bp):
ATT
Found at i:38540 original size:26 final size:26
Alignment explanation
Indices: 38430--38878 Score: 298
Period size: 26 Copynumber: 17.7 Consensus size: 26
38420 TTATTCCATA
* *
38430 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATC
* * *
38454 ATTAATATTAAATCAATATTATAA-A
1 ATTATTATTAAATCATTATTATAATC
* * *
38479 ATCATTACTAAATCATTATTA-AACC
1 ATTATTATTAAATCATTATTATAATC
* * *
38504 ATTACTATTAAATTATTATTATAATG
1 ATTATTATTAAATCATTATTATAATC
* *
38530 ATTATTATTAAATCATTATTATTATT
1 ATTATTATTAAATCATTATTATAATC
*
38556 ATTATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATC
* *
38582 ATTATTACTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATC
* *
38608 ATTATTACTAAATCATTATTATAATA
1 ATTATTATTAAATCATTATTATAATC
* *
38634 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATTAAATCATTATTATAATC
* *
38659 CTTAAATATTAAAATCATTATTA-AATC
1 ATT-ATTATT-AAATCATTATTATAATC
*
38686 ATTATTA-T-AATGATTATTATTAA--
1 ATTATTATTAAATCATTATTA-TAATC
* *
38709 ATAATTATTATAATGATTATTACTAAATC
1 ATTATTATTA-AATCATTATTA-T-AATC
*
38738 ATTATTA-T-AATGATTATTACTAAATC
1 ATTATTATTAAATCATTATTA-T-AATC
* *
38764 ATTATTA-TAATTTCATTACTAGTAATC
1 ATTATTATTAA-ATCATTATTA-TAATC
* *
38791 ---ATTAGTAAATCATTAGTATTAA--
1 ATTATTATTAAATCATTATTA-TAATC
*
38813 A-TA--ATTAAAT-ATTAATAATAAATC
1 ATTATTATTAAATCATT-ATTAT-AATC
* *
38837 ATTATTAAT-AATAATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATC
* *
38861 ATTAGTATCAAATCATTA
1 ATTATTATTAAATCATTA
38879 AATATTTAAA
Statistics
Matches: 343, Mismatches: 54, Indels: 55
0.76 0.12 0.12
Matches are distributed among these distances:
21 4 0.01
22 10 0.03
23 16 0.05
24 37 0.11
25 63 0.18
26 169 0.49
27 29 0.08
28 9 0.03
29 6 0.02
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTATTATTAAATCATTATTATAATC
Found at i:38669 original size:116 final size:116
Alignment explanation
Indices: 38559--38767 Score: 375
Period size: 116 Copynumber: 1.8 Consensus size: 116
38549 TATTATTATT
*
38559 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTACTAAATCAT
1 ATTATTAAATCATTATTATAATGATTATTACTAAATAATTATTATAATGATTATTACTAAATCAT
38624 TATTATAATAATTATTA-TCAAATCATTACTAAATCCTTAAATATTAAAATC
66 TATTATAATAATTATTACT-AAATCATTACTAAATCCTTAAATATTAAAATC
*
38675 ATTATTAAATCATTATTATAATGATTATTATTAAATAATTATTATAATGATTATTACTAAATCAT
1 ATTATTAAATCATTATTATAATGATTATTACTAAATAATTATTATAATGATTATTACTAAATCAT
*
38740 TATTATAATGATTATTACTAAATCATTA
66 TATTATAATAATTATTACTAAATCATTA
38768 TTATAATTTC
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
116 88 0.99
117 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (116 bp):
ATTATTAAATCATTATTATAATGATTATTACTAAATAATTATTATAATGATTATTACTAAATCAT
TATTATAATAATTATTACTAAATCATTACTAAATCCTTAAATATTAAAATC
Found at i:38772 original size:52 final size:51
Alignment explanation
Indices: 38443--39197 Score: 249
Period size: 52 Copynumber: 14.5 Consensus size: 51
38433 ATTAGTAATA
* * *
38443 ATTATTAAATCATTAATATTAAATCAATATTATAAAATCATTACTA-AATC---
1 ATTATTAAATCATTATTA-T-AATCATTATTAT-AAATCATTATTATAATCATT
* * * *
38493 ATTATTAAACCATTACTATTAAATTATTATTAT-AATGATTATTATTAAATCATT
1 ATTATTAAATCATTATTA-T-AATCATTATTATAAATCATTATTA-T-AATCATT
* * *
38547 ATTATTATTATTATTATTA-AATCATTATTAT-AATGATTATTACTAAATCATT
1 ATTATTA-AATCATTATTATAATCATTATTATAAATCATTATTA-T-AATCATT
* * *
38599 ATTA-T-AATGATTATTACTAAATCATTATTAT-AATAATTATTATCAA--ATC
1 ATTATTAAATCATTATTA-T-AATCATTATTATAAATCATTATTAT-AATCATT
* * * *
38648 ATTACTAAATCCTTAAATATTAAAATCATTA-T-TAAATCATTATTATAATGATT
1 ATTATTAAAT-C---ATTATTATAATCATTATTATAAATCATTATTATAATCATT
* * *
38701 ATTATTAAATAATTATTATAATGATTATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATCATTATTA-TAAATCATTATTATAATCATT
* * *
38753 ATTACTAAATCATTATTATAATTTCATTACTAGT-AATCATTAGTA-AATCATT
1 ATTATTAAATCATTATTATAA--TCATTATTA-TAAATCATTATTATAATCATT
* *
38805 AGTATTAAAT-A--ATTA-AAT-ATTAATAATAAATCATTATTAATAAT-A--
1 ATTATTAAATCATTATTATAATCATT-ATTATAAATCATTATT-ATAATCATT
* * * * *
38850 ATTATTAAATCATTAGTATCAAATCATTAAATATTTAAA-AATTATTAATAAATTTGACT
1 ATTATTAAATCATTATTAT--AATCATT--AT-TATAAATCATTATT-AT-AA--TCATT
* * * * * * *
38909 ATGTA-TAAAT--TTAAATTCGAGTAGTCCA-CACTTGTACACTCATTTGTTATTATTCCATA
1 AT-TATTAAATCATT--ATT--A-TAAT-CATTA-TTATA-AATCA-TTATTA-TAAT-CATT
* * * * *
38968 ATTATTAGTAATAATTATTA-AATCATTAGTATTAAATAATTATTATAA-AATA
1 ATTATTA--AATCATTATTATAATCATTATTA-TAAATCATTATTATAATCATT
* * * *
39020 ATTACTAAATCATTATTA-AATTATTACTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATCATTATTA-TAAATCATTATTATAATCATT
* * * *
39071 ATTACTAAATCATTATTATAATGATTATTATCAAATCATTACTA-AATCATCAA
1 ATTATTAAATCATTATTATAATCATTATTAT-AAATCATTATTATAATCAT--T
* * * *
39124 ATCATTAAAT-ATTA--A-AATCATT-TTTTAAATTATTATTA-ATTTCATT
1 ATTATTAAATCATTATTATAATCATTATTATAAATCATTATTATA-ATCATT
*
39170 ATTACT-AATCATTATTACTAAATCATTA
1 ATTATTAAATCATTATTA-T-AATCATTA
39198 AATATTAATA
Statistics
Matches: 543, Mismatches: 86, Indels: 150
0.70 0.11 0.19
Matches are distributed among these distances:
45 16 0.03
46 21 0.04
47 13 0.02
48 25 0.05
49 38 0.07
50 67 0.12
51 51 0.09
52 159 0.29
53 49 0.09
54 23 0.04
55 18 0.03
56 7 0.01
57 8 0.01
58 7 0.01
59 17 0.03
60 7 0.01
61 14 0.03
62 1 0.00
63 2 0.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (51 bp):
ATTATTAAATCATTATTATAATCATTATTATAAATCATTATTATAATCATT
Found at i:38791 original size:116 final size:115
Alignment explanation
Indices: 38559--38805 Score: 363
Period size: 116 Copynumber: 2.1 Consensus size: 115
38549 TATTATTATT
*
38559 ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTACTAAATCAT
1 ATTATTAAATCATTATTATAATGATTATTACTAAATAATTATTATAATGATTATTACTAAATCAT
*
38624 TATTATAATAATTATTATCAAATCATTACTAAATCCTTAAATATTAAAATC
66 TATTATAATAATTATTATCAAATCATTACTAAAT-CTTAAATACTAAAATC
*
38675 ATTATTAAATCATTATTATAATGATTATTATTAAATAATTATTATAATGATTATTACTAAATCAT
1 ATTATTAAATCATTATTATAATGATTATTACTAAATAATTATTATAATGATTATTACTAAATCAT
* * * * *
38740 TATTATAATGATTATTA-CTAAATCATTATTATAAT-TTCATTACTAGTAATC
66 TATTATAATAATTATTATC-AAATCATTACTA-AATCTTAAATACTA-AAATC
*
38791 ATTAGTAAATCATTA
1 ATTATTAAATCATTA
38806 GTATTAAATA
Statistics
Matches: 119, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
115 8 0.07
116 108 0.91
117 3 0.03
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (115 bp):
ATTATTAAATCATTATTATAATGATTATTACTAAATAATTATTATAATGATTATTACTAAATCAT
TATTATAATAATTATTATCAAATCATTACTAAATCTTAAATACTAAAATC
Found at i:38826 original size:21 final size:22
Alignment explanation
Indices: 38796--38840 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
38786 TAATCATTAG
* *
38796 TAAATCATTAGTATTAAATAAT
1 TAAATCATTAATAATAAATAAT
*
38818 TAAAT-ATTAATAATAAATCAT
1 TAAATCATTAATAATAAATAAT
38839 TA
1 TA
38841 TTAATAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATCATTAATAATAAATAAT
Found at i:39002 original size:14 final size:14
Alignment explanation
Indices: 38981--39197 Score: 115
Period size: 14 Copynumber: 16.1 Consensus size: 14
38971 ATTAGTAATA
38981 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
38995 AGTATTAAATAATT
1 ATTATTAAATCATT
*
39009 ATTA-TAAA--ATA
1 ATTATTAAATCATT
*
39020 ATTACTAAATC---
1 ATTATTAAATCATT
*
39031 ATTATTAAATTATT
1 ATTATTAAATCATT
*
39045 ACTATTAAATCATT
1 ATTATTAAATCATT
*
39059 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
39071 ATTACTAAATCATT
1 ATTATTAAATCATT
*
39085 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
39097 ATTATCAAATCATT
1 ATTATTAAATCATT
*
39111 ACTAAATCATCAAATCATT
1 A-T---T-ATTAAATCATT
*
39130 AAATATTAAAATCATT
1 -ATTATT-AAATCATT
39146 -TT-TT-AA--ATT
1 ATTATTAAATCATT
*
39155 ATTATTAATTTCATT
1 ATTATTAA-ATCATT
*
39170 ATTACT-AATCATT
1 ATTATTAAATCATT
*
39183 ATTACTAAATCATT
1 ATTATTAAATCATT
39197 A
1 A
39198 AATATTAATA
Statistics
Matches: 159, Mismatches: 20, Indels: 48
0.70 0.09 0.21
Matches are distributed among these distances:
9 3 0.02
10 2 0.01
11 19 0.12
12 25 0.16
13 20 0.13
14 57 0.36
15 11 0.07
16 9 0.06
18 1 0.01
19 11 0.07
20 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:39079 original size:26 final size:26
Alignment explanation
Indices: 38968--39111 Score: 145
Period size: 25 Copynumber: 5.7 Consensus size: 26
38958 TTATTCCATA
* * *
38968 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTACTAAATCATTATTATAATG
* * * *
38992 ATTAGTATTAAATAATTATTATAA-A
1 ATTATTACTAAATCATTATTATAATG
* *
39017 ATAATTACTAAATCATTATTA-AATT
1 ATTATTACTAAATCATTATTATAATG
* *
39042 ATTACTATTAAATCATTATTATAATG
1 ATTATTACTAAATCATTATTATAATG
39068 ATTATTACTAAATCATTATTATAATG
1 ATTATTACTAAATCATTATTATAATG
39094 ATTATTA-TCAAATCATTA
1 ATTATTACT-AAATCATTA
39112 CTAAATCATC
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
24 9 0.09
25 47 0.47
26 45 0.45
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (26 bp):
ATTATTACTAAATCATTATTATAATG
Found at i:39183 original size:13 final size:14
Alignment explanation
Indices: 39165--39197 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
39155 ATTATTAATT
39165 TCATTATTACT-AA
1 TCATTATTACTAAA
39178 TCATTATTACTAAA
1 TCATTATTACTAAA
39192 TCATTA
1 TCATTA
39198 AATATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.45
Consensus pattern (14 bp):
TCATTATTACTAAA
Found at i:39213 original size:49 final size:48
Alignment explanation
Indices: 39160--39441 Score: 372
Period size: 49 Copynumber: 5.8 Consensus size: 48
39150 AAATTATTAT
*
39160 TAATTTCATTATTACTAATCATTATTACTAAATCATTAAATATTAATAA
1 TAATTTCATTATTACTAATCATTACTA-TAAATCATTAAATATTAATAA
*
39209 TAATTTCATTGTTACTAATCATTACTATCAAATCATTAAATATTAATAA
1 TAATTTCATTATTACTAATCATTACTAT-AAATCATTAAATATTAATAA
39258 TAATTTCATTATTACTAATCATTACTACTAAATCATTAAATATTAATAA
1 TAATTTCATTATTACTAATCATTACTA-TAAATCATTAAATATTAATAA
* *
39307 TATTTTCATTATTACTAATCATTACTACCAAATCATTAAATATTAATAA
1 TAATTTCATTATTACTAATCATTACTA-TAAATCATTAAATATTAATAA
* * * *
39356 TAATTTCATTATTACTAATCATTATTAAATAATTATTATAATTTTAA-ATA
1 TAATTTCATTATTACTAATCATTACTATA-AATCATTA-AATATTAATA-A
* * *
39406 TAAATTCATTATTA--AATCATGATTATCAAATCATTA
1 TAATTTCATTATTACTAATCATTACTAT-AAATCATTA
39442 CTAAATCAAA
Statistics
Matches: 213, Mismatches: 14, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
48 19 0.09
49 172 0.81
50 22 0.10
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.44
Consensus pattern (48 bp):
TAATTTCATTATTACTAATCATTACTATAAATCATTAAATATTAATAA
Found at i:39262 original size:98 final size:98
Alignment explanation
Indices: 39160--39441 Score: 419
Period size: 98 Copynumber: 2.9 Consensus size: 98
39150 AAATTATTAT
*
39160 TAATTTCATTATTACTAATCATTATTACTAAATCATTAAATATTAATAATAATTTCATTGTTACT
1 TAATTTCATTATTACTAATCATTATTACTAAATCATTAAATATTAATAATAATTTCATTATTACT
39225 AATCATTACTATCAAATCATTAAATATTAATAA
66 AATCATTACTATCAAATCATTAAATATTAATAA
* *
39258 TAATTTCATTATTACTAATCATTACTACTAAATCATTAAATATTAATAATATTTTCATTATTACT
1 TAATTTCATTATTACTAATCATTATTACTAAATCATTAAATATTAATAATAATTTCATTATTACT
*
39323 AATCATTACTACCAAATCATTAAATATTAATAA
66 AATCATTACTATCAAATCATTAAATATTAATAA
* * * *
39356 TAATTTCATTATTACTAATCATTATTA-AATAATTATTATAATTTTAA-ATATAAATTCATTATT
1 TAATTTCATTATTACTAATCATTATTACTA-AATCATTA-AATATTAATA-ATAATTTCATTATT
* *
39419 A--AATCATGATTATCAAATCATTA
63 ACTAATCATTACTATCAAATCATTA
39442 CTAAATCAAA
Statistics
Matches: 168, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
97 20 0.12
98 128 0.76
99 20 0.12
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.44
Consensus pattern (98 bp):
TAATTTCATTATTACTAATCATTATTACTAAATCATTAAATATTAATAATAATTTCATTATTACT
AATCATTACTATCAAATCATTAAATATTAATAA
Found at i:42468 original size:8 final size:8
Alignment explanation
Indices: 42419--42474 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
42409 ATATTACTAA
*
42419 TAATGATT
1 TAATAATT
42427 TAATAATTAT
1 TAATAA-T-T
* *
42437 TATTAATC
1 TAATAATT
42445 TAATAATT
1 TAATAATT
*
42453 TGAT-ATT
1 TAATAATT
42460 TAATAATT
1 TAATAATT
42468 TAATAAT
1 TAATAAT
42475 AATATGATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
7 6 0.16
8 24 0.63
9 2 0.05
10 6 0.16
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (8 bp):
TAATAATT
Found at i:42784 original size:17 final size:18
Alignment explanation
Indices: 42752--42795 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
42742 AAATATATTT
42752 TTTTAAAACAACAATAATA
1 TTTT-AAACAACAATAATA
* *
42771 TTTTAAAC-ACAATATTT
1 TTTTAAACAACAATAATA
42788 TTTTAAAC
1 TTTTAAAC
42796 GGAAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 4 0.17
19 4 0.17
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTTAAACAACAATAATA
Found at i:43277 original size:43 final size:48
Alignment explanation
Indices: 43220--43330 Score: 135
Period size: 50 Copynumber: 2.4 Consensus size: 48
43210 GTTTAAAGAC
*
43220 ACTAACAAATTAATTAATTATTTTTT-TAT-AT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAATTATTTTTTATATAATATATATATAACTTAA
* *
43263 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAA-TTATTTTTTATATAATAT-ATATATAACTTAA
43313 ACTAACAAACTAA-TAATT
1 ACTAACAAACTAATTAATT
43331 TATACTAACA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
43 15 0.27
44 8 0.14
45 3 0.05
46 2 0.04
47 1 0.02
48 1 0.02
49 5 0.09
50 21 0.38
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (48 bp):
ACTAACAAACTAATTAATTATTTTTTATATAATATATATATAACTTAA
Found at i:43337 original size:21 final size:21
Alignment explanation
Indices: 43304--43352 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
43294 AATATAATAT
43304 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
43325 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
43346 ATTAACT
1 A-TAACT
43353 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:44056 original size:2 final size:2
Alignment explanation
Indices: 44049--44079 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44039 AGTTACCGTG
44049 TA 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 TA T
44080 TTGCAAGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45795 original size:23 final size:22
Alignment explanation
Indices: 45752--45818 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
45742 CTTGTGAGCA
*
45752 CATAAATAAAAATAAACATATT
1 CATAAATAAAAATAAAAATATT
* *
45774 CATAAATATTAAATAAATATATT
1 CATAAATA-AAAATAAAAATATT
*
45797 CATGAATAAAAAATAAAAATAT
1 CATAAAT-AAAAATAAAAATAT
45819 ATATTTACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
22 8 0.21
23 29 0.76
24 1 0.03
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (22 bp):
CATAAATAAAAATAAAAATATT
Found at i:46736 original size:23 final size:23
Alignment explanation
Indices: 46705--46789 Score: 125
Period size: 23 Copynumber: 3.7 Consensus size: 23
46695 ACAGGTAAAA
*
46705 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
46728 ATATAATGTAATAAGTTGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
46751 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
**
46774 ATATAATAAAATAGGT
1 ATATAATGTAATAGGT
46790 TAATTACTAG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:46864 original size:110 final size:109
Alignment explanation
Indices: 46723--46923 Score: 321
Period size: 110 Copynumber: 1.8 Consensus size: 109
46713 TAATAGGTAG
* * *
46723 CGCTTATATAATGTAATAAGTTGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAG
1 CGCTTAAATAATATAATAAGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATA-
*
46788 GTTAATTACTAGAAACATTATCAAGCACAATAACATATTAAGTAC
65 ATTAATTACTAGAAACATTATCAAGCACAATAACATATTAAGTAC
* *
46833 CGCTTAAATAATATAATAGGTAGCGCTTATATAATGTAATATGTAGCGCTTATATAATAAAATAA
1 CGCTTAAATAATATAATAAGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAA
* *
46898 TTAATTACTGGAAACATTTTCAAGCA
66 TTAATTACTAGAAACATTATCAAGCA
46924 TTTCAACATA
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
109 24 0.29
110 59 0.71
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (109 bp):
CGCTTAAATAATATAATAAGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAA
TTAATTACTAGAAACATTATCAAGCACAATAACATATTAAGTAC
Found at i:46890 original size:23 final size:23
Alignment explanation
Indices: 46713--46896 Score: 112
Period size: 23 Copynumber: 8.2 Consensus size: 23
46703 AAATATGATG
*
46713 TAATAGGTAGCGCTTATATAATG
1 TAATAGGTAGCGCTTATATAATA
* * *
46736 TAATAAGTTGCGCTTATATAATG
1 TAATAGGTAGCGCTTATATAATA
46759 TAATAGGTAGCGCTTATATAATA
1 TAATAGGTAGCGCTTATATAATA
* * *
46782 AAATAGGTTA---ATTACTAGAA-A
1 TAATAGG-TAGCGCTTA-TATAATA
* * *** * *
46803 CATTATCAAGCAC--A-ATAACA
1 TAATAGGTAGCGCTTATATAATA
* * * *
46823 TATTAAGTACCGCTTAAATAATA
1 TAATAGGTAGCGCTTATATAATA
*
46846 TAATAGGTAGCGCTTATATAATG
1 TAATAGGTAGCGCTTATATAATA
*
46869 TAATATGTAGCGCTTATATAATA
1 TAATAGGTAGCGCTTATATAATA
*
46892 AAATA
1 TAATA
46897 ATTAATTACT
Statistics
Matches: 122, Mismatches: 30, Indels: 18
0.72 0.18 0.11
Matches are distributed among these distances:
19 3 0.02
20 9 0.07
21 8 0.07
22 5 0.04
23 95 0.78
24 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (23 bp):
TAATAGGTAGCGCTTATATAATA
Found at i:47406 original size:87 final size:86
Alignment explanation
Indices: 47261--47494 Score: 276
Period size: 87 Copynumber: 2.7 Consensus size: 86
47251 TAACAAATTA
* ** * *
47261 AATAATTAACATATTTTATTATAT-CAC-TACCTATTATGTTATATAAGTAT-TACCTAATATGT
1 AATAATTAACATATTTTATTATATAAACATACCTATTACATTATATAAAT-TGTACCTAATATAT
** * *
47323 TATTGTGTTTGATAATATTTTT
65 TATTGTACTTAATAATATTTTC
* * *
47345 AATAATTAACCTATTTTATTATATAAACGATACCTATTACACTATATAAATTGTACATAATATAT
1 AATAATTAACATATTTTATTATATAAAC-ATACCTATTACATTATATAAATTGTACCTAATATAT
47410 TATTGTACTTAATAATATTTTC
65 TATTGTACTTAATAATATTTTC
* * * *
47432 GATAATTAACATATTTTATTATATAAATATTACATATTACATTATATAAACTGTACCTAATAT
1 AATAATTAACATATTTTATTATATAAACA-TACCTATTACATTATATAAATTGTACCTAATAT
47495 TTAAATACTT
Statistics
Matches: 126, Mismatches: 19, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
84 23 0.18
85 2 0.02
86 2 0.02
87 99 0.79
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (86 bp):
AATAATTAACATATTTTATTATATAAACATACCTATTACATTATATAAATTGTACCTAATATATT
ATTGTACTTAATAATATTTTC
Found at i:47416 original size:17 final size:18
Alignment explanation
Indices: 47394--47428 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
47384 CACTATATAA
47394 ATTGTACATAAT-ATATT
1 ATTGTACATAATAATATT
*
47411 ATTGTACTTAATAATATT
1 ATTGTACATAATAATATT
47429 TTCGATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (18 bp):
ATTGTACATAATAATATT
Done.