Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002125.1 Hibiscus syriacus cultivar Beakdansim tig00004353_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: 46441
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:182 original size:21 final size:21
Alignment explanation
Indices: 158--239 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 21
148 TTGGGAGGGA
*
158 CCTCTTCAACGATGACAGTGG
1 CCTCTTGAACGATGACAGTGG
* **
179 CCTCTTGAACGGTGGGAG-GG
1 CCTCTTGAACGATGACAGTGG
* ** * *
199 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGACAGTGG
220 CCTCTTGAACGATGACAGTG
1 CCTCTTGAACGATGACAGTG
240 AGTCGAGCTT
Statistics
Matches: 45, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
20 14 0.31
21 31 0.69
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGTGG
Found at i:213 original size:41 final size:42
Alignment explanation
Indices: 149--230 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 42
139 TCTAGAATGT
*
149 TGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACGG
* ** *
191 TGGGAGGGA-CTCTTGAGGGATGATAGGGGCCTCTTGAACG
1 TGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACG
231 ATGACAGTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 26 0.74
42 9 0.26
ACGTcount: A:0.21, C:0.20, G:0.38, T:0.22
Consensus pattern (42 bp):
TGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACGG
Found at i:782 original size:30 final size:31
Alignment explanation
Indices: 701--795 Score: 120
Period size: 30 Copynumber: 3.0 Consensus size: 31
691 TCTGAAACTT
701 AAAATCGCAACGCGAAAATGACTATCGCAACG
1 AAAATCGCAACGCG-AAATGACTATCGCAACG
* * **
733 AGAGAATTGCAATGCGAAATGAAAATCGCAAC-
1 A-A-AATCGCAACGCGAAATGACTATCGCAACG
765 AAAATCGCAACGCGAAATGACTATCGCAACG
1 AAAATCGCAACGCGAAATGACTATCGCAACG
796 CGAAAATGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
30 24 0.46
31 1 0.02
32 2 0.04
33 15 0.29
34 10 0.19
ACGTcount: A:0.44, C:0.22, G:0.20, T:0.14
Consensus pattern (31 bp):
AAAATCGCAACGCGAAATGACTATCGCAACG
Found at i:804 original size:20 final size:20
Alignment explanation
Indices: 768--835 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
758 TCGCAACAAA
768 ATCGCAACGCG-AAATGACT
1 ATCGCAACGCGAAAATGACT
787 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
807 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
827 ATCGCAACG
1 ATCGCAACG
836 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 11 0.25
20 33 0.75
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:899 original size:53 final size:53
Alignment explanation
Indices: 842--944 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
832 AACGAGAGAA
* * * *
842 TCGCAATACAAT-TTTTATTTCTCATTGCGATTCTTTCGTTGCGATAGTCAAAT
1 TCGCAATACAATAATAT-TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
* * *
895 TCGCATTGCGATAATATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 TCGCAATACAATAATATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
945 TTTTCGCATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 40 0.95
54 2 0.05
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (53 bp):
TCGCAATACAATAATATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
Found at i:905 original size:20 final size:19
Alignment explanation
Indices: 880--925 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
870 GATTCTTTCG
*
880 TTGCGATAGTCAAATTCGCA
1 TTGCGATAAT-AAATTCGCA
**
900 TTGCGATAATATTTTCGCA
1 TTGCGATAATAAATTCGCA
919 TTGCGAT
1 TTGCGAT
926 TCTCTCGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (19 bp):
TTGCGATAATAAATTCGCA
Found at i:951 original size:53 final size:53
Alignment explanation
Indices: 859--960 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 53
849 ACAATTTTTA
* *
859 TTTCTCATTGCGATTCTTTCGTTGCGATAGTCAAATTCGCATTGCGATAATAT
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAATAT
**
912 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGATA
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATA
961 GTAAACTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (53 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCATTGCGATAATAT
Found at i:958 original size:20 final size:20
Alignment explanation
Indices: 880--962 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
870 GATTCTTTCG
**
880 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
900 TTGCGATAAT-ATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
919 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
933 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
953 TTGCGATAGT
1 TTGCGATAGT
963 AAACTATTCT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 7 0.14
16 6 0.12
17 1 0.02
18 4 0.08
19 14 0.27
20 19 0.37
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:2823 original size:20 final size:20
Alignment explanation
Indices: 2800--2859 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
2790 CTGAAACTTT
2800 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
2820 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
2840 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
2859 A
1 A
2860 TCGCATTGCG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 6 0.17
20 30 0.83
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:2904 original size:20 final size:20
Alignment explanation
Indices: 2879--2925 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2869 GATTCTCTCG
2879 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
2899 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
2919 TTGCGAT
1 TTGCGAT
2926 TCACTCGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:2945 original size:34 final size:34
Alignment explanation
Indices: 2902--2980 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 34
2892 ATTCGCATTG
*
2902 CGATAGTCATTTTCGCGTTGCGATTCACTCGTTA
1 CGATAGTCATTTTCGCATTGCGATTCACTCGTTA
*
2936 CGATAGTCATTTTCGCATTGCGATTCACTCGTTG
1 CGATAGTCATTTTCGCATTGCGATTCACTCGTTA
2970 CGATAGTCATT
1 CGATAGTCATT
2981 CTCGGTTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (34 bp):
CGATAGTCATTTTCGCATTGCGATTCACTCGTTA
Found at i:3635 original size:20 final size:20
Alignment explanation
Indices: 3506--3637 Score: 140
Period size: 20 Copynumber: 6.5 Consensus size: 20
3496 GCTATGTAAA
*
3506 TCGCATTGCGATAGT-CGTAT
1 TCGCATTGCGAT-TTACGTAT
*
3526 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
*
3546 TCACATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
3566 TCACATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
* * **
3586 TCGCATTGTGATTTTCCAAAT
1 TCGCATTGCGA-TTTACGTAT
*
3607 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
3627 TCGTATTGCGA
1 TCGCATTGCGA
3638 ATTAGGAAAA
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
19 1 0.01
20 77 0.84
21 14 0.15
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:3660 original size:21 final size:21
Alignment explanation
Indices: 3634--3679 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3624 TATTCGTATT
3634 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
3655 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
3676 GCGA
1 GCGA
3680 TAGTCAATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:4567 original size:21 final size:20
Alignment explanation
Indices: 4540--4637 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
4530 AATCAGTTTC
4540 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
4561 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
4582 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
4602 CCAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGATTTT
*
4622 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
4638 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 3
0.75 0.22 0.04
Matches are distributed among these distances:
20 29 0.49
21 30 0.51
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:4693 original size:20 final size:20
Alignment explanation
Indices: 4604--4814 Score: 232
Period size: 20 Copynumber: 10.6 Consensus size: 20
4594 GCGATTTTCC
* ** *
4604 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
4624 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
4644 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
4664 -AACCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
4683 AAATAGCAACGCGTATCTGT
1 AAATCGCAACGCGTATCCGT
*
4703 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
4723 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4743 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
*
4763 AAAATCGCAACGTGTATCCGT
1 -AAATCGCAACGCGTATCCGT
*
4784 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
4804 AAATCGCAACG
1 AAATCGCAACG
4815 AATCTGTAAA
Statistics
Matches: 164, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
19 20 0.12
20 124 0.76
21 19 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:4709 original size:79 final size:81
Alignment explanation
Indices: 4604--4814 Score: 243
Period size: 79 Copynumber: 2.6 Consensus size: 81
4594 GCGATTTTCC
* * *
4604 AAATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGT-AAC
1 AAATCGCAACGCGTATCTGTAAATCGCAACGCGTAAC-CATAAATCGCAACGCGTATCCGTAAAC
*
4667 CGCAACG-TGTATCCGT-
65 CGCAACGAT-AATCCGTA
* * * * *
4683 AAATAGCAACGCGTATCTGTAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGTAAATC
1 AAATCGCAACGCGTATCTGTAAATCGCAACGCGTAACCATAAATCGCAACGCGTATCCGTAAACC
4748 GCAACGATAATCCGTA
66 GCAACGATAATCCGTA
* * * *
4764 AAATCGCAACGTGTATCCGTAAATCGCAACG-ATAATCCGTAAATCGCAACG
1 AAATCGCAACGCGTATCTGTAAATCGCAACGCGTAA-CCATAAATCGCAACG
4815 AATCTGTAAA
Statistics
Matches: 112, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
79 50 0.45
80 19 0.17
81 43 0.38
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.19
Consensus pattern (81 bp):
AAATCGCAACGCGTATCTGTAAATCGCAACGCGTAACCATAAATCGCAACGCGTATCCGTAAACC
GCAACGATAATCCGTA
Found at i:4793 original size:61 final size:58
Alignment explanation
Indices: 4643--4831 Score: 229
Period size: 61 Copynumber: 3.2 Consensus size: 58
4633 CGCGAACACA
* * * *
4643 TAAATCGCAACGCGTATCCGT-AACCGCAACGTGTATCCGTAAATAGCAACGCGTATCTG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACG-GTATCCGTAAATCGCAACG-ATATCCG
*
4702 TAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACG-GTATCCGTAAATCGCAACGAT-ATCCG
* * *
4762 TAAAATCGCAACGTGTATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGA-ATCTG
1 T-AAATCGCAACGCGTATCCGTAAATCGCAACGGT-ATCCGTAAATCGCAACGATATCCG
*
4821 TAAATCACAAC
1 TAAATCGCAAC
4832 ACTGAAATTT
Statistics
Matches: 115, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
58 9 0.08
59 26 0.23
60 33 0.29
61 47 0.41
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (58 bp):
TAAATCGCAACGCGTATCCGTAAATCGCAACGGTATCCGTAAATCGCAACGATATCCG
Found at i:5362 original size:20 final size:20
Alignment explanation
Indices: 5337--5522 Score: 223
Period size: 20 Copynumber: 9.3 Consensus size: 20
5327 AGAAGTAGTA
*
5337 CGCAACGCGTATCCGTAAAC
1 CGCAACGCGTATCCGTAAAT
*
5357 CGCAACGTGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
5377 CGCAACGCGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
*
5397 CGCAATGCGTATCCGTAAAT
1 CGCAACGCGTATCCGTAAAT
*
5417 CGCAACGCGTATCCATAAAT
1 CGCAACGCGTATCCGTAAAT
*
5437 CGCAACG-ATAATCCGTAAAT
1 CGCAACGCGT-ATCCGTAAAT
* * *
5457 CGCAACGAGAATCTGTAAAT
1 CGCAACGCGTATCCGTAAAT
*
5477 CGCAACG-ATAATCCGTAAAT
1 CGCAACGCGT-ATCCGTAAAT
* * *
5497 CGCAACGAGAATCTGTAAAT
1 CGCAACGCGTATCCGTAAAT
*
5517 CACAAC
1 CGCAAC
5523 ACTGAAATTT
Statistics
Matches: 144, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 143 0.99
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (20 bp):
CGCAACGCGTATCCGTAAAT
Found at i:8766 original size:20 final size:20
Alignment explanation
Indices: 8735--8798 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
8725 TTTTGGTTGA
8735 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
8755 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
8775 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
8796 AAT
1 AAT
8799 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:8787 original size:21 final size:21
Alignment explanation
Indices: 8733--8797 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
8723 TCTTTTGGTT
8733 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
8754 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
8774 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
8795 GAA
1 GAA
8798 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:8820 original size:19 final size:19
Alignment explanation
Indices: 8733--8858 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
8723 TCTTTTGGTT
*
8733 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
8752 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
8774 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
8791 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
8807 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
8824 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
8838 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
8857 GA
1 GA
8859 TTTTGGTTTC
Statistics
Matches: 82, Mismatches: 10, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
12 8 0.10
14 13 0.16
15 2 0.02
16 3 0.04
17 4 0.05
18 1 0.01
19 24 0.29
20 12 0.15
21 11 0.13
22 4 0.05
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:8831 original size:31 final size:32
Alignment explanation
Indices: 8774--8853 Score: 144
Period size: 31 Copynumber: 2.5 Consensus size: 32
8764 CGCAACGAGA
8774 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAAC-AGAGAATCGCAACGC
8807 GAAATGAAAATCGCAAC-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACAGAGAATCGCAACGC
8838 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
8854 TGCGATTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
31 30 0.64
33 17 0.36
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (32 bp):
GAAATGAAAATCGCAACAGAGAATCGCAACGC
Found at i:8889 original size:14 final size:14
Alignment explanation
Indices: 8870--8926 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
8860 TTTGGTTTCG
8870 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
8884 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
8903 CGTTACGATTCTCT
1 CGTTGCGATTCTCT
8917 CGTTGCGATT
1 CGTTGCGATT
8927 TTCATTTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:8902 original size:33 final size:33
Alignment explanation
Indices: 8854--8933 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
8844 AAAATCGCAA
** *
8854 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
8887 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
8920 TGCGATTTTCATTT
1 TGCGATTTTCATTT
8934 TTCTCGTTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
Found at i:8939 original size:21 final size:21
Alignment explanation
Indices: 8914--8987 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
8904 GTTACGATTC
8914 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
8935 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
8956 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
8977 TCTCGTTGCGA
1 TCTCGTTGCGA
8988 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:9109 original size:33 final size:33
Alignment explanation
Indices: 9067--9137 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
9057 AATACTAACT
9067 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
9100 TGAAAATCGCAACGAGAGAATCGCACCGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
9133 TGAAA
1 TGAAA
9138 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:9539 original size:20 final size:20
Alignment explanation
Indices: 9514--9706 Score: 237
Period size: 20 Copynumber: 9.6 Consensus size: 20
9504 CTTTAAAAAT
9514 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
9534 CGCGTTGCGATTTTACGGATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
9556 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
9575 CGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
*
9595 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
9615 CGCGTTGCTATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
9635 CACGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
9655 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
9675 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
9695 CGCGTTGCGATT
1 CGCGTTGCGATT
9707 CTGGAAAATC
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.01
20 129 0.86
21 17 0.11
22 2 0.01
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:9831 original size:18 final size:18
Alignment explanation
Indices: 9797--9846 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
9787 ATTCTGGGGA
9797 TCGCGTTGCGA-TTTATT
1 TCGCGTTGCGATTTTATT
9814 TCGCGTTGCGATTTTATT
1 TCGCGTTGCGATTTTATT
9832 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
9847 GTTGGTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 11 0.34
18 21 0.66
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (18 bp):
TCGCGTTGCGATTTTATT
Found at i:13264 original size:47 final size:49
Alignment explanation
Indices: 13207--13299 Score: 154
Period size: 48 Copynumber: 1.9 Consensus size: 49
13197 ATACTTTGAT
*
13207 TATTTATTAGGTTCTTTA-TTATTTTATCTCATAAA-CTTTAATTACTA
1 TATTTATTAGGTTATTTATTTATTTTATCTCATAAACCTTTAATTACTA
*
13254 TATTTTTTAGGTTATTTATTTATTTTATCTCATAAACCTTTAATTA
1 TATTTATTAGGTTATTTATTTATTTTATCTCATAAACCTTTAATTA
13300 TTTATTAGGC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 16 0.38
48 17 0.40
49 9 0.21
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.57
Consensus pattern (49 bp):
TATTTATTAGGTTATTTATTTATTTTATCTCATAAACCTTTAATTACTA
Found at i:16563 original size:447 final size:448
Alignment explanation
Indices: 15729--16632 Score: 1535
Period size: 447 Copynumber: 2.0 Consensus size: 448
15719 AGGACAAGAA
*
15729 ACAACCATTTTATTAGGCCACAGTAGGGTCTTTTTAGCGAAGAAGAAGCATTTTAGTGAAGCTTG
1 ACAACCATTTTATTAGGCCACAGTAGGGTCTCTTTAGCGAAGAAGAAGCATTTTAGTGAAGCTTG
*
15794 TTTGAAAGATTGCACTGCTTCCTGATCTCACCCTTGTTACCGGTGAGGGTTGCTCTCGGAGAGGA
66 TTTGAAAGATTGCACTGCTTCCTGA-CTCACCCTTGGTACCGGTGAGGGTTGCTCTCGGAGAGGA
15859 GAGTAATGGCCCTGGAGAACTCCGTGAAGAAATAGTCTTGGCTCTTGGCCATTTTCTTCACATAA
130 GAGTAATGGCCCTGGAGAACTCCGTGAAGAAATAGTCTTGGCTCTTGGCCATTTTCTTCACATAA
*
15924 GGTCTGGTCCTCTTGTGATAAGCCAGTTGGTGGTCCACAATCAACAAGCCCTTGTTGTCCAGGAT
195 GGTCTGGTCCTCTTGTCATAAGCCAGTTGGTGGTCCACAATCAACAAGCCCTTGTTGTCCAGGAT
*
15989 GTTTCTATAGTAGTTGTTGTCCAGAACCATGGGTGTCCCCCGGTCGTTTCTCACGTATTGCACCG
260 GTTTCTATAGTAGTTGTTGTCCAGAACCATGGGTGTCCCCCGGTCGTTTCTCACGTACTGCACCG
* *
16054 CTTTGGGGACTGGGATTTGATCAGTGCACTTACGGAGCATGTGTGGAATATGGTCGGGGTTGAGC
325 CCTTGGGGACTGGGATTTGATCAGGGCACTTACGGAGCATGTGTGGAATATGGTCGGGGTTGAGC
16119 TCAGGGCCAA-C-CTCTGAGTACAGAAGGTGCACCAGCTTCACACAGTGAGTTCTGCCG
390 TCAGGGCCAACCGCTCTGAGTACAGAAGGTGCACCAGCTTCACACAGTGAGTTCTGCCG
* * *
16176 ACAACCATTTTATTCGGCCACAGTCGGGTCTCTTTAGCGAAGAAGAAGCATTTTAGTGGAGCTTG
1 ACAACCATTTTATTAGGCCACAGTAGGGTCTCTTTAGCGAAGAAGAAGCATTTTAGTGAAGCTTG
* * *
16241 TTTGCAAGATTGCACTGCTTCCTGA-TCACCCTTGGTACGGGTGAGAGGGTTGTTCTCGGAGAGG
66 TTTGAAAGATTGCACTGCTTCCTGACTCACCCTTGGTACCGGT--GAGGGTTGCTCTCGGAGAGG
*
16305 AGAGTAATGGCCCTGGAGAACTCCTTGAAGAAATAGTCTTGGCTCTTGGCCATTTTCTTCACATA
129 AGAGTAATGGCCCTGGAGAACTCCGTGAAGAAATAGTCTTGGCTCTTGGCCATTTTCTTCACATA
16370 AGGTCTGGTCCTCTTGTCATAAGCCAGTTGGTGGTCCACAATCAACAAGCCCTTGTTGTCCAGGA
194 AGGTCTGGTCCTCTTGTCATAAGCCAGTTGGTGGTCCACAATCAACAAGCCCTTGTTGTCCAGGA
*
16435 TGTTTCTATAGTTGTTGTTGTCCAGAACCATGGGTGTCCCCCGGTCGTTTCTCACGTACTGCACC
259 TGTTTCTATAGTAGTTGTTGTCCAGAACCATGGGTGTCCCCCGGTCGTTTCTCACGTACTGCACC
* *
16500 GCCTTGGGGTCTGGGATTTGATCAGGGCACTTATGGAGCATGTGTGGAATATGGTCGGGGTTGAG
324 GCCTTGGGGACTGGGATTTGATCAGGGCACTTACGGAGCATGTGTGGAATATGGTCGGGGTTGAG
* * * *
16565 CTCAGGGTCAACCTCTGGGCTCTGGGTACAGACGGTGCACCAGCTTCACGCAGTGAGTTCTGCCG
389 CTCAGGGCCAA-C-C---GCTCTGAGTACAGAAGGTGCACCAGCTTCACACAGTGAGTTCTGCCG
16630 ACA
1 ACA
16633 CTGTGTGCTC
Statistics
Matches: 428, Mismatches: 20, Indels: 11
0.93 0.04 0.02
Matches are distributed among these distances:
445 15 0.04
447 366 0.86
450 1 0.00
454 46 0.11
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (448 bp):
ACAACCATTTTATTAGGCCACAGTAGGGTCTCTTTAGCGAAGAAGAAGCATTTTAGTGAAGCTTG
TTTGAAAGATTGCACTGCTTCCTGACTCACCCTTGGTACCGGTGAGGGTTGCTCTCGGAGAGGAG
AGTAATGGCCCTGGAGAACTCCGTGAAGAAATAGTCTTGGCTCTTGGCCATTTTCTTCACATAAG
GTCTGGTCCTCTTGTCATAAGCCAGTTGGTGGTCCACAATCAACAAGCCCTTGTTGTCCAGGATG
TTTCTATAGTAGTTGTTGTCCAGAACCATGGGTGTCCCCCGGTCGTTTCTCACGTACTGCACCGC
CTTGGGGACTGGGATTTGATCAGGGCACTTACGGAGCATGTGTGGAATATGGTCGGGGTTGAGCT
CAGGGCCAACCGCTCTGAGTACAGAAGGTGCACCAGCTTCACACAGTGAGTTCTGCCG
Found at i:19868 original size:4 final size:4
Alignment explanation
Indices: 19861--20059 Score: 79
Period size: 4 Copynumber: 49.0 Consensus size: 4
19851 ATTTTGTTTG
* ** * * *
19861 ATTT ATTT ATTT ATTC ATTT ATTT A-GA ATCT ATTT GTTT -TTG ACTTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT
* * * *
19908 -TTT ATTC ATTC ATTT ATTT -GTT ATTC ATTT -TTT ATTT -TTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
** ** * * * *
19952 ATAC ATTT ATTT ATTT -TGA AATT ATTT ATTT GTTT GTTT CAAATTT GTTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ---ATTT ATTT
* *
20002 ATTT ATTT ATTT CGAATTT ATTC ATTT ATTT ATTT GTTT CAAATTT ATTT
1 ATTT ATTT ATTT ---ATTT ATTT ATTT ATTT ATTT ATTT ---ATTT ATTT
20052 ATTT ATTT
1 ATTT ATTT
20060 GAAGGGATAT
Statistics
Matches: 144, Mismatches: 34, Indels: 34
0.68 0.16 0.16
Matches are distributed among these distances:
3 15 0.10
4 117 0.81
5 2 0.01
7 10 0.07
ACGTcount: A:0.24, C:0.06, G:0.05, T:0.66
Consensus pattern (4 bp):
ATTT
Found at i:19931 original size:19 final size:19
Alignment explanation
Indices: 19909--19963 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
19899 TTTGACTTTT
19909 TTATTCATTCATTTATTTG
1 TTATTCATTCATTTATTTG
* *
19928 TTATTCATT-TTTTATTTT
1 TTATTCATTCATTTATTTG
* *
19946 TTATTTATACATTTATTT
1 TTATTCATTCATTTATTT
19964 ATTTTGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 14 0.47
19 16 0.53
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (19 bp):
TTATTCATTCATTTATTTG
Found at i:19939 original size:38 final size:40
Alignment explanation
Indices: 19857--19964 Score: 123
Period size: 42 Copynumber: 2.7 Consensus size: 40
19847 AATAATTTTG
**
19857 TTTGATTTATTTATTTATTCATTTATTTAGAATCTATTTGTT
1 TTTGATTT-TTTATTTATTCATTTATTTAG-ATCTATTCATT
*
19899 TTTGACTTTTTTATTCATTCATTTATTT-G-T-TATTCATT
1 TTTGA-TTTTTTATTTATTCATTTATTTAGATCTATTCATT
* *
19937 TTTTATTTTTTATTTATACATTTATTTA
1 TTTGATTTTTTATTTATTCATTTATTTA
19965 TTTTGAAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
37 20 0.34
38 10 0.17
39 1 0.02
41 1 0.02
42 23 0.40
43 3 0.05
ACGTcount: A:0.22, C:0.06, G:0.05, T:0.67
Consensus pattern (40 bp):
TTTGATTTTTTATTTATTCATTTATTTAGATCTATTCATT
Found at i:19976 original size:23 final size:23
Alignment explanation
Indices: 19909--20036 Score: 88
Period size: 23 Copynumber: 5.8 Consensus size: 23
19899 TTTGACTTTT
*
19909 TTATTCATTCATTTA-TTTG---
1 TTATTCATTTATTTATTTTGAAA
** *
19928 TTATTCATTT-TTTATTTTTTAT
1 TTATTCATTTATTTATTTTGAAA
*
19950 TTATACATTTATTTATTTTGAAA
1 TTATTCATTTATTTATTTTGAAA
* * * *
19973 TTATTTATTTGTTT-GTTTCAAA
1 TTATTCATTTATTTATTTTGAAA
* * * *
19995 TTTGTTTATTTATTTATTTCGAAT
1 -TTATTCATTTATTTATTTTGAAA
20019 TTATTCATTTATTTATTT
1 TTATTCATTTATTTATTT
20037 GTTTCAAATT
Statistics
Matches: 83, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
18 4 0.05
19 12 0.14
22 15 0.18
23 48 0.58
24 4 0.05
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.66
Consensus pattern (23 bp):
TTATTCATTTATTTATTTTGAAA
Found at i:20003 original size:27 final size:27
Alignment explanation
Indices: 19973--20060 Score: 103
Period size: 27 Copynumber: 3.4 Consensus size: 27
19963 TATTTTGAAA
*
19973 TTATTTATTTGTTTGTTTCAAATTTGT
1 TTATTTATTTGTTTGTTTCAAATTTAT
* *
20000 TTATTTA----TTTATTTCGAATTTAT
1 TTATTTATTTGTTTGTTTCAAATTTAT
* *
20023 TCATTTATTTATTTGTTTCAAATTTAT
1 TTATTTATTTGTTTGTTTCAAATTTAT
20050 TTATTTATTTG
1 TTATTTATTTG
20061 AAGGGATATG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
23 19 0.39
27 30 0.61
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.66
Consensus pattern (27 bp):
TTATTTATTTGTTTGTTTCAAATTTAT
Found at i:20051 original size:23 final size:23
Alignment explanation
Indices: 19956--20060 Score: 104
Period size: 23 Copynumber: 4.4 Consensus size: 23
19946 TTATTTATAC
* *
19956 ATTTATTTATTTTGAAA-TTATTT
1 ATTTATTT-GTTTCAAATTTATTT
* *
19979 ATTTGTTTGTTTCAAATTTGTTT
1 ATTTATTTGTTTCAAATTTATTT
* *
20002 ATTTATTTATTTCGAATTTATTCATTT
1 ATTTATTTGTTTC-AA---ATTTATTT
20029 ATTTATTTGTTTCAAATTTATTT
1 ATTTATTTGTTTCAAATTTATTT
20052 ATTTATTTG
1 ATTTATTTG
20061 AAGGGATATG
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
22 6 0.09
23 39 0.58
24 2 0.03
26 2 0.03
27 18 0.27
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.65
Consensus pattern (23 bp):
ATTTATTTGTTTCAAATTTATTT
Found at i:20963 original size:18 final size:18
Alignment explanation
Indices: 20937--20971 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20927 ACTAAATATT
20937 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
20955 TGTCTCGAATGACCACT
1 TGTCCCGAAGGACCACT
20972 GATAATCCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:24699 original size:29 final size:29
Alignment explanation
Indices: 24656--24794 Score: 244
Period size: 29 Copynumber: 4.8 Consensus size: 29
24646 TTTTATATGT
24656 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
24684 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
24713 TCATATAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
24742 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
24771 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
24795 ATATCACATA
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
28 7 0.07
29 93 0.89
30 5 0.05
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:25242 original size:64 final size:63
Alignment explanation
Indices: 25173--25329 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 63
25163 TAATGAAGGT
* **
25173 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TTAA-AA
25236 G
63 G
* * *
25237 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
*
25300 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
25330 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 67 0.85
65 9 0.11
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
Found at i:25389 original size:21 final size:21
Alignment explanation
Indices: 25363--25419 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
25353 TTTAACCTTG
25363 ATGCATCGATGCACTATGAAT
1 ATGCATCGATGCACTATGAAT
25384 ATGCATCGATGCACTATGAAT
1 ATGCATCGATGCACTATGAAT
25405 ATGCATCGATGCACT
1 ATGCATCGATGCACT
25420 CTTCCCAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (21 bp):
ATGCATCGATGCACTATGAAT
Found at i:26202 original size:12 final size:12
Alignment explanation
Indices: 26170--26218 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
26160 ATATAGATGA
* *
26170 TGATGATGTTGA
1 TGATGATGGTGG
*
26182 TGGTGATGGTGG
1 TGATGATGGTGG
26194 TGATGATGGTGG
1 TGATGATGGTGG
26206 T-A-G-TGGTGG
1 TGATGATGGTGG
26215 TGAT
1 TGAT
26219 TATCAAAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
9 7 0.23
10 2 0.06
11 1 0.03
12 21 0.68
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.37
Consensus pattern (12 bp):
TGATGATGGTGG
Found at i:26412 original size:23 final size:23
Alignment explanation
Indices: 26341--26413 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
26331 AATTTGTAAC
26341 TTTTTTTAGTTATTCGAACTGCA
1 TTTTTTTAGTTATTCGAACTGCA
*
26364 TTGTTTTAGTTATTCGAACTGCA
1 TTTTTTTAGTTATTCGAACTGCA
* *
26387 TTTTTTTAGTTAATCGAACTTCA
1 TTTTTTTAGTTATTCGAACTGCA
26410 TTTT
1 TTTT
26414 CTTTCTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.53
Consensus pattern (23 bp):
TTTTTTTAGTTATTCGAACTGCA
Found at i:26817 original size:4 final size:4
Alignment explanation
Indices: 26808--26843 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
26798 TAAATGGGAA
26808 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
26844 CTAATCGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:29541 original size:9 final size:9
Alignment explanation
Indices: 29527--29552 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29517 ACGGTCAACG
29527 GTCGGGTCA
1 GTCGGGTCA
29536 GTCGGGTCA
1 GTCGGGTCA
29545 GTCGGGTC
1 GTCGGGTC
29553 GGGTCATACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.23, G:0.46, T:0.23
Consensus pattern (9 bp):
GTCGGGTCA
Found at i:29603 original size:20 final size:20
Alignment explanation
Indices: 29567--29625 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
29557 CATACCGATC
*
29567 AAACCGGTTAGAACCGGTTGA
1 AAACCGGTCA-AACCGGTTGA
*
29588 AAACTGGTCAAACCGGTTGA
1 AAACCGGTCAAACCGGTTGA
29608 AAACCGGTCAAACCGGTT
1 AAACCGGTCAAACCGGTT
29626 TTCAGCCCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 27 0.77
21 8 0.23
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (20 bp):
AAACCGGTCAAACCGGTTGA
Found at i:29613 original size:11 final size:10
Alignment explanation
Indices: 29567--29625 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 10
29557 CATACCGATC
29567 AAACCGGTTA
1 AAACCGGTTA
*
29577 GAACCGGTTGA
1 AAACCGGTT-A
* *
29588 AAACTGG-TC
1 AAACCGGTTA
29597 AAACCGGTTGA
1 AAACCGGTT-A
*
29608 AAACCGG-TC
1 AAACCGGTTA
29617 AAACCGGTT
1 AAACCGGTT
29626 TTCAGCCCTC
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
9 13 0.34
10 12 0.32
11 13 0.34
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (10 bp):
AAACCGGTTA
Found at i:30507 original size:97 final size:97
Alignment explanation
Indices: 30341--30536 Score: 374
Period size: 97 Copynumber: 2.0 Consensus size: 97
30331 TTTTGTAAAT
30341 ATTCGGGTTGTTACAATTCTCCCCCTCTACAAGAAATTTCATCCTCGAAATTTACCTTATGAGAA
1 ATTCGGGTTGTTACAATTCTCCCCCTCTACAAGAAATTTCATCCTCGAAATTTACCTTATGAGAA
*
30406 CAGTTGAGGAAATTGAGCTTCCATTGACTCCA
66 CAGTTGAGGAAATTGAGCCTCCATTGACTCCA
*
30438 ATTCGGGTTGTTACAATTCTCCCCCTCTACAAGAAATTTCGTCCTCGAAATTTACCTTATGAGAA
1 ATTCGGGTTGTTACAATTCTCCCCCTCTACAAGAAATTTCATCCTCGAAATTTACCTTATGAGAA
30503 CAGTTGAGGAAATTGAGCCTCCATTGACTCCA
66 CAGTTGAGGAAATTGAGCCTCCATTGACTCCA
30535 AT
1 AT
30537 GTCTCCCAAG
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (97 bp):
ATTCGGGTTGTTACAATTCTCCCCCTCTACAAGAAATTTCATCCTCGAAATTTACCTTATGAGAA
CAGTTGAGGAAATTGAGCCTCCATTGACTCCA
Found at i:36853 original size:13 final size:13
Alignment explanation
Indices: 36835--36860 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36825 AAGGAAGTCA
36835 ACGGTCAATGGTC
1 ACGGTCAATGGTC
36848 ACGGTCAATGGTC
1 ACGGTCAATGGTC
36861 GGGTCGAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (13 bp):
ACGGTCAATGGTC
Found at i:36896 original size:19 final size:19
Alignment explanation
Indices: 36872--36923 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
36862 GGTCGAGTCG
36872 GGTCAAACCGGTTCGGAA-C
1 GGTCAAACCGGTTC-GAACC
*
36891 GGTCAAATCGGTTCGAACC
1 GGTCAAACCGGTTCGAACC
36910 GGTCAGAACCGGTT
1 GGTCA-AACCGGTT
36924 AAAAATTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.10
19 19 0.66
20 7 0.24
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCGAACC
Found at i:39025 original size:23 final size:23
Alignment explanation
Indices: 38976--39034 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
38966 GATTTTAAAA
* *
38976 AAAATA-AAAATATTTTAAATTT
1 AAAATATAAAATATTTAAAACTT
38998 AAAATATAAAATATTTAAAACCTT
1 AAAATATAAAATATTTAAAA-CTT
39022 -AAATATAATAATA
1 AAAATATAA-AATA
39035 CCAAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 6 0.19
23 20 0.62
24 6 0.19
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATATAAAATATTTAAAACTT
Found at i:42066 original size:21 final size:21
Alignment explanation
Indices: 42042--42093 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
42032 ATAGATCTCC
*
42042 ACATCAGTATCGTGAAGTGTT
1 ACATCAGCATCGTGAAGTGTT
42063 ACATCAGCATCGTGAAGTGTT
1 ACATCAGCATCGTGAAGTGTT
42084 ACATCAGCAT
1 ACATCAGCAT
42094 TATAACGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (21 bp):
ACATCAGCATCGTGAAGTGTT
Found at i:43073 original size:61 final size:61
Alignment explanation
Indices: 42968--43088 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 61
42958 TTTGAGGTCG
*
42968 TATCCCACCGTGGATTAACTAATATTCCAAGTTTTGGCCCTCATCAATCCTCTACAAATCA
1 TATCCCACCGTGGATTAACTAATAATCCAAGTTTTGGCCCTCATCAATCCTCTACAAATCA
* * *
43029 TATCCCACCGTAGGATTAACTAATAATCCAAG-TTTGGCCGTCATCAATCCTTTGCAAATC
1 TATCCCACCGT-GGATTAACTAATAATCCAAGTTTTGGCCCTCATCAATCCTCTACAAATC
43089 GTTTTAAAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 36 0.65
62 19 0.35
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.31
Consensus pattern (61 bp):
TATCCCACCGTGGATTAACTAATAATCCAAGTTTTGGCCCTCATCAATCCTCTACAAATCA
Found at i:44497 original size:45 final size:45
Alignment explanation
Indices: 44424--44555 Score: 126
Period size: 45 Copynumber: 2.9 Consensus size: 45
44414 AGATATAACT
* * * *
44424 TCTGAAGGAACGCA-ATTGTATGGCACAATAACTGATGACACTTTC
1 TCTGAAGGAAAGCATTTTG-ATGGTACAATAACTGATGACACTTGC
*
44469 AT-TGAAGGAAAGCATTTTGATGGTACAATAATTGATGACAC-TGC
1 -TCTGAAGGAAAGCATTTTGATGGTACAATAACTGATGACACTTGC
* * * * *
44513 TGCTGAAGGGAAGCATTTGGATGGTGCAATAGCTGAAGACACT
1 T-CTGAAGGAAAGCATTTTGATGGTACAATAACTGATGACACT
44556 GTTACTGGAG
Statistics
Matches: 71, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
43 1 0.01
44 2 0.03
45 64 0.90
46 4 0.06
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (45 bp):
TCTGAAGGAAAGCATTTTGATGGTACAATAACTGATGACACTTGC
Done.