Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007344.1 Hibiscus syriacus cultivar Beakdansim tig00019677_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: 97209
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1132 original size:2 final size:2
Alignment explanation
Indices: 1125--1175 Score: 77
Period size: 2 Copynumber: 25.5 Consensus size: 2
1115 ATACTACTCT
1125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1166 CTC TA TA TA T
1 -TA TA TA TA T
1176 TTTTTTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 43 0.96
3 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1401 original size:7 final size:6
Alignment explanation
Indices: 1373--1402 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1363 CGAATTGAGT
1373 ATTTTA ATTTTA ATTTTA ATTTCTA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTT-TA ATTTT
1403 TCGTAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:2635 original size:28 final size:28
Alignment explanation
Indices: 2599--2653 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2589 AAAGTAATTC
*
2599 GCGATGTTTG-ATAAACAAACGCCGCTAA
1 GCGACGTTTGTATAAA-AAACGCCGCTAA
* *
2627 GCGACGTTTGTTTAAAAAACGTCGCTA
1 GCGACGTTTGTATAAAAAACGCCGCTA
2654 TAGATCTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (28 bp):
GCGACGTTTGTATAAAAAACGCCGCTAA
Found at i:2688 original size:43 final size:43
Alignment explanation
Indices: 2627--2715 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 43
2617 ACGCCGCTAA
* * * *
2627 GCGACGTTTGTTTAAAAAACGTCGCTATAGATCTTGACCTTTT
1 GCGACATTTGTTTAAAAAACGCCGATATAGATCTTAACCTTTT
* *
2670 GCGACATTTGTTTGAAAAAGGCCGATATAGATCTTAACCTTTT
1 GCGACATTTGTTTAAAAAACGCCGATATAGATCTTAACCTTTT
2713 GCG
1 GCG
2716 TCGTTTTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (43 bp):
GCGACATTTGTTTAAAAAACGCCGATATAGATCTTAACCTTTT
Found at i:7446 original size:46 final size:46
Alignment explanation
Indices: 7393--7913 Score: 777
Period size: 46 Copynumber: 11.5 Consensus size: 46
7383 GTATTAACAT
* *
7393 ATCCTTTCAGGCCTTTTAATTATGGCATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* * *
7439 ATCCTTTCATGCATTTTAATTATGGAAACCTTTTATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* * *
7485 ATCATTTCATGCATTTTAATTATGCCATCCTTTCATGACTTAATG-
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* *
7530 ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGT
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
7576 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* *
7622 ATCCTTTCATGCATTTTAATTATAGCATCATTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
*
7668 ATCCTTTCATGCATTTTAATTATGGCATCCTTTTATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* * *
7714 ATCCTATCATGC--CTT-A--AT-GCATCCTTTCATGCCTTATTGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
*
7754 ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* *
7800 ATCCTTTCATACATTTTAATTATGACATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
* * * *
7846 ATCCCTTCATGCATTTTAATTATGACATCCTTTCATCCCTTAATTC
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
*
7892 ATCATTTCATGCATTTTAATTA
1 ATCCTTTCATGCATTTTAATTA
7914 CTCTAAAACT
Statistics
Matches: 432, Mismatches: 36, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
40 31 0.07
41 2 0.00
42 2 0.00
43 2 0.00
44 2 0.00
45 44 0.10
46 349 0.81
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (46 bp):
ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGC
Found at i:7705 original size:26 final size:25
Alignment explanation
Indices: 7481--7913 Score: 266
Period size: 20 Copynumber: 19.0 Consensus size: 25
7471 TTATGCCTTA
*
7481 ATGCATCATTTCATGCATTTTAATT
1 ATGCATCCTTTCATGCATTTTAATT
*
7506 ATGCCATCCTTTCATG-A-CTT-A--
1 ATG-CATCCTTTCATGCATTTTAATT
7527 ATG-ATCCTTTCATGCATTTTAATT
1 ATGCATCCTTTCATGCATTTTAATT
*
7551 ATGACATCCTTTCATGC--CTT-A--
1 ATG-CATCCTTTCATGCATTTTAATT
*
7572 ATGTATCCTTTCATGCATTTTAATT
1 ATGCATCCTTTCATGCATTTTAATT
*
7597 ATGGCATCCTTTCATGC--CTT-A--
1 AT-GCATCCTTTCATGCATTTTAATT
7618 ATGCATCCTTTCATGCATTTTAATT
1 ATGCATCCTTTCATGCATTTTAATT
* *
7643 ATAGCATCATTTCATGC--CTT-A--
1 AT-GCATCCTTTCATGCATTTTAATT
7664 ATGCATCCTTTCATGCATTTTAATT
1 ATGCATCCTTTCATGCATTTTAATT
* *
7689 ATGGCATCCTTTTATGC--CTT-A--
1 AT-GCATCCTTTCATGCATTTTAATT
* *
7710 ATGCATCCTATCATGC--CTT-A--
1 ATGCATCCTTTCATGCATTTTAATT
*
7730 ATGCATCCTTTCATGC--CTT-A-T
1 ATGCATCCTTTCATGCATTTTAATT
7751 -TGCATCCTTTCATGCATTTTAATT
1 ATGCATCCTTTCATGCATTTTAATT
*
7775 ATGACATCCTTTCATGC--CTT-A--
1 ATG-CATCCTTTCATGCATTTTAATT
*
7796 ATGCATCCTTTCATACATTTTAATT
1 ATGCATCCTTTCATGCATTTTAATT
*
7821 ATGACATCCTTTCATGC--CTT-A--
1 ATG-CATCCTTTCATGCATTTTAATT
*
7842 ATGCATCCCTTCATGCATTTTAATT
1 ATGCATCCTTTCATGCATTTTAATT
**
7867 ATGACATCCTTTCAT-C-CCTTAA-T
1 ATG-CATCCTTTCATGCATTTTAATT
*
7890 -T-CATCATTTCATGCATTTTAATT
1 ATGCATCCTTTCATGCATTTTAATT
7913 A
1 A
7914 CTCTAAAACT
Statistics
Matches: 327, Mismatches: 32, Indels: 99
0.71 0.07 0.22
Matches are distributed among these distances:
19 11 0.03
20 124 0.38
21 21 0.06
22 18 0.06
23 15 0.05
24 22 0.07
25 19 0.06
26 97 0.30
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (25 bp):
ATGCATCCTTTCATGCATTTTAATT
Found at i:7836 original size:178 final size:182
Alignment explanation
Indices: 7393--7904 Score: 759
Period size: 178 Copynumber: 2.8 Consensus size: 182
7383 GTATTAACAT
* *
7393 ATCCTTTCAGGCCTTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
* * * *
7458 TTATGGA-AACCTTTTATGCCTTAATGCATCATTTCATGCATTTTAATTATGCCATCCTTTCATG
66 TTAT-GACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATG
* * *
7522 ACTTAATG-ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGT
130 CCTTAATGCATCCTTTCATGCA-CTTAA-TATGACATCCTTTCATGCCTTAATGC
7576 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
* * *
7641 TTAT-AGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTTATG
66 TTATGA-CATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATG
* *
7705 CCTTAATGCATCCTATCATGC-CTT-A-ATG-CATCCTTTCATGCCTTATTGC
130 CCTTAATGCATCCTTTCATGCACTTAATATGACATCCTTTCATGCCTTAATGC
* *
7754 ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATACATTTTAA
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
* *
7819 TTATGACATCCTTTCATGCCTTAATGCATCCCTTCATGCATTTTAATTATGACATCCTTTCATCC
66 TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATGC
* *
7884 CTTAATTCATCATTTCATGCA
131 CTTAATGCATCCTTTCATGCA
7905 TTTTAATTAC
Statistics
Matches: 301, Mismatches: 23, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
178 157 0.52
179 4 0.01
181 2 0.01
182 2 0.01
183 125 0.42
184 11 0.04
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.43
Consensus pattern (182 bp):
ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
TTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATGC
CTTAATGCATCCTTTCATGCACTTAATATGACATCCTTTCATGCCTTAATGC
Found at i:7837 original size:224 final size:226
Alignment explanation
Indices: 7393--7913 Score: 807
Period size: 224 Copynumber: 2.3 Consensus size: 226
7383 GTATTAACAT
* *
7393 ATCCTTTCAGGCCTTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
* *
7458 TTATGGAAACCTTTTATGCCTTAATGCATCATTTCATGCATTTTAATTATGCCATCCTTTCATGA
65 TTATGGAAACCTTTTATGCCTTAATGCATCATATCATGCA-CTTAA-TATGCCATCCTTTCATGA
* *
7523 CTTAATGATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGTATCCTTTCATGC
128 CTTAATGATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATAC
*
7588 ATTTTAATTATGGCATCCTTTCATGCCTTAATGC
193 ATTTTAATTATGACATCCTTTCATGCCTTAATGC
*
7622 ATCCTTTCATGCATTTTAATTATAGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTAT-GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
* * * *
7687 TTATGGCATCCTTTTATGCCTTAATGCATCCTATCATGC-CTT-A-ATG-CATCCTTTCATGCCT
65 TTATGGAAACCTTTTATGCCTTAATGCATCATATCATGCACTTAATATGCCATCCTTTCATGACT
*
7748 TATTGCATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATACA
130 TAATG-ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATACA
7813 TTTTAATTATGACATCCTTTCATGCCTTAATGC
194 TTTTAATTATGACATCCTTTCATGCCTTAATGC
* * * *
7846 ATCCCTTCATGCATTTTAATTATGACATCCTTTCATCCCTTAATTCATCATTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTATG-CATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
7911 TTA
65 TTA
7914 CTCTAAAACT
Statistics
Matches: 271, Mismatches: 19, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
223 19 0.07
224 153 0.56
226 1 0.00
227 2 0.01
229 96 0.35
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (226 bp):
ATCCTTTCATGCATTTTAATTATGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAAT
TATGGAAACCTTTTATGCCTTAATGCATCATATCATGCACTTAATATGCCATCCTTTCATGACTT
AATGATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATACATT
TTAATTATGACATCCTTTCATGCCTTAATGC
Found at i:8466 original size:95 final size:95
Alignment explanation
Indices: 8289--8498 Score: 271
Period size: 95 Copynumber: 2.2 Consensus size: 95
8279 TTGATACTAG
* * * * *
8289 TACCCTGGTACCGATACTTCTAAACTATAGTACCGATACCCCCTTTCGGTATTGATATCAATTTT
1 TACCATGGTATCGATACTACTAAACTATAGTACCGATACCCCCTTTCGGTATTGATACCAATTCT
* *
8354 AACTTCTACGTTTCCTGGTATCGATACCCT
66 AACTTCGACGTTGCCTGGTATCGATACCCT
** * * *
8384 TACCATGGTATCGATACTACTCTACTATGGTACCTATA-CCCCTTTACGGTATTGATACCGATTC
1 TACCATGGTATCGATACTACTAAACTATAGTACCGATACCCCCTTT-CGGTATTGATACCAATTC
*
8448 TAGA-TTCGATGTTGCCTGGTATCGATACCCT
65 TA-ACTTCGACGTTGCCTGGTATCGATACCCT
8479 TACCATGGTATCGATACTAC
1 TACCATGGTATCGATACTAC
8499 CTCGTAGGTA
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
94 7 0.07
95 92 0.92
96 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (95 bp):
TACCATGGTATCGATACTACTAAACTATAGTACCGATACCCCCTTTCGGTATTGATACCAATTCT
AACTTCGACGTTGCCTGGTATCGATACCCT
Found at i:14671 original size:20 final size:20
Alignment explanation
Indices: 14648--14686 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
14638 TTTTCACGTA
*
14648 TTAACATATCCTTTCATGCC
1 TTAACACATCCTTTCATGCC
**
14668 TTAATGCATCCTTTCATGC
1 TTAACACATCCTTTCATGC
14687 ATTTTAATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.28, G:0.08, T:0.41
Consensus pattern (20 bp):
TTAACACATCCTTTCATGCC
Found at i:14709 original size:26 final size:26
Alignment explanation
Indices: 14673--14875 Score: 174
Period size: 26 Copynumber: 8.5 Consensus size: 26
14663 ATGCCTTAAT
14673 GCATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
*
14699 GCATCCTTTCATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
*
14719 GCAT-CATTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
* **
14744 GTATCCTTTCATATATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
* *
14770 ACATCCTTTCATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
14790 GCATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
* *
14816 GAATCCTTTCATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
* *
14836 GCATCATTTCGTGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
14862 GCATCCTTTCATGC
1 GCATCCTTTCATGC
14876 GCTAATGCAT
Statistics
Matches: 136, Mismatches: 22, Indels: 38
0.69 0.11 0.19
Matches are distributed among these distances:
19 8 0.06
20 28 0.21
21 8 0.06
22 5 0.04
23 5 0.04
24 8 0.06
25 7 0.05
26 67 0.49
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAATTATG
Found at i:14744 original size:45 final size:46
Alignment explanation
Indices: 14655--14755 Score: 177
Period size: 45 Copynumber: 2.2 Consensus size: 46
14645 GTATTAACAT
*
14655 ATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGC
1 ATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAATTATGGC
*
14701 ATCCTTTCATGCCTTAATGCAT-CATTCATGCATTTTAATTATGGT
1 ATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAATTATGGC
14746 ATCCTTTCAT
1 ATCCTTTCAT
14756 ATATTTTAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
45 31 0.58
46 22 0.42
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (46 bp):
ATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAATTATGGC
Found at i:14752 original size:71 final size:72
Alignment explanation
Indices: 14675--14829 Score: 258
Period size: 71 Copynumber: 2.2 Consensus size: 72
14665 GCCTTAATGC
*
14675 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCAT-CATTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAA
*
14739 TTATGGT
66 TTATGGA
** *
14746 ATCCTTTCATATATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAA
14811 TTATGGA
66 TTATGGA
14818 ATCCTTTCATGC
1 ATCCTTTCATGC
14830 CTTAATGCAT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
71 45 0.59
72 31 0.41
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.45
Consensus pattern (72 bp):
ATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCATTCATGCATTTTAA
TTATGGA
Found at i:14796 original size:20 final size:20
Alignment explanation
Indices: 14771--14845 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
14761 TTAATTATGA
14771 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
14791 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGC--CTT-A--AT-G
*
14817 AATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
14837 CATCATTTC
1 CATCCTTTC
14846 GTGCATTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
20 21 0.48
21 2 0.05
22 2 0.05
23 2 0.05
24 2 0.05
25 2 0.05
26 13 0.30
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:14887 original size:46 final size:46
Alignment explanation
Indices: 14758--14890 Score: 214
Period size: 46 Copynumber: 2.9 Consensus size: 46
14748 CCTTTCATAT
* *
14758 ATTTTAATTATGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
14804 ATTTTAATTATGGAATCCTTTCATGCCTTAATGCATCATTTCGTGC
1 ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
14850 ATTTTAATTATGGCATCCTTTCATGCGC-TAATGCATCATTT
1 ATTTTAATTATGGCATCCTTTCATGC-CTTAATGCATCATTT
14891 ACTCTAAAAC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
46 80 0.99
47 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (46 bp):
ATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:19174 original size:16 final size:16
Alignment explanation
Indices: 19153--19211 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
19143 ATAAATGAAT
19153 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
19169 ATAAACGAATACGAAC
1 ATAAACGAACACGAAC
* *
19185 ATAAATGAACATGAAC
1 ATAAACGAACACGAAC
19201 ATAAACGAACA
1 ATAAACGAACA
19212 TAAACGTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:19194 original size:26 final size:26
Alignment explanation
Indices: 19165--19215 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
19155 AAACGAACAC
*
19165 GAACATAAACGA-ATACGAACATAAAT
1 GAACATAAAC-ATAAACGAACATAAAT
*
19191 GAACATGAACATAAACGAACATAAA
1 GAACATAAACATAAACGAACATAAA
19216 CGTTGGAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.59, C:0.16, G:0.12, T:0.14
Consensus pattern (26 bp):
GAACATAAACATAAACGAACATAAAT
Found at i:19212 original size:16 final size:16
Alignment explanation
Indices: 19147--19212 Score: 87
Period size: 16 Copynumber: 4.1 Consensus size: 16
19137 TAATAAATAA
*
19147 ATGAATATAAACGAAC
1 ATGAACATAAACGAAC
* *
19163 ACGAACATAAACGAAT
1 ATGAACATAAACGAAC
* *
19179 ACGAACATAAATGAAC
1 ATGAACATAAACGAAC
19195 ATGAACATAAACGAAC
1 ATGAACATAAACGAAC
19211 AT
1 AT
19213 AAACGTTGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.17, G:0.12, T:0.15
Consensus pattern (16 bp):
ATGAACATAAACGAAC
Found at i:19448 original size:12 final size:12
Alignment explanation
Indices: 19415--19454 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
19405 CTCAATACTG
19415 GATTCTAAGCTC
1 GATTCTAAGCTC
19427 GATTC-AAGCTC
1 GATTCTAAGCTC
*
19438 GATTCTGAGCTC
1 GATTCTAAGCTC
19450 GATTC
1 GATTC
19455 GAGATCGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (12 bp):
GATTCTAAGCTC
Found at i:19462 original size:23 final size:23
Alignment explanation
Indices: 19415--19462 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
19405 CTCAATACTG
*
19415 GATTCTAAGCTCGATTCAAGCTC
1 GATTCTAAGCTCGATTCAAGATC
* *
19438 GATTCTGAGCTCGATTCGAGATC
1 GATTCTAAGCTCGATTCAAGATC
19461 GA
1 GA
19463 CATTGCCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (23 bp):
GATTCTAAGCTCGATTCAAGATC
Found at i:20347 original size:24 final size:24
Alignment explanation
Indices: 20314--20391 Score: 104
Period size: 24 Copynumber: 3.2 Consensus size: 24
20304 TTGGGTTAAC
* * *
20314 CATAAATGAATGAACACAAACGAA
1 CATAACTGAAAGAACATAAACGAA
20338 CATAACTGAACA-AACATAAACGAA
1 CATAACTGAA-AGAACATAAACGAA
*
20362 CATAACCGAAAGAACATAAACGAA
1 CATAACTGAAAGAACATAAACGAA
20386 CATAAC
1 CATAAC
20392 CGAACGTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.02
24 47 0.98
ACGTcount: A:0.58, C:0.21, G:0.10, T:0.12
Consensus pattern (24 bp):
CATAACTGAAAGAACATAAACGAA
Found at i:20392 original size:24 final size:25
Alignment explanation
Indices: 20325--20396 Score: 112
Period size: 24 Copynumber: 3.0 Consensus size: 25
20315 ATAAATGAAT
* *
20325 GAACACAAACGAACATAACTGAACA
1 GAACATAAACGAACATAACCGAACA
20350 -AACATAAACGAACATAACCGAA-A
1 GAACATAAACGAACATAACCGAACA
20373 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
20397 GTTCACGAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.02
24 42 0.98
ACGTcount: A:0.57, C:0.24, G:0.11, T:0.08
Consensus pattern (25 bp):
GAACATAAACGAACATAACCGAACA
Found at i:23803 original size:3 final size:3
Alignment explanation
Indices: 23797--23842 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
23787 CAAAAAAATG
23797 TAA TAA TAAA TAA TAA TAA -AA -AA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
23840 TAA
1 TAA
23843 CGATAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.15
3 31 0.77
4 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:23815 original size:13 final size:13
Alignment explanation
Indices: 23797--23842 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
23787 CAAAAAAATG
23797 TAATAATAAATAA
1 TAATAATAAATAA
*
23810 TAATAAAAAATAA
1 TAATAATAAATAA
23823 TAATAAT-AATAA
1 TAATAATAAATAA
23835 TAA-AATAA
1 TAATAATAA
23843 CGATAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 3 0.10
12 9 0.30
13 18 0.60
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:24180 original size:43 final size:43
Alignment explanation
Indices: 24132--24296 Score: 124
Period size: 40 Copynumber: 3.8 Consensus size: 43
24122 TAAGGTGATA
* *
24132 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTAAGGTTG
* ** *
24175 ACACGGCTCCTACGTGATGAGGAGATCTGG---TCTGGGGATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTTG
* * ** ** *
24215 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-AAGGT--TG
*
24261 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCT
24297 CTAGGGATCA
Statistics
Matches: 96, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
40 34 0.35
42 1 0.01
43 29 0.30
44 2 0.02
46 29 0.30
47 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (43 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTTG
Found at i:24656 original size:15 final size:15
Alignment explanation
Indices: 24632--24675 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
24622 AAGATGATCT
*
24632 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
24647 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
24662 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
24676 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:24728 original size:31 final size:30
Alignment explanation
Indices: 24664--24738 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 30
24654 AGAGAAAATG
*
24664 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
*
24695 TTTCAAGTGAAACAAACTCAAAGAT-TTTGTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTT-TA
* *
24726 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
24739 TGCCTCAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 26 0.68
32 9 0.24
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:24859 original size:27 final size:27
Alignment explanation
Indices: 24828--24881 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
24818 CAAAATTTTG
24828 TTTC-AAAGGAAACAAACTCAAAGATTT
1 TTTCAAAAGG-AACAAACTCAAAGATTT
*
24855 TTTCAAAAGGAACAGACTCAAAGATTT
1 TTTCAAAAGGAACAAACTCAAAGATTT
24882 ATCTCAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (27 bp):
TTTCAAAAGGAACAAACTCAAAGATTT
Found at i:24888 original size:28 final size:28
Alignment explanation
Indices: 24832--24888 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
24822 ATTTTGTTTC
*
24832 AAAGGAAACAAACTCAAAGATTTTTTCA
1 AAAGGAAACAAACTCAAAGATTTTCTCA
*
24860 AAAGG-AACAGACTCAAAGATTTATCTCA
1 AAAGGAAACAAACTCAAAGATTT-TCTCA
24888 A
1 A
24889 GAGAAACTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (28 bp):
AAAGGAAACAAACTCAAAGATTTTCTCA
Found at i:25287 original size:105 final size:106
Alignment explanation
Indices: 25150--25347 Score: 292
Period size: 105 Copynumber: 1.9 Consensus size: 106
25140 ACGATCTCAA
* *
25150 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGGATCTCAAAGG-GAAAAGGTCTC
1 GTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAGGTCTC
25214 AAGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
66 AAGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
* * * * *
25255 GTGAGATTAATTTTGTTTTAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAATGTCT
1 GTGAGATCAACTTTG-TTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAGGTCT
* *
25319 CAAGCGAGACGAAGTTTGTTTTAAGAGAA
65 CAAGCGAGACGAAATTTGTTTTAAAAGAA
25348 TTTGTCTCAA
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
105 42 0.51
106 40 0.49
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.30
Consensus pattern (106 bp):
GTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAAGGTCTC
AAGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCTAAG
Found at i:25354 original size:36 final size:36
Alignment explanation
Indices: 25314--25450 Score: 163
Period size: 36 Copynumber: 3.8 Consensus size: 36
25304 AAGGAAAAAA
* * *
25314 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
* *
25350 TGTCTCAAACGAGACAAAATTTGTTTT--GAGAAAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAA-T
**
25385 TGTCTCAAGCGAGACAAAATTTGCTTCGAA-AGAAAT
1 TGTCTCAAGCGAGACAAAATTTG-TTTTAAGAGAAAT
25421 TGTCTCAAGCGAGACAAAAATTTGTTTTAA
1 TGTCTCAAGCGAGAC-AAAATTTGTTTTAA
25451 AATTCTCAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
34 5 0.06
35 22 0.26
36 45 0.53
37 13 0.15
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
Found at i:25424 original size:71 final size:72
Alignment explanation
Indices: 25314--25448 Score: 193
Period size: 71 Copynumber: 1.9 Consensus size: 72
25304 AAGGAAAAAA
* * ** *
25314 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATTTGTCTCAAACGAGAC-AAAATTTGTTTTG
1 TGTCTCAAGCGAGACAAAATTTGTTCGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTG
25378 AGAAAGC
66 AGAAAGC
*
25385 TGTCTCAAGCGAGACAAAATTTGCTTCGAA-AGAAATTGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTG-TTCGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTT
25449 AAAATTCTCA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
71 40 0.71
72 16 0.29
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (72 bp):
TGTCTCAAGCGAGACAAAATTTGTTCGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTG
AGAAAGC
Found at i:25820 original size:4 final size:4
Alignment explanation
Indices: 25804--25849 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
25794 GCAAATTTTA
*
25804 TATG TAT- TATG TATG TATG --TG TATA TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
25849 T
1 T
25850 TTTCTCGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 3 0.08
4 32 0.86
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:25834 original size:18 final size:17
Alignment explanation
Indices: 25806--25841 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
25796 AAATTTTATA
25806 TGTATTATGTATGTATG
1 TGTATTATGTATGTATG
25823 TGTATATATGTATGTATG
1 TGTAT-TATGTATGTATG
25841 T
1 T
25842 ATGTATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (17 bp):
TGTATTATGTATGTATG
Found at i:33082 original size:3 final size:3
Alignment explanation
Indices: 33076--33124 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
33066 CAAAAAAATG
33076 TAA TAA TAAA TAA TAA TAA -AA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
33120 -AA TAA
1 TAA TAA
33125 CGATAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.14
3 34 0.79
4 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:33094 original size:13 final size:13
Alignment explanation
Indices: 33076--33119 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
33066 CAAAAAAATG
33076 TAATAATAAATAA
1 TAATAATAAATAA
*
33089 TAATAAAAAATAA
1 TAATAATAAATAA
33102 TAATAAT-AATAA
1 TAATAATAAATAA
33114 TAATAA
1 TAATAA
33120 AATAACGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAATAATAAATAA
Found at i:33096 original size:25 final size:25
Alignment explanation
Indices: 33068--33121 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
33058 TTGGCCTGCA
*
33068 AAAAAAT-GTAATAATAAATAATAAT
1 AAAAAATAATAATAAT-AATAATAAT
33093 AAAAAATAATAATAATAATAATAAT
1 AAAAAATAATAATAATAATAATAAT
33118 AAAA
1 AAAA
33122 TAACGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (25 bp):
AAAAAATAATAATAATAATAATAAT
Found at i:34788 original size:16 final size:16
Alignment explanation
Indices: 34752--34792 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
34742 ATAAAAATTT
*
34752 AATTTCATAG-ATAAA
1 AATTTTATAGTATAAA
34767 AA-TTTATAGTATAAA
1 AATTTTATAGTATAAA
34782 AATTTTATAGT
1 AATTTTATAGT
34793 TTCATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 6 0.26
15 9 0.39
16 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (16 bp):
AATTTTATAGTATAAA
Found at i:37213 original size:35 final size:34
Alignment explanation
Indices: 37152--37221 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 34
37142 TTTTATTACT
*
37152 TCAACATACTTTTTCATTTTACTTAAACTCTTGCC
1 TCAACATACTTTTTAATTTTA-TTAAACTCTTGCC
*
37187 TCAACATACTTTTATAATTTCT-TTAAACTTTTGCC
1 TCAACATACTTTT-TAATTT-TATTAAACTCTTGCC
37222 ATAGCATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 25 0.81
36 5 0.16
37 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (34 bp):
TCAACATACTTTTTAATTTTATTAAACTCTTGCC
Found at i:37991 original size:53 final size:53
Alignment explanation
Indices: 37928--38091 Score: 258
Period size: 53 Copynumber: 3.1 Consensus size: 53
37918 ACTAAGGTCA
*
37928 CGAAATGGTAATTCACAAACTTATTATGAATACCAT-GAGTGCACACATAGTGC
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGA-TGCACACATAGTGC
*
37981 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGT
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGC
* * *
38034 CGAAATGGTAATTCAAAAACTCATTATGAATACCATGGATGCATACACAGTGC
1 CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGC
*
38087 TGAAA
1 CGAAA
38092 GTACACAAAG
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 101 0.98
54 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (53 bp):
CGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGC
Found at i:42600 original size:2 final size:2
Alignment explanation
Indices: 42593--42622 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42583 AAATACATAC
42593 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
42623 TAAATACATC
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44012 original size:90 final size:89
Alignment explanation
Indices: 43902--44073 Score: 308
Period size: 90 Copynumber: 1.9 Consensus size: 89
43892 CTGACTATTT
* *
43902 AATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATTTGATTAGGA
1 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAGGA
43967 TAACTTGGATATAAAAGGATTAATA
65 TAACTTGGATATAAAAGGATTAATA
43992 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGAT
1 AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGAT
*
44057 AACTTGGCTATAAAAGG
66 AACTTGGATATAAAAGG
44074 GTGTGTTAGG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 33 0.42
90 46 0.58
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (89 bp):
AATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGAT
AACTTGGATATAAAAGGATTAATA
Found at i:55868 original size:20 final size:20
Alignment explanation
Indices: 55843--55914 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
55833 CCAAGGTTCC
*
55843 AGTATCGATACTCGCATATG
1 AGTATCAATACTCGCATATG
*
55863 AGTATCAATACTCACATATG
1 AGTATCAATACTCGCATATG
55883 AGTATCAATACTCGCATATG
1 AGTATCAATACTCGCATATG
55903 AGTATCAATACT
1 AGTATCAATACT
55915 TCCCATAACC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (20 bp):
AGTATCAATACTCGCATATG
Found at i:60490 original size:174 final size:174
Alignment explanation
Indices: 60178--60526 Score: 671
Period size: 175 Copynumber: 2.0 Consensus size: 174
60168 GCATCTAAAC
60178 CTAAAAGAAGAATAACAACACCAAAGGGGAAAAAACATGATATACGGTTGCACAAGTGCTTGAGG
1 CTAAAAGAAGAATAACAACACCAAAGGGGAAAAAACATGATATACGGTTGCACAAGTGCTTGAGG
60243 AAGACCAACAGGAGAGGGGAAAAAAGAAAAAGTTTGGGTTTGATTAATCATTTGATGTGATCATC
66 AAGACCAACAGGAGAGGGGAAAAAAGAAAAAGTTTGGGTTTGATTAATCATTTGATGTGATCATC
60308 CAAAAAAAACGATACAATATTCAAAGTTCCTTTTTTATTGTCTT
131 CAAAAAAAACGATACAATATTCAAAGTTCCTTTTTTATTGTCTT
*
60352 CTAAAAGAAGAATAACAACACCCAAGGGGAAAAAACATGATATACGGTTGCACAAGTGCTTGAGG
1 CTAAAAGAAGAATAACAACACCAAAGGGGAAAAAACATGATATACGGTTGCACAAGTGCTTGAGG
*
60417 AAGACCAACAGGAGAGGGGAAAAAAAGGAAAAGTTTGGGTTTGATTAATCATTTGATGTGATCAT
66 AAGACCAACAGGAGAGGGG-AAAAAAGAAAAAGTTTGGGTTTGATTAATCATTTGATGTGATCAT
60482 CCAAAAAAAACGATACAATATTCAAAGTTCCTTTTTTATTGTCTT
130 CCAAAAAAAACGATACAATATTCAAAGTTCCTTTTTTATTGTCTT
60527 TTACCCTTTT
Statistics
Matches: 172, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
174 83 0.48
175 89 0.52
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (174 bp):
CTAAAAGAAGAATAACAACACCAAAGGGGAAAAAACATGATATACGGTTGCACAAGTGCTTGAGG
AAGACCAACAGGAGAGGGGAAAAAAGAAAAAGTTTGGGTTTGATTAATCATTTGATGTGATCATC
CAAAAAAAACGATACAATATTCAAAGTTCCTTTTTTATTGTCTT
Found at i:63085 original size:3 final size:3
Alignment explanation
Indices: 63071--63152 Score: 67
Period size: 3 Copynumber: 27.0 Consensus size: 3
63061 ATTGGGCTTG
* * * *
63071 TAA TATA TAA TAA TAA TATT TAT TAA TAA TAA TAA AAA T-T TAA TAA
1 TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
63117 TTA TAA TAA TTA TAA TAA TAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
63153 AACGGTAAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
2 1 0.02
3 56 0.90
4 5 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:63824 original size:22 final size:22
Alignment explanation
Indices: 63797--63847 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
63787 CATTATGAAC
63797 TTCTTCTTCCTCTTCAGATAGG
1 TTCTTCTTCCTCTTCAGATAGG
63819 TTCTTCTTCCTCTTCAGATAGG
1 TTCTTCTTCCTCTTCAGATAGG
63841 TTCTTCT
1 TTCTTCT
63848 CATTATGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.12, C:0.27, G:0.12, T:0.49
Consensus pattern (22 bp):
TTCTTCTTCCTCTTCAGATAGG
Found at i:63827 original size:42 final size:39
Alignment explanation
Indices: 63740--63825 Score: 154
Period size: 39 Copynumber: 2.2 Consensus size: 39
63730 GGTTGATCAA
* *
63740 GTTCTTCTCATTATGAACTTCTTTTTCGTCTTCAGATAG
1 GTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAG
63779 GTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAG
1 GTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAG
63818 GTTCTTCT
1 GTTCTTCT
63826 TCCTCTTCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.16, C:0.23, G:0.12, T:0.49
Consensus pattern (39 bp):
GTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAG
Found at i:72830 original size:15 final size:15
Alignment explanation
Indices: 72810--72841 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
72800 TGCAATGAAT
72810 AATGAATGTATGCAA
1 AATGAATGTATGCAA
72825 AATGAATGTATGCAA
1 AATGAATGTATGCAA
72840 AA
1 AA
72842 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:76078 original size:25 final size:25
Alignment explanation
Indices: 76028--76086 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
76018 TTAATACTTG
76028 AAAATAAAATAAAAACATTAATAAA
1 AAAATAAAATAAAAACATTAATAAA
* * *
76053 AAAATAATATATAAATATT-ATGAAA
1 AAAATAAAATAAAAACATTAAT-AAA
*
76078 ATAATAAAA
1 AAAATAAAA
76087 ATTTTGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (25 bp):
AAAATAAAATAAAAACATTAATAAA
Found at i:78383 original size:3 final size:3
Alignment explanation
Indices: 78375--78461 Score: 77
Period size: 3 Copynumber: 29.0 Consensus size: 3
78365 CTGTAATATG
* * * *
78375 TAA TAA TAA TATT TAT TAA TAA TAA TAA AAA T-A TAA TAA TAA TTA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
78420 TAA TTA TAA CAA TTA TAA TAA TTA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
78462 AACGGACAAA
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
2 2 0.03
3 62 0.94
4 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:81226 original size:9 final size:9
Alignment explanation
Indices: 81212--81251 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
81202 GTGGCTGAAA
81212 ACCGGTTTG
1 ACCGGTTTG
81221 ACCGGTTTCG
1 ACCGGTTT-G
*
81231 ACCAGTTTG
1 ACCGGTTTG
*
81240 ACCGGTCTG
1 ACCGGTTTG
81249 ACC
1 ACC
81252 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:81273 original size:17 final size:17
Alignment explanation
Indices: 81251--81283 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
81241 CCGGTCTGAC
81251 CCGACCCGACCGTTGAA
1 CCGACCCGACCGTTGAA
81268 CCGACCCGACCGTTGA
1 CCGACCCGACCGTTGA
81284 CCGTTGACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.42, G:0.24, T:0.12
Consensus pattern (17 bp):
CCGACCCGACCGTTGAA
Found at i:81287 original size:7 final size:7
Alignment explanation
Indices: 81275--81305 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
81265 GAACCGACCC
81275 GACCGTT
1 GACCGTT
81282 GACCGTT
1 GACCGTT
81289 GACCG-T
1 GACCGTT
81295 GACCGTT
1 GACCGTT
81302 GACC
1 GACC
81306 TCCTTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:81299 original size:13 final size:14
Alignment explanation
Indices: 81275--81305 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
81265 GAACCGACCC
81275 GACCGTTGACCGTT
1 GACCGTTGACCGTT
81289 GACCG-TGACCGTT
1 GACCGTTGACCGTT
81302 GACC
1 GACC
81306 TCCTTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:88417 original size:17 final size:17
Alignment explanation
Indices: 88395--88433 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
88385 CGAACCGATC
*
88395 TGACCCGACCCGACTGT
1 TGACCCGACCCGACCGT
88412 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
88429 TGACC
1 TGACC
88434 GTTGACCGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.44, G:0.23, T:0.15
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:88447 original size:6 final size:7
Alignment explanation
Indices: 88423--88460 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
88413 GACCCGACCC
88423 GACCGTT
1 GACCGTT
88430 GACCGTT
1 GACCGTT
88437 GACCG-T
1 GACCGTT
88443 GACCGTT
1 GACCGTT
*
88450 AACCGTT
1 GACCGTT
88457 GACC
1 GACC
88461 TCCTTTAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:88447 original size:13 final size:14
Alignment explanation
Indices: 88423--88460 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
88413 GACCCGACCC
88423 GACCGTTGACCGTT
1 GACCGTTGACCGTT
88437 GACCG-TGACCGTT
1 GACCGTTGACCGTT
*
88450 AACCGTTGACC
1 GACCGTTGACC
88461 TCCTTTAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:88448 original size:20 final size:20
Alignment explanation
Indices: 88423--88460 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
88413 GACCCGACCC
*
88423 GACCGTTGACCGTTGACCGT
1 GACCGTTAACCGTTGACCGT
88443 GACCGTTAACCGTTGACC
1 GACCGTTAACCGTTGACC
88461 TCCTTTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (20 bp):
GACCGTTAACCGTTGACCGT
Found at i:90847 original size:15 final size:16
Alignment explanation
Indices: 90827--90859 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
90817 ATATTTTTTT
*
90827 ATTAATTTTAA-AATA
1 ATTAATATTAATAATA
90842 ATTAATATTAATAATA
1 ATTAATATTAATAATA
90858 AT
1 AT
90860 ATTTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAATATTAATAATA
Found at i:90989 original size:28 final size:29
Alignment explanation
Indices: 90945--91008 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
90935 ATCATAGTCT
* * *
90945 TAATATTTTATTTATAAAA-TTATATAAA
1 TAATATTTTAATAATAAAACTGATATAAA
*
90973 TAATATTTTAATAATAAAACTGATGTAAA
1 TAATATTTTAATAATAAAACTGATATAAA
91002 TAATATT
1 TAATATT
91009 AAATAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (29 bp):
TAATATTTTAATAATAAAACTGATATAAA
Done.