Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008009.1 Hibiscus syriacus cultivar Beakdansim tig00110471_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: 287486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4165 original size:21 final size:21
Alignment explanation
Indices: 4139--4186 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
4129 CCTAATATTG
4139 CAATGTCAAAATTAGGTACAA
1 CAATGTCAAAATTAGGTACAA
*
4160 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTACAA
*
4181 TAATGT
1 CAATGT
4187 TTGAAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTACAA
Found at i:7177 original size:23 final size:24
Alignment explanation
Indices: 7145--7207 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
7135 AACGACTAAA
7145 AATGTATCATAAAGACAG-AGAAT
1 AATGTATCATAAAGACAGAAGAAT
* **
7168 AATGTGTCATAAAGGTAGAAGAAT
1 AATGTATCATAAAGACAGAAGAAT
* *
7192 -ACGTTTCATAAAGACA
1 AATGTATCATAAAGACA
7208 AAATTATTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
23 27 0.84
24 5 0.16
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (24 bp):
AATGTATCATAAAGACAGAAGAAT
Found at i:9867 original size:20 final size:20
Alignment explanation
Indices: 9827--9867 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
9817 TTAGTTATAT
* * *
9827 TCTATTATTTTTATTATAAA
1 TCTAATATTTTTATAACAAA
9847 TCTAATATTTTTATAACAAA
1 TCTAATATTTTTATAACAAA
9867 T
1 T
9868 AAGATAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (20 bp):
TCTAATATTTTTATAACAAA
Found at i:10115 original size:22 final size:22
Alignment explanation
Indices: 10090--10137 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
10080 CTCGAGTTTC
*
10090 TTTCGATTCGGGTTAATTTCGA
1 TTTCGATTCGGGTTAATTTCAA
** *
10112 TTTCGATTTTGGTTGATTTCAA
1 TTTCGATTCGGGTTAATTTCAA
10134 TTTC
1 TTTC
10138 ACTAAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.12, G:0.19, T:0.52
Consensus pattern (22 bp):
TTTCGATTCGGGTTAATTTCAA
Found at i:19556 original size:83 final size:83
Alignment explanation
Indices: 19412--19682 Score: 389
Period size: 83 Copynumber: 3.2 Consensus size: 83
19402 CTGAATGAAA
* * *
19412 TCGAACTCGTCAGGTCTTTAGTTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATG
1 TCGAACTCG-AAGGTCTTT-GTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
19477 TGCCTTGGAGCTGAGCGTAG
64 TGCCTTGGAGCTGAGCGTAG
** * * * * *
19497 TCGAACTCGAAGGTCTTTGTTGGCAGATTGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
* *
19562 CCTTTGAGCTGAGCGTGG
66 CCTTGGAGCTGAGCGTAG
* * *
19580 TCGAACTCGAAGGTTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTATGAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
19645 CCTTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
19663 TCGAACTCGAAGGTCTTTGT
1 TCGAACTCGAAGGTCTTTGT
19683 GTTTCAAGAG
Statistics
Matches: 161, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
83 144 0.89
84 8 0.05
85 9 0.06
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
CCTTGGAGCTGAGCGTAG
Found at i:19730 original size:28 final size:28
Alignment explanation
Indices: 19684--19774 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 28
19674 GGTCTTTGTG
*
19684 TTTCAAGAGAAA-TATTTTCAAAGGTTTT
1 TTTCAAGAGAAACGA-TTTCAAAGGTTTT
19712 TTTCAAGAGAAACGATTTCAAAGGTTTTTTGT
1 TTTCAAGAGAAACGATTTCAAAGG---TTT-T
* *
19744 GTTTCAAGAGAAACGACTTCAAAGGATTT
1 -TTTCAAGAGAAACGATTTCAAAGGTTTT
19773 TT
1 TT
19775 GTGTTTCAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
28 23 0.43
29 2 0.04
30 2 0.04
31 3 0.06
32 1 0.02
33 23 0.43
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (28 bp):
TTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:19753 original size:33 final size:32
Alignment explanation
Indices: 19672--19790 Score: 149
Period size: 33 Copynumber: 3.8 Consensus size: 32
19662 GTCGAACTCG
* *
19672 AAGGTCTTTGTGTTTCAAGAGAAA-TATTTTCA
1 AAGGTTTTTGTGTTTCAAGAGAAACGA-TTTCA
19704 AAGG--TTT-T-TTTCAAGAGAAACGATTTCA
1 AAGGTTTTTGTGTTTCAAGAGAAACGATTTCA
*
19732 AAGGTTTTTTGTGTTTCAAGAGAAACGACTTCA
1 AAGG-TTTTTGTGTTTCAAGAGAAACGATTTCA
19765 AAGGATTTTTGTGTTTCAAGAGAAAC
1 AAGG-TTTTTGTGTTTCAAGAGAAAC
19791 TGTCTCCAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
28 21 0.27
29 2 0.03
30 3 0.04
31 3 0.04
32 5 0.06
33 44 0.56
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (32 bp):
AAGGTTTTTGTGTTTCAAGAGAAACGATTTCA
Found at i:19895 original size:37 final size:36
Alignment explanation
Indices: 19845--19948 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 36
19835 AAAATTGGTG
19845 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTCA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTCA
* **
19882 TTTCAAGTGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCA
* * *
19918 GTTCAAAAAGAAACTGTCTCAAGGGAGACAA
1 TTTC-AAGAGAAACTGTCTCAAGAGAGACAA
19949 TGGTGAGCAC
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 5 0.08
37 54 0.92
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.22
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCA
Found at i:20493 original size:106 final size:106
Alignment explanation
Indices: 20071--21163 Score: 1902
Period size: 106 Copynumber: 10.3 Consensus size: 106
20061 TGTTTCGAGG
* *
20071 CCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
* *
20135 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTTGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
20176 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
* * *
20240 CGGTCCCTTCGCCGTGAAGTTGAACTTACGTTGTCTTGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
20281 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTTATTGACAAC
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA---GTTGTTTGTTGACAAC
20346 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
63 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
20390 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
20455 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
20496 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
20561 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
20602 GCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
20667 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
20708 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
20773 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
20814 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAAAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
20879 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
20920 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
20985 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
21026 CCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
*
21091 TGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
21132 CCAATATCCTTCGTTGTGAAGTTGAAATTGGC
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGGC
21164 ACTCGAGCAA
Statistics
Matches: 957, Mismatches: 27, Indels: 7
0.97 0.03 0.01
Matches are distributed among these distances:
105 149 0.16
106 708 0.74
108 4 0.00
109 96 0.10
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:26676 original size:106 final size:106
Alignment explanation
Indices: 26509--27227 Score: 1305
Period size: 106 Copynumber: 6.8 Consensus size: 106
26499 TTGTTGGTTA
26509 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
26574 TTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTA
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
26615 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
26680 CTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTG
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
26721 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
26786 CTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTATTTG
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
*
26827 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATACTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
26892 CTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTTG
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
26933 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
26998 CTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAGTTGTTTG
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
*
27039 TTGACAA-CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCATTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
27103 TTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTG
66 CTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
*
27144 TTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
1 TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
27209 TTGTGAAGTTGAAATTGGC
66 CTGTGAAGTTGAAATTGGC
27228 ACTCGAGCAA
Statistics
Matches: 597, Mismatches: 15, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
105 101 0.17
106 496 0.83
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
CTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG
Found at i:35762 original size:30 final size:30
Alignment explanation
Indices: 35726--35798 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
35716 CCCGAAGGAC
*
35726 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
35756 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAA
*
35786 CTATCCATAGGTC
1 CTATCCAGAGGTC
35799 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCAGTAA
Found at i:35838 original size:31 final size:31
Alignment explanation
Indices: 35784--35876 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
35774 GATCCTCAGT
* *
35784 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
35815 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
35846 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
35877 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:38742 original size:23 final size:23
Alignment explanation
Indices: 38709--38798 Score: 117
Period size: 23 Copynumber: 3.9 Consensus size: 23
38699 GTCGAGGGTT
*
38709 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
* * * * *
38732 TTATATGGTCCTTTGGGACAAAC
1 CTATGTGGTCATTCGGGACAAAA
*
38755 CTATGTGGTCATTCGAGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
38778 CTATGTGGTCATTCGGGACAA
1 CTATGTGGTCATTCGGGACAA
38799 TTTCTATGTT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAA
Found at i:40799 original size:27 final size:27
Alignment explanation
Indices: 40762--40828 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
40752 TTAATGACAC
40762 ACAA-ATTTTGTGTGCTATTACTCATA
1 ACAATATTTTGTGTGCTATTACTCATA
40788 ACAATATTTTGTGTGCTATTACTCATA
1 ACAATATTTTGTGTGCTATTACTCATA
40815 ACAATATCTTTGTG
1 ACAATAT-TTTGTG
40829 CATTTTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 4 0.10
27 29 0.74
28 6 0.15
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (27 bp):
ACAATATTTTGTGTGCTATTACTCATA
Found at i:41025 original size:15 final size:16
Alignment explanation
Indices: 40994--41027 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40984 TCTAATTTAA
40994 TTATTTAATAACTATT
1 TTATTTAATAACTATT
*
41010 TTATTT-ATATCTATT
1 TTATTTAATAACTATT
41025 TTA
1 TTA
41028 CCGTCAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTTAATAACTATT
Found at i:51787 original size:12 final size:12
Alignment explanation
Indices: 51770--51795 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
51760 TGACTACTCA
51770 TCGCTCTCGCCT
1 TCGCTCTCGCCT
51782 TCGCTCTCGCCT
1 TCGCTCTCGCCT
51794 TC
1 TC
51796 TTCTTCGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.50, G:0.15, T:0.35
Consensus pattern (12 bp):
TCGCTCTCGCCT
Found at i:55714 original size:20 final size:20
Alignment explanation
Indices: 55689--56024 Score: 294
Period size: 20 Copynumber: 16.6 Consensus size: 20
55679 GATTTTCCAG
* * *
55689 AATCGCAACGCGGATATGAA
1 AATCGCAACGCGAATACGTA
* **
55709 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
55729 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
55748 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
55770 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
55790 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
55811 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
55831 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
55851 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
55871 AATCGCAACGC--ATATCTGTA
1 AATCGCAACGCGAATA-C-GTA
*
55891 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
55911 AATCGCAACGC--ATATCTGTA
1 AATCGCAACGCGAATA-C-GTA
*
55931 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
55951 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
55971 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
*
55992 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
56012 AATCGCAACGCGA
1 AATCGCAACGCGA
56025 TTTTTAAAGC
Statistics
Matches: 264, Mismatches: 33, Indels: 38
0.79 0.10 0.11
Matches are distributed among these distances:
18 7 0.03
19 4 0.02
20 190 0.72
21 55 0.21
22 8 0.03
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:55901 original size:60 final size:61
Alignment explanation
Indices: 55750--56021 Score: 331
Period size: 60 Copynumber: 4.5 Consensus size: 61
55740 GATTCTGACT
* * *
55750 ATCGCAACG-AGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCA-TATCCGT-AAATCGCAACGAGAATACGTAAATCGCAACGACAATACGTAAA
* *
55812 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGAGAATACGT-AA
1 ATCGCAACGCATATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGACAATACGTAAA
*
55872 ATCGCAACGCATATCTGTAAATCGCAACGAGAATACGTAAATCGCAACG-C-ATATCTGT-AA
1 ATCGCAACGCATATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGACAATA-C-GTAAA
* * * * * *
55932 ATCGCAACG-AGAATACGTAAATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCA-TATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGACAATACGTAAA
* *
55993 ATCGCAACGCGTATCTGTAAATCGCAACG
1 ATCGCAACGCATATCCGTAAATCGCAACG
56022 CGATTTTTAA
Statistics
Matches: 182, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
58 3 0.02
59 2 0.01
60 95 0.52
61 63 0.35
62 19 0.10
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (61 bp):
ATCGCAACGCATATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGACAATACGTAAA
Found at i:56609 original size:20 final size:19
Alignment explanation
Indices: 56581--56652 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
56571 TTCTAAACTT
56581 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
*
56601 AAAAGCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
56621 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
56642 AAAATCGCAAC
1 AAAATCGCAAC
56653 GCGAAACCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.51, C:0.19, G:0.18, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:56692 original size:19 final size:19
Alignment explanation
Indices: 56670--56810 Score: 104
Period size: 19 Copynumber: 7.8 Consensus size: 19
56660 CAAAATTGCA
56670 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
56689 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
*
56703 TTGCGATTTTAATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
56722 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
56736 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
** * *
56755 TTGCGATAGTCATTTCCACA
1 TTGCGATTTTCATTT-CGCG
** *
56775 TTGCGATAGTCATTCTCTCG
1 TTGCGATTTTCATT-TCGCG
56795 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
56811 AACCAAAAGA
Statistics
Matches: 96, Mismatches: 14, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
14 20 0.21
16 5 0.05
17 5 0.05
19 35 0.36
20 30 0.31
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:56706 original size:14 final size:14
Alignment explanation
Indices: 56687--56743 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
56677 TTTCATTTCG
56687 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
56701 CGTTGCGATTTTAATTTCG
1 CGTTGCGA---T--TCTCT
56720 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
56734 CGTTGCGATT
1 CGTTGCGATT
56744 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 21 0.62
16 1 0.03
17 1 0.03
19 11 0.32
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:56712 original size:33 final size:33
Alignment explanation
Indices: 56670--56761 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
56660 CAAAATTGCA
56670 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
56703 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
56736 TTGCGATTTTCATTTCGCGTTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
56762 AGTCATTTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:56808 original size:20 final size:19
Alignment explanation
Indices: 56731--56801 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 19
56721 GTTGCGATTC
**
56731 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATAGTCATT
*
56750 TCGCGTTGCGATAGTCATT
1 TCTCGTTGCGATAGTCATT
* *
56769 TCCACATTGCGATAGTCATT
1 T-CTCGTTGCGATAGTCATT
56789 CTCTCGTTGCGAT
1 -TCTCGTTGCGAT
56802 TTTCATTTCA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 17 0.40
20 25 0.58
21 1 0.02
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (19 bp):
TCTCGTTGCGATAGTCATT
Found at i:58701 original size:94 final size:93
Alignment explanation
Indices: 58413--58791 Score: 634
Period size: 94 Copynumber: 4.1 Consensus size: 93
58403 TAGATTGCTT
* * *
58413 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGCTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
58478 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
58507 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACA-TGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
58571 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
58600 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
*
58665 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
58694 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTTTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
58759 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
58787 AGTAA
1 AGTAA
58792 TGCAATTCAT
Statistics
Matches: 272, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
92 20 0.07
93 75 0.28
94 177 0.65
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:58728 original size:187 final size:187
Alignment explanation
Indices: 58413--58791 Score: 654
Period size: 187 Copynumber: 2.0 Consensus size: 187
58403 TAGATTGCTT
*
58413 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGCTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGCTAAT
*
58478 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
66 ATTTGTCTTTTGTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
58543 TGTGTATTCTTTAACA-TGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
58600 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAAT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGCTAAT
*
58665 ATTTGTC-TTTGTTTTATCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAA
66 ATTTGTCTTTTGTTTTATCTTTTGGTTG-AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAA
* *
58729 CTGTGTATTCTTTAATACTTTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
130 CTGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
58787 AGTAA
1 AGTAA
58792 TGCAATTCAT
Statistics
Matches: 182, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
186 19 0.10
187 125 0.69
188 38 0.21
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (187 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTGAAGCTAAT
ATTTGTCTTTTGTTTTATCTTTTGGTTGAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAAC
TGTGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:58895 original size:19 final size:19
Alignment explanation
Indices: 58855--58947 Score: 107
Period size: 19 Copynumber: 4.8 Consensus size: 19
58845 CACAAAACTT
*
58855 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
*
58876 AATATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
58895 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
58914 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAA-TG
*
58933 ATAATCGCAACGCGA
1 AAAATCGCAACGCGA
58948 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
19 52 0.81
21 12 0.19
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:59004 original size:20 final size:20
Alignment explanation
Indices: 58979--59061 Score: 112
Period size: 20 Copynumber: 4.2 Consensus size: 20
58969 CTCTCGTTGT
**
58979 GATAGTCAAATTCGCATTGC
1 GATAGTCATTTTCGCATTGC
* *
58999 GATAGTCATTTTCGTATTGT
1 GATAGTCATTTTCGCATTGC
*
59019 TATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
*
59039 GATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCATTGC
59059 GAT
1 GAT
59062 TTTAAGTTTC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:59035 original size:40 final size:40
Alignment explanation
Indices: 58975--59052 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
58965 GATTCTCTCG
58975 TTGTGATAGTCAAATTCGCATTGCGATAGTCATTTTCGTA
1 TTGTGATAGTCAAATTCGCATTGCGATAGTCATTTTCGTA
* **
59015 TTGTTATAGTCATTTTCGCATTGCGATAGTCATTTTCG
1 TTGTGATAGTCAAATTCGCATTGCGATAGTCATTTTCG
59053 CGTTGCGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.44
Consensus pattern (40 bp):
TTGTGATAGTCAAATTCGCATTGCGATAGTCATTTTCGTA
Found at i:60975 original size:33 final size:34
Alignment explanation
Indices: 60922--61002 Score: 110
Period size: 33 Copynumber: 2.4 Consensus size: 34
60912 CTATCGCAAC
** *
60922 GCGAAAATGACTATCGCAACGAGAGAATCACAAT
1 GCGAAAATGAAAATCACAACGAGAGAATCACAAT
* *
60956 GCG-AAATGAAAATCACAACGAGCGAATCGCAAT
1 GCGAAAATGAAAATCACAACGAGAGAATCACAAT
60989 GCGAAAATGAAAAT
1 GCGAAAATGAAAAT
61003 TGCAACGTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
33 28 0.68
34 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (34 bp):
GCGAAAATGAAAATCACAACGAGAGAATCACAAT
Found at i:61017 original size:25 final size:25
Alignment explanation
Indices: 60987--61034 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
60977 GCGAATCGCA
*
60987 ATGCGAAAATGAAAATTGCAACGTG
1 ATGCGAAAATGAAAATCGCAACGTG
61012 ATGCGAAAATGAAAATCGCAACG
1 ATGCGAAAATGAAAATCGCAACG
61035 CGAAACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.17
Consensus pattern (25 bp):
ATGCGAAAATGAAAATCGCAACGTG
Found at i:61065 original size:19 final size:19
Alignment explanation
Indices: 61043--61149 Score: 134
Period size: 19 Copynumber: 5.8 Consensus size: 19
61033 CGCGAAACTA
*
61043 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
61062 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
61080 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
61096 ATTTCGCATTACGATTTTC
1 ATTTCGCATTGCGATTTTC
*
61115 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
61134 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
61150 CTCTCGTTGC
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 3 0.04
18 4 0.05
19 43 0.57
20 12 0.16
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:61111 original size:33 final size:33
Alignment explanation
Indices: 61049--61171 Score: 147
Period size: 33 Copynumber: 3.5 Consensus size: 33
61039 ACTAATTTCG
61049 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* *
61083 CGTTGCGATTTTCATTTCGCATTACGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCGCATTGCGA--TTCA---CT
*
61121 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
61154 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
61172 CGCGTTGCAT
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
33 29 0.38
34 14 0.18
35 4 0.05
36 3 0.04
38 27 0.35
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:61134 original size:38 final size:38
Alignment explanation
Indices: 61043--61149 Score: 152
Period size: 38 Copynumber: 2.9 Consensus size: 38
61033 CGCGAAACTA
61043 ATTTCGCGTTGCGATTTTCATTTTCGCATTGCGA--TTC
1 ATTTCGCGTTGCGATTTTCA-TTTCGCATTGCGATTTTC
* *
61080 A---CTCGTTGCGATTTTCATTTCGCATTACGATTTTC
1 ATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTC
61115 ATTTCGCGTTGCGATTTTCATTTCGCATTGCGATT
1 ATTTCGCGTTGCGATTTTCATTTCGCATTGCGATT
61150 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
33 12 0.20
34 15 0.25
35 4 0.07
37 1 0.02
38 29 0.48
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (38 bp):
ATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:61209 original size:14 final size:14
Alignment explanation
Indices: 61190--61225 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
61180 ATTGTTTAAT
61190 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
61204 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
61218 TGATTTGT
1 TGATTTGT
61226 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:61371 original size:33 final size:33
Alignment explanation
Indices: 61325--61409 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
61315 TCGCAACGCG
**
61325 GAAATGACTATCGCAACGAGAGAATCACAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
* *
61358 GAAATGAAAATCGCAACGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGC
61391 GAAAATGAAAATCGCAACG
1 G-AAATGAAAATCGCAACG
61410 CGAAACTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 30 0.64
34 17 0.36
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCACAATGC
Found at i:61485 original size:34 final size:34
Alignment explanation
Indices: 61435--61552 Score: 168
Period size: 34 Copynumber: 3.5 Consensus size: 34
61425 GGTGCGATTT
*
61435 TCATTTT-GCATTGCGATTCTCTTGTTGCGATAG
1 TCATTTTCGCATTGCGATTCTCTCGTTGCGATAG
* * **
61468 TCATTTTCGCATTGCGATTCACTCGTTACGATTT
1 TCATTTTCGCATTGCGATTCTCTCGTTGCGATAG
61502 TCA-TTTCGCATTGCGATTCTCTCGTTGCGATAG
1 TCATTTTCGCATTGCGATTCTCTCGTTGCGATAG
*
61535 TCATTTTCGCGTTGCGAT
1 TCATTTTCGCATTGCGAT
61553 AGGCAATTCC
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
33 36 0.49
34 37 0.51
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.43
Consensus pattern (34 bp):
TCATTTTCGCATTGCGATTCTCTCGTTGCGATAG
Found at i:61549 original size:20 final size:20
Alignment explanation
Indices: 61524--61610 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
61514 GCGATTCTCT
*
61524 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
* *
61544 CGTTGCGATAGGCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
61564 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
61584 TGTTGCGATAGTCA-TT-CG
1 CGTTGCGATAGTCATTTCCG
61602 CGTTGCGAT
1 CGTTGCGAT
61611 TTCCGTGTTG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
18 10 0.17
19 2 0.03
20 46 0.79
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:63768 original size:14 final size:15
Alignment explanation
Indices: 63749--63785 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
63739 TCCCGTGGCA
63749 TTTTCTTCGGGGA-T
1 TTTTCTTCGGGGATT
*
63763 TTTTCTTTGGGGATT
1 TTTTCTTCGGGGATT
63778 TTTTCTTC
1 TTTTCTTC
63786 TTCTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.05, C:0.14, G:0.22, T:0.59
Consensus pattern (15 bp):
TTTTCTTCGGGGATT
Found at i:64878 original size:20 final size:20
Alignment explanation
Indices: 64855--64895 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
64845 TTGCGATAGT
* *
64855 CAGAATCTCGTTGCGATTTA
1 CAGAATCACATTGCGATTTA
*
64875 CAGATTCACATTGCGATTTA
1 CAGAATCACATTGCGATTTA
64895 C
1 C
64896 GTATTCGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (20 bp):
CAGAATCACATTGCGATTTA
Found at i:64901 original size:20 final size:20
Alignment explanation
Indices: 64863--65093 Score: 175
Period size: 20 Copynumber: 11.5 Consensus size: 20
64853 GTCAGAATCT
*
64863 CGTTGCGATTTACAG-ATTCA
1 CGTTGCGATTTAC-GTATTCG
*
64883 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
* *
64903 TGTTGCAATTTTACGTATT-G
1 CGTTGCGA-TTTACGTATTCG
* * *
64923 TCGTTGCAATTTACGGATACG
1 -CGTTGCGATTTACGTATTCG
* * * *
64944 CATTACGTTTTACGTATTCT
1 CGTTGCGATTTACGTATTCG
*
64964 CGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTAC-GTATTCG
*
64984 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCG
* *
65004 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCG
* *
65024 CGTTGCGATAGT-CAG-AATCG
1 CGTTGCGAT-TTAC-GTATTCG
** *
65044 CGTTGCGATTTATATGTTCG
1 CGTTGCGATTTACGTATTCG
* *
65064 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCG
65084 CGTTGCGATT
1 CGTTGCGATT
65094 CTGGAAAATC
Statistics
Matches: 165, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.02
20 141 0.85
21 21 0.13
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCG
Found at i:64917 original size:21 final size:21
Alignment explanation
Indices: 64891--64934 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
64881 CACATTGCGA
64891 TTTACGTATTCGT-GTTGCAAT
1 TTTACGTATT-GTCGTTGCAAT
64912 TTTACGTATTGTCGTTGCAAT
1 TTTACGTATTGTCGTTGCAAT
64933 TT
1 TT
64935 ACGGATACGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (21 bp):
TTTACGTATTGTCGTTGCAAT
Found at i:65016 original size:60 final size:61
Alignment explanation
Indices: 64855--65093 Score: 195
Period size: 60 Copynumber: 4.0 Consensus size: 61
64845 TTGCGATAGT
* * * *
64855 CAGA-ATCTCGTTGCGATTTACAG-ATTCACATTGCGATTTACGTATTCGTGTTGCAATTTTA
1 CAGATATCGCGTTGCGATTTAC-GTATTCGCATTGCGATTTACGTATTCGCGTTGCGA-TTTA
* * * * * * *
64916 C-G-TATTGTCGTTGCAATTTACGGATACGCATTACGTTTTACGTATTCTCGTTGCGATTTA
1 CAGATATCG-CGTTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTA
* * * * *
64976 CAGATA-CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATAGT-
1 CAGATATCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCGTTGCGAT-TTA
** * * * *
65036 CAGA-ATCGCGTTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 CAGATATCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCGTTGCGATT
65094 CTGGAAAATC
Statistics
Matches: 140, Mismatches: 31, Indels: 16
0.75 0.17 0.09
Matches are distributed among these distances:
59 1 0.01
60 95 0.68
61 42 0.30
62 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (61 bp):
CAGATATCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTA
Found at i:65025 original size:40 final size:40
Alignment explanation
Indices: 64863--65032 Score: 207
Period size: 40 Copynumber: 4.2 Consensus size: 40
64853 GTCAGAATCT
* * * *
64863 CGTTGCGATTTACAG-ATTCACATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCTCGTTGCGATTTACGGATACG
* * * *
64903 TGTTGCAATTTTACGTATTGTCGTTGCAATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACG
* * * *
64944 CATTACGTTTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
64984 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
65024 CGTTGCGAT
1 CGTTGCGAT
65033 AGTCAGAATC
Statistics
Matches: 108, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
40 81 0.75
41 27 0.25
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:65111 original size:21 final size:21
Alignment explanation
Indices: 65081--65160 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
65071 ATTTTCATAT
*
65081 TCGCGTTGCGATTCTGGAAAA
1 TCGCATTGCGATTCTGGAAAA
* * **
65102 TCGCAATGCGAATT-TGTACTA
1 TCGCATTGCG-ATTCTGGAAAA
** *
65123 TCGCATTGCGATTCTTCATAA
1 TCGCATTGCGATTCTGGAAAA
65144 TCGCATTGCGATTCTGG
1 TCGCATTGCGATTCTGG
65161 GAACTAATTT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTCTGGAAAA
Found at i:65868 original size:2 final size:2
Alignment explanation
Indices: 65861--65892 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
65851 AAAAATTTAA
*
65861 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65893 TATTTTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101298 original size:24 final size:24
Alignment explanation
Indices: 101253--101301 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
101243 ATACTTTTAA
* ** *
101253 TAAATTAAAATAAATTATATATTT
1 TAAATGAAAATAAAAGAAATATTT
101277 TAAATGAAAATAAAAGAAATATTT
1 TAAATGAAAATAAAAGAAATATTT
101301 T
1 T
101302 TTAAATTAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (24 bp):
TAAATGAAAATAAAAGAAATATTT
Found at i:101367 original size:23 final size:22
Alignment explanation
Indices: 101308--101361 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
101298 TTTTTTAAAT
*
101308 TAAGTTAGTAATAAAATATATTTAA
1 TAAGTTAAT-ATAAAA-ATATTT-A
101333 TAAGTTAATATAAAAATATTT-
1 TAAGTTAATATAAAAATATTTA
101354 TAAGTTAA
1 TAAGTTAA
101362 CATATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 8 0.29
23 6 0.21
24 6 0.21
25 8 0.29
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
TAAGTTAATATAAAAATATTTA
Found at i:101725 original size:39 final size:39
Alignment explanation
Indices: 101637--101725 Score: 92
Period size: 39 Copynumber: 2.3 Consensus size: 39
101627 AATGTTAATG
* *
101637 TGAAATAATTTAAGAAATGAAGAATTTAGAACGTTACGG
1 TGAAATAATTTAAGAAATGAAGAATTTAAAACGTTACGC
* * * *
101676 TGTCAA-AATTTAAGAAATTAAGATTTTAAAATGTTA-GAC
1 TG-AAATAATTTAAGAAATGAAGAATTTAAAACGTTACG-C
101715 TGAAATAATTT
1 TGAAATAATTT
101726 GAGGATCATG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
38 3 0.08
39 35 0.88
40 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.34
Consensus pattern (39 bp):
TGAAATAATTTAAGAAATGAAGAATTTAAAACGTTACGC
Found at i:103326 original size:25 final size:25
Alignment explanation
Indices: 103298--103347 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
103288 TTTAGCACCA
103298 TATCACTACATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
*
103323 TATCCCTACATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
103348 GCCCATAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (25 bp):
TATCACTACATGTTTATGCTTCAGT
Found at i:107332 original size:25 final size:25
Alignment explanation
Indices: 107304--107353 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
107294 TTTAGCACCA
107304 TATCACTACATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
*
107329 TATCCCTACATGTTTATGCTTCAGT
1 TATCACTACATGTTTATGCTTCAGT
107354 ACCCCTAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (25 bp):
TATCACTACATGTTTATGCTTCAGT
Found at i:109408 original size:14 final size:14
Alignment explanation
Indices: 109389--109416 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
109379 ATGAAGCTTA
109389 CCCAAGGTTCCATG
1 CCCAAGGTTCCATG
109403 CCCAAGGTTCCATG
1 CCCAAGGTTCCATG
109417 ATACATGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (14 bp):
CCCAAGGTTCCATG
Found at i:117136 original size:43 final size:43
Alignment explanation
Indices: 117075--117175 Score: 166
Period size: 43 Copynumber: 2.3 Consensus size: 43
117065 AAACAGATCC
* *
117075 GATATTTAGCGGCGTTTGTAGTCACAAACATCGCAATAGATTT
1 GATATGTAGCGGCGTTTGTAGTCACAAACACCGCAATAGATTT
* *
117118 GATATGTAGCGGCGTTTGTAGTCACAAACGCCGCAATTGATTT
1 GATATGTAGCGGCGTTTGTAGTCACAAACACCGCAATAGATTT
117161 GATATGTAGCGGCGT
1 GATATGTAGCGGCGT
117176 GTCCGGCAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
GATATGTAGCGGCGTTTGTAGTCACAAACACCGCAATAGATTT
Found at i:117641 original size:28 final size:28
Alignment explanation
Indices: 117572--117626 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 28
117562 TTCTCTGAAA
117572 TGTTGCT-TCTCT-CTT-T-GCTTCTAT
1 TGTTGCTCTCTCTGCTTCTCGCTTCTAT
117596 TGTTGCTCTCTCTGCTTCTCGCTTCT-T
1 TGTTGCTCTCTCTGCTTCTCGCTTCTAT
117623 TGTT
1 TGTT
117627 TGCTTCTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.26
25 5 0.19
26 3 0.11
27 6 0.22
28 6 0.22
ACGTcount: A:0.02, C:0.27, G:0.15, T:0.56
Consensus pattern (28 bp):
TGTTGCTCTCTCTGCTTCTCGCTTCTAT
Found at i:120648 original size:20 final size:20
Alignment explanation
Indices: 120623--120661 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
120613 CGAACGCCTT
* *
120623 TAAAAAAATAAACGAACACC
1 TAAAAAAACAAACAAACACC
120643 TAAAAAAACAAACAAACAC
1 TAAAAAAACAAACAAACAC
120662 AAACATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.69, C:0.21, G:0.03, T:0.08
Consensus pattern (20 bp):
TAAAAAAACAAACAAACACC
Found at i:122916 original size:200 final size:200
Alignment explanation
Indices: 122573--122973 Score: 786
Period size: 200 Copynumber: 2.0 Consensus size: 200
122563 AAAATAAATA
122573 TTTTTCACGGGATCTATATTATGACTTCCAACTGCTCTACTGTTTGTGATGTAAGTCTATCCTTT
1 TTTTTCACGGGATCTATATTATGACTTCCAACTGCTCTACTGTTTGTGATGTAAGTCTATCCTTT
122638 TCAACATACGACTGTTTTCTTCTTTATTTTCTGTTGATATTACACTCCCATTTTTCGACAAATTC
66 TCAACATACGACTGTTTTCTTCTTTATTTTCTGTTGATATTACACTCCCATTTTTCGACAAATTC
122703 CGAGCTTGAAATGATCTACCCCGCAGTATCATTATGATGTTGATCAGTTTCCTCGGCAGAGAATA
131 CGAGCTTGAAATGATCTACCCCGCAGTATCATTATGATGTTGATCAGTTTCCTCGGCAGAGAATA
122768 CAGTC
196 CAGTC
122773 TTTTTCACGGGATCTATATTATGACTTCCAACTGCTCTACTGTTTGTGATGTAAGTCTATCCTTT
1 TTTTTCACGGGATCTATATTATGACTTCCAACTGCTCTACTGTTTGTGATGTAAGTCTATCCTTT
122838 TCAACATACGACTGTTTTTCTTCTTTATTTTCTGTTGATA-TACACTCCCATTTTTCGACAAATT
66 TCAACATACGACTG-TTTTCTTCTTTATTTTCTGTTGATATTACACTCCCATTTTTCGACAAATT
122902 CCGAGCTTGAAATGATCTACCCCGCAGTATCATTATGATGTTGATCAGTTTCCTCGGCAGAGAAT
130 CCGAGCTTGAAATGATCTACCCCGCAGTATCATTATGATGTTGATCAGTTTCCTCGGCAGAGAAT
122967 ACAGTC
195 ACAGTC
122973 T
1 T
122974 CTGATAACCT
Statistics
Matches: 200, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
200 175 0.88
201 25 0.12
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (200 bp):
TTTTTCACGGGATCTATATTATGACTTCCAACTGCTCTACTGTTTGTGATGTAAGTCTATCCTTT
TCAACATACGACTGTTTTCTTCTTTATTTTCTGTTGATATTACACTCCCATTTTTCGACAAATTC
CGAGCTTGAAATGATCTACCCCGCAGTATCATTATGATGTTGATCAGTTTCCTCGGCAGAGAATA
CAGTC
Found at i:124981 original size:2 final size:2
Alignment explanation
Indices: 124974--125000 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
124964 ATCCTGATCA
124974 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
125001 ATAAACCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:128151 original size:59 final size:59
Alignment explanation
Indices: 128013--128186 Score: 185
Period size: 59 Copynumber: 3.0 Consensus size: 59
128003 GATTTGGGGA
* * ** * *
128013 ATGAAATTGGAAGATTTAAAAGTTTGGGGACTAATTTAGAATGCGAGTCATAGTTTGATG
1 ATGAAATTGGAATATTCAAAAGTTT-AAGACTAATTTAGAATGAGAGTCATAGTTTGAGG
**
128073 ATGAAATTGGAATGCTCAAAAGTTTAAGACTAATTTAGAATGAGTA-TCATAGTTTGAGG
1 ATGAAATTGGAATATTCAAAAGTTTAAGACTAATTTAGAATGAG-AGTCATAGTTTGAGG
* * * *
128132 ATGAAATTAGAATATTC-AAAGTTTAGAAACT-ATATAG-ATGAGAGCCATAGTTTGA
1 ATGAAATTGGAATATTCAAAAGTTTA-AGACTAATTTAGAATGAGAGTCATAGTTTGA
128187 AAAATATGTG
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
56 1 0.01
57 15 0.15
58 13 0.13
59 46 0.47
60 22 0.23
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.32
Consensus pattern (59 bp):
ATGAAATTGGAATATTCAAAAGTTTAAGACTAATTTAGAATGAGAGTCATAGTTTGAGG
Found at i:130535 original size:52 final size:53
Alignment explanation
Indices: 130435--130540 Score: 189
Period size: 52 Copynumber: 2.0 Consensus size: 53
130425 GCAGAGACTG
130435 AGCAGGGAGTAGCGCAGGCAATTATTCGCTCTGTTATCGACTTAAGAGGGACC
1 AGCAGGGAGTAGCGCAGGCAATTATTCGCTCTGTTATCGACTTAAGAGGGACC
130488 AGCAGGGAGTAGCGCAGGCAA-TATTCGCT-TGTTATCGACTTTAAGAGGGACC
1 AGCAGGGAGTAGCGCAGGCAATTATTCGCTCTGTTATCGAC-TTAAGAGGGACC
130540 A
1 A
130541 TGGCCTAAGG
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
51 10 0.19
52 21 0.40
53 21 0.40
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (53 bp):
AGCAGGGAGTAGCGCAGGCAATTATTCGCTCTGTTATCGACTTAAGAGGGACC
Found at i:131386 original size:13 final size:13
Alignment explanation
Indices: 131368--131395 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
131358 TAATTAATGT
131368 TTCATATTTAAAC
1 TTCATATTTAAAC
131381 TTCATATTTAAAC
1 TTCATATTTAAAC
131394 TT
1 TT
131396 TCGGTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (13 bp):
TTCATATTTAAAC
Found at i:135904 original size:15 final size:15
Alignment explanation
Indices: 135884--135920 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
135874 TTCCACCAAA
135884 GCCACGCCTGAAAGC
1 GCCACGCCTGAAAGC
135899 GCCACGCCTGAAAGC
1 GCCACGCCTGAAAGC
135914 GCCACGC
1 GCCACGC
135921 TCACCTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.43, G:0.27, T:0.05
Consensus pattern (15 bp):
GCCACGCCTGAAAGC
Found at i:141994 original size:13 final size:13
Alignment explanation
Indices: 141976--142001 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
141966 GGATAGAGGC
141976 CGCATAAATGAGA
1 CGCATAAATGAGA
141989 CGCATAAATGAGA
1 CGCATAAATGAGA
142002 ATGCTTCGAT
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:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (13 bp):
CGCATAAATGAGA
Found at i:146997 original size:3 final size:3
Alignment explanation
Indices: 146989--147014 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
146979 GAAGAAAAAA
146989 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
147015 ACCCTGGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:149236 original size:3 final size:3
Alignment explanation
Indices: 149224--149314 Score: 121
Period size: 3 Copynumber: 29.7 Consensus size: 3
149214 TTTAAAAAAA
* * *
149224 TAT TAC TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
149272 TAT T-T GTATT TAT TAT TAT TAT TAT TAT TAT TAT TAAT TAT TA
1 TAT TAT -TA-T TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA
149315 CCATACCTAA
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
2 1 0.01
3 71 0.91
4 5 0.06
5 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:149866 original size:144 final size:144
Alignment explanation
Indices: 149617--149950 Score: 352
Period size: 144 Copynumber: 2.3 Consensus size: 144
149607 GCAAAACCAT
* * * * *
149617 CACGAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGGCGATGGATTGAAGAAAATAA
1 CACGAACAACATACTTAAATTTCAGGACGATCAGACGGTGGACGGCGATGAATCGAAGAAAAAAA
* * * * *
149682 GCCGAACGATTTTTGGCCTCTTGCAGGTGATCGGATCTCTGATCAACATTCCAAACGGTGAAAAG
66 GCCGAACGATTTTTGGCCTCTCGCAGATGATCGGAACTCTGATCAACATTCCAAACAGTCAAAAG
* **** *
149747 TTGTGTTATGTCAA
131 GTGCACGAGGTCAA
* * * *
149761 CACGAACATCATACTTAAATTTGAGGATGATC-GACGGTGGACGTG-G-TGAATCGGAGAAAACA
1 CACGAACAACATACTTAAATTTCAGGACGATCAGACGGTGGACG-GCGATGAATCGAAGAAAA-A
* * * * *
149823 AATCCGAACGGTTTTTGGCCTCTCGCCGATGATTGGGAACTCTGATCAACATTCCGAACAGTCAA
64 AAGCCGAACGATTTTTGGCCTCTCGCAGATGA-TCGGAACTCTGATCAACATTCCAAACAGTCAA
149888 AAGGTGCACGAGGTCAA
128 AAGGTGCACGAGGTCAA
* *
149905 CACGAACAACATA-TTGAAATTTTAGGACGATCGGACGGTGGCACGG
1 CACGAACAACATACTT-AAATTTCAGGACGATCAGACGGTGG-ACGG
149951 TAGCGCAGCA
Statistics
Matches: 156, Mismatches: 28, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
142 11 0.07
143 41 0.26
144 92 0.59
145 9 0.06
146 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (144 bp):
CACGAACAACATACTTAAATTTCAGGACGATCAGACGGTGGACGGCGATGAATCGAAGAAAAAAA
GCCGAACGATTTTTGGCCTCTCGCAGATGATCGGAACTCTGATCAACATTCCAAACAGTCAAAAG
GTGCACGAGGTCAA
Found at i:150103 original size:29 final size:28
Alignment explanation
Indices: 150071--150135 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
150061 TGAATATATA
*
150071 TGTTTTCTTGATTTTA-ACACTTTAGTTTC
1 TGTTTT-TT-ATTTTAGACACTTAAGTTTC
*
150100 TGTTATTTTATTTTAGTCACTTAAGTTTC
1 TGTT-TTTTATTTTAGACACTTAAGTTTC
150129 TGTTTTT
1 TGTTTTT
150136 ACTATATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 9 0.28
29 21 0.66
30 2 0.06
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.62
Consensus pattern (28 bp):
TGTTTTTTATTTTAGACACTTAAGTTTC
Found at i:151941 original size:12 final size:12
Alignment explanation
Indices: 151883--151941 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
151873 CAAAAATCAA
*
151883 AACAGAATTCAT
1 AACAGAATTCAG
*
151895 ATCAG-ATATCAG
1 AACAGAAT-TCAG
*
151907 AACAGAATCCAG
1 AACAGAATTCAG
*
151919 ATCAGAA-TCAG
1 AACAGAATTCAG
151930 AACAGAATTCAG
1 AACAGAATTCAG
151942 GTAACGTATC
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
11 11 0.30
12 24 0.65
13 2 0.05
ACGTcount: A:0.47, C:0.19, G:0.15, T:0.19
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:151957 original size:24 final size:23
Alignment explanation
Indices: 151878--151964 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
151868 GACATCAAAA
* * *
151878 ATCAAAACAGAATTCATATCAGAT
1 ATCAGAACAGAATTCAGATAAG-T
* * *
151902 ATCAGAACAGAATCCAGATCAGA
1 ATCAGAACAGAATTCAGATAAGT
*
151925 ATCAGAACAGAATTCAGGTAACGT
1 ATCAGAACAGAATTCAGATAA-GT
*
151949 ATCAGAACATAATTCA
1 ATCAGAACAGAATTCA
151965 ATTCGGAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.34
24 35 0.66
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (23 bp):
ATCAGAACAGAATTCAGATAAGT
Found at i:154415 original size:15 final size:15
Alignment explanation
Indices: 154395--154423 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
154385 GTCAACAATG
154395 GTCAACGGTCAACGA
1 GTCAACGGTCAACGA
154410 GTCAACGGTCAACG
1 GTCAACGGTCAACG
154424 GGTCGGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (15 bp):
GTCAACGGTCAACGA
Found at i:154427 original size:8 final size:7
Alignment explanation
Indices: 154394--154424 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
154384 GGTCAACAAT
154394 GGTCAAC
1 GGTCAAC
154401 GGTCAAC
1 GGTCAAC
154408 GAGTCAAC
1 G-GTCAAC
154416 GGTCAAC
1 GGTCAAC
154423 GG
1 GG
154425 GTCGGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.29, C:0.26, G:0.32, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:156558 original size:24 final size:23
Alignment explanation
Indices: 156524--156593 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 23
156514 AAATGGAGAT
156524 ATCAGAAATCAAAACAGAATTCAC
1 ATCAG-AATCAAAACAGAATTCAC
* * * *
156548 ATCAGATATCAGAACATAATCCAG
1 ATCAGA-ATCAAAACAGAATTCAC
156572 ATCAGAATCAAAACAGAATTCA
1 ATCAGAATCAAAACAGAATTCA
156594 GGTAACGTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 14 0.37
24 24 0.63
ACGTcount: A:0.51, C:0.20, G:0.10, T:0.19
Consensus pattern (23 bp):
ATCAGAATCAAAACAGAATTCAC
Found at i:161177 original size:24 final size:24
Alignment explanation
Indices: 161150--161259 Score: 100
Period size: 24 Copynumber: 4.6 Consensus size: 24
161140 GTAAATGGAG
* *
161150 ATATCAGAAATCAAAATAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
161174 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
161198 AAATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
161221 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
* *
161245 ATTTCGGAAATCAGA
1 ATATCAGAAATCAGA
161260 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
22 2 0.03
23 16 0.23
24 49 0.71
25 2 0.03
ACGTcount: A:0.47, C:0.16, G:0.15, T:0.22
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:161222 original size:12 final size:12
Alignment explanation
Indices: 161184--161245 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
161174 ATATCAGATA
161184 TCAGAACAGAAT
1 TCAGAACAGAAT
*
161196 CCA-AATCAGAA-
1 TCAGAA-CAGAAT
161207 TCAGAACAGAAT
1 TCAGAACAGAAT
*
161219 TCAGGTAAC-GTA-
1 TCA-G-AACAGAAT
161231 TCAGAACAGAAT
1 TCAGAACAGAAT
161243 TCA
1 TCA
161246 TTTCGGAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
10 3 0.08
11 12 0.31
12 18 0.46
13 3 0.08
14 3 0.08
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (12 bp):
TCAGAACAGAAT
Found at i:164928 original size:6 final size:6
Alignment explanation
Indices: 164919--164947 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
164909 TTGTAAAGTT
164919 ATGTAA ATGTAA ATGTAA ATGTAA ATGTA
1 ATGTAA ATGTAA ATGTAA ATGTAA ATGTA
164948 TGACAGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
ATGTAA
Found at i:169484 original size:3 final size:3
Alignment explanation
Indices: 169476--169502 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
169466 ATTTGATTTG
169476 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
169503 AGTGTTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:169744 original size:17 final size:17
Alignment explanation
Indices: 169709--169788 Score: 79
Period size: 17 Copynumber: 4.6 Consensus size: 17
169699 ATGTTTAAAA
* *
169709 TTATCAAATGATTTTCAG
1 TTATCAGAT-ATTTACAG
169727 TTATCAGATATTTACAG
1 TTATCAGATATTTACAG
* *
169744 TTATCAGATAATTACAA
1 TTATCAGATATTTACAG
* * *
169761 ATATAATATATTTTACAG
1 TTATCAGATA-TTTACAG
169779 TTATCAGATA
1 TTATCAGATA
169789 CATATTAATA
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
17 29 0.59
18 20 0.41
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (17 bp):
TTATCAGATATTTACAG
Found at i:172511 original size:13 final size:13
Alignment explanation
Indices: 172493--172517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
172483 AGCCATTAGT
172493 TTCATAATTAATA
1 TTCATAATTAATA
172506 TTCATAATTAAT
1 TTCATAATTAAT
172518 GTGAAATGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCATAATTAATA
Found at i:180810 original size:49 final size:49
Alignment explanation
Indices: 180753--180869 Score: 164
Period size: 49 Copynumber: 2.4 Consensus size: 49
180743 CTGTTTCAAC
* * * *
180753 TAAAAATGGGTTTGAATCATCTTCTTCCTACTTTTTATGTGGTCA-ATTA
1 TAAAAATGGGGTTGAATCATATTATTCCTACTTTTTATATGGT-ATATTA
*
180802 TAAAAATGGGGTTGAATCATATTATTCCTACTTTTTATATGGTATATTC
1 TAAAAATGGGGTTGAATCATATTATTCCTACTTTTTATATGGTATATTA
*
180851 TAAAAACGGGGTTGAATCA
1 TAAAAATGGGGTTGAATCA
180870 ACTAAAAACA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 1 0.02
49 60 0.98
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (49 bp):
TAAAAATGGGGTTGAATCATATTATTCCTACTTTTTATATGGTATATTA
Found at i:185244 original size:536 final size:537
Alignment explanation
Indices: 183974--186658 Score: 4949
Period size: 537 Copynumber: 5.0 Consensus size: 537
183964 AAAAATACAT
*
183974 TTTTTTTCTTGGCCATGCAATATTTTACCTCAGGTTCATCAAAGACTTCTCAAAGATAACACAAT
1 TTTTTTTCTTGGCCATGCAAGATTTTACCTCAGGTTCATCAAAGACTTCTCAAAGATAACACAAT
184039 CGTTGTGTAATCTACTTCAAAAAGATAAAGTCTTTGATTTCAACCAAGAATGCAAGGAATTGTTC
66 CGTTGTGTAATCTACTTCAAAAAGATAAAGTCTTTGATTTCAACCAAGAATGCAAGGAATTGTTC
* *
184104 ATCATTTTGAAGGAAAAACTAATATCAGCTCTGATTGTACAAATGCCAAATTGGGATTATCCTTT
131 GTCATTTTGAAGGAAAAACTAATATCAGCTCCGATTGTACAAATGCCAAATTGGGATTATCCTTT
*
184169 CGAGATCATTTATGATTCCTCAGACACTAGTGTTGGAGTAGTTCTCAGTTAAAAAGTCAGCAAAA
196 CGAGATCATGTATGATTCCTCAGACACTAGTGTTGGAGTAGTTCTCAGTTAAAAAGTCAGCAAAA
184234 TACCGCATGTCATTGCCTATGCATCACACACCTTAGATTCAGAGCAGAAAAATTACTCTATAACC
261 TACCGCATGTCATTGCCTATGCATCACACACCTTAGATTCAGAGCAGAAAAATTACTCTATAACC
184299 GAAAAAGAATTTTTTACTATAATATTTGCTTTGGAAAAATTTAGATCATATTTGCTGGGAACTAA
326 GAAAAAGAATTTTTTACTATAATATTTGCTTTGGAAAAATTTAGATCATATTTGCTGGGAACTAA
*
184364 TATTGTTGTTTATTCTGACCATGCAACATTACGATATTTAATGAGCAAAAAGTAAGTGAAGCCGA
391 TATTGTTGTTTATTCTGACCATGCAACATTACGATATTTAATGAGCAAAAAGTAAGCGAAGCCGA
184429 GACTTATCCGTTGAATTTTACCCCTTCAAGAATTTAATTTAAAAATCAAGGATAAGAAAGGATGT
456 GACTTATCCGTTGAATTTTACCCCTTCAAGAATTTAATTTAAAAATCAAGGATAAGAAAGGATGT
184494 GAGAATTTGGTGCTCGA
521 GAGAATTTGGTGCTCGA
184511 TTTTTTTCTTGGCCATGCAAGATTTTACCTCAGGTTCATCAAAGACTTCTCAAAGATAACACAAT
1 TTTTTTTCTTGGCCATGCAAGATTTTACCTCAGGTTCATCAAAGACTTCTCAAAGATAACACAAT
*
184576 CGTTGTGTAATCTACTTCAAAAAGATAAAGTCTTTAATTTCAACCAAGAATGCAAGGAATTGTTC
66 CGTTGTGTAATCTACTTCAAAAAGATAAAGTCTTTGATTTCAACCAAGAATGCAAGGAATTGTTC
* *
184641 GTCACTTTGAAGGAAAAACTAATATCAGCTCCGATTGTACAAATGCCAAATTGGGATTATTCTTT
131 GTCATTTTGAAGGAAAAACTAATATCAGCTCCGATTGTACAAATGCCAAATTGGGATTATCCTTT
184706 CGAGATCATGTATGATTCCTCAGACACTAGTGTTGGAGTAGTTCTCAGTTAAAAAGTCAGCAAAA
196 CGAGATCATGTATGATTCCTCAGACACTAGTGTTGGAGTAGTTCTCAGTTAAAAAGTCAGCAAAA
*
184771 TACCGCATGTCATTGCCTATGCATCACACACCTTAAATTCAGAGCAGAAAAATTACTCTATAACC
261 TACCGCATGTCATTGCCTATGCATCACACACCTTAGATTCAGAGCAGAAAAATTACTCTATAACC
184836 GAAAAAGAATTTTTTACTATAATATTTGCTTTGGAAAAATTTAGATCATATTTGCTGGGAACTAA
326 GAAAAAGAATTTTTTACTATAATATTTGCTTTGGAAAAATTTAGATCATATTTGCTGGGAACTAA
184901 TATTGTTGTTTATTCTGACCATGCAACATTACGATATTTAATGAGCAAAAA-TAAGCGAAGCCGA
391 TATTGTTGTTTATTCTGACCATGCAACATTACGATATTTAATGAGCAAAAAGTAAGCGAAGCCGA
184965 GACTTATCCGTTGAATTTTACCCCTTCAAGAATTTAATTTAAAAATCAAGGATAAGAAAGGATGT
456 GACTTATCCGTTGAATTTTACCCCTTCAAGAATTTAATTTAAAAATCAAGGATAAGAAAGGATGT
185030 GAGAATTTGGTGCTCGA
521 GAGAATTTGGTGCTCGA
185047 TTTTTTTCTTGGCCATGCAAGATTTTACCTCAGGTTCATCAAAGACTTCTCAAAGATAACACAAT
1 TTTTTTTCTTGGCCATGCAAGATTTTACCTCAGGTTCATCAAAGACTTCTCAAAGATAACACAAT
185112 CGTTGTGTAATCTACTTCAAAAAGATAAAGTCTTTGATTTCAACCAAGAATGCAAGGAATTGTTC
66 CGTTGTGTAATCTACTTCAAAAAGATAAAGTCTTTGATTTCAACCAAGAATGCAAGGAATTGTTC
*
185177 GTCATTTTAAAGGAAAAACTAATATCAGCTCCGATTGTACAAATGCCAAATTGGGATTATCCTTT
131 GTCATTTTGAAGGAAAAACTAATATCAGCTCCGATTGTACAAATGCCAAATTGGGATTATCCTTT
*
185242 CGAGATCATGTATGATTCCTCAGACACTAGTGTTGGAGTAGTTCACAGTTAAAAAGTCAGCAAAA
196 CGAGATCATGTATGATTCCTCAGACACTAGTGTTGGAGTAGTTCTCAGTTAAAAAGTCAGCAAAA
* * * * *
185307 TACCGCAAGTCATTGCATATGCATCACACACCTTAGATTTATAGCATAAAAATTACTCTATAACC
261 TACCGCATGTCATTGCCTATGCATCACACACCTTAGATTCAGAGCAGAAAAATTACTCTATAACC
* *
185372 GAAAAAGAATTTTTTACTATAATATTTTCTTTGGAAAAATTTATATCATATTTGCTGGGAACTAA
326 GAAAAAGAATTTTTTACTATAATATTTGCTTTGGAAAAATTTAGATCATATTTGCTGGGAACTAA
*
185437 TATTGTTGTTTATTCTGACCATGCAACATTACGATATTTAATGAGCAAAAAGTAAGCGAAGCGGA
391 TATTGTTGTTTATTCTGACCATGCAACATTACGATATTTAATGAGCAAAAAGTAAGCGAAGCCGA
185502 GACTTATCCGTTGAATTTTACCCCTTCAAGAATTTAATTTAAAAATCAAGGATAAGAAAGGATGT
456 GACTTATCCGTTGAATTTTACCCCTTCAAGAATTTAATTTAAAAATCAAGGATAAGAAAGGATGT
185567 GAGAATTTGGTGCTCGA
521 GAGAATTTGGTGCTCGA
* *
185584 TTTTTTTCTTGGCCATGCAAGATTTTACCTCAGGTTCATCAAAGACTTCTAAAAGATAACATAAT
1 TTTTTTTCTTGGCCATGCAAGATTTTACCTCAGGTTCATCAAAGACTTCTCAAAGATAACACAAT
* * *
185649 CATTGTGTAATCTACTTCAAAAAGATAAAGTCTTTGATTTCAACAAAAAATGCAAGGAATTGTTC
66 CGTTGTGTAATCTACTTCAAAAAGATAAAGTCTTTGATTTCAACCAAGAATGCAAGGAATTGTTC
185714 GTCATTTTGAAGGAAAAACTAATATCAGCTCCGATTGTACAAATGCCAAATTGGGATTATCCTTT
131 GTCATTTTGAAGGAAAAACTAATATCAGCTCCGATTGTACAAATGCCAAATTGGGATTATCCTTT
*
185779 CGAGATCATGTATGATTCCTCAGACACTAGTGTTGGAGTAGTTCACAGTTAAAAAGTCAGCAAAA
196 CGAGATCATGTATGATTCCTCAGACACTAGTGTTGGAGTAGTTCTCAGTTAAAAAGTCAGCAAAA
* * * *
185844 TACCGCATGTCATTGCATATGCATCACACACCTTAGATTTATAGCATAAAAATTACTCTATAACC
261 TACCGCATGTCATTGCCTATGCATCACACACCTTAGATTCAGAGCAGAAAAATTACTCTATAACC
* *
185909 GAAAAAGAATTTTTTACTATAATATTTTCTTTGGAAAAATTTATATCATATTTGCTGGGAACTAA
326 GAAAAAGAATTTTTTACTATAATATTTGCTTTGGAAAAATTTAGATCATATTTGCTGGGAACTAA
**
185974 TATTGTTGTTTATTCTGACCATGCAACATTACGATATTTAATGAGCAAAAAGTAAGCGAAGTGGA
391 TATTGTTGTTTATTCTGACCATGCAACATTACGATATTTAATGAGCAAAAAGTAAGCGAAGCCGA
186039 GACTTATCCGTTGAATTTTACCCCTTCAAGAATTTAATTTAAAAATCAAGGATAAGAAAGGATGT
456 GACTTATCCGTTGAATTTTACCCCTTCAAGAATTTAATTTAAAAATCAAGGATAAGAAAGGATGT
186104 GAGAATTTGGTGCTCGA
521 GAGAATTTGGTGCTCGA
* *
186121 TTTTTTTCTTGGCCATGCAAGATTTTACCTCAGGTTCATCAAAGACTTCTAAAAGATAACATAAT
1 TTTTTTTCTTGGCCATGCAAGATTTTACCTCAGGTTCATCAAAGACTTCTCAAAGATAACACAAT
* * * *
186186 CATTGTGTAATCTACTTCAAAAAGATAAAGTATTTGATTTCAACAAAAAATGCAAGGAATTGTTC
66 CGTTGTGTAATCTACTTCAAAAAGATAAAGTCTTTGATTTCAACCAAGAATGCAAGGAATTGTTC
186251 GTCATTTTGAAGGAAAAACTAATATCAGCTCCGATTGTACAAATGCCAAATTGGGATTATCCTTT
131 GTCATTTTGAAGGAAAAACTAATATCAGCTCCGATTGTACAAATGCCAAATTGGGATTATCCTTT
*
186316 CGAGATCATGTATGATTCCTCAGACACTAGTGTTGGAGTAGTTCTAAGTTAAAAAGTCAGCAAAA
196 CGAGATCATGTATGATTCCTCAGACACTAGTGTTGGAGTAGTTCTCAGTTAAAAAGTCAGCAAAA
* *
186381 TACCGCATGTCATTGCCTATGCATCACACACCTTAGATTCAGAGAAGAAAAAGTACTCTATAACC
261 TACCGCATGTCATTGCCTATGCATCACACACCTTAGATTCAGAGCAGAAAAATTACTCTATAACC
186446 GAAAAAGAATTTTTTACTATAATATTTGCTTTGGAAAAATTTAGATCATATTTGCTGGGAACTAA
326 GAAAAAGAATTTTTTACTATAATATTTGCTTTGGAAAAATTTAGATCATATTTGCTGGGAACTAA
* * * *
186511 TATTTTTGTTTATTCCGACCATGCAACATTACGATATTTAATGAGCAAAAAGTAAGCAAAGCTGA
391 TATTGTTGTTTATTCTGACCATGCAACATTACGATATTTAATGAGCAAAAAGTAAGCGAAGCCGA
186576 GACTTATCCGTTGAATTTTACCCCTTCAAGAATTTAATTTAAAAATCAAGGATAAGAAAGGATGT
456 GACTTATCCGTTGAATTTTACCCCTTCAAGAATTTAATTTAAAAATCAAGGATAAGAAAGGATGT
186641 GAGAATTTGGTGCTCGA
521 GAGAATTTGGTGCTCGA
186658 T
1 T
186659 CAATTAAGCA
Statistics
Matches: 2100, Mismatches: 47, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
536 522 0.25
537 1578 0.75
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (537 bp):
TTTTTTTCTTGGCCATGCAAGATTTTACCTCAGGTTCATCAAAGACTTCTCAAAGATAACACAAT
CGTTGTGTAATCTACTTCAAAAAGATAAAGTCTTTGATTTCAACCAAGAATGCAAGGAATTGTTC
GTCATTTTGAAGGAAAAACTAATATCAGCTCCGATTGTACAAATGCCAAATTGGGATTATCCTTT
CGAGATCATGTATGATTCCTCAGACACTAGTGTTGGAGTAGTTCTCAGTTAAAAAGTCAGCAAAA
TACCGCATGTCATTGCCTATGCATCACACACCTTAGATTCAGAGCAGAAAAATTACTCTATAACC
GAAAAAGAATTTTTTACTATAATATTTGCTTTGGAAAAATTTAGATCATATTTGCTGGGAACTAA
TATTGTTGTTTATTCTGACCATGCAACATTACGATATTTAATGAGCAAAAAGTAAGCGAAGCCGA
GACTTATCCGTTGAATTTTACCCCTTCAAGAATTTAATTTAAAAATCAAGGATAAGAAAGGATGT
GAGAATTTGGTGCTCGA
Found at i:188633 original size:16 final size:17
Alignment explanation
Indices: 188603--188634 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
188593 AATATTGAAA
188603 CTTGAACTCAAAAAAGG
1 CTTGAACTCAAAAAAGG
188620 CTTGAACT-AAAAAAG
1 CTTGAACTCAAAAAAG
188635 AATTTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (17 bp):
CTTGAACTCAAAAAAGG
Found at i:195591 original size:20 final size:20
Alignment explanation
Indices: 195562--195642 Score: 74
Period size: 20 Copynumber: 3.9 Consensus size: 20
195552 CAGAACCCCA
*
195562 GGGGGTATCGATTCCCTTAT
1 GGGGGAATCGATTCCCTTAT
*
195582 GGGGGAATCGGTTCCCCTTCAAAT
1 GGGGGAATCGATT-CCCTT---AT
* *
195606 -GGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTTAT
*
195625 GGGGGTATCGATTCCCTT
1 GGGGGAATCGATTCCCTT
195643 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
19 2 0.04
20 25 0.50
21 5 0.10
22 4 0.08
23 12 0.24
24 2 0.04
ACGTcount: A:0.16, C:0.23, G:0.31, T:0.30
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTTAT
Found at i:203497 original size:21 final size:20
Alignment explanation
Indices: 203466--203551 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 20
203456 TTAACCAGAA
*
203466 CCCTAGGGGGGTATCGATTC
1 CCCTAGGGGGGAATCGATTC
*
203486 CCCTATGGGGGGAATCGGTTC
1 CCCTA-GGGGGGAATCGATTC
* *
203507 CCCTTCAAAGGGGGAATCGGTTC
1 CCC-T--AGGGGGGAATCGATTC
* *
203530 CCTCAAGTGGGG-ATCGATTC
1 CC-CTAGGGGGGAATCGATTC
203550 CC
1 CC
203552 TCTGCACTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
20 14 0.26
21 21 0.39
22 1 0.02
23 16 0.30
24 2 0.04
ACGTcount: A:0.17, C:0.27, G:0.33, T:0.23
Consensus pattern (20 bp):
CCCTAGGGGGGAATCGATTC
Found at i:221220 original size:83 final size:83
Alignment explanation
Indices: 221111--221435 Score: 457
Period size: 83 Copynumber: 4.0 Consensus size: 83
221101 GGAAATATAT
*
221111 ATTTAATATT-TAAATTTAAACA-ATATTATTATATATTTAAATTTAGATATTAAAAGAGTTTAG
1 ATTTAATATTATAAATTTAAA-AGATATTATAATATATTTAAATTTAGATATTAAAAGAGTTTAG
* *
221174 GTTGGAGTGAAACTCTGAG
65 GTTGGAGTAAAACTCTCAG
* * *
221193 ATTTAATATTATAAATTTAAAAGATATTATAACATGTTTAAATTTAGATATTAAAAGAGTTTTGG
1 ATTTAATATTATAAATTTAAAAGATATTATAATATATTTAAATTTAGATATTAAAAGAGTTTAGG
221258 TTGGAGTAAAACTCTCAG
66 TTGGAGTAAAACTCTCAG
* * *
221276 GTTTAATATTATAAATTTAAAAGATATTATAATATGTTTAAATTTAGATATTAAAAGAGTTTTGG
1 ATTTAATATTATAAATTTAAAAGATATTATAATATATTTAAATTTAGATATTAAAAGAGTTTAGG
* *
221341 TTAGAGTAAAACTCTCAT
66 TTGGAGTAAAACTCTCAG
* * *
221359 ATTTAATATTTTAAATTTAAAAGATATTATTATCTA-TT---TTTAGATATTAAAAGAGTTTTA-
1 ATTTAATATTATAAATTTAAAAGATATTATAATATATTTAAATTTAGATATTAAAAGAG-TTTAG
221419 GTTGGAGTAAAACTCTC
65 GTTGGAGTAAAACTCTC
221436 TCGAAATTCC
Statistics
Matches: 223, Mismatches: 17, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
79 33 0.15
80 3 0.01
82 13 0.06
83 174 0.78
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.42
Consensus pattern (83 bp):
ATTTAATATTATAAATTTAAAAGATATTATAATATATTTAAATTTAGATATTAAAAGAGTTTAGG
TTGGAGTAAAACTCTCAG
Found at i:222515 original size:40 final size:42
Alignment explanation
Indices: 222459--222578 Score: 138
Period size: 40 Copynumber: 2.9 Consensus size: 42
222449 ATAGATCCGT
* * *
222459 ACCTTAGTGGCATTTGTTA-TAAAAATGCCATAATAGAGG-CA
1 ACCTTAGTGGCGTTTGTTACT-AAAACGCCACAATAGAGGTCA
*
222500 A-CTTAGTGGCGTTTGTTACTAAAACGCCACAATAGAGGTGA
1 ACCTTAGTGGCGTTTGTTACTAAAACGCCACAATAGAGGTCA
* * * *
222541 ACCTTAGTGGTGTTTGTCACTAAAACGCCGCTATAGAG
1 ACCTTAGTGGCGTTTGTTACTAAAACGCCACAATAGAG
222579 CCGTACCTTG
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
40 32 0.47
41 4 0.06
42 32 0.47
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (42 bp):
ACCTTAGTGGCGTTTGTTACTAAAACGCCACAATAGAGGTCA
Found at i:222557 original size:42 final size:41
Alignment explanation
Indices: 222459--222620 Score: 134
Period size: 42 Copynumber: 4.0 Consensus size: 41
222449 ATAGATCCGT
* * *
222459 ACCTTAGTGGCATTTGTTATAAAAATGCCATAATAGAGGCA
1 ACCTTAGTGGCATTTGTTATAAAAACGCCACAATAGAGGGA
*
222500 A-CTTAGTGGCGTTTGTTACT-AAAACGCCACAATAGAGGTGA
1 ACCTTAGTGGCATTTGTTA-TAAAAACGCCACAATAGAGG-GA
** * * * * *
222541 ACCTTAGTGGTGTTTGTCACT-AAAACGCCGCTATAGAGCCGT
1 ACCTTAGTGGCATTTGTTA-TAAAAACGCCACAATAGAG-GGA
** *
222583 ACCTT-GTGTAATTTGTTATAAAAACACCACAATAGAGG
1 ACCTTAGTGGCATTTGTTATAAAAACGCCACAATAGAGG
222621 CCACAATGGA
Statistics
Matches: 98, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
40 33 0.34
41 27 0.28
42 38 0.39
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (41 bp):
ACCTTAGTGGCATTTGTTATAAAAACGCCACAATAGAGGGA
Found at i:236652 original size:12 final size:12
Alignment explanation
Indices: 236637--236678 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
236627 AGCTGAAGCA
236637 AGAGAAGCA-GG
1 AGAGAAGCAGGG
*
236648 -GAG-AGCAGCG
1 AGAGAAGCAGGG
236658 AGAGAAGCAGGG
1 AGAGAAGCAGGG
236670 AGAGAAGCA
1 AGAGAAGCA
236679 AATAGAGCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 4 0.15
10 4 0.15
11 3 0.12
12 15 0.58
ACGTcount: A:0.43, C:0.12, G:0.45, T:0.00
Consensus pattern (12 bp):
AGAGAAGCAGGG
Found at i:236675 original size:33 final size:33
Alignment explanation
Indices: 236637--236699 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
236627 AGCTGAAGCA
**
236637 AGAGAAGCAGGGAGAGCAGCGAGAGAAGCAGGG
1 AGAGAAGCAAAGAGAGCAGCGAGAGAAGCAGGG
*
236670 AGAGAAGCAAATAGAGCAGCGAGAGAAGCA
1 AGAGAAGCAAAGAGAGCAGCGAGAGAAGCA
236700 TAGAGAAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.41, T:0.02
Consensus pattern (33 bp):
AGAGAAGCAAAGAGAGCAGCGAGAGAAGCAGGG
Found at i:236699 original size:12 final size:11
Alignment explanation
Indices: 236637--236699 Score: 53
Period size: 12 Copynumber: 5.8 Consensus size: 11
236627 AGCTGAAGCA
236637 AGAGAAGCAGG
1 AGAGAAGCAGG
236648 -GAG-AGCAGCG
1 AGAGAAGCAG-G
236658 AGAGAAGCAGGG
1 AGAGAAGCA-GG
*
236670 AGAGAAGCA-A
1 AGAGAAGCAGG
*
236680 ATAG-AGCAGCG
1 AGAGAAGCAG-G
236691 AGAGAAGCA
1 AGAGAAGCA
236700 TAGAGAAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
9 9 0.22
10 7 0.17
11 6 0.15
12 18 0.44
13 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.41, T:0.02
Consensus pattern (11 bp):
AGAGAAGCAGG
Found at i:236702 original size:19 final size:20
Alignment explanation
Indices: 236631--236704 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
236621 AAGCGAAGCT
* *
236631 GAAGCAAGAGAAGCAGGGAGA
1 GAAGCAATAG-AGCAGCGAGA
* * * *
236652 GCAGCGAGAGAAGCAGGGAGA
1 GAAGCAATAG-AGCAGCGAGA
236673 GAAGCAAATAGAGCAGCGAGA
1 GAAGC-AATAGAGCAGCGAGA
236694 GAAGC-ATAGAG
1 GAAGCAATAGAG
236705 AAGTAGCATT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 6 0.13
21 37 0.80
22 3 0.07
ACGTcount: A:0.45, C:0.12, G:0.41, T:0.03
Consensus pattern (20 bp):
GAAGCAATAGAGCAGCGAGA
Found at i:241938 original size:2 final size:2
Alignment explanation
Indices: 241927--242002 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
241917 CAGTTATGTC
241927 TA TA -A 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
241968 TA TA 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 TA TA T
242003 TGTTATGATT
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:242202 original size:31 final size:31
Alignment explanation
Indices: 242167--242226 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
242157 AAAACATAAT
242167 ATATAGTCATTTTTACTTT-TAGTTAATTAAG
1 ATATAGTCATTTTTA-TTTCTAGTTAATTAAG
*
242198 ATATAGTCATTTTTATTTCTATTTAATTA
1 ATATAGTCATTTTTATTTCTAGTTAATTA
242227 TGGTGTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.55
Consensus pattern (31 bp):
ATATAGTCATTTTTATTTCTAGTTAATTAAG
Found at i:242684 original size:2 final size:2
Alignment explanation
Indices: 242677--242705 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
242667 TTTATAACAT
242677 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 T
242706 TACTTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:242775 original size:26 final size:27
Alignment explanation
Indices: 242720--242803 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 27
242710 TTTTTAAGAT
242720 TTTTA-TATTAATTT-A-TTAAATATA
1 TTTTATTATTAATTTAATTTAAATATA
*
242744 TTTTATTATGAATTTAATTTAAA-ATA
1 TTTTATTATTAATTTAATTTAAATATA
* *
242770 TTTTATTTTTAATTTATTTTAAATATA
1 TTTTATTATTAATTTAATTTAAATATA
*
242797 TGTTATT
1 TTTTATT
242804 TTTATCCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.10
25 8 0.16
26 24 0.47
27 14 0.27
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTTATTATTAATTTAATTTAAATATA
Found at i:242846 original size:30 final size:29
Alignment explanation
Indices: 242718--242933 Score: 90
Period size: 30 Copynumber: 7.6 Consensus size: 29
242708 CTTTTTTAAG
* * *
242718 ATTTTTATATTAATTTATTAAATATATTTT
1 ATTTTTATTTTAACTT-TTAAAAATATTTT
* * *
242748 ATTATGAATTTAA--TTT-AAAATATTTT
1 ATTTTTATTTTAACTTTTAAAAATATTTT
* * *
242774 ATTTTTAATTT-A-TTTTAAATATATGTT
1 ATTTTTATTTTAACTTTTAAAAATATTTT
***
242801 ATTTTTATCCAAACTTTTAAAAAATATTTT
1 ATTTTTATTTTAACTTTT-AAAAATATTTT
* ** * *
242831 ATTATTATTTTAACTTTCCAAAGT-TTAT
1 ATTTTTATTTTAACTTTTAAAAATATTTT
* *
242859 A-TTTTATCTTAA--TTTACCAAATATATTAT
1 ATTTTTATTTTAACTTTTA--AAA-ATATTTT
* * * *
242888 ATTATTATTATAAATTATTAAATATATTTT
1 ATTTTTATTTTAACTT-TTAAAAATATTTT
* *
242918 ATTCTTATATTAACTT
1 ATTTTTATTTTAACTT
242934 CAAAATATTT
Statistics
Matches: 136, Mismatches: 37, Indels: 26
0.68 0.19 0.13
Matches are distributed among these distances:
25 3 0.02
26 21 0.15
27 29 0.21
28 7 0.05
29 13 0.10
30 57 0.42
31 2 0.01
32 1 0.01
33 3 0.02
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (29 bp):
ATTTTTATTTTAACTTTTAAAAATATTTT
Found at i:242892 original size:27 final size:27
Alignment explanation
Indices: 242822--242892 Score: 65
Period size: 27 Copynumber: 2.6 Consensus size: 27
242812 AACTTTTAAA
* *
242822 AAATATTTTATTATTATTTTAACTTTCC
1 AAATATATTA-TATTATCTTAACTTTCC
* *
242850 AAAGTTTA-TATTTTATCTTAA-TTTACC
1 AAA-TATATTATATTATCTTAACTTT-CC
242877 AAATATATTATATTAT
1 AAATATATTATATTAT
242893 TATTATAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
26 6 0.18
27 21 0.62
28 5 0.15
29 2 0.06
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (27 bp):
AAATATATTATATTATCTTAACTTTCC
Found at i:242919 original size:21 final size:22
Alignment explanation
Indices: 242877--242919 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
242867 TTAATTTACC
*
242877 AAATATATTATATTATTATTAT
1 AAATATATTAAATTATTATTAT
242899 AAAT-TATTAAATATATT-TTAT
1 AAATATATTAAAT-TATTATTAT
242920 TCTTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATATATTAAATTATTATTAT
Found at i:243000 original size:25 final size:24
Alignment explanation
Indices: 242971--243032 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 24
242961 TTAAATTAGA
242971 TTAATAATAAAATATATTTA-ATAAG
1 TTAATAATAAAA-ATATTTATA-AAG
*
242996 TTAAT-ATAAAAATATTTTTAAAG
1 TTAATAATAAAAATATTTATAAAG
243019 TTAATATATAAAAA
1 TTAATA-ATAAAAA
243033 AAATTTGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 14 0.42
24 7 0.21
25 12 0.36
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (24 bp):
TTAATAATAAAAATATTTATAAAG
Found at i:243019 original size:23 final size:26
Alignment explanation
Indices: 242971--243031 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
242961 TTAAATTAGA
242971 TTAATA-ATAAAATATATTTAATAAG
1 TTAATATATAAAATATATTTAATAAG
*
242996 TTAATATA-AAAATAT-TTTTA-AAG
1 TTAATATATAAAATATATTTAATAAG
243019 TTAATATATAAAA
1 TTAATATATAAAA
243032 AAAATTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 11 0.33
24 8 0.24
25 13 0.39
26 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
TTAATATATAAAATATATTTAATAAG
Found at i:243148 original size:21 final size:21
Alignment explanation
Indices: 243124--243165 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
243114 TTTTGGCTCA
243124 ATGGTTGGGTACGTGCTTAGT
1 ATGGTTGGGTACGTGCTTAGT
243145 ATGGTTGGGTACGTGCTTAGT
1 ATGGTTGGGTACGTGCTTAGT
243166 TTTTTAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
ATGGTTGGGTACGTGCTTAGT
Found at i:243466 original size:31 final size:31
Alignment explanation
Indices: 243405--243469 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
243395 TTATCACATC
* **
243405 TTAATTAAATAAAAATGAAAGTGATGATATA
1 TTAATTAAATAAAAATGAAAGTAACCATATA
243436 TTAATTAAATAAAAATGAAAGTAACCATATA
1 TTAATTAAATAAAAATGAAAGTAACCATATA
243467 TTA
1 TTA
243470 TGTTTTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.32
Consensus pattern (31 bp):
TTAATTAAATAAAAATGAAAGTAACCATATA
Found at i:244874 original size:14 final size:14
Alignment explanation
Indices: 244838--244889 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
244828 AATAAATAAT
*
244838 TTTAAATTAATTTAA
1 TTTAAA-TATTTTAA
*
244853 TTTAAAATATTTTTA
1 TTT-AAATATTTTAA
**
244868 TTTAAATATTAAAA
1 TTTAAATATTTTAA
244882 TTTAAATA
1 TTTAAATA
244890 ATTATAAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 16 0.52
15 12 0.39
16 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAAATATTTTAA
Found at i:245587 original size:16 final size:16
Alignment explanation
Indices: 245568--245601 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
245558 CAATATACGA
245568 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
245584 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
245600 AT
1 AT
245602 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:245678 original size:14 final size:16
Alignment explanation
Indices: 245642--245678 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
245632 TATTAATGTA
245642 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
245659 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
245674 T-AATA
1 TGAATA
245679 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:246345 original size:130 final size:130
Alignment explanation
Indices: 246141--246388 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
246131 AATTTTCTTC
* * * *
246141 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACATATGTCAGAT
1 TAATTAGGTGGTGACATGCGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* ** *
246206 TCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
246271 TAATTAGGTGGTGACATGCGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGCGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
246336 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
246389 TATATAAATA
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGCGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:246837 original size:35 final size:35
Alignment explanation
Indices: 246787--246862 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
246777 AATTGAATTT
* *
246787 AATTGAATTATTTTGGAATTTAGGGTTGAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
* *
246822 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
246857 AATTGA
1 AATTGA
246863 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
Found at i:252689 original size:101 final size:100
Alignment explanation
Indices: 252572--252836 Score: 243
Period size: 99 Copynumber: 2.6 Consensus size: 100
252562 ACACAACTTG
* * **
252572 CAATGTTAGAATTATAAACATGTTTTGTCTTA-TGATTGCATAATAAAAACGATTTAAAACATAT
1 CAATGTTATACTTATAAACATGTTTTGTCTTACTTTTTGCATAATAAAAACG-TTTAAAACATAT
* * *
252636 AATC-TTAACGGTTGAGAATTTAAAAAAGTGAAACCTA
65 AA-CATAAACGGTTGA-AAGTTAAAAAAGCGAAACCTA
* * * * *
252673 CAATGTTATACTTATAAACCTATTTTGTATTACTTTTTG-ATAATATAAAA-GTTTTAAACATGT
1 CAATGTTATACTTATAAACATGTTTTGTCTTACTTTTTGCATAATA-AAAACGTTTAAAACATAT
* * **
252736 AACATAAACGGTTGATAGTTAAAAAGGCGCTACCTA
65 AACATAAACGGTTGAAAGTTAAAAAAGCGAAACCTA
* * * * * *
252772 TAATGTTATACATATAAACTTGTTTT-TGCTTATTTTTTTCATAATAAAAACGGTTTGAAACATA
1 CAATGTTATACTTATAAACATGTTTTGT-CTTACTTTTTGCATAATAAAAAC-GTTTAAAACATA
252836 T
64 T
252837 GCTCCTGTTT
Statistics
Matches: 132, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
98 1 0.01
99 50 0.38
100 28 0.21
101 45 0.34
102 8 0.06
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.38
Consensus pattern (100 bp):
CAATGTTATACTTATAAACATGTTTTGTCTTACTTTTTGCATAATAAAAACGTTTAAAACATATA
ACATAAACGGTTGAAAGTTAAAAAAGCGAAACCTA
Found at i:254790 original size:99 final size:98
Alignment explanation
Indices: 254603--254978 Score: 343
Period size: 99 Copynumber: 3.8 Consensus size: 98
254593 CTTATAACTT
* * * *
254603 AACCAA-TTTGTATTAATTTTTCATAATGT-CTA-AGGTTT-AAGCTTATAACTTATCCAATTAA
1 AACCAAGTTTGT-TTACTTTTTCATAATATAC-ACAGATTTCAA-CTTATAACTTAACCAATTAA
** *
254664 CATAACAACAAGGCACAACTTATAATGTTATACAAGA
63 CATAACAACAAGGTGCAACATATAATGTTAT-CAAGA
* * **
254701 AATCAGGTTTAGTTTACTTTTTCATAATATACACAG-TTTCAGGTTATAACTTAACCAATTAACA
1 AACCAAGTTT-GTTTACTTTTTCATAATATACACAGATTTCAACTTATAACTTAACCAATTAACA
* * *
254765 TAAAAACAAGGTGCAACATATAATGTTATCTAGG
65 TAACAACAAGGTGCAACATATAATGTTATCAAGA
* * ** * *
254799 AACCATGTTTGTTTAAATTTTTTCATAATATACAC-GATTTCAACTTATAACGCAACCAGTTAAA
1 AACCAAGTTTGTTT--ACTTTTTCATAATATACACAGATTTCAACTTATAACTTAACCAATTAAC
* * * *
254863 ATAACACCAAGGTGCAACCTATAATATTATCTAGGA
64 ATAACAACAAGGTGCAACATATAATGTTATC-AAGA
* * ** * *
254899 AACCAAGTTTGTATTACTTTTTCATAATATAC-GAGCTTTCTTCCTATAACTTAACCAGTTAACA
1 AACCAAGTTTGT-TTACTTTTTCATAATATACACAGATTTCAACTTATAACTTAACCAATTAACA
*
254963 TAACACCAAGGTGCAA
65 TAACAACAAGGTGCAA
254979 TCGGTAACAT
Statistics
Matches: 228, Mismatches: 39, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
97 4 0.02
98 16 0.07
99 188 0.82
100 18 0.08
101 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (98 bp):
AACCAAGTTTGTTTACTTTTTCATAATATACACAGATTTCAACTTATAACTTAACCAATTAACAT
AACAACAAGGTGCAACATATAATGTTATCAAGA
Found at i:261909 original size:33 final size:33
Alignment explanation
Indices: 261867--261984 Score: 148
Period size: 33 Copynumber: 3.6 Consensus size: 33
261857 TTAACTTACT
* * *
261867 GATGAGTTGTTTGTTGGTTGGTCGAGATTTTTG
1 GATGAGTTGTTGGTTGATTGGTCGAGATTTTTC
*
261900 GATGAGTTGTTGGTTGATTGGTCTAGATTTTTC
1 GATGAGTTGTTGGTTGATTGGTCGAGATTTTTC
* *
261933 GATGAGTGGTTGGTT-ATTTGGTCGAGATTTTTT
1 GATGAGTTGTTGGTTGA-TTGGTCGAGATTTTTC
* *
261966 GATGAGCTATTGGTTGATT
1 GATGAGTTGTTGGTTGATT
261985 TTTTCTATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 1 0.01
33 71 0.97
34 1 0.01
ACGTcount: A:0.15, C:0.04, G:0.33, T:0.47
Consensus pattern (33 bp):
GATGAGTTGTTGGTTGATTGGTCGAGATTTTTC
Found at i:264717 original size:19 final size:19
Alignment explanation
Indices: 264693--264734 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
264683 AAATAAGTTG
* *
264693 GTTGTTATGTGAAGAATAA
1 GTTGTTATCTAAAGAATAA
264712 GTTGTTATCTAAAGAATAA
1 GTTGTTATCTAAAGAATAA
264731 GTTG
1 GTTG
264735 CAACAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (19 bp):
GTTGTTATCTAAAGAATAA
Found at i:266530 original size:2 final size:2
Alignment explanation
Indices: 266523--266598 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
266513 TGTTATTTTG
266523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
266565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
266599 GTAAATTTAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:270551 original size:69 final size:69
Alignment explanation
Indices: 270440--270579 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
270430 TTGAATACAA
270440 AGGTTTTATTGCTATACTGTAGATATTTTGACATTCCTAAGGGATGTAGAATATTGTGTTTATTA
1 AGGTTTTATTGCTATACTGTAGATATTTTGACATTCCTAAGGGATGTAGAATATTGTGTTTATTA
270505 TAAG
66 TAAG
270509 AGGTTTTATTGCTATACTGTAGATATTTTGACATTCCTAAGGGATGTAGAATATTGTGTTTATTA
1 AGGTTTTATTGCTATACTGTAGATATTTTGACATTCCTAAGGGATGTAGAATATTGTGTTTATTA
270574 TAAG
66 TAAG
270578 AG
1 AG
270580 AGTACAATTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (69 bp):
AGGTTTTATTGCTATACTGTAGATATTTTGACATTCCTAAGGGATGTAGAATATTGTGTTTATTA
TAAG
Found at i:280746 original size:17 final size:18
Alignment explanation
Indices: 280724--280759 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
280714 CTCAAAATCA
*
280724 TCTC-TTTGTTTTTGTTT
1 TCTCTTTTGTTTTTATTT
280741 TCTCTTTTGTTTTTATTT
1 TCTCTTTTGTTTTTATTT
280759 T
1 T
280760 GCATATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.03, C:0.11, G:0.08, T:0.78
Consensus pattern (18 bp):
TCTCTTTTGTTTTTATTT
Done.