Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008653.1 Hibiscus syriacus cultivar Beakdansim tig00111644_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: 1778368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1308743 original size:31 final size:32
Alignment explanation
Indices: 1308695--1308767 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
1308685 TCGGGCCGGG
1308695 TATATATATTAAATTAAATATAAA-TATT-ATA
1 TATATATATTAAATTAAAT-TAAATTATTAATA
* *
1308726 TATATATTTTAATTTAAATTAAATTTATTAATA
1 TATATATATTAAATTAAATTAAA-TTATTAATA
1308759 TATATATAT
1 TATATATAT
1308768 ATATAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 4 0.11
31 17 0.47
32 4 0.11
33 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATATATTAAATTAAATTAAATTATTAATA
Found at i:1308813 original size:12 final size:12
Alignment explanation
Indices: 1308796--1308825 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1308786 ATTTATCGGC
1308796 CGGGTATCGAGT
1 CGGGTATCGAGT
*
1308808 CGGGTATCGGGT
1 CGGGTATCGAGT
1308820 CGGGTA
1 CGGGTA
1308826 ATCAGGGCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.17, G:0.47, T:0.23
Consensus pattern (12 bp):
CGGGTATCGAGT
Found at i:1309325 original size:20 final size:20
Alignment explanation
Indices: 1309230--1309328 Score: 144
Period size: 20 Copynumber: 5.0 Consensus size: 20
1309220 AATCACAATT
* *
1309230 CGATTATGACTATCGCAATG
1 CGATTCTGACTATCGCAACG
1309250 CGATTCTGACTATCGCAACG
1 CGATTCTGACTATCGCAACG
*
1309270 CGATTCTGATTATCGCAACG
1 CGATTCTGACTATCGCAACG
*
1309290 CGATTCTGACTATCGCAATG
1 CGATTCTGACTATCGCAACG
* *
1309310 CGATTCTGATTGTCGCAAC
1 CGATTCTGACTATCGCAAC
1309329 ACTGAATTTC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (20 bp):
CGATTCTGACTATCGCAACG
Found at i:1310200 original size:24 final size:24
Alignment explanation
Indices: 1310143--1310202 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1310133 TAGTCAGTAT
1310143 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
1310167 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
1310191 TCGAATTTTGAT
1 TCGAAATTTGAT
1310203 GATGTTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:1312448 original size:18 final size:18
Alignment explanation
Indices: 1312425--1312459 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1312415 AGAAAAAGGC
*
1312425 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1312443 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1312460 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1312749 original size:34 final size:34
Alignment explanation
Indices: 1312658--1312828 Score: 144
Period size: 34 Copynumber: 4.9 Consensus size: 34
1312648 GAATTTGACT
* * **
1312658 ATCGCAACGCGAATTTGATTATCACAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
*
1312692 ATCACAACGCGAATTTGACTATCGCAACGAAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
* **
1312726 ATCGCAACGCGAATTTGACTATCGCAGCGTGAATTTGATT
1 ATCGCAACGCGAATTTGACTATCGCAAC--GAA----AAA
* * * * *
1312766 ATCGCAACGGGTATTCGACTATCGCAATGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
* * *
1312800 ATCGCAAAGCGTATTAGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
1312829 CGAATTGACT
Statistics
Matches: 110, Mismatches: 21, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
34 81 0.74
36 3 0.03
38 2 0.02
40 24 0.22
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
Found at i:1312774 original size:74 final size:74
Alignment explanation
Indices: 1312696--1312834 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 74
1312686 TCAAAAATCA
* * * * *
1312696 CAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGAATTTGACTATCGCAGCGTGAATT
1 CAACGCGAATTCGACTATCGCAACGAAAAAATCGCAAAGCGAATTAGACTATCGCAACGCGAATT
1312761 TGATTATCG
66 TGATTATCG
* * * * *
1312770 CAACGGGTATTCGACTATCGCAATGAGAAAATCGCAAAGCGTATTAGACTATCGCAACGCGAATT
1 CAACGCGAATTCGACTATCGCAACGAAAAAATCGCAAAGCGAATTAGACTATCGCAACGCGAATT
1312835 GACTTTCGCG
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
74 55 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (74 bp):
CAACGCGAATTCGACTATCGCAACGAAAAAATCGCAAAGCGAATTAGACTATCGCAACGCGAATT
TGATTATCG
Found at i:1312788 original size:20 final size:20
Alignment explanation
Indices: 1312630--1312792 Score: 116
Period size: 20 Copynumber: 8.8 Consensus size: 20
1312620 TTACACATTC
*
1312630 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1312650 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
1312670 ATTTGATTATCACAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
1312689 A----A-AATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
1312704 ATTTGACTATCGCAA--CGA
1 ATTTGACTATCGCAACGCGA
**
1312722 A----AAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1312738 ATTTGACTATCGCAGCGTGA
1 ATTTGACTATCGCAACGCGA
* * *
1312758 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
*
1312778 ATTCGACTATCGCAA
1 ATTTGACTATCGCAA
1312793 TGAGAAAATC
Statistics
Matches: 111, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
14 17 0.15
15 3 0.03
16 4 0.04
18 4 0.04
19 3 0.03
20 80 0.72
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1312843 original size:19 final size:20
Alignment explanation
Indices: 1312800--1312843 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1312790 CAATGAGAAA
*
1312800 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
1312820 ATCGCAACGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
1312839 TTCGC
1 ATCGC
1312844 GTTGCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:1312862 original size:20 final size:21
Alignment explanation
Indices: 1312833--1312890 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
1312823 GCAACGCGAA
1312833 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
1312853 TTG-GCTTTCGCATTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
1312873 TTGAG-TTTAGCGTTGCGA
1 TTGAGCTTTCGCGTTGCGA
1312891 AAGTGTACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.28, T:0.43
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:1313049 original size:14 final size:14
Alignment explanation
Indices: 1312989--1313050 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
1312979 CACAAATAAG
*
1312989 AATTATTTACACATC
1 AATT-TTTACAAATC
**
1313004 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
1313019 AACTTTTACAAATC
1 AATTTTTACAAATC
*
1313033 AATTTTTGCAAATC
1 AATTTTTACAAATC
1313047 AATT
1 AATT
1313051 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.37
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:1314544 original size:42 final size:42
Alignment explanation
Indices: 1314465--1314557 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1314455 CCTCTTCAAC
* * *
1314465 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
1314507 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
1314549 GATGACAGG
1 GATGACAGG
1314558 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:1315066 original size:18 final size:18
Alignment explanation
Indices: 1315043--1315126 Score: 105
Period size: 18 Copynumber: 4.4 Consensus size: 18
1315033 GAAACTTAAA
1315043 ATCGCAACACGAATGACT
1 ATCGCAACACGAATGACT
1315061 ATCGCAACACGAATGACT
1 ATCGCAACACGAATGACT
*
1315079 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG--AATGACT
**
1315099 ATCGCAACGTGAATTTGACT
1 ATCGCAACACGAA--TGACT
1315119 ATCGCAAC
1 ATCGCAAC
1315127 GAGAGAATCG
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
18 30 0.50
20 30 0.50
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (18 bp):
ATCGCAACACGAATGACT
Found at i:1315097 original size:20 final size:20
Alignment explanation
Indices: 1315054--1315127 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
1315044 TCGCAACACG
*
1315054 AATGACTATCGCAACACG--
1 AATGACTATCGCAACGCGAA
1315072 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
1315092 AATGACTATCGCAACGTGAA
1 AATGACTATCGCAACGCGAA
**
1315112 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
1315128 AGAGAATCGC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
18 17 0.34
20 33 0.66
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:1315368 original size:18 final size:18
Alignment explanation
Indices: 1315345--1315394 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1315335 TTTACTAAGC
1315345 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
1315363 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
1315381 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
1315395 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:1317137 original size:20 final size:20
Alignment explanation
Indices: 1317114--1317167 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1317104 GAAACTTAAA
1317114 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
**
1317134 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAAAATGACT
* *
1317154 ATTGCAACGCGAAA
1 ATCGCAACACGAAA
1317168 CTAAAATCGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:1317591 original size:22 final size:22
Alignment explanation
Indices: 1317565--1317606 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1317555 AGATAGACGG
1317565 ATTTCG-CTAGAGATGGGGACTA
1 ATTTCGTC-AGAGATGGGGACTA
*
1317587 ATTTCGTCGGAGATGGGGAC
1 ATTTCGTCAGAGATGGGGAC
1317607 AGATGTCGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.24, C:0.14, G:0.36, T:0.26
Consensus pattern (22 bp):
ATTTCGTCAGAGATGGGGACTA
Found at i:1317807 original size:20 final size:20
Alignment explanation
Indices: 1317782--1317855 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
1317772 GCGCTTTGAA
1317782 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
1317802 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* * *
1317822 AATCTCGTTGCGATAGTTAG
1 AATCGCATTGCGATAGTCAG
1317842 AATCGCATTGCGAT
1 AATCGCATTGCGAT
1317856 TTACATATTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:1317867 original size:20 final size:20
Alignment explanation
Indices: 1317844--1317894 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1317834 ATAGTTAGAA
1317844 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1317864 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1317884 TCGCATTGCGA
1 TCGCATTGCGA
1317895 ATTCGGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1317918 original size:21 final size:21
Alignment explanation
Indices: 1317891--1317957 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
1317881 TATTCGCATT
**
1317891 GCGAATTCGGAAAATCGCAAC
1 GCGAATTTAGAAAATCGCAAC
* *
1317912 GCTAATTTAGAAAATCGCAAT
1 GCGAATTTAGAAAATCGCAAC
*
1317933 GCGAATTTAGAAAATCGCAAT
1 GCGAATTTAGAAAATCGCAAC
1317954 GCGA
1 GCGA
1317958 TTCTAACTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (21 bp):
GCGAATTTAGAAAATCGCAAC
Found at i:1321283 original size:18 final size:18
Alignment explanation
Indices: 1321260--1321294 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1321250 AGAAAAAGGC
*
1321260 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1321278 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1321295 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1321490 original size:20 final size:20
Alignment explanation
Indices: 1321465--1321678 Score: 124
Period size: 20 Copynumber: 11.7 Consensus size: 20
1321455 TTACACATTC
1321465 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1321485 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
1321505 ATTTGATTATCACAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
1321524 A----A-AATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
1321539 ATTTGACTATCGCAA--CGA
1 ATTTGACTATCGCAACGCGA
**
1321557 A----AAAATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1321573 ATTTGACTATCGCAGCGTGA
1 ATTTGACTATCGCAACGCGA
* * * *
1321593 ATTTAATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
* *
1321613 ATTCGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
1321633 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
1321647 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1321667 A-TTGACTTTCGC
1 ATTTGACTATCGC
1321679 GTTGCGATTT
Statistics
Matches: 146, Mismatches: 30, Indels: 37
0.69 0.14 0.17
Matches are distributed among these distances:
14 27 0.18
15 3 0.02
16 5 0.03
18 5 0.03
19 12 0.08
20 94 0.64
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1321584 original size:34 final size:34
Alignment explanation
Indices: 1321493--1321663 Score: 162
Period size: 34 Copynumber: 4.9 Consensus size: 34
1321483 GAATTTGACT
* * **
1321493 ATCGCAACGCGAATTTGATTATCACAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
*
1321527 ATCACAACGCGAATTTGACTATCGCAACGAAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
* *
1321561 ATCGCAACGCGAATTTGACTATCGCAGCGTGAATTTAATT
1 ATCGCAACGCGAATTTGACTATCGCAAC--GAA---AA-A
* * * *
1321601 ATCGCAACGGGTATTCGACTATCGCAACGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
* * *
1321635 ATCGCAAAGCGTATTAGACTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
1321664 CGAATTGACT
Statistics
Matches: 114, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
34 81 0.71
35 2 0.02
36 3 0.03
38 2 0.02
39 2 0.02
40 24 0.21
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAAAAA
Found at i:1321609 original size:74 final size:74
Alignment explanation
Indices: 1321531--1321669 Score: 197
Period size: 74 Copynumber: 1.9 Consensus size: 74
1321521 TCAAAAATCA
* * * * *
1321531 CAACGCGAATTTGACTATCGCAACGAAAAAATCGCAACGCGAATTTGACTATCGCAGCGTGAATT
1 CAACGCGAATTCGACTATCGCAACGAAAAAATCGCAAAGCGAATTAGACTATCGCAACGCGAATT
1321596 TAATTATCG
66 TAATTATCG
* * * *
1321605 CAACGGGTATTCGACTATCGCAACGAGAAAATCGCAAAGCGTATTAGACTATCGCAACGCGAATT
1 CAACGCGAATTCGACTATCGCAACGAAAAAATCGCAAAGCGAATTAGACTATCGCAACGCGAATT
1321670 GACTTTCGCG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
74 56 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (74 bp):
CAACGCGAATTCGACTATCGCAACGAAAAAATCGCAAAGCGAATTAGACTATCGCAACGCGAATT
TAATTATCG
Found at i:1321697 original size:20 final size:21
Alignment explanation
Indices: 1321668--1321725 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
1321658 GCAACGCGAA
1321668 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
1321688 TTG-GCTTTCGCATTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
1321708 TTGAG-TTTAGCGTTGCGA
1 TTGAGCTTTCGCGTTGCGA
1321726 AAGTGTACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.17, G:0.28, T:0.43
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:1323359 original size:21 final size:21
Alignment explanation
Indices: 1323335--1323391 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
1323325 GGATGATAGG
1323335 GGCCTCTTGAACGATAGGGGA
1 GGCCTCTTGAACGATAGGGGA
1323356 GGCCTCTTGAACGATAGGGGA
1 GGCCTCTTGAACGATAGGGGA
1323377 GGCCTCTTGAACGAT
1 GGCCTCTTGAACGAT
1323392 GACATGTGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (21 bp):
GGCCTCTTGAACGATAGGGGA
Found at i:1323363 original size:42 final size:42
Alignment explanation
Indices: 1323265--1323392 Score: 118
Period size: 42 Copynumber: 3.0 Consensus size: 42
1323255 TCTAGAATGT
* * *
1323265 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGA
* ** *
1323307 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGA
* **
1323349 TAGGG-GAGGCCTCTTGAACGAT-AGGGGAGGCCTCTTGAACGA
1 T-GGGAGAGGACTCTTGAACGATGACAGG-GGCCTCTTGAACGA
1323391 TG
1 TG
1323393 ACATGTGAGT
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
41 4 0.06
42 61 0.86
43 6 0.08
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:1323905 original size:18 final size:19
Alignment explanation
Indices: 1323882--1323927 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1323872 GAAACTTAAA
1323882 ATCGCAACACG-AATGACT
1 ATCGCAACACGAAATGACT
*
1323900 ATCGCAACGCGAAAATGACT
1 ATCGCAACACG-AAATGACT
1323920 ATCGCAAC
1 ATCGCAAC
1323928 GAGAGAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.40
20 15 0.60
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAACACGAAATGACT
Found at i:1323979 original size:20 final size:20
Alignment explanation
Indices: 1323954--1324021 Score: 127
Period size: 20 Copynumber: 3.4 Consensus size: 20
1323944 GAGATTCTCT
1323954 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1323974 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1323994 CGTTGCAATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1324014 CGTTGCGA
1 CGTTGCGA
1324022 AAGTAAACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1324194 original size:18 final size:18
Alignment explanation
Indices: 1324173--1324218 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
1324163 CTAAGCAATA
1324173 TAAGTGAAATGGTTAATC
1 TAAGTGAAATGGTTAATC
1324191 TAAGTGAAATGGTTAATC
1 TAAGTGAAATGGTTAATC
1324209 TAAGTGAAAT
1 TAAGTGAAAT
1324219 TACGAGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (18 bp):
TAAGTGAAATGGTTAATC
Found at i:1325990 original size:20 final size:20
Alignment explanation
Indices: 1325940--1326013 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
1325930 GAAACTTAAA
* **
1325940 ATCGCAACACAAAAATGAAA
1 ATCGCAACACGAAAATGACT
*
1325960 ATTGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
**
1325980 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAAAATGACT
* *
1326000 ATTGCAACGCGAAA
1 ATCGCAACACGAAA
1326014 CTAAAATCGC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:1326420 original size:22 final size:22
Alignment explanation
Indices: 1326390--1326446 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
1326380 GATGGAGATA
1326390 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* * *
1326412 GACTGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
1326434 GACGGATGTCGCC
1 GACGGATTTCGCC
1326447 TTAGAGAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:1326638 original size:20 final size:20
Alignment explanation
Indices: 1326613--1326683 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
1326603 GCGCTTTGAA
*
1326613 AATCGCATTGTGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
1326633 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
1326653 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
1326673 AATCGCATTGC
1 AATCGCATTGC
1326684 AATTTACATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:1326704 original size:40 final size:40
Alignment explanation
Indices: 1326611--1326765 Score: 125
Period size: 40 Copynumber: 3.8 Consensus size: 40
1326601 TGGCGCTTTG
* * * *
1326611 AAAATCGCATTGTGATAGTCAGAATCGCGTTGCGATAGT-C
1 AAAATCGCATTGCGATAGTCAGAATCGCATTGCAAT-TTAC
* *
1326651 AGAATCGCGTTGCGATAGTCAGAATCGCATTGCAATTTAC
1 AAAATCGCATTGCGATAGTCAGAATCGCATTGCAATTTAC
* * * * ** *
1326691 ATATTCGCATTGCGAT-TTCGGAAAATCGCAACGCGAATTTAG
1 AAAATCGCATTGCGATAGTC--AGAATCGCATTGC-AATTTAC
* *
1326733 AAAATCGCAATGCGATAGTCAGAATCGCGTTGC
1 AAAATCGCATTGCGATAGTCAGAATCGCATTGC
1326766 GAATCTGGAA
Statistics
Matches: 88, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
39 3 0.03
40 45 0.51
41 19 0.22
42 19 0.22
43 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (40 bp):
AAAATCGCATTGCGATAGTCAGAATCGCATTGCAATTTAC
Found at i:1327274 original size:27 final size:27
Alignment explanation
Indices: 1327243--1327301 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
1327233 GAACAAAGTA
*
1327243 TTAATAACGACCATTAGATTAATAAAT
1 TTAATAACGACCACTAGATTAATAAAT
* * *
1327270 TTAATTATGATCACTAGATTAATAAAT
1 TTAATAACGACCACTAGATTAATAAAT
1327297 TTAAT
1 TTAAT
1327302 TTCTATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (27 bp):
TTAATAACGACCACTAGATTAATAAAT
Found at i:1328492 original size:21 final size:21
Alignment explanation
Indices: 1328468--1328516 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1328458 AATATTTTTG
*
1328468 ATTAATCGATTAATTCGATGA
1 ATTAATCGATTAATTCAATGA
1328489 ATTAATCGATTAATTCAATGA
1 ATTAATCGATTAATTCAATGA
1328510 ATTAATC
1 ATTAATC
1328517 AATTTTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (21 bp):
ATTAATCGATTAATTCAATGA
Found at i:1334119 original size:15 final size:17
Alignment explanation
Indices: 1334097--1334136 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
1334087 CGGGCCAAGT
1334097 ATATATATTTAAAT-TA
1 ATATATATTTAAATATA
1334113 A-ATATA--TAAATATA
1 ATATATATTTAAATATA
1334127 ATATATATTT
1 ATATATATTT
1334137 TTAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 7
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.25
14 3 0.15
15 10 0.50
16 1 0.05
17 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATTTAAATATA
Found at i:1334155 original size:19 final size:19
Alignment explanation
Indices: 1334103--1334160 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
1334093 AAGTATATAT
* *
1334103 ATTTAAATTAAATATATAA
1 ATTTAAATTAAATTTTTAA
* *
1334122 ATAT-AATATATATTTTTAA
1 ATTTAAAT-TAAATTTTTAA
1334141 ATTTAAATTAAATTTATTAA
1 ATTTAAATTAAATTT-TTAA
1334161 TATTATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 3 0.10
19 20 0.67
20 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTAAATTAAATTTTTAA
Found at i:1334309 original size:37 final size:38
Alignment explanation
Indices: 1334259--1334331 Score: 130
Period size: 37 Copynumber: 1.9 Consensus size: 38
1334249 ACTAAACCTG
1334259 TCCCCGTCCCCGTTTAACATAAAC-GTTTTTTCCCTCA
1 TCCCCGTCCCCGTTTAACATAAACAGTTTTTTCCCTCA
*
1334296 TCCCCGTCCCCGTTTAGCATAAACAGTTTTTTCCCT
1 TCCCCGTCCCCGTTTAACATAAACAGTTTTTTCCCT
1334332 TCACCATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 23 0.68
38 11 0.32
ACGTcount: A:0.18, C:0.37, G:0.10, T:0.36
Consensus pattern (38 bp):
TCCCCGTCCCCGTTTAACATAAACAGTTTTTTCCCTCA
Found at i:1337540 original size:43 final size:43
Alignment explanation
Indices: 1337479--1337561 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
1337469 AATATTTTTT
* *
1337479 GAAAAATGTTTTCTAATGTTTGATACCTGTAATTGGTTTTACA
1 GAAAAATGTTTTCCAATGTTTGATACCTATAATTGGTTTTACA
*
1337522 GAAAATAT-TTTTCCAATGTTTGATAGCTATAATTGGTTTT
1 GAAAA-ATGTTTTCCAATGTTTGATACCTATAATTGGTTTT
1337562 CCACGATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 34 0.94
44 2 0.06
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (43 bp):
GAAAAATGTTTTCCAATGTTTGATACCTATAATTGGTTTTACA
Found at i:1338462 original size:19 final size:18
Alignment explanation
Indices: 1338412--1338462 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
1338402 CTATTGAACA
1338412 AATAT-TTATATTTTAAT
1 AATATATTATATTTTAAT
1338429 AATATATTATCATTTTAAT
1 AATATATTAT-ATTTTAAT
* *
1338448 AGTATTTTAATATTT
1 AATATATT-ATATTT
1338463 ATGCCAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 18 0.62
20 2 0.07
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
AATATATTATATTTTAAT
Found at i:1344763 original size:36 final size:36
Alignment explanation
Indices: 1344722--1344824 Score: 163
Period size: 36 Copynumber: 2.9 Consensus size: 36
1344712 AATGTGCTGG
*
1344722 ACATTGATACA-GAAATGTACCAAAGCTGATATGATA
1 ACATTGATACACG-AATGTACCAAAGCTGATATAATA
*
1344758 ACATTGATACACGAATGTACCAAAGCTAATATAATA
1 ACATTGATACACGAATGTACCAAAGCTGATATAATA
*
1344794 ACATTAATACACGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1344825 ATGGATAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 61 0.98
37 1 0.02
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATAATA
Found at i:1351627 original size:226 final size:227
Alignment explanation
Indices: 1351232--1351688 Score: 862
Period size: 226 Copynumber: 2.0 Consensus size: 227
1351222 TGCCTAAAAA
*
1351232 TTTTGTTTCATTTAAAAACCCTCTTATTCTAACTTTTAAAAAATCTATTTTAAAGTATATCTCAA
1 TTTTGTTTCATTTAAAAACACTCTTATTCTAACTTTTAAAAAATCTATTTTAAAGTATATCTCAA
**
1351297 CTATAATTTATTTCTTTGTCACATGAAAATAAATTCATTTGTTAATCAGTAATTTTGCTAAACCA
66 CTATAATTTATTTCTTTGAAACATGAAAATAAATTCATTTGTTAATCAGTAATTTTGCTAAACCA
1351362 TGTCTTTTCGTGAAATGTTTTAAAAACATAATAATGTAATATATTCTTTTCATGCATAGATACTG
131 TGTCTTTTCGTGAAATGTTTTAAAAACATAATAATGTAATATATTCTTTTCATGCATAGATACTG
*
1351427 ATAAAACTAAACTAAGTAAAATAAACTAATTT
196 ATAAAACTAAACTAAGTAAAATAAACTAAATT
*
1351459 TTTTGTTTCATTTGAAAACACTCTTATTCTAACTTTT-AAAAATCTATTTTAAAGTATATCTCAA
1 TTTTGTTTCATTTAAAAACACTCTTATTCTAACTTTTAAAAAATCTATTTTAAAGTATATCTCAA
1351523 CTATAATTTATTTCTTTGAAACATGAAAATAAATTCATTTGTTAATCAGTAATTTTGCTAAACCA
66 CTATAATTTATTTCTTTGAAACATGAAAATAAATTCATTTGTTAATCAGTAATTTTGCTAAACCA
1351588 TGTCTTTTCGTGAAATGTTTTAAAAACATAATAATGTAATATATTCTTTTCATGCATAGATACTG
131 TGTCTTTTCGTGAAATGTTTTAAAAACATAATAATGTAATATATTCTTTTCATGCATAGATACTG
1351653 ATAAAACTAAACTAAGTAAAATAAACTAAATT
196 ATAAAACTAAACTAAGTAAAATAAACTAAATT
1351685 TTTT
1 TTTT
1351689 CTAATTTACT
Statistics
Matches: 225, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
226 190 0.84
227 35 0.16
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (227 bp):
TTTTGTTTCATTTAAAAACACTCTTATTCTAACTTTTAAAAAATCTATTTTAAAGTATATCTCAA
CTATAATTTATTTCTTTGAAACATGAAAATAAATTCATTTGTTAATCAGTAATTTTGCTAAACCA
TGTCTTTTCGTGAAATGTTTTAAAAACATAATAATGTAATATATTCTTTTCATGCATAGATACTG
ATAAAACTAAACTAAGTAAAATAAACTAAATT
Found at i:1352329 original size:36 final size:36
Alignment explanation
Indices: 1352289--1352391 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
1352279 ACGGTGCTGG
1352289 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* * * *
1352325 ACATTGATACACTAATATACCAAAGCTAATATGCTA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
*
1352361 ACATTGATACAAGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
1352392 ATGGATAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:1356325 original size:416 final size:416
Alignment explanation
Indices: 1355554--1356386 Score: 1323
Period size: 416 Copynumber: 2.0 Consensus size: 416
1355544 AAATTTAAAA
* * *
1355554 GGGGTAAAATACTCTTTTGGTCATTCTCCTTTATTTTCCCTTAAAAACTCATCCTACTATTCCAA
1 GGGGTAAAATACTCTTTTGGTCATTCTCCTTTATTTTCCCTCAAAAACTCATCCCACAATTCCAA
* *
1355619 CATTTGGGCCCAACTCAGGCTCAATTTCAACTAAACTTGGTCCAAGCTATTCTAATAGGTCAATT
66 CACTTGGGCCCAACTCAGGCTCAATTTCAACTAAACTTGGTCCAAGCTATTCTAACAGGTCAATT
*
1355684 GGGCTCAAAATATGGGTCTCGGGTTAACCCAAACTACTAACCTGAGATTCAGAGAGTTACAACTC
131 GGGCTCAAAATATAGGTCTCGGGTTAACCCAAACTACTAACCTGAGATTCAGAGAGTTACAACTC
* * *
1355749 TCCCCTCTTAATAAAAATTTATTCCTCGAAATTTTACTTGGATAGAAAAGATGGGAATATTGGAG
196 TCCCCTCTTAATAAAAATTTATTCATCGAAATTTTACTTGGATAGAAAAGATGGGAATACTAGAG
*
1355814 TTGCATGTCTTCCTCGGTTTCCCAAGTAGCTTCCTCGACTCCATGATTCCTCCAAAACACCTTTA
261 TTGCATGTCTTCCTCGGTTTCCCAAGTAACTTCCTCGACTCCATGATTCCTCCAAAACACCTTTA
* ***
1355879 CCAAAGGAATTTTCTTATTTCTTAACTCTTTCACCT-ATTTGGCTAAAATTTGGATCGACTCTTC
326 CCAAAGGAATTTTCTCATTTCTTAACTCTTTCACCTCA-AAAGCTAAAATTTGGATCGACTCTTC
* *
1355943 TTTGTAGGTCATGTCGGGGTTCAACTT
390 TTTGTAGGCCATGTCGGGGCTCAACTT
** *
1355970 GGGGTAAAATACTCTTTTGGTTC-TTCTCCTTTATTTTCTGTCAAAAACTCATCCCACAATTCTA
1 GGGGTAAAATACTCTTTTGG-TCATTCTCCTTTATTTTCCCTCAAAAACTCATCCCACAATTCCA
* *
1356034 ACACTTGGGCCCAAGTCAGGC-CTAATTTCAACTAAACTTGGTCCAAGCTATTCTAACAGGTCAT
65 ACACTTGGGCCCAACTCAGGCTC-AATTTCAACTAAACTTGGTCCAAGCTATTCTAACAGGTCAA
* * * * ** *
1356098 TTGGGCTTAAAATATAGTTCTTGGGTTGACCCAAGTTACTAACCTGAGATTCAGGGCA-TTACAA
129 TTGGGCTCAAAATATAGGTCTCGGGTTAACCCAAACTACTAACCTGAGATTCAGAG-AGTTACAA
* *
1356162 CTCTCCCCTTTTAATAAAAATTTCTTCATCGAAATTTTACTTGGATAGAAAAGATGGGAATACTA
193 CTCTCCCCTCTTAATAAAAATTTATTCATCGAAATTTTACTTGGATAGAAAAGATGGGAATACTA
1356227 GAGTTGCATGTCTTCCTCGGTTTCCCAAGTAACTTCCTCGACTCCATGATTCCTCCAAAACACCT
258 GAGTTGCATGTCTTCCTCGGTTTCCCAAGTAACTTCCTCGACTCCATGATTCCTCCAAAACACCT
*
1356292 TTACCAAATGAATTTTCTCATTTCTTAACTCTTTCACCTCAAAAGCTAAAATTTGGATCGACTCT
323 TTACCAAAGGAATTTTCTCATTTCTTAACTCTTTCACCTCAAAAGCTAAAATTTGGATCGACTCT
1356357 TCTTTGTAGGCCATGTCGGGGCTCAACTT
388 TCTTTGTAGGCCATGTCGGGGCTCAACTT
1356386 G
1 G
1356387 ACTTGCTCTA
Statistics
Matches: 382, Mismatches: 31, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
415 1 0.00
416 377 0.99
417 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (416 bp):
GGGGTAAAATACTCTTTTGGTCATTCTCCTTTATTTTCCCTCAAAAACTCATCCCACAATTCCAA
CACTTGGGCCCAACTCAGGCTCAATTTCAACTAAACTTGGTCCAAGCTATTCTAACAGGTCAATT
GGGCTCAAAATATAGGTCTCGGGTTAACCCAAACTACTAACCTGAGATTCAGAGAGTTACAACTC
TCCCCTCTTAATAAAAATTTATTCATCGAAATTTTACTTGGATAGAAAAGATGGGAATACTAGAG
TTGCATGTCTTCCTCGGTTTCCCAAGTAACTTCCTCGACTCCATGATTCCTCCAAAACACCTTTA
CCAAAGGAATTTTCTCATTTCTTAACTCTTTCACCTCAAAAGCTAAAATTTGGATCGACTCTTCT
TTGTAGGCCATGTCGGGGCTCAACTT
Found at i:1360168 original size:23 final size:22
Alignment explanation
Indices: 1360129--1360188 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
1360119 ATATAAAATG
*
1360129 TCCCGAAGAACCGCGTAGAATTA
1 TCCCGAAG-ACCACGTAGAATTA
*
1360152 TCCCGAATGACCACGTAGAATTG
1 TCCCGAA-GACCACGTAGAATTA
1360175 TCCCGAAGGACCAC
1 TCCCGAA-GACCAC
1360189 ATATATGTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.32, C:0.30, G:0.22, T:0.17
Consensus pattern (22 bp):
TCCCGAAGACCACGTAGAATTA
Found at i:1361393 original size:22 final size:23
Alignment explanation
Indices: 1361337--1361420 Score: 82
Period size: 22 Copynumber: 3.7 Consensus size: 23
1361327 TATTCGCCAT
* * *
1361337 TAAATTTTATGAAATTAATATTTC
1 TAAATATTATAAAATT-ATATTAC
*
1361361 TAAGTATTATAAAATTATATTAC
1 TAAATATTATAAAATTATATTAC
*
1361384 -AAATATTATAAAATTATA-TCC
1 TAAATATTATAAAATTATATTAC
* *
1361405 TAAAAATAATAAAATT
1 TAAATATTATAAAATT
1361421 GATTTTAACT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 2 0.04
22 30 0.59
23 6 0.12
24 13 0.25
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATATTATAAAATTATATTAC
Found at i:1364146 original size:40 final size:40
Alignment explanation
Indices: 1364070--1364146 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
1364060 ATTTTTTATT
* *
1364070 TTGAGTCAAACTTCAAAATTTAATTTCAGGAGTTTTCGAA
1 TTGAGTCAAACTTCAAAATTTAAATTCAGGAATTTTCGAA
*
1364110 TTGAGTCGAAC-TCTAAAATTTAAATTC-GTGAATTTTC
1 TTGAGTCAAACTTC-AAAATTTAAATTCAG-GAATTTTC
1364147 TAATAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 3 0.09
40 29 0.91
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (40 bp):
TTGAGTCAAACTTCAAAATTTAAATTCAGGAATTTTCGAA
Found at i:1366840 original size:15 final size:16
Alignment explanation
Indices: 1366813--1366848 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1366803 ATATTTAGCT
*
1366813 GGGCGGGCGGGATGTG
1 GGGCGGGCGGGATGCG
1366829 GGGCGGGC-GGATGCG
1 GGGCGGGCGGGATGCG
1366844 GGGCG
1 GGGCG
1366849 AGTAATGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.06, C:0.17, G:0.69, T:0.08
Consensus pattern (16 bp):
GGGCGGGCGGGATGCG
Found at i:1371455 original size:105 final size:105
Alignment explanation
Indices: 1371297--1371488 Score: 384
Period size: 105 Copynumber: 1.8 Consensus size: 105
1371287 ATAATGGATC
1371297 TAAAATAATAATAATAATTTATTATTGAGATGATTTTATCTATATTATAATAATTATTAAATGCA
1 TAAAATAATAATAATAATTTATTATTGAGATGATTTTATCTATATTATAATAATTATTAAATGCA
1371362 AATCAATCTTGAAATTATTGTAATAAAAAGATTCTTATGA
66 AATCAATCTTGAAATTATTGTAATAAAAAGATTCTTATGA
1371402 TAAAATAATAATAATAATTTATTATTGAGATGATTTTATCTATATTATAATAATTATTAAATGCA
1 TAAAATAATAATAATAATTTATTATTGAGATGATTTTATCTATATTATAATAATTATTAAATGCA
1371467 AATCAATCTTGAAATTATTGTA
66 AATCAATCTTGAAATTATTGTA
1371489 TCTATATTAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 87 1.00
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (105 bp):
TAAAATAATAATAATAATTTATTATTGAGATGATTTTATCTATATTATAATAATTATTAAATGCA
AATCAATCTTGAAATTATTGTAATAAAAAGATTCTTATGA
Found at i:1383675 original size:38 final size:38
Alignment explanation
Indices: 1383633--1383719 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
1383623 TATAAGTTTA
*
1383633 TAAATAATATA-TTCATATTTCAATTGAATATAAATTCC
1 TAAATAATATATTTCA-ATTTCAATTGAATATAAATCCC
* * *
1383671 TAAATAACATATTTGAATTTGAATTGAATATAAATCCC
1 TAAATAATATATTTCAATTTCAATTGAATATAAATCCC
*
1383709 TAAATAGTATA
1 TAAATAATATA
1383720 ATATTACTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 39 0.93
39 3 0.07
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (38 bp):
TAAATAATATATTTCAATTTCAATTGAATATAAATCCC
Found at i:1385693 original size:22 final size:23
Alignment explanation
Indices: 1385659--1385712 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
1385649 AGTTTCCTTT
1385659 TAATA-TATATATA-TATATATTA
1 TAATATTATATATATTAT-TATTA
1385681 TAATATTAT-TATATTATTATTA
1 TAATATTATATATATTATTATTA
1385703 -AATTATTATA
1 TAA-TATTATA
1385713 CAACCCGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
21 2 0.07
22 20 0.71
23 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TAATATTATATATATTATTATTA
Found at i:1386506 original size:13 final size:13
Alignment explanation
Indices: 1386488--1386517 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1386478 TGAATGGTGG
1386488 TCGGTGGTGGCTA
1 TCGGTGGTGGCTA
1386501 TCGGTGGTGGCTA
1 TCGGTGGTGGCTA
1386514 TCGG
1 TCGG
1386518 GGACTGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.07, C:0.17, G:0.47, T:0.30
Consensus pattern (13 bp):
TCGGTGGTGGCTA
Found at i:1396024 original size:2 final size:2
Alignment explanation
Indices: 1396017--1396066 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
1396007 TGTCGTTTTA
1396017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1396057 AT -T AT -T AT AT
1 AT AT AT AT AT AT
1396067 TATTATTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1397230 original size:15 final size:16
Alignment explanation
Indices: 1397210--1397250 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1397200 AAATTACATG
1397210 TTTAGTCTCTATA-AT
1 TTTAGTCTCTATATAT
*
1397225 TTTAGT-TATATATAT
1 TTTAGTCTCTATATAT
*
1397240 TTTAATCTCTA
1 TTTAGTCTCTA
1397251 ATTATTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.24
15 13 0.62
16 3 0.14
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (16 bp):
TTTAGTCTCTATATAT
Found at i:1399001 original size:75 final size:76
Alignment explanation
Indices: 1398911--1399089 Score: 245
Period size: 75 Copynumber: 2.4 Consensus size: 76
1398901 AAGTCGAATA
* *
1398911 TCAAGACTCAAACCACAATATTAAGTTTAGAATAGTAAAATCCATAAACAAATCACAATATTAAA
1 TCAAGACTCAAACCACAATATTAAGTCTAGAATAATAAAATCCATAAACAAATCACAATATTAAA
1398976 ATGTCAAAT-T
66 ATGTCAAATCT
* * * * * *
1398986 TCAAGATTCAAACCACAATATTAACTCTAGAATAATAAAATTCATAATCAAATCATACTATTAAA
1 TCAAGACTCAAACCACAATATTAAGTCTAGAATAATAAAATCCATAAACAAATCACAATATTAAA
*
1399051 GTGTCAAATCT
66 ATGTCAAATCT
* *
1399062 T-AAGACTCAAACCATAATATCAAGTCTA
1 TCAAGACTCAAACCACAATATTAAGTCTA
1399090 AAAAAATATT
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 88 0.98
76 2 0.02
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (76 bp):
TCAAGACTCAAACCACAATATTAAGTCTAGAATAATAAAATCCATAAACAAATCACAATATTAAA
ATGTCAAATCT
Found at i:1399753 original size:7 final size:7
Alignment explanation
Indices: 1399741--1399765 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1399731 ACTAGAGTTG
1399741 AAAATTT
1 AAAATTT
1399748 AAAATTT
1 AAAATTT
1399755 AAAATTT
1 AAAATTT
1399762 AAAA
1 AAAA
1399766 CTAACAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:1401710 original size:25 final size:25
Alignment explanation
Indices: 1401672--1401721 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1401662 TTTTTCATTG
1401672 CTTAATAGTATGTACATTATGTTCT
1 CTTAATAGTATGTACATTATGTTCT
*
1401697 CTTAATAGTTTGTACATTATGTTCT
1 CTTAATAGTATGTACATTATGTTCT
1401722 ATTATCTAAA
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:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (25 bp):
CTTAATAGTATGTACATTATGTTCT
Found at i:1405106 original size:25 final size:25
Alignment explanation
Indices: 1405059--1405107 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1405049 CAAGTTTGTG
* **
1405059 TTCTAGTCGAGCTTTAATTTTTTAT
1 TTCTAGTCGAGCTTGAAAATTTTAT
*
1405084 TTCTAGTGGAGCTTGAAAATTTTA
1 TTCTAGTCGAGCTTGAAAATTTTA
1405108 AGCTCGTGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.49
Consensus pattern (25 bp):
TTCTAGTCGAGCTTGAAAATTTTAT
Found at i:1408282 original size:16 final size:17
Alignment explanation
Indices: 1408249--1408282 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1408239 AAGATCTATG
1408249 ATATGAACATAAGAGATA
1 ATATGAACAT-AGAGATA
1408267 ATATGAACAT-GAGATA
1 ATATGAACATAGAGATA
1408283 TGTGATTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
ATATGAACATAGAGATA
Found at i:1410215 original size:19 final size:17
Alignment explanation
Indices: 1410187--1410225 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
1410177 TGTTTGAAGG
1410187 AAGTTAAAGATTGATAGAA
1 AAGTTAAAGA-TGATA-AA
*
1410206 AAGTTTAAGATGATAAA
1 AAGTTAAAGATGATAAA
1410223 AAG
1 AAG
1410226 GGATATGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.26
Consensus pattern (17 bp):
AAGTTAAAGATGATAAA
Found at i:1412260 original size:16 final size:17
Alignment explanation
Indices: 1412227--1412260 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1412217 AAGATCTATG
1412227 ATATGAACATAAGAGATA
1 ATATGAACAT-AGAGATA
1412245 ATATGAACAT-GAGATA
1 ATATGAACATAGAGATA
1412261 TGTGATTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
ATATGAACATAGAGATA
Found at i:1415453 original size:103 final size:103
Alignment explanation
Indices: 1415231--1415453 Score: 394
Period size: 103 Copynumber: 2.2 Consensus size: 103
1415221 GAGGGTCTAC
1415231 GTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
1 GTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
* *
1415296 ATCCTTGGCATATGTATATGATTCTTAAGGAATGATAT
66 ATCCCTAGCATATGTATATGATTCTTAAGGAATGATAT
*
1415334 GTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
1 GTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
*
1415399 ATCCCTAGTATATGTATATGATTCTTAAGGAATGATAT
66 ATCCCTAGCATATGTATATGATTCTTAAGGAATGATAT
1415437 GTGGTCCTT-GTGGACAT
1 GTGGTCCTTCG-GGACAT
1415454 TATTATATGG
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 1 0.01
103 113 0.99
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
GTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTG
ATCCCTAGCATATGTATATGATTCTTAAGGAATGATAT
Found at i:1415497 original size:23 final size:23
Alignment explanation
Indices: 1415471--1415529 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
1415461 TGGCACTATG
1415471 GTGCAATTCTACGCGGCACTCCA
1 GTGCAATTCTACGCGGCACTCCA
* * *
1415494 GTGCAATTCTACGTGGCACTTCG
1 GTGCAATTCTACGCGGCACTCCA
*
1415517 GTGCAATTATACG
1 GTGCAATTCTACG
1415530 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GTGCAATTCTACGCGGCACTCCA
Found at i:1417387 original size:31 final size:28
Alignment explanation
Indices: 1417336--1417426 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
1417326 TATTTAAGTA
* *
1417336 CTAAA-TATTTTTTG-CTAAAATAAGTAC
1 CTAAAGTATTTTATGTC-AAAATAGGTAC
*
1417363 CTAAAGTTATATTT-TCGATCAAAATAGGTAT
1 CTAAAG-TAT-TTTAT-G-TCAAAATAGGTAC
*
1417394 CTATAGTATTTTATGTCAAAATAGGTAC
1 CTAAAGTATTTTATGTCAAAATAGGTAC
1417422 CTAAA
1 CTAAA
1417427 TTGTTTAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
27 5 0.10
28 16 0.31
29 8 0.15
30 8 0.15
31 14 0.27
32 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (28 bp):
CTAAAGTATTTTATGTCAAAATAGGTAC
Found at i:1420114 original size:20 final size:21
Alignment explanation
Indices: 1420073--1420114 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1420063 TACACATATA
*
1420073 TTAAGAGAAAAAACTTCTAAT
1 TTAAGAGAAAAAACTTCGAAT
1420094 TTAA-AGAAGAAAACTT-GAAT
1 TTAAGAGAA-AAAACTTCGAAT
1420114 T
1 T
1420115 CCAAAAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (21 bp):
TTAAGAGAAAAAACTTCGAAT
Found at i:1420520 original size:31 final size:31
Alignment explanation
Indices: 1420482--1420553 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
1420472 TAATTTTTTG
*
1420482 TTTTAGTACCCGACAT-TT-ACTTTTTGTTTCA
1 TTTTAGTACCC-A-ATGTTAACTTTTTGTTTAA
*
1420513 TTTTAGTACCCATTGTTAACTTTTTGTTTAA
1 TTTTAGTACCCAATGTTAACTTTTTGTTTAA
1420544 TTTTAGTACC
1 TTTTAGTACC
1420554 TAAATTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
29 1 0.03
30 3 0.08
31 33 0.89
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.53
Consensus pattern (31 bp):
TTTTAGTACCCAATGTTAACTTTTTGTTTAA
Found at i:1427705 original size:23 final size:23
Alignment explanation
Indices: 1427679--1427722 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1427669 GTTGAGAACG
*
1427679 AACTTTTAAAATT-TCAGGAGACA
1 AACTTATAAAATTCT-AGGAGACA
1427702 AACTTATAAAATTCTAGGAGA
1 AACTTATAAAATTCTAGGAGA
1427723 ATAAAAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (23 bp):
AACTTATAAAATTCTAGGAGACA
Found at i:1428102 original size:18 final size:19
Alignment explanation
Indices: 1428079--1428116 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1428069 TTGTAGAAAC
1428079 TATTTTTA-GATTCAAAAA
1 TATTTTTATGATTCAAAAA
*
1428097 TATTTTTATGTTTCAAAAA
1 TATTTTTATGATTCAAAAA
1428116 T
1 T
1428117 CAGAGTCGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
TATTTTTATGATTCAAAAA
Found at i:1434512 original size:34 final size:34
Alignment explanation
Indices: 1434446--1434513 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
1434436 TAATAGACTA
* * * * *
1434446 GAATTACATAAGATACATATTACATTCTAACCCT
1 GAATAACATAAGATACACATAACACTCCAACCCT
*
1434480 GAATAACATAAGATAGACATAACACTCCAACCCT
1 GAATAACATAAGATACACATAACACTCCAACCCT
1434514 CGATAATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.25
Consensus pattern (34 bp):
GAATAACATAAGATACACATAACACTCCAACCCT
Found at i:1441756 original size:120 final size:119
Alignment explanation
Indices: 1441540--1441776 Score: 447
Period size: 120 Copynumber: 2.0 Consensus size: 119
1441530 GAAGCCTTTT
*
1441540 ATTATGAAATTTGTTGAGGATTTTTACAATGGAAGGAAATGGGAGCATGGGTCAATCATGCATTT
1 ATTATGAAATTTGTTGAGGATTTTCACAATGGAAGGAAATGGGAGCATGGGTCAATCATGCATTT
1441605 ATAACTTTGATCCCCAAGATCCGAAATCCTGAAGGTATCGAAGACTACAGACCG
66 ATAACTTTGATCCCCAAGATCCGAAATCCTGAAGGTATCGAAGACTACAGACCG
1441659 ATTATGAAATTTGTTGAGGATTTTCACAATGGAAGGAAATGGGAGCATGTGGTCAATCATGCATT
1 ATTATGAAATTTGTTGAGGATTTTCACAATGGAAGGAAATGGGAGCATG-GGTCAATCATGCATT
*
1441724 TATAACTTTGATCCCCAAGATCCGAAATCCTGAAGGTATCGAAGACTATAGAC
65 TATAACTTTGATCCCCAAGATCCGAAATCCTGAAGGTATCGAAGACTACAGAC
1441777 TGATAAGCCT
Statistics
Matches: 115, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
119 48 0.42
120 67 0.58
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (119 bp):
ATTATGAAATTTGTTGAGGATTTTCACAATGGAAGGAAATGGGAGCATGGGTCAATCATGCATTT
ATAACTTTGATCCCCAAGATCCGAAATCCTGAAGGTATCGAAGACTACAGACCG
Found at i:1442319 original size:19 final size:20
Alignment explanation
Indices: 1442286--1442325 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
1442276 TTTGAAAATG
1442286 GCAATCTATTTTACATGTTT
1 GCAATCTATTTTACATGTTT
1442306 GCAATCTA-TTTACATGTTT
1 GCAATCTATTTTACATGTTT
1442325 G
1 G
1442326 GTACGATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (20 bp):
GCAATCTATTTTACATGTTT
Found at i:1449077 original size:34 final size:35
Alignment explanation
Indices: 1449034--1449112 Score: 124
Period size: 34 Copynumber: 2.3 Consensus size: 35
1449024 ATGAAGGCAA
1449034 GTTTAGAGTTTTAGTTTTTTAT-AAAAAAAGACAG
1 GTTTAGAGTTTTAGTTTTTTATAAAAAAAAGACAG
* *
1449068 GTTTAGAGTTTTTGTTTTTTATAAAAAAAAGGCAG
1 GTTTAGAGTTTTAGTTTTTTATAAAAAAAAGACAG
*
1449103 ATTTAGAGTT
1 GTTTAGAGTT
1449113 GGATGTGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 21 0.51
35 20 0.49
ACGTcount: A:0.35, C:0.03, G:0.19, T:0.43
Consensus pattern (35 bp):
GTTTAGAGTTTTAGTTTTTTATAAAAAAAAGACAG
Found at i:1455657 original size:17 final size:16
Alignment explanation
Indices: 1455608--1455658 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1455598 CATTTTAGTA
*
1455608 AAAAT-TTTATTTTTT
1 AAAATATTTAATTTTT
* *
1455623 AAAATAATATCATTTTT
1 AAAAT-ATTTAATTTTT
1455640 AAAATATTTAATTATTT
1 AAAATATTTAATT-TTT
1455657 AA
1 AA
1455659 CAAAAGAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 5 0.18
16 6 0.21
17 17 0.61
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATATTTAATTTTT
Found at i:1465407 original size:119 final size:121
Alignment explanation
Indices: 1465223--1465461 Score: 446
Period size: 119 Copynumber: 2.0 Consensus size: 121
1465213 GAGCTAAATT
1465223 ACAGAGGGGATTTTGAAGGTCTCGGGTTGAGGGAAATTGATAATTTGGAGGGGAGTGAACAAGCC
1 ACAGAGGGGATTTTGAAGGTCTCGGGTTGAGGGAAATTGATAATTTGGAGGGGAGTGAACAAGCC
*
1465288 CAATCCGAAGAA-T-TATGAGTCATCCTCCAATTTAAAAATCATTCCTTCTGGGCC
66 CAATCCAAAGAATTATATGAGTCATCCTCCAATTTAAAAATCATTCCTTCTGGGCC
*
1465342 ACAGAGGGGATTTTGAAGGTCTCGGGTTGAGGGAAATTGATAATTTTGAGGGGAGTGAACAAGCC
1 ACAGAGGGGATTTTGAAGGTCTCGGGTTGAGGGAAATTGATAATTTGGAGGGGAGTGAACAAGCC
1465407 CAATCCAAAGAATTATATGAGTCATCCTCCAATTTAAAAATCATTCCTTCTGGGC
66 CAATCCAAAGAATTATATGAGTCATCCTCCAATTTAAAAATCATTCCTTCTGGGC
1465462 TAGTAGTTAA
Statistics
Matches: 116, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
119 75 0.65
120 1 0.01
121 40 0.34
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (121 bp):
ACAGAGGGGATTTTGAAGGTCTCGGGTTGAGGGAAATTGATAATTTGGAGGGGAGTGAACAAGCC
CAATCCAAAGAATTATATGAGTCATCCTCCAATTTAAAAATCATTCCTTCTGGGCC
Found at i:1472480 original size:587 final size:586
Alignment explanation
Indices: 1471327--1472502 Score: 2226
Period size: 587 Copynumber: 2.0 Consensus size: 586
1471317 GCCCATCACC
1471327 TCTCACTGCTCCATCAACATTGAATTTAAAGAAATCTGTAGGAGGTGAAGACCAGTAGATAGCCT
1 TCTCACTGCTCCATCAACATTGAATTTAAAGAAATCTGTAGGAGGTGAAGACCAGTAGATAGCCT
* *
1471392 TATTCGATTTATAGGAAATAGAGTGAAATGTATCTGCCAATGTTGGATCTCCTACTAGTATGTCA
66 TATTCGATTTATAGAAAATAGAGTGAAATGTATCTGCCAACGTTGGATCTCCTACTAGTATGTCA
*
1471457 ACCTGAATATTAGCATTAGGGAATTTCGCTAAAAACCATTTAGCTAATATAACCCTGGAAATGAA
131 ACCTGAATATTAGCATTAGGGAATTTCGCTAAAAACCATTTAGCTAATATAACCCTGGAAATAAA
*
1471522 GAACAAAGAATAAGTATCTAGTTTCCAGTTCTCAAACACCACTGAGTTCCTAGCTTTCCATAAAG
196 GAACAAAGAAGAAGTATCTAGTTTCCAGTTCTCAAACACCACTGAGTTCCTAGCTTTCCATAAAG
*
1471587 ACCATAGAACGACTCCTGGAATAACTTCCAAATAGTAGACTGCTCCCTTAGATAAGACCAGGAAC
261 ACCATAGAACGACTCCTGGAATAACTTCCAAATAGTAGACTGCTCCCTTAGATAAGACCAGAAAC
*
1471652 AAAGAAGGGAAGAAGGTTCTTGAGGCATAACTGAAGAGATATCCCATAGTCTTAGAAATCTATAC
326 AAAAAAGGGAAGAAGGTTCTTGAGGCATAACTGAAGAGATATCCCATAGTCTTAGAAATCTATAC
1471717 CACAATTCCTCTGCAACCGAGCACGAAATAAACAGATGATGGATTGTTTCCTCATATTTATGACA
391 CACAATTCCTCTGCAACCGAGCACGAAATAAACAGATGATGGATTGTTTCCTCATATTTATGACA
1471782 TAAAGTACACAGAACATCTTCTATCGAAATCCCTCTTTTCTTCAATTCCACTCTAACCGCCAATT
456 TAAAGTACACAGAACATCTTCTATCGAAATCCCTCTTTTCTTCAATTCCACTCTAACCGCCAATT
*
1471847 TTTGATGAGTAATCTGCCAAAGAAATGTTTCTAATCTAGGAGGAGCCATTCCAGACCACACCCAT
521 TTTGATGAGTAATCTGCCAAAGAAATGTTACTAATCTAGGAGGAGCCATTCCAGACCACACCCAT
1471912 T
586 T
*
1471913 TCTCACTGCTCCATCAACATTGAATTTAAAGAAATCTGTAGGAGGTGGAGACCAGTAGATAGCCT
1 TCTCACTGCTCCATCAACATTGAATTTAAAGAAATCTGTAGGAGGTGAAGACCAGTAGATAGCCT
*
1471978 TCTTCGATTTATAGAAAATAGAGTGAAATGTATCTGCCAACGTTGGATCTCCTACTAGTATGTCA
66 TATTCGATTTATAGAAAATAGAGTGAAATGTATCTGCCAACGTTGGATCTCCTACTAGTATGTCA
* *
1472043 ACCTGAATATTAGCATTAGGGAATTTCGCTAAAAATCATTTAGCTAATCTAACCCTGGAAATAAA
131 ACCTGAATATTAGCATTAGGGAATTTCGCTAAAAACCATTTAGCTAATATAACCCTGGAAATAAA
*
1472108 GAACAAAGAAGAAGTATCTAGTTTCCAGTTCTCAAACACCACTGAGTTCTTAGCTTTCCATAAAG
196 GAACAAAGAAGAAGTATCTAGTTTCCAGTTCTCAAACACCACTGAGTTCCTAGCTTTCCATAAAG
1472173 ACCATAGAACGACTCCTGGAATAAACTTCCAAATAGTAGACTGCTCCCTTAGATAAGACCAGAAA
261 ACCATAGAACGACTCCTGGAAT-AACTTCCAAATAGTAGACTGCTCCCTTAGATAAGACCAGAAA
1472238 CAAAAAAGGGAAGAAGGTTCTTGAGGCATAACTGAAGAGATATCCCATAGTCTTAGAAATCTATA
325 CAAAAAAGGGAAGAAGGTTCTTGAGGCATAACTGAAGAGATATCCCATAGTCTTAGAAATCTATA
1472303 CCACAATTCCTCTGCAACCGAGCACGAAATAAACAGATGATGGATTGTTTCCTCATATTTATGAC
390 CCACAATTCCTCTGCAACCGAGCACGAAATAAACAGATGATGGATTGTTTCCTCATATTTATGAC
*
1472368 ATAAAGTACACAGAGCATCTTCTATCGAAATCCCTCTTTTCTTCAATTCCACTCTAACCGCCAAT
455 ATAAAGTACACAGAACATCTTCTATCGAAATCCCTCTTTTCTTCAATTCCACTCTAACCGCCAAT
1472433 TTTTGATGAGTAATCTGCCAAAGAAATGTTACTAATCTAGGAGGAGCCATTCCAGACCACACCCA
520 TTTTGATGAGTAATCTGCCAAAGAAATGTTACTAATCTAGGAGGAGCCATTCCAGACCACACCCA
1472498 TT
585 TT
1472500 TCT
1 TCT
1472503 TCCACTGAAA
Statistics
Matches: 576, Mismatches: 13, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
586 273 0.47
587 303 0.53
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (586 bp):
TCTCACTGCTCCATCAACATTGAATTTAAAGAAATCTGTAGGAGGTGAAGACCAGTAGATAGCCT
TATTCGATTTATAGAAAATAGAGTGAAATGTATCTGCCAACGTTGGATCTCCTACTAGTATGTCA
ACCTGAATATTAGCATTAGGGAATTTCGCTAAAAACCATTTAGCTAATATAACCCTGGAAATAAA
GAACAAAGAAGAAGTATCTAGTTTCCAGTTCTCAAACACCACTGAGTTCCTAGCTTTCCATAAAG
ACCATAGAACGACTCCTGGAATAACTTCCAAATAGTAGACTGCTCCCTTAGATAAGACCAGAAAC
AAAAAAGGGAAGAAGGTTCTTGAGGCATAACTGAAGAGATATCCCATAGTCTTAGAAATCTATAC
CACAATTCCTCTGCAACCGAGCACGAAATAAACAGATGATGGATTGTTTCCTCATATTTATGACA
TAAAGTACACAGAACATCTTCTATCGAAATCCCTCTTTTCTTCAATTCCACTCTAACCGCCAATT
TTTGATGAGTAATCTGCCAAAGAAATGTTACTAATCTAGGAGGAGCCATTCCAGACCACACCCAT
T
Found at i:1478171 original size:20 final size:20
Alignment explanation
Indices: 1478146--1478236 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
1478136 TAAATTAAAT
*
1478146 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
1478166 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
1478186 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
1478198 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
1478218 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
1478237 TTATTTTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:1478223 original size:52 final size:52
Alignment explanation
Indices: 1478145--1478292 Score: 262
Period size: 53 Copynumber: 2.8 Consensus size: 52
1478135 CTAAATTAAA
*
1478145 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
*
1478197 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTTTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
1478250 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
1478293 ATGTTGCTAA
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 8 0.09
52 35 0.38
53 50 0.54
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:1478276 original size:20 final size:20
Alignment explanation
Indices: 1478251--1478290 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1478241 TTTATTAGTT
*
1478251 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
1478271 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
1478291 TTATGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:1481995 original size:16 final size:16
Alignment explanation
Indices: 1481974--1482005 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1481964 GTTATAGATT
1481974 GAAATTTTGGGATTTG
1 GAAATTTTGGGATTTG
*
1481990 GAAATTTTGGGTTTTG
1 GAAATTTTGGGATTTG
1482006 AGATGATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (16 bp):
GAAATTTTGGGATTTG
Found at i:1484901 original size:19 final size:19
Alignment explanation
Indices: 1484888--1484948 Score: 95
Period size: 19 Copynumber: 3.2 Consensus size: 19
1484878 AATCGTAATG
1484888 CGATCTCTAAATCGCAACA
1 CGATCTCTAAATCGCAACA
* *
1484907 CGATCTCAAAATCACAACA
1 CGATCTCTAAATCGCAACA
*
1484926 CGATCTCTAAATCGCAATA
1 CGATCTCTAAATCGCAACA
1484945 CGAT
1 CGAT
1484949 AGTCCAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.21
Consensus pattern (19 bp):
CGATCTCTAAATCGCAACA
Found at i:1484969 original size:21 final size:21
Alignment explanation
Indices: 1484945--1484992 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1484935 AATCGCAATA
1484945 CGATAGTCCAAATTCGCGTTG
1 CGATAGTCCAAATTCGCGTTG
*
1484966 CGATAGTCCGAATTCGCGTTG
1 CGATAGTCCAAATTCGCGTTG
1484987 CGATAG
1 CGATAG
1484993 CACTGTTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (21 bp):
CGATAGTCCAAATTCGCGTTG
Found at i:1485006 original size:21 final size:21
Alignment explanation
Indices: 1484982--1485044 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
1484972 TCCGAATTCG
*
1484982 CGTTGCGATAGCACTGTTTAC
1 CGTTGCGATAGCACTGTTCAC
1485003 CGTTGCGATAGCACTGTTCAC
1 CGTTGCGATAGCACTGTTCAC
1485024 CGTTGCGATAGCACTGTTCAC
1 CGTTGCGATAGCACTGTTCAC
1485045 ATTGCGAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (21 bp):
CGTTGCGATAGCACTGTTCAC
Found at i:1485228 original size:16 final size:17
Alignment explanation
Indices: 1485201--1485252 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
1485191 TTTATTTATG
1485201 ATAAACTATAAATTTTAA
1 ATAAA-TATAAATTTTAA
* *
1485219 A-CAATATAAA-ATTAA
1 ATAAATATAAATTTTAA
*
1485234 ATAAATATAAATTCTAA
1 ATAAATATAAATTTTAA
1485251 AT
1 AT
1485253 TATTTATGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
15 5 0.19
16 14 0.52
17 7 0.26
18 1 0.04
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAATATAAATTTTAA
Found at i:1485632 original size:16 final size:17
Alignment explanation
Indices: 1485605--1485656 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
1485595 TTTATTTATG
1485605 ATAAACTATAAATTTTAA
1 ATAAA-TATAAATTTTAA
*
1485623 AT-AATATAAA-ATTAA
1 ATAAATATAAATTTTAA
*
1485638 ATAAATATAAATTCTAA
1 ATAAATATAAATTTTAA
1485655 AT
1 AT
1485657 TATTTATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 14 0.48
17 7 0.24
18 2 0.07
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAATATAAATTTTAA
Found at i:1485786 original size:21 final size:21
Alignment explanation
Indices: 1485760--1485908 Score: 235
Period size: 21 Copynumber: 7.1 Consensus size: 21
1485750 ATGTGAACAG
1485760 AACGGTGAACAGTGCTATCGC
1 AACGGTGAACAGTGCTATCGC
* * *
1485781 AACGGTGAACAATACCATCGC
1 AACGGTGAACAGTGCTATCGC
* *
1485802 AATGGTGAACAGTGCTATCAC
1 AACGGTGAACAGTGCTATCGC
*
1485823 AACGGTGAACAGTGTTATCGC
1 AACGGTGAACAGTGCTATCGC
*
1485844 AAAGGTGAACAGTGCTATCGC
1 AACGGTGAACAGTGCTATCGC
1485865 AACGGTGAACAGTGCTATCGC
1 AACGGTGAACAGTGCTATCGC
1485886 AACGGTGAACAGTGCTATCGC
1 AACGGTGAACAGTGCTATCGC
1485907 AA
1 AA
1485909 TGATTTTGGA
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 114 1.00
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.19
Consensus pattern (21 bp):
AACGGTGAACAGTGCTATCGC
Found at i:1485992 original size:21 final size:21
Alignment explanation
Indices: 1485963--1486015 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1485953 ATAGTCAGAA
*
1485963 TCGCATTGCGATTTTACAAAT
1 TCGCGTTGCGATTTTACAAAT
*
1485984 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTACAAAT
1486005 TCGCGTTGCGA
1 TCGCGTTGCGA
1486016 ATTTGATACC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATTTTACAAAT
Found at i:1486865 original size:158 final size:158
Alignment explanation
Indices: 1486603--1486915 Score: 583
Period size: 158 Copynumber: 2.0 Consensus size: 158
1486593 TGCACTCCTT
1486603 AATGTATCAGTACACTTTGAACATCTTCCCAGATTTTACTCTTGAGGTGTATCTGTAACATCCTC
1 AATGTATCAGTACACTTTGAACATCTTCCCAGATTTTACTCTTGAGGTGTATCTGTAACATCCTC
1486668 AATACCGATTTAGTGACTAAATTATAAAATTTTAGAATTTAGTGATAAAAG-TAGAATAGTTGAA
66 AATACCGATTTAGTGACTAAATTATAAAATTTTAGAATTTAGTGATAAAAGCT-GAATAGTTGAA
1486732 TAGTTCAATGATTTATTTGAAAATATCAC
130 TAGTTCAATGATTTATTTGAAAATATCAC
*
1486761 AATGTATCGGTACACTTTGAACATCTTCCCAGATTTTACTCTTGAGGTGTATCTGTAACATCCTC
1 AATGTATCAGTACACTTTGAACATCTTCCCAGATTTTACTCTTGAGGTGTATCTGTAACATCCTC
* *
1486826 AATATCGATTTAGTGACTAAATTGTAAAATTTTAGAATTTAGTGATAAAAGCTGAATAGTTGAAT
66 AATACCGATTTAGTGACTAAATTATAAAATTTTAGAATTTAGTGATAAAAGCTGAATAGTTGAAT
1486891 AGTTCAATGATTTATTTGAAAATAT
131 AGTTCAATGATTTATTTGAAAATAT
1486916 TACCTGAAAG
Statistics
Matches: 151, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
158 150 0.99
159 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (158 bp):
AATGTATCAGTACACTTTGAACATCTTCCCAGATTTTACTCTTGAGGTGTATCTGTAACATCCTC
AATACCGATTTAGTGACTAAATTATAAAATTTTAGAATTTAGTGATAAAAGCTGAATAGTTGAAT
AGTTCAATGATTTATTTGAAAATATCAC
Found at i:1488004 original size:18 final size:18
Alignment explanation
Indices: 1487981--1488015 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1487971 AGGGTTATAC
1487981 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1487999 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1488016 AATATTTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1488654 original size:21 final size:21
Alignment explanation
Indices: 1488628--1488669 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1488618 CGATATTTTT
*
1488628 ATGCATCGATGCACTGTAGCA
1 ATGCATCGATGCACTATAGCA
1488649 ATGCATCGATGCACTATAGCA
1 ATGCATCGATGCACTATAGCA
1488670 CTGTTCACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
ATGCATCGATGCACTATAGCA
Found at i:1495257 original size:24 final size:24
Alignment explanation
Indices: 1495229--1495282 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1495219 TTAAGGATAT
1495229 ATTAATCTTGTATATATATTTTTA
1 ATTAATCTTGTATATATATTTTTA
1495253 ATTAATCTTGTATATATATTTTTA
1 ATTAATCTTGTATATATATTTTTA
1495277 ATTAAT
1 ATTAAT
1495283 TACTAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTAATCTTGTATATATATTTTTA
Found at i:1495291 original size:24 final size:24
Alignment explanation
Indices: 1495229--1495291 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
1495219 TTAAGGATAT
**
1495229 ATTAATCTTGTATATATATTTTTA
1 ATTAATCTACTATATATATTTTTA
**
1495253 ATTAATCTTGTATATATATTTTTA
1 ATTAATCTACTATATATATTTTTA
1495277 ATTAAT-TACTA-ATAT
1 ATTAATCTACTATATAT
1495292 CTAATCTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.11
23 3 0.08
24 30 0.81
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.56
Consensus pattern (24 bp):
ATTAATCTACTATATATATTTTTA
Found at i:1508017 original size:24 final size:25
Alignment explanation
Indices: 1507990--1508038 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1507980 ATTTTATGTT
1507990 AAGAG-AT-AATTTATAAAAATTTAA
1 AAGAGAATAAATTTAT-AAAATTTAA
1508014 AAGAGAATAAATTTATAAAATTTAA
1 AAGAGAATAAATTTATAAAATTTAA
1508039 GGGCGAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.22
25 11 0.48
26 7 0.30
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
AAGAGAATAAATTTATAAAATTTAA
Found at i:1508304 original size:28 final size:25
Alignment explanation
Indices: 1508254--1508304 Score: 66
Period size: 28 Copynumber: 1.9 Consensus size: 25
1508244 TAGATTTTTA
*
1508254 AAAATTTTATTTTTTGAAAAAATTC
1 AAAATTTTATTTTTTAAAAAAATTC
1508279 AAAATTATTATTATTTTCAAAAAAAT
1 AAAATT-TTATT-TTTT-AAAAAAAT
1508305 CTAATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 5 0.23
27 4 0.18
28 7 0.32
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAATTTTATTTTTTAAAAAAATTC
Found at i:1512505 original size:17 final size:18
Alignment explanation
Indices: 1512466--1512504 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1512456 TATTTTTATC
*
1512466 AAAAGAAAAAAAAACCAA
1 AAAATAAAAAAAAACCAA
*
1512484 AAAATAAAAAAAATCCAA
1 AAAATAAAAAAAAACCAA
1512502 AAA
1 AAA
1512505 TTATAAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.82, C:0.10, G:0.03, T:0.05
Consensus pattern (18 bp):
AAAATAAAAAAAAACCAA
Found at i:1515798 original size:31 final size:31
Alignment explanation
Indices: 1515731--1515790 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1515721 CAATTTAAGG
*
1515731 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1515762 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1515791 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:1516034 original size:21 final size:21
Alignment explanation
Indices: 1515995--1516036 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1515985 ATTTGAATAT
* *
1515995 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGATACCGATTCCC
*
1516016 TATGAAGGGATACCTATTCCC
1 TATGAAGGGATACCGATTCCC
1516037 CCATTCTGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (21 bp):
TATGAAGGGATACCGATTCCC
Found at i:1516729 original size:14 final size:16
Alignment explanation
Indices: 1516710--1516751 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
1516700 CTTTATCCTT
1516710 TTGTTTTG-CTT-ATC
1 TTGTTTTGTCTTAATC
1516724 TTGTTTTGTCTTAATC
1 TTGTTTTGTCTTAATC
*
1516740 TTCTATTTGTCT
1 TTGT-TTTGTCT
1516752 CAATTTCCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 8 0.33
15 3 0.12
16 6 0.25
17 7 0.29
ACGTcount: A:0.10, C:0.14, G:0.12, T:0.64
Consensus pattern (16 bp):
TTGTTTTGTCTTAATC
Found at i:1517269 original size:20 final size:20
Alignment explanation
Indices: 1517227--1517270 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1517217 TTTCCGCACC
* * *
1517227 GATACCCTAGGGTGGGTATT
1 GATACCCTAGGATGAGTAAT
*
1517247 GATACCCTAGGATTAGTAAT
1 GATACCCTAGGATGAGTAAT
1517267 GATA
1 GATA
1517271 GTGTTGGCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (20 bp):
GATACCCTAGGATGAGTAAT
Found at i:1520195 original size:18 final size:20
Alignment explanation
Indices: 1520153--1520233 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 20
1520143 GTTACAATTG
* * *
1520153 TATAAAAAAAT-TTAAAAAG
1 TATAAAAATATATTGAAAAT
1520172 TA-AAAAATATA-TGAAAAT
1 TATAAAAATATATTGAAAAT
* *
1520190 T-T-AAAATTTATTTAAAAT
1 TATAAAAATATATTGAAAAT
* *
1520208 TATAAAAATATTTTATAAAAT
1 TATAAAAATATATT-GAAAAT
1520229 TATAA
1 TATAA
1520234 TTTTTAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
17 7 0.14
18 20 0.41
19 3 0.06
20 8 0.16
21 11 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
TATAAAAATATATTGAAAAT
Found at i:1520462 original size:26 final size:25
Alignment explanation
Indices: 1520423--1520486 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
1520413 TTAAGACTAA
* *
1520423 TTTA-TTTTAGAAAATATTTTTTATT
1 TTTATTTTTA-AAAATATATTTAATT
1520448 TTTATTATTTAAAAATATATTTAATT
1 TTTATT-TTTAAAAATATATTTAATT
1520474 TTTATTTTTAAAA
1 TTTATTTTTAAAA
1520487 TTTAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 11 0.31
26 20 0.57
27 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTATTTTTAAAAATATATTTAATT
Found at i:1521925 original size:15 final size:15
Alignment explanation
Indices: 1521907--1521956 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
1521897 AAATTTATAA
1521907 ATTAAAAATATAAAG
1 ATTAAAAATATAAAG
* *
1521922 ATTAAATATTGTAAA-
1 ATTAAA-AATATAAAG
1521937 ATT-AAAATATAAAG
1 ATTAAAAATATAAAG
*
1521951 ACTAAA
1 ATTAAA
1521957 TTTAAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
13 6 0.22
14 4 0.15
15 11 0.41
16 6 0.22
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (15 bp):
ATTAAAAATATAAAG
Found at i:1522207 original size:20 final size:20
Alignment explanation
Indices: 1522184--1522223 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1522174 TCGAGAAAGA
*
1522184 GGAAAAGAATGTAATATGGT
1 GGAAAAGAATATAATATGGT
*
1522204 GGAAAATAATATAATATGGT
1 GGAAAAGAATATAATATGGT
1522224 TATTTATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28
Consensus pattern (20 bp):
GGAAAAGAATATAATATGGT
Found at i:1523651 original size:21 final size:21
Alignment explanation
Indices: 1523626--1523703 Score: 147
Period size: 21 Copynumber: 3.7 Consensus size: 21
1523616 TTTCTAGTAG
1523626 TTACTGTTATTATTTAGACTA
1 TTACTGTTATTATTTAGACTA
1523647 TTACTGTTATTATTTAGACTA
1 TTACTGTTATTATTTAGACTA
1523668 TTACTGTTATTATTTAGACTA
1 TTACTGTTATTATTTAGACTA
*
1523689 TTACTGCTATTATTT
1 TTACTGTTATTATTT
1523704 CTGTTTCTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.54
Consensus pattern (21 bp):
TTACTGTTATTATTTAGACTA
Found at i:1525093 original size:17 final size:17
Alignment explanation
Indices: 1525067--1525117 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1525057 TTTGGGGAGG
*
1525067 ATGAGGAAGGAGATAAA
1 ATGAGAAAGGAGATAAA
1525084 ATGAGAAAGGAGGAATAAA
1 ATGAGAAAGGA-G-ATAAA
1525103 AT--GAAAGGA-ATAAA
1 ATGAGAAAGGAGATAAA
1525117 A
1 A
1525118 ATCTTCATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.19
17 17 0.55
18 1 0.03
19 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (17 bp):
ATGAGAAAGGAGATAAA
Found at i:1525334 original size:17 final size:18
Alignment explanation
Indices: 1525312--1525349 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1525302 AGGGTGTTGT
*
1525312 ATATTTAAA-ATTTAAAA
1 ATATTTAAACAGTTAAAA
1525329 ATATTTAAACAGTTAAAA
1 ATATTTAAACAGTTAAAA
1525347 ATA
1 ATA
1525350 AATATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
ATATTTAAACAGTTAAAA
Found at i:1525395 original size:18 final size:17
Alignment explanation
Indices: 1525373--1525422 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
1525363 TTTTTGAAAG
1525373 AAAAAATATATAAAATA
1 AAAAAATATATAAAATA
*
1525390 TTAAAAATATA-AGAAATA
1 -AAAAAATATATA-AAATA
1525408 AAAAAAT-TATAAAAT
1 AAAAAATATATAAAAT
1525423 GATAAAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 6 0.21
17 8 0.29
18 14 0.50
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAAAAATATATAAAATA
Found at i:1526446 original size:23 final size:24
Alignment explanation
Indices: 1526420--1526488 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
1526410 GAGTCGAAAG
1526420 TTCTATGCGGTCCTTC-GGAGC-AA
1 TTCTATGCGGTCCTTCGGGA-CAAA
*
1526443 TTCTATGTGGTCCTTCGGGACAAA
1 TTCTATGCGGTCCTTCGGGACAAA
* *
1526467 TTCTACGCTGTCCTTCGGGACA
1 TTCTATGCGGTCCTTCGGGACA
1526489 TTTCTACGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 16 0.40
24 24 0.60
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (24 bp):
TTCTATGCGGTCCTTCGGGACAAA
Found at i:1526479 original size:24 final size:23
Alignment explanation
Indices: 1526420--1526496 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
1526410 GAGTCGAAAG
* *
1526420 TTCTATGCGGTCCTTC-GGAGCAA
1 TTCTACGCTGTCCTTCGGGA-CAA
*
1526443 TTCTATG-TGGTCCTTCGGGACAAA
1 TTCTACGCT-GTCCTTCGGGAC-AA
*
1526467 TTCTACGCTGTCCTTCGGGACAT
1 TTCTACGCTGTCCTTCGGGACAA
1526490 TTCTACG
1 TTCTACG
1526497 TGGTTCTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
23 23 0.49
24 23 0.49
25 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34
Consensus pattern (23 bp):
TTCTACGCTGTCCTTCGGGACAA
Found at i:1530961 original size:18 final size:18
Alignment explanation
Indices: 1530938--1530972 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1530928 ATCATTAACT
* *
1530938 AAATATGAATAATAAAAC
1 AAATATAAAAAATAAAAC
1530956 AAATATAAAAAATAAAA
1 AAATATAAAAAATAAAA
1530973 ATGAAGTGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (18 bp):
AAATATAAAAAATAAAAC
Found at i:1537544 original size:29 final size:28
Alignment explanation
Indices: 1537508--1537681 Score: 91
Period size: 29 Copynumber: 6.0 Consensus size: 28
1537498 TTGTAATTAT
1537508 TGTTTTAGCCCTTTAAGTTTCTATATTTG
1 TGTTTTAGCCCTTTAAGTTTCTAT-TTTG
* * *
1537537 TGTTTTAGTCCTTTAAATTT-TGTTATTG
1 TGTTTTAGCCCTTTAAGTTTCTATT-TTG
* * * * *
1537565 TTGTTTAATCCCTTAAAGTTTATATTTTAC
1 -TGTTTTAGCCCTTTAAGTTTCTATTTT-G
* * * **
1537595 TG-TTTAGTCCTTTAAGTGTTTGTAATTAC
1 TGTTTTAGCCCTTTAA--GTTTCTATTTTG
* *
1537624 TGTTTTAGGCTTTTAAGTTTCTATTTTG
1 TGTTTTAGCCCTTTAAGTTTCTATTTTG
* * * *
1537652 ATATTTTAACCCCTTCAGTTTCTATATTTG
1 -TGTTTTAGCCCTTTAAGTTTCTAT-TTTG
1537682 CTATTTAGTC
Statistics
Matches: 107, Mismatches: 29, Indels: 17
0.70 0.19 0.11
Matches are distributed among these distances:
27 1 0.01
28 22 0.21
29 58 0.54
30 26 0.24
ACGTcount: A:0.20, C:0.12, G:0.13, T:0.55
Consensus pattern (28 bp):
TGTTTTAGCCCTTTAAGTTTCTATTTTG
Found at i:1537559 original size:58 final size:57
Alignment explanation
Indices: 1537497--1537651 Score: 177
Period size: 58 Copynumber: 2.7 Consensus size: 57
1537487 GCTCTGTTTA
1537497 TTTGTAATTATTGTTTTAGCCCTTTAAGTTTCTATATTTGTGTTTTAGTCCTTTAAAT-
1 TTTGTAATTATTGTTTTAGCCCTTTAAGTTTCTAT-TTTGTG-TTTAGTCCTTTAAATG
* * * * * * * *
1537555 TTTGTTATTGTTGTTTAATCCCTTAAAGTTTATATTTTACTGTTTAGTCCTTTAAGTG
1 TTTGTAATTATTGTTTTAGCCCTTTAAGTTTCTATTTT-GTGTTTAGTCCTTTAAATG
* * *
1537613 TTTGTAATTACTGTTTTAGGCTTTTAAGTTTCTATTTTG
1 TTTGTAATTATTGTTTTAGCCCTTTAAGTTTCTATTTTG
1537652 ATATTTTAAC
Statistics
Matches: 77, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
57 17 0.22
58 60 0.78
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.57
Consensus pattern (57 bp):
TTTGTAATTATTGTTTTAGCCCTTTAAGTTTCTATTTTGTGTTTAGTCCTTTAAATG
Found at i:1540418 original size:21 final size:20
Alignment explanation
Indices: 1540332--1540489 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1540322 AAATGACCAA
**
1540332 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1540351 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1540371 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1540391 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1540412 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1540433 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1540453 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1540474 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1540490 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1540480 original size:20 final size:20
Alignment explanation
Indices: 1540456--1540704 Score: 259
Period size: 20 Copynumber: 12.5 Consensus size: 20
1540446 CGATTTTCCA
** *
1540456 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
1540476 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
1540496 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
1540516 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
1540536 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
1540556 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1540576 -ATTCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1540595 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1540615 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1540635 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1540655 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1540675 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
1540695 AAATCACAAC
1 AAATCGCAAC
1540705 ACTGAAATTT
Statistics
Matches: 200, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.09
20 182 0.91
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:1541425 original size:24 final size:24
Alignment explanation
Indices: 1541386--1541432 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1541376 AAATTTGGTC
1541386 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1541410 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1541433 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1541624 original size:12 final size:12
Alignment explanation
Indices: 1541607--1541631 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1541597 ATATAATCCT
1541607 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1541619 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1541631 G
1 G
1541632 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1543980 original size:19 final size:19
Alignment explanation
Indices: 1543935--1544037 Score: 144
Period size: 19 Copynumber: 5.6 Consensus size: 19
1543925 GAAATGAAAA
*
1543935 TCGCATTGCGATTCTCATT
1 TCGCATTGCGATTTTCATT
1543954 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
1543974 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1543990 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1544007 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1544026 TCGCATTGCGAT
1 TCGCATTGCGAT
1544038 AGTCAATTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 37 0.49
20 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1544133 original size:14 final size:14
Alignment explanation
Indices: 1544114--1544167 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1544104 CGGAAATGAA
1544114 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1544128 AATCGCAATGCGAAATG
1 AATCGCAA--CGAGA-G
*
1544145 AAATCGCAACAAGAG
1 -AATCGCAACGAGAG
1544160 AATCGCAA
1 AATCGCAA
1544168 TGCGAAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 16 0.48
15 1 0.03
16 7 0.21
17 1 0.03
18 8 0.24
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1544154 original size:32 final size:33
Alignment explanation
Indices: 1544096--1544186 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1544086 CCATTACATT
*
1544096 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACAAGAGAA
1544130 TCGCAATGCGAAATG-AAATCGCAACAAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACAAGAGAA
1544162 TCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
1544187 TGCGAAATGA
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
32 31 0.56
33 15 0.27
34 9 0.16
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACAAGAGAA
Found at i:1544184 original size:19 final size:19
Alignment explanation
Indices: 1544096--1544243 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
1544086 CCATTACATT
1544096 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
1544116 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
1544130 TCGCAATGCGAAATG-AAA
1 TCGCAATGCGAAATGAAAA
*
1544148 TCGCAA--C--AA-GAGAA
1 TCGCAATGCGAAATGAAAA
1544162 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
1544181 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
1544200 TCGCAA--CG--A-GATAA
1 TCGCAATGCGAAATGAAAA
*
1544214 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
1544233 TCGCATTGCGA
1 TCGCAATGCGA
1544244 TTCTCCCATT
Statistics
Matches: 104, Mismatches: 8, Indels: 33
0.72 0.06 0.23
Matches are distributed among these distances:
13 1 0.01
14 30 0.29
15 2 0.02
16 6 0.06
17 3 0.03
18 13 0.12
19 43 0.41
20 6 0.06
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Done.