Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 78 of 193
Found at i:25717080 original size:13 final size:13
Alignment explanation
Indices: 25717062--25717086 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25717052 TAAGTTAAAA
25717062 ATGCTAAAAATGC
1 ATGCTAAAAATGC
25717075 ATGCTAAAAATG
1 ATGCTAAAAATG
25717087 ATAAAATGGG
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:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Found at i:25731570 original size:27 final size:27
Alignment explanation
Indices: 25731532--25731673 Score: 140
Period size: 27 Copynumber: 5.3 Consensus size: 27
25731522 AAGCAATTAA
* * *
25731532 CGATATTCTGTATTTTGCTCGAATGAG
1 CGATATTTTGTATCTGGCTCGAATGAG
*
25731559 CGATATTTTGTATTTGGCTCGAATGAG
1 CGATATTTTGTATCTGGCTCGAATGAG
* * *
25731586 CGATATTCTATATCTGGCTCGAATGAA
1 CGATATTTTGTATCTGGCTCGAATGAG
* * * * *
25731613 TGATATCTTATATCTGGCTTGAATGAT
1 CGATATTTTGTATCTGGCTCGAATGAG
* * *
25731640 CGATATTTTGTAGCTAGCTCGAACGAG
1 CGATATTTTGTATCTGGCTCGAATGAG
*
25731667 CAATATT
1 CGATATT
25731674 CTGTTATTGT
Statistics
Matches: 95, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 95 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (27 bp):
CGATATTTTGTATCTGGCTCGAATGAG
Found at i:25734296 original size:26 final size:26
Alignment explanation
Indices: 25734267--25734353 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 26
25734257 ATGAGCATGC
25734267 CCAGAATTGTCGCTGTA-GAAACTTGT
1 CCAGAATTGTCGCTGTATG-AACTTGT
* **
25734293 CCAGAATTATCGCTACATGAA-TATGT
1 CCAGAATTGTCGCTGTATGAACT-TGT
* * *
25734319 CCAGAGTTGTCGCTGTATGAGCATGT
1 CCAGAATTGTCGCTGTATGAACTTGT
25734345 CCAGAATTG
1 CCAGAATTG
25734354 AGCCTAAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
25 1 0.02
26 46 0.96
27 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (26 bp):
CCAGAATTGTCGCTGTATGAACTTGT
Found at i:25734331 original size:52 final size:52
Alignment explanation
Indices: 25734253--25734352 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 52
25734243 ACTAATGTCA
* *
25734253 CTACATGAGCATGCCCAGAATTGTCGCTGTA-GAAACTTGTCCAGAATTATCG
1 CTACATGAACATGCCCAGAATTGTCGCTGTATG-AACATGTCCAGAATTATCG
* * * *
25734305 CTACATGAATATGTCCAGAGTTGTCGCTGTATGAGCATGTCCAGAATT
1 CTACATGAACATGCCCAGAATTGTCGCTGTATGAACATGTCCAGAATT
25734353 GAGCCTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 40 0.98
53 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (52 bp):
CTACATGAACATGCCCAGAATTGTCGCTGTATGAACATGTCCAGAATTATCG
Found at i:25741979 original size:37 final size:36
Alignment explanation
Indices: 25741935--25742070 Score: 191
Period size: 37 Copynumber: 3.7 Consensus size: 36
25741925 CAGTAGCACA
*
25741935 AAGCCTACTAGGCACATAGCCTGAAAACATCGGCATG
1 AAGCCTACTAGGCACAAAGCCTGAAAACA-CGGCATG
* * *
25741972 AAACCTACTAGGTACAAAGCCTGAAAACACCGGCACG
1 AAGCCTACTAGGCACAAAGCCTGAAAACA-CGGCATG
*
25742009 AAGCCTACTAGGCACATAGCCTGAAAACACTGGCATG
1 AAGCCTACTAGGCACAAAGCCTGAAAACAC-GGCATG
*
25742046 AAGCCTACTAGGCACAAAACCTGAA
1 AAGCCTACTAGGCACAAAGCCTGAA
25742071 TTTTTAGATG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
36 1 0.01
37 86 0.99
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.14
Consensus pattern (36 bp):
AAGCCTACTAGGCACAAAGCCTGAAAACACGGCATG
Found at i:25742029 original size:74 final size:74
Alignment explanation
Indices: 25741930--25742070 Score: 230
Period size: 74 Copynumber: 1.9 Consensus size: 74
25741920 GATTACAGTA
* *
25741930 GCACAAAGCCTACTAGGCACATAGCCTGAAAACA-TCGGCATGAAACCTACTAGGTACAAAGCCT
1 GCACAAAGCCTACTAGGCACATAGCCTGAAAACACT-GGCATGAAACCTACTAGGCACAAAACCT
25741994 GAAAACACCG
65 GAAAACACCG
* *
25742004 GCACGAAGCCTACTAGGCACATAGCCTGAAAACACTGGCATGAAGCCTACTAGGCACAAAACCTG
1 GCACAAAGCCTACTAGGCACATAGCCTGAAAACACTGGCATGAAACCTACTAGGCACAAAACCTG
25742069 AA
66 AA
25742071 TTTTTAGATG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 61 0.98
75 1 0.02
ACGTcount: A:0.38, C:0.28, G:0.20, T:0.13
Consensus pattern (74 bp):
GCACAAAGCCTACTAGGCACATAGCCTGAAAACACTGGCATGAAACCTACTAGGCACAAAACCTG
AAAACACCG
Found at i:25755557 original size:28 final size:28
Alignment explanation
Indices: 25755515--25755569 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
25755505 CAATGGCACG
* *
25755515 TCACTGTAAATGACAAACTCCTTTCCTA
1 TCACTGTAAACGACAAACTACTTTCCTA
25755543 TCACTGTAAACGACAAACTACTTTCCT
1 TCACTGTAAACGACAAACTACTTTCCT
25755570 GTCTTTGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (28 bp):
TCACTGTAAACGACAAACTACTTTCCTA
Found at i:25759534 original size:18 final size:18
Alignment explanation
Indices: 25759511--25759549 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
25759501 TGATCCAGTA
*
25759511 ATGCTCTTACGAGCAAGT
1 ATGCTCTGACGAGCAAGT
*
25759529 ATGCTCTGACGAGCTAGT
1 ATGCTCTGACGAGCAAGT
25759547 ATG
1 ATG
25759550 GTCAAACGAG
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:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (18 bp):
ATGCTCTGACGAGCAAGT
Found at i:25759558 original size:18 final size:18
Alignment explanation
Indices: 25759526--25759574 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
25759516 CTTACGAGCA
**
25759526 AGTATGCTCTGACGAG-C
1 AGTATGCTCAAACGAGTC
*
25759543 TAGTATGGTCAAACGAGTC
1 -AGTATGCTCAAACGAGTC
25759562 AGTATGCTCAAAC
1 AGTATGCTCAAAC
25759575 AAGCCTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (18 bp):
AGTATGCTCAAACGAGTC
Found at i:25760815 original size:16 final size:16
Alignment explanation
Indices: 25760794--25760824 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25760784 ATAATTTGAA
25760794 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
25760810 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
25760825 AGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:25761670 original size:26 final size:26
Alignment explanation
Indices: 25761611--25761663 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
25761601 TTCTGGGCAT
25761611 AATTCTGGACACGTTCATGCAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
*
25761637 AATTCTGGACATGTTCATGCAGCGAC
1 AATTCTGGACACGTTCATGCAGCGAC
25761663 A
1 A
25761664 TTCCTGGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (26 bp):
AATTCTGGACACGTTCATGCAGCGAC
Found at i:25761695 original size:37 final size:38
Alignment explanation
Indices: 25761654--25761740 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
25761644 GACATGTTCA
*
25761654 TGCAGCGACA-TTCCTGGGTGCA-ATTGAAGAATACTTT
1 TGCAGCGACAGTT-CTGGATGCAGATTGAAGAATACTTT
* * *
25761691 TGCAGCGATAGTTCTGGATGCAGTTTGAAGAATATTTT
1 TGCAGCGACAGTTCTGGATGCAGATTGAAGAATACTTT
*
25761729 TGCAGCAACAGT
1 TGCAGCGACAGT
25761741 ATTGGGTGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
37 17 0.40
38 25 0.60
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (38 bp):
TGCAGCGACAGTTCTGGATGCAGATTGAAGAATACTTT
Found at i:25765694 original size:37 final size:38
Alignment explanation
Indices: 25765653--25765757 Score: 99
Period size: 38 Copynumber: 2.8 Consensus size: 38
25765643 AGACATGTTC
*
25765653 ATGCAGTGACATTCTTGGGTGCAA-TTGAAGAATAC-TT
1 ATGCAGCGACATTCTTGGGTGCAATTTGAAGAAT-CTTT
* * *
25765690 ATGCAGGGATAGTT-TTGGATGCAATTTGAAGAATCTTT
1 ATGCAGCGACA-TTCTTGGGTGCAATTTGAAGAATCTTT
* * * *
25765728 ATGTAGCAACATACTTGGGTGCATTTTGAA
1 ATGCAGCGACATTCTTGGGTGCAATTTGAA
25765758 AATATTCCTG
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
37 20 0.37
38 34 0.63
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (38 bp):
ATGCAGCGACATTCTTGGGTGCAATTTGAAGAATCTTT
Found at i:25770242 original size:22 final size:22
Alignment explanation
Indices: 25770212--25770261 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
25770202 CATAAGTGGA
* *
25770212 ATTACTTAAGATTAA-ATAAGAG
1 ATTAATTAAG-TTAATATAAAAG
*
25770234 ATTAATTAAGTTAATTTAAAAG
1 ATTAATTAAGTTAATATAAAAG
25770256 ATTAAT
1 ATTAAT
25770262 ATTTACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (22 bp):
ATTAATTAAGTTAATATAAAAG
Found at i:25782854 original size:91 final size:92
Alignment explanation
Indices: 25782694--25782902 Score: 277
Period size: 91 Copynumber: 2.3 Consensus size: 92
25782684 TTAAGGGTGT
* *
25782694 AAAAAG-CCTTCAAAATTTTT--AAAAAAAGCAATTAAGTTCAAACTTTTATTTTGCACTCACTT
1 AAAAAGACCTTCAAACTTTTTCAAAAAAAAGCAATTAAGTTCAAACTTTTATTTTGCACTCAATT
*
25782756 GGATACTTGAACTTTCAAAATGTAT-A
66 GGATACTTGAACTTTCAAAATGCATAA
* ***
25782782 AAAAAGACCCTCAAACTTTTTCAAAAAAAAGCAATTAA-TCTCCTGCTTTTATTTTGCACTCAAT
1 AAAAAGACCTTCAAACTTTTTCAAAAAAAAGCAATTAAGT-TCAAACTTTTATTTTGCACTCAAT
25782846 TAGG-TACTTGAACTTTCAAAATGCATAA
65 T-GGATACTTGAACTTTCAAAATGCATAA
* *
25782874 AAAAAAACCTTTAAACTTTTTCAAAAAAA
1 AAAAAGACCTTCAAACTTTTTCAAAAAAA
25782903 GTCATTAAGC
Statistics
Matches: 105, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
88 6 0.06
89 12 0.11
90 1 0.01
91 57 0.54
92 29 0.28
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.33
Consensus pattern (92 bp):
AAAAAGACCTTCAAACTTTTTCAAAAAAAAGCAATTAAGTTCAAACTTTTATTTTGCACTCAATT
GGATACTTGAACTTTCAAAATGCATAA
Found at i:25782928 original size:91 final size:91
Alignment explanation
Indices: 25782714--25782928 Score: 251
Period size: 91 Copynumber: 2.4 Consensus size: 91
25782704 CAAAATTTTT
* ** *
25782714 AAAAAAAGCAATTAAG-TTCAAACTTTTATTTTGCACTCACTTGGATACTTGAACTTTCAAAATG
1 AAAAAAAGCAATTAAGCTCCTGA-TTTTATTTTGCACTCAATTGGATACTTGAACTTTCAAAATG
* *
25782778 TATAAAAAAGACCCTCAAACTTTTTCA
65 CATAAAAAAAACCCTCAAACTTTTTCA
* *
25782805 AAAAAAAGCAATTAATCTCCTGCTTTTATTTTGCACTCAATTAGG-TACTTGAACTTTCAAAATG
1 AAAAAAAGCAATTAAGCTCCTGATTTTATTTTGCACTCAATT-GGATACTTGAACTTTCAAAATG
* *
25782869 CATAAAAAAAAACCTTTAAACTTTTTC-
65 CAT-AAAAAAAACCCTCAAACTTTTTCA
*
25782896 AAAAAAAGTC-ATTAAGC-CCTTGATTTTTTTTTG
1 AAAAAAAG-CAATTAAGCTCC-TGATTTTATTTTG
25782929 TTTTTTGCAT
Statistics
Matches: 106, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
90 2 0.02
91 79 0.75
92 25 0.24
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (91 bp):
AAAAAAAGCAATTAAGCTCCTGATTTTATTTTGCACTCAATTGGATACTTGAACTTTCAAAATGC
ATAAAAAAAACCCTCAAACTTTTTCA
Found at i:25783137 original size:20 final size:21
Alignment explanation
Indices: 25783103--25783182 Score: 63
Period size: 24 Copynumber: 3.6 Consensus size: 21
25783093 TAAATTTTAT
* *
25783103 TAAAAATTAGAAAAAGAATTA
1 TAAAAATTAGAAAAAAAAGTA
*
25783124 TAAAAATT-GTAAAAAAAGTA
1 TAAAAATTAGAAAAAAAAGTA
* *
25783144 TAAAAATAATTGTAAAAAAAATTA
1 TAAAAAT--TAG-AAAAAAAAGTA
25783168 TAAAATATATAGAAA
1 TAAAA-AT-TAGAAA
25783183 TATAGAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 16 0.33
21 8 0.17
22 1 0.02
23 4 0.08
24 17 0.35
25 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.26
Consensus pattern (21 bp):
TAAAAATTAGAAAAAAAAGTA
Found at i:25783139 original size:11 final size:11
Alignment explanation
Indices: 25783125--25783163 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
25783115 AAAGAATTAT
25783125 AAAAATTGTAA
1 AAAAATTGTAA
* *
25783136 AAAAAGTATAA
1 AAAAATTGTAA
25783147 AAATAATTGTAA
1 AAA-AATTGTAA
25783159 AAAAA
1 AAAAA
25783164 ATTATAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (11 bp):
AAAAATTGTAA
Found at i:25783140 original size:12 final size:12
Alignment explanation
Indices: 25783104--25783172 Score: 56
Period size: 12 Copynumber: 6.1 Consensus size: 12
25783094 AAATTTTATT
*
25783104 AAAAATTAGAAA
1 AAAAATTATAAA
*
25783116 AAGAATTAT---
1 AAAAATTATAAA
*
25783125 AAAAATTGT-AA
1 AAAAATTATAAA
*
25783136 AAAAAGTATAAA
1 AAAAATTATAAA
* *
25783148 AATAATTGTAAA
1 AAAAATTATAAA
25783160 AAAAATTATAAA
1 AAAAATTATAAA
25783172 A
1 A
25783173 TATATAGAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
9 7 0.16
11 7 0.16
12 29 0.67
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:25783154 original size:23 final size:24
Alignment explanation
Indices: 25783128--25783172 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
25783118 GAATTATAAA
25783128 AATTGT-AAAAAAAGTATAAAAAT
1 AATTGTAAAAAAAAGTATAAAAAT
*
25783151 AATTGTAAAAAAAATTATAAAA
1 AATTGTAAAAAAAAGTATAAAA
25783173 TATATAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (24 bp):
AATTGTAAAAAAAAGTATAAAAAT
Found at i:25783173 original size:23 final size:23
Alignment explanation
Indices: 25783113--25783174 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
25783103 TAAAAATTAG
*
25783113 AAAAAGAATTAT-AAA-AATTGT
1 AAAAAAAATTATAAAATAATTGT
*
25783134 -AAAAAAAGTATAAAAATAATTGT
1 AAAAAAAATTAT-AAAATAATTGT
25783157 AAAAAAAATTATAAAATA
1 AAAAAAAATTATAAAATA
25783175 TATAGAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.26
22 3 0.09
23 12 0.35
24 10 0.29
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (23 bp):
AAAAAAAATTATAAAATAATTGT
Found at i:25783256 original size:19 final size:18
Alignment explanation
Indices: 25783219--25783270 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
25783209 AGGTCGTAAG
25783219 AAAAATTATAAAAATGTA
1 AAAAATTATAAAAATGTA
*
25783237 AATAAA-TATAAAATTCGTA
1 AA-AAATTATAAAAAT-GTA
25783256 AAAAATTATAAAAAT
1 AAAAATTATAAAAAT
25783271 TATTGTACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (18 bp):
AAAAATTATAAAAATGTA
Found at i:25783543 original size:18 final size:20
Alignment explanation
Indices: 25783510--25783555 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
25783500 AAATGATAAA
25783510 AATAAAAATCAATAAAGTTT
1 AATAAAAATCAATAAAGTTT
* *
25783530 -ATAAAAAT-ATTAAATTTT
1 AATAAAAATCAATAAAGTTT
25783548 AATAAAAA
1 AATAAAAA
25783556 AAATATAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAAAAATCAATAAAGTTT
Found at i:25783571 original size:31 final size:31
Alignment explanation
Indices: 25783529--25783587 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
25783519 CAATAAAGTT
25783529 TATAAAAATA-TTAAATTTTAATAAAAAAAA
1 TATAAAAATATTTAAATTTTAATAAAAAAAA
*
25783559 TATAGAAAATATTTAAATTTTATTAAAAA
1 TATA-AAAATATTTAAATTTTAATAAAAA
25783588 TTAGAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 4 0.15
31 6 0.23
32 16 0.62
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (31 bp):
TATAAAAATATTTAAATTTTAATAAAAAAAA
Found at i:25783586 original size:32 final size:30
Alignment explanation
Indices: 25783529--25783587 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
25783519 CAATAAAGTT
*
25783529 TATAAAAATATTAAATTTTAATAAAAAAAA
1 TATAAAAATATTAAAATTTAATAAAAAAAA
* * *
25783559 TATAGAAAATATTTAAATTTTATTAAAAA
1 TATA-AAAATATTAAAATTTAATAAAAAA
25783588 TTAGAAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (30 bp):
TATAAAAATATTAAAATTTAATAAAAAAAA
Found at i:25783617 original size:22 final size:21
Alignment explanation
Indices: 25783582--25783652 Score: 81
Period size: 21 Copynumber: 3.2 Consensus size: 21
25783572 TAAATTTTAT
*
25783582 TAAAAATTAG-AAAAAGAATTA
1 TAAAAATT-GTAAAAAAAATTA
*
25783603 TAAAAATTGTAAAAAAAAGTA
1 TAAAAATTGTAAAAAAAATTA
25783624 TAAATAATTGTAAAAAAAAATTTA
1 TAAA-AATTGT-AAAAAAAA-TTA
25783648 TAAAA
1 TAAAA
25783653 TATATAGAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
20 1 0.02
21 21 0.49
22 6 0.14
23 9 0.21
24 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (21 bp):
TAAAAATTGTAAAAAAAATTA
Found at i:25783619 original size:24 final size:23
Alignment explanation
Indices: 25783592--25783652 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
25783582 TAAAAATTAG
25783592 AAAAAGAATTATAAAAATTGTAAA
1 AAAAAG-ATTATAAAAATTGTAAA
25783616 AAAAAG--TATAAATAATTGTAAA
1 AAAAAGATTATAAA-AATTGTAAA
25783638 AAAAA-ATTTATAAAA
1 AAAAAGA-TTATAAAA
25783653 TATATAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
21 6 0.18
22 14 0.42
23 1 0.03
24 12 0.36
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (23 bp):
AAAAAGATTATAAAAATTGTAAA
Found at i:25783729 original size:25 final size:24
Alignment explanation
Indices: 25783699--25783755 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
25783689 AGGTCGTAAG
*
25783699 AAAATTATAAAAAATAAATAAATAT
1 AAAATTATAAAAAAT-AATAAAAAT
*
25783724 AAAATTCATAAAAAATTATAAAAAT
1 AAAATT-ATAAAAAATAATAAAAAT
25783749 -AAATTAT
1 AAAATTAT
25783756 TGTACTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 2 0.07
24 5 0.17
25 13 0.45
26 9 0.31
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAATTATAAAAAATAATAAAAAT
Found at i:25787292 original size:19 final size:19
Alignment explanation
Indices: 25787265--25787304 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
25787255 AAATTAGTTG
* *
25787265 TAAGCAGTTTATTGTTTGT
1 TAAGCAGTTCATTGTTAGT
*
25787284 TAAGTAGTTCATTGTTAGT
1 TAAGCAGTTCATTGTTAGT
25787303 TA
1 TA
25787305 GGATGTTCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (19 bp):
TAAGCAGTTCATTGTTAGT
Found at i:25791926 original size:20 final size:21
Alignment explanation
Indices: 25791895--25791940 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
25791885 ATAATAATTG
25791895 GTTAATTAAAAGAAAAAGTAA
1 GTTAATTAAAAGAAAAAGTAA
25791916 GTTAA-TAAAAGAAAAAGTAA
1 GTTAATTAAAAGAAAAAGTAA
25791936 GTTAA
1 GTTAA
25791941 CATATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (21 bp):
GTTAATTAAAAGAAAAAGTAA
Found at i:25800800 original size:25 final size:25
Alignment explanation
Indices: 25800747--25800792 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
25800737 GTTAGATCCA
25800747 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAATTCTAAAAAGATAATTAG
*
25800772 AATTAAA-TCTAAACA-ATAATT
1 AATTAAATTCTAAAAAGATAATT
25800793 CACTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTAG
Found at i:25801872 original size:9 final size:9
Alignment explanation
Indices: 25801860--25801894 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
25801850 TTTTTATCTT
25801860 TTTTTTCAA
1 TTTTTTCAA
25801869 TTTTTTTCAA
1 -TTTTTTCAA
25801879 TTTTTTCAA
1 TTTTTTCAA
25801888 TTTTTTC
1 TTTTTTC
25801895 TTTTTCTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTTCAA
Found at i:25801872 original size:10 final size:10
Alignment explanation
Indices: 25801859--25801893 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
25801849 CTTTTTATCT
25801859 TTTTTTTCAA
1 TTTTTTTCAA
25801869 TTTTTTTCAA
1 TTTTTTTCAA
25801879 -TTTTTTCAA
1 TTTTTTTCAA
25801888 TTTTTT
1 TTTTTT
25801894 CTTTTTCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:25801872 original size:19 final size:19
Alignment explanation
Indices: 25801829--25801899 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
25801819 GCTCAAACAT
* *
25801829 ATTTTTATCTTTTTCTTCTT
1 ATTTTTATCTTTTTTTTC-A
*
25801849 CTTTTTATCTTTTTTTTCA
1 ATTTTTATCTTTTTTTTCA
* **
25801868 ATTTTTTTCAATTTTTTCA
1 ATTTTTATCTTTTTTTTCA
25801887 ATTTTT-TCTTTTT
1 ATTTTTATCTTTTT
25801900 CTAAATAATA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 5 0.12
19 21 0.50
20 16 0.38
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.75
Consensus pattern (19 bp):
ATTTTTATCTTTTTTTTCA
Found at i:25801873 original size:20 final size:20
Alignment explanation
Indices: 25801830--25801893 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
25801820 CTCAAACATA
* *
25801830 TTTTTATCTTTTTCTTC-TT
1 TTTTTATCTTTTTTTTCAAT
25801849 CTTTTTATCTTTTTTTTCAAT
1 -TTTTTATCTTTTTTTTCAAT
**
25801870 TTTTT-TCAATTTTTTCAAT
1 TTTTTATCTTTTTTTTCAAT
25801889 TTTTT
1 TTTTT
25801894 CTTTTTCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
19 17 0.44
20 21 0.54
21 1 0.03
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTATCTTTTTTTTCAAT
Found at i:25802534 original size:57 final size:57
Alignment explanation
Indices: 25802471--25802584 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
25802461 GAAAAAATTC
25802471 ACTCTAATAGGGTATGAGAAAATTACTTAAACACAATAAATAATTCAGGGATTTTAT
1 ACTCTAATAGGGTATGAGAAAATTACTTAAACACAATAAATAATTCAGGGATTTTAT
*
25802528 ACTCTAATGGGGTATGAGAAAATTACTTAAACACAATAAATAATTCAGGGATTTTAT
1 ACTCTAATAGGGTATGAGAAAATTACTTAAACACAATAAATAATTCAGGGATTTTAT
25802585 CACAATTATA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.32
Consensus pattern (57 bp):
ACTCTAATAGGGTATGAGAAAATTACTTAAACACAATAAATAATTCAGGGATTTTAT
Found at i:25802876 original size:5 final size:5
Alignment explanation
Indices: 25802866--25802932 Score: 57
Period size: 5 Copynumber: 12.4 Consensus size: 5
25802856 GTGCATAATC
25802866 AAATA AAATAAA AAATA AAATA AAATA AAACT- AAA-A AAATGA AAATGA
1 AAATA AAAT--A AAATA AAATA AAATA AAA-TA AAATA AAAT-A AAAT-A
25802914 AAATGA AAATAA AAATA AA
1 AAAT-A AAAT-A AAATA AA
25802933 TGTACTAATT
Statistics
Matches: 55, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
4 3 0.05
5 24 0.44
6 23 0.42
7 5 0.09
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (5 bp):
AAATA
Found at i:25802883 original size:12 final size:11
Alignment explanation
Indices: 25802866--25802932 Score: 64
Period size: 12 Copynumber: 5.6 Consensus size: 11
25802856 GTGCATAATC
25802866 AAATAAAATAAA
1 AAATAAAAT-AA
25802878 AAATAAAAT-A
1 AAATAAAATAA
25802888 AAATAAAACTAAAA
1 AAATAAAA-T--AA
*
25802902 AAATGAAAATGA
1 AAAT-AAAATAA
25802914 AAATGAAAATAA
1 AAAT-AAAATAA
25802926 AAATAAA
1 AAATAAA
25802933 TGTACTAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
10 9 0.19
11 4 0.08
12 25 0.52
14 6 0.12
15 4 0.08
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:25802885 original size:6 final size:6
Alignment explanation
Indices: 25802866--25802932 Score: 50
Period size: 6 Copynumber: 11.2 Consensus size: 6
25802856 GTGCATAATC
* * *
25802866 AAAT-A AAATAA AAA-ATA AAAT-A AAATAA AACTAAAA AAATGA AAATGA
1 AAATAA AAATAA AAATA-A AAATAA AAATAA AA--ATAA AAATAA AAATAA
*
25802914 AAATGA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA A
25802933 TGTACTAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
5 10 0.19
6 37 0.71
8 5 0.10
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:25802922 original size:20 final size:19
Alignment explanation
Indices: 25802866--25802916 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
25802856 GTGCATAATC
*
25802866 AAATAAAATAAAA--AATA
1 AAATAAAATAAAACTAAAA
25802883 AAATAAAATAAAACTAAAA
1 AAATAAAATAAAACTAAAA
25802902 AAATGAAAATGAAAA
1 AAAT-AAAAT-AAAA
25802917 TGAAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 13 0.45
19 7 0.24
20 5 0.17
21 4 0.14
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (19 bp):
AAATAAAATAAAACTAAAA
Found at i:25804980 original size:19 final size:21
Alignment explanation
Indices: 25804958--25805011 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
25804948 AAAAGAACCT
25804958 ATAAAAATAAAAAAAT-T-AA
1 ATAAAAATAAAAAAATATAAA
25804977 ATAAAAA-ACAAAAAATATGAAA
1 ATAAAAATA-AAAAAATAT-AAA
*
25804999 ATAAAAGTAAAAA
1 ATAAAAATAAAAA
25805012 TGGCTAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 1 0.03
22 12 0.41
23 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.17
Consensus pattern (21 bp):
ATAAAAATAAAAAAATATAAA
Found at i:25805085 original size:46 final size:48
Alignment explanation
Indices: 25804980--25805085 Score: 112
Period size: 46 Copynumber: 2.3 Consensus size: 48
25804970 AAATTAAATA
****
25804980 AAAAACAAAAAATATGAAAATAAAAGTAAAAATGGCTAAATAAAGGGG
1 AAAAACAAAAAATATGAAAATAAAAGTAAAAATGGCTAAATAAAAAAC
* * *
25805028 GAAAA-ATAAAATAT-AAAATAAAATTAAAAAT-GC-AAATAATAAAAC
1 AAAAACAAAAAATATGAAAATAAAAGTAAAAATGGCTAAATAA-AAAAC
25805073 AAAAACAAAAAAT
1 AAAAACAAAAAAT
25805086 GGCTAAAGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
44 6 0.13
45 7 0.15
46 22 0.47
47 8 0.17
48 4 0.09
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (48 bp):
AAAAACAAAAAATATGAAAATAAAAGTAAAAATGGCTAAATAAAAAAC
Found at i:25809029 original size:20 final size:20
Alignment explanation
Indices: 25809004--25809044 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
25808994 TCACTTTATT
*
25809004 ACTTGAATATGATTGTGTAC
1 ACTTGAATACGATTGTGTAC
25809024 ACTTGAATACGATTGTGTAC
1 ACTTGAATACGATTGTGTAC
25809044 A
1 A
25809045 GTTCCGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (20 bp):
ACTTGAATACGATTGTGTAC
Found at i:25814884 original size:9 final size:9
Alignment explanation
Indices: 25814853--25814892 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
25814843 AAAATAAAAG
25814853 TTATTTATT
1 TTATTTATT
* *
25814862 TATTTTTATG
1 T-TATTTATT
25814872 TTATTTATT
1 TTATTTATT
25814881 TTATTTATT
1 TTATTTATT
25814890 TTA
1 TTA
25814893 AAATTGATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (9 bp):
TTATTTATT
Found at i:25816519 original size:3 final size:3
Alignment explanation
Indices: 25816462--25816501 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
25816452 CTTCAATAGC
25816462 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
25816502 TCCTAAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:25824838 original size:24 final size:24
Alignment explanation
Indices: 25824811--25824905 Score: 145
Period size: 24 Copynumber: 4.0 Consensus size: 24
25824801 TGACTCAAAG
*
25824811 AAATAAACAGAGTTTAATTGAAAC
1 AAATAAACAGAGTTCAATTGAAAC
*
25824835 AAATAAACAAAGTTCAATTGAAAC
1 AAATAAACAGAGTTCAATTGAAAC
25824859 AAATAAACAGAGTTCAATTGAAAC
1 AAATAAACAGAGTTCAATTGAAAC
* * *
25824883 AATTAAACAGAGTTTAACTGAAA
1 AAATAAACAGAGTTCAATTGAAA
25824906 GATTATTTCT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.55, C:0.11, G:0.12, T:0.23
Consensus pattern (24 bp):
AAATAAACAGAGTTCAATTGAAAC
Found at i:25826846 original size:24 final size:24
Alignment explanation
Indices: 25826818--25826900 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 24
25826808 TAGACTAATA
**
25826818 AGAGTTTGGCTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
25826842 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * * *
25826866 AGAGTTCAATTGAAACAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
25826890 AGAGTTTAACT
1 AGAGTTTAACT
25826901 GAAAGATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:25826903 original size:24 final size:24
Alignment explanation
Indices: 25826830--25826904 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
25826820 AGTTTGGCTC
25826830 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
25826854 AAACAAATAAACAGAGTTCAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
25826878 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
25826902 AAA
1 AAA
25826905 GATTATTTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.55, C:0.11, G:0.12, T:0.23
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:25834386 original size:6 final size:6
Alignment explanation
Indices: 25834375--25834406 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
25834365 TCTTGACTTC
*
25834375 CTCCTT CTCCTT CTCCTT CTCCTT CTCTTT CT
1 CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CT
25834407 TTTTCTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (6 bp):
CTCCTT
Found at i:25835575 original size:20 final size:20
Alignment explanation
Indices: 25835550--25835663 Score: 76
Period size: 20 Copynumber: 5.8 Consensus size: 20
25835540 TTTATTGTTT
25835550 TTCCTCATAATTTTTGGTAC
1 TTCCTCATAATTTTTGGTAC
*
25835570 TTCCTCGT-ATGTTTTGGTAC
1 TTCCTCATAAT-TTTTGGTAC
* *
25835590 ATT-CTTATAATTTTTGGCAC
1 -TTCCTCATAATTTTTGGTAC
* * *
25835610 TTCCTCA-AGCTTTATAGTA-
1 TTCCTCATA-ATTTTTGGTAC
* **
25835629 TTCTCTTATAATTTTTAATAC
1 TTC-CTCATAATTTTTGGTAC
25835650 TTCCTCAT-ATTTTT
1 TTCCTCATAATTTTT
25835664 TTAATATTTC
Statistics
Matches: 72, Mismatches: 14, Indels: 17
0.70 0.14 0.17
Matches are distributed among these distances:
19 14 0.19
20 50 0.69
21 8 0.11
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.52
Consensus pattern (20 bp):
TTCCTCATAATTTTTGGTAC
Found at i:25835684 original size:21 final size:21
Alignment explanation
Indices: 25835636--25835685 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
25835626 GTATTCTCTT
25835636 ATAA-TTTTTAATACTTCCTC
1 ATAATTTTTTAATACTTCCTC
* * *
25835656 ATATTTTTTTAATATTTCTTC
1 ATAATTTTTTAATACTTCCTC
*
25835677 GTAATTTTT
1 ATAATTTTT
25835686 GTTGCATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (21 bp):
ATAATTTTTTAATACTTCCTC
Found at i:25835740 original size:18 final size:17
Alignment explanation
Indices: 25835718--25835770 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
25835708 TTAGTCAGAT
25835718 TTTTTTGTACTTCCTCA
1 TTTTTTGTACTTCCTCA
* *
25835735 TGTTTTGGTACATCCTCA
1 T-TTTTTGTACTTCCTCA
*
25835753 TTTTTTGATACTTTCTCA
1 TTTTTTG-TACTTCCTCA
25835771 AGTCTTATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 6 0.21
18 23 0.79
ACGTcount: A:0.15, C:0.21, G:0.09, T:0.55
Consensus pattern (17 bp):
TTTTTTGTACTTCCTCA
Found at i:25835740 original size:20 final size:20
Alignment explanation
Indices: 25835697--25835734 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25835687 TTGCATTATC
*
25835697 TTTTTTTGTACTTAGTCAGA
1 TTTTTTTGTACTTACTCAGA
*
25835717 TTTTTTTGTACTTCCTCA
1 TTTTTTTGTACTTACTCA
25835735 TGTTTTGGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.58
Consensus pattern (20 bp):
TTTTTTTGTACTTACTCAGA
Found at i:25835837 original size:25 final size:25
Alignment explanation
Indices: 25835809--25835857 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
25835799 TATACTTATA
*
25835809 TTTTTTGTA-TTCTCTCATAATTTTC
1 TTTTTTGTACATCT-TCATAATTTTC
25835834 TTTTTTGTACATCTTCATAATTTT
1 TTTTTTGTACATCTTCATAATTTT
25835858 TGGTGCATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.18, C:0.14, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTGTACATCTTCATAATTTTC
Found at i:25836083 original size:20 final size:20
Alignment explanation
Indices: 25835834--25836182 Score: 120
Period size: 20 Copynumber: 17.9 Consensus size: 20
25835824 CATAATTTTC
* * *
25835834 TTTTTTGTACATCTTCATAA
1 TTTTTGGTACTTCCTCATAA
* * * *
25835854 TTTTTGGTGCATCCTTAT-T
1 TTTTTGGTACTTCCTCATAA
*
25835873 TTTTTGGTA-TCCCTCATAA
1 TTTTTGGTACTTCCTCATAA
* * * *
25835892 TTTTTTGTATTTGCTCATAT
1 TTTTTGGTACTTCCTCATAA
* * * **
25835912 TTTTTTGTACTTCATTATGT
1 TTTTTGGTACTTCCTCATAA
* *
25835932 TTTTTAGCA-TTCTCTCATAA
1 TTTTTGGTACTTC-CTCATAA
* *
25835952 TTTTT--TA-TACATC-TAA
1 TTTTTGGTACTTCCTCATAA
* * *
25835968 GTTTTT-GTACATACTTATAA
1 -TTTTTGGTACTTCCTCATAA
*
25835988 TTTTTGGTACTCCCTCATAA
1 TTTTTGGTACTTCCTCATAA
* * *
25836008 TTTTTTGTAATTCCTC-TTA
1 TTTTTGGTACTTCCTCATAA
* *
25836027 TTTTTGGAACTTCCTAATAA
1 TTTTTGGTACTTCCTCATAA
** *
25836047 TTTTTGACACATT-TTCATAA
1 TTTTTGGTAC-TTCCTCATAA
*
25836067 TTTTTGGTACTTCTTCAT--
1 TTTTTGGTACTTCCTCATAA
* * *
25836085 TTTCTTTGCACTTTCTCATAA
1 TTT-TTGGTACTTCCTCATAA
* *
25836106 TTCTTGATA-TT-CTACCATAA
1 TTTTTGGTACTTCCT--CATAA
**
25836126 TTTTTTATACTTCCTCAT-A
1 TTTTTGGTACTTCCTCATAA
* *
25836145 TGTTTTGGTGCTTCCTTATATA
1 T-TTTTGGTACTTCCTCATA-A
25836167 TTTTT--TACTTCCTCAT
1 TTTTTGGTACTTCCTCAT
25836183 GTTATTTTGG
Statistics
Matches: 240, Mismatches: 68, Indels: 43
0.68 0.19 0.12
Matches are distributed among these distances:
16 3 0.01
17 7 0.03
18 15 0.06
19 65 0.27
20 136 0.57
21 10 0.04
22 4 0.02
ACGTcount: A:0.21, C:0.17, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTTTGGTACTTCCTCATAA
Found at i:25836347 original size:20 final size:20
Alignment explanation
Indices: 25836322--25836391 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
25836312 TACTTTCTTT
25836322 TTTTTTGTATTCCCTCAAAA
1 TTTTTTGTATTCCCTCAAAA
* *
25836342 TTTTTTTTACTT-CCTC-ATA
1 TTTTTTGTA-TTCCCTCAAAA
*
25836361 TTTTTTAGTATACCCTCAAAA
1 TTTTTT-GTATTCCCTCAAAA
25836382 TTTTTTGTAT
1 TTTTTTGTAT
25836392 GATTTGGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 9 0.22
20 22 0.54
21 10 0.24
ACGTcount: A:0.23, C:0.17, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTTGTATTCCCTCAAAA
Found at i:25836609 original size:17 final size:17
Alignment explanation
Indices: 25836587--25836621 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
25836577 CAGTATGCAA
25836587 GGATGAATCTTTTTGAG
1 GGATGAATCTTTTTGAG
25836604 GGATGAATCTTTTTGAG
1 GGATGAATCTTTTTGAG
25836621 G
1 G
25836622 AAACGAGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.31, T:0.40
Consensus pattern (17 bp):
GGATGAATCTTTTTGAG
Found at i:25848918 original size:90 final size:90
Alignment explanation
Indices: 25848746--25848919 Score: 231
Period size: 90 Copynumber: 1.9 Consensus size: 90
25848736 TGATACGAAT
* * * * ** *
25848746 CGTATCAAGCTTCGGCTTAGCAGGCTTTTGAGCTGGTGAAATGATGTGATAACTCAAGCTACAAC
1 CGTATCAAGCTTCAGCTTAGCAGGATTTTGAGCCGGTGAAACGATGAAATAACCCAAGCTACAAC
* *
25848811 TTAGCAGGCTTTTGAGCCGATAAAA
66 TTAGCAGGCGTTAGAGCCGATAAAA
***
25848836 CGTATCAAGCTTCAGCTTAGCAGGATTTTGAGCCGGTGAAACGATGAAATAACCCAAGCTACGGT
1 CGTATCAAGCTTCAGCTTAGCAGGATTTTGAGCCGGTGAAACGATGAAATAACCCAAGCTACAAC
*
25848901 TTAGCATGCGTTAGAGCCG
66 TTAGCAGGCGTTAGAGCCG
25848920 GTGAAGTAGA
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
90 71 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (90 bp):
CGTATCAAGCTTCAGCTTAGCAGGATTTTGAGCCGGTGAAACGATGAAATAACCCAAGCTACAAC
TTAGCAGGCGTTAGAGCCGATAAAA
Found at i:25849684 original size:62 final size:62
Alignment explanation
Indices: 25849601--25849735 Score: 236
Period size: 62 Copynumber: 2.2 Consensus size: 62
25849591 CAGTCGTGGT
25849601 TAGGCCGTGTACCAAACTGTGCAACCACTACACTTATTTATGAAATTTCACACGATCGTGGCC
1 TAGGCCGTGTACCAAACTGTGCAACCACTACACTTATTTATGAAATTTCA-ACGATCGTGGCC
* *
25849664 TAGGCCGTGTACCAGA-TGTGCAACCACTACACTTATTTATGAAATTTCAACGATCGTGGTC
1 TAGGCCGTGTACCAAACTGTGCAACCACTACACTTATTTATGAAATTTCAACGATCGTGGCC
25849725 TAGGCCGTGTA
1 TAGGCCGTGTA
25849736 TTAGGTCGTG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
61 22 0.31
62 33 0.47
63 15 0.21
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (62 bp):
TAGGCCGTGTACCAAACTGTGCAACCACTACACTTATTTATGAAATTTCAACGATCGTGGCC
Found at i:25850623 original size:28 final size:28
Alignment explanation
Indices: 25850582--25850824 Score: 203
Period size: 28 Copynumber: 8.8 Consensus size: 28
25850572 CTCATATTCA
* *
25850582 TATGCGTTTCCGCTCGCCAGTTTATACT
1 TATGCGTTTACGCTCGCCAGCTTATACT
* *
25850610 TATGTGTTTACGCTCGCGAGCTTATACT
1 TATGCGTTTACGCTCGCCAGCTTATACT
* * *
25850638 TACGCGTTTACGCTTGCCAACTTATACT
1 TATGCGTTTACGCTCGCCAGCTTATACT
*
25850666 TACGCGTTTACGCTCGCCAGCTTATACT
1 TATGCGTTTACGCTCGCCAGCTTATACT
* * **
25850694 TATGCGTTTAAGCTCGCCAACTTGCAC-
1 TATGCGTTTACGCTCGCCAGCTTATACT
* * * *
25850721 -A--CATTTATGCTCGTCAGCTTATTCAT
1 TATGCGTTTACGCTCGCCAGCTTATAC-T
* *
25850747 T-TGCGTTTACACTCGCCAGCTTATTCAT
1 TATGCGTTTACGCTCGCCAGCTTATAC-T
* * *
25850775 T-TGCATTTACACTCGCCAGCTTATTCAT
1 TATGCGTTTACGCTCGCCAGCTTATAC-T
* *
25850803 T-TGCGTTTACTCTCGCTAGCTT
1 TATGCGTTTACGCTCGCCAGCTT
25850825 GCACACATTT
Statistics
Matches: 179, Mismatches: 31, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
24 16 0.09
26 1 0.01
28 162 0.91
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.38
Consensus pattern (28 bp):
TATGCGTTTACGCTCGCCAGCTTATACT
Found at i:25850752 original size:52 final size:52
Alignment explanation
Indices: 25850672--25850924 Score: 274
Period size: 52 Copynumber: 4.8 Consensus size: 52
25850662 TACTTACGCG
* * * *
25850672 TTTACGCTCGCCAGCTTATAC-TTATGCGTTTAAGCTCGCCAACTTGCACACA
1 TTTACGCTCGTCAGCTTATTCATT-TGCGTTTACGCTCGCCAGCTTGCACACA
* * * **
25850724 TTTATGCTCGTCAGCTTATTCATTTGCGTTTACACTCGCCAGCTTATTCATTTGCA
1 TTTACGCTCGTCAGCTTATTCATTTGCGTTTACGCTCGCCAGC-T-TGCA--CACA
* * * *
25850780 TTTACACTCGCCAGCTTATTCATTTGCGTTTACTCTCGCTAGCTTGCACACA
1 TTTACGCTCGTCAGCTTATTCATTTGCGTTTACGCTCGCCAGCTTGCACACA
* * * * *
25850832 TTTACACTCGTCAGTTTAGTCATTTGCATTTACGCTCGCCAGCTTGCACACG
1 TTTACGCTCGTCAGCTTATTCATTTGCGTTTACGCTCGCCAGCTTGCACACA
* *
25850884 TTTATGCTAGTCAGCTTATTCATTTGCGTTTACGCTCGCCA
1 TTTACGCTCGTCAGCTTATTCATTTGCGTTTACGCTCGCCA
25850925 ACTTATTCAT
Statistics
Matches: 166, Mismatches: 30, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
52 116 0.70
53 3 0.02
54 6 0.04
55 1 0.01
56 40 0.24
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.37
Consensus pattern (52 bp):
TTTACGCTCGTCAGCTTATTCATTTGCGTTTACGCTCGCCAGCTTGCACACA
Found at i:25850784 original size:108 final size:108
Alignment explanation
Indices: 25850672--25850876 Score: 286
Period size: 108 Copynumber: 1.9 Consensus size: 108
25850662 TACTTACGCG
* **
25850672 TTTACGCTCGCCAGCTTATAC-TTATGCGTTTAAGCTCGCCAACTTGCACACATTTATGCTCGTC
1 TTTACACTCGCCAGCTTATACATT-TGCGTTTAAGCTCGCCAACTTGCACACATTTACACTCGTC
* *
25850736 AGCTTATTCATTTGCGTTTACACTCGCCAGCTTATTCATTTGCA
65 AGCTTAGTCATTTGCATTTACACTCGCCAGCTTATTCATTTGCA
* ** * *
25850780 TTTACACTCGCCAGCTTATTCATTTGCGTTTACTCTCGCTAGCTTGCACACATTTACACTCGTCA
1 TTTACACTCGCCAGCTTATACATTTGCGTTTAAGCTCGCCAACTTGCACACATTTACACTCGTCA
* *
25850845 GTTTAGTCATTTGCATTTACGCTCGCCAGCTT
66 GCTTAGTCATTTGCATTTACACTCGCCAGCTT
25850877 GCACACGTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
108 82 0.98
109 2 0.02
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (108 bp):
TTTACACTCGCCAGCTTATACATTTGCGTTTAAGCTCGCCAACTTGCACACATTTACACTCGTCA
GCTTAGTCATTTGCATTTACACTCGCCAGCTTATTCATTTGCA
Found at i:25850791 original size:80 final size:80
Alignment explanation
Indices: 25850669--25850938 Score: 241
Period size: 80 Copynumber: 3.4 Consensus size: 80
25850659 TTATACTTAC
* * * * *
25850669 GCGTTTACGCTCGCCAGCTTATAC-TTATGCGTTTA-AGCTCGCCAACTTGCACACATTTATGCT
1 GCGTTTACACTCGCCAGCTTATTCATT-TGCATTTACA-CTCGCCAGCTTGCACACGTTTATGCT
25850732 CGTCAGCTTATTCATTT
64 CGTCAGCTTATTCATTT
* **
25850749 GCGTTTACACTCGCCAGCTTATTCATTTGCATTTACACTCGCCAGCTTATTCATTTGCGTTTACT
1 GCGTTTACACTCGCCAGCTTATTCATTTGCATTTACACTCGCCAGC-T-TGCA--CACGTTTA-T
* *
25850814 -CTCG-CTAGC-T-TGCA--C
61 GCTCGTC-AGCTTATTCATTT
* * * * * * *
25850829 ACATTTACACTCGTCAGTTTAGTCATTTGCATTTACGCTCGCCAGCTTGCACACGTTTATGCTAG
1 GCGTTTACACTCGCCAGCTTATTCATTTGCATTTACACTCGCCAGCTTGCACACGTTTATGCTCG
25850894 TCAGCTTATTCATTT
66 TCAGCTTATTCATTT
* *
25850909 GCGTTTACGCTCGCCAACTTATTCATTTGC
1 GCGTTTACACTCGCCAGCTTATTCATTTGC
25850939 GTTTGATTCA
Statistics
Matches: 147, Mismatches: 29, Indels: 28
0.72 0.14 0.14
Matches are distributed among these distances:
75 1 0.01
76 12 0.08
77 2 0.01
78 6 0.04
79 1 0.01
80 100 0.68
81 4 0.03
82 6 0.04
83 2 0.01
84 12 0.08
85 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (80 bp):
GCGTTTACACTCGCCAGCTTATTCATTTGCATTTACACTCGCCAGCTTGCACACGTTTATGCTCG
TCAGCTTATTCATTT
Found at i:25853777 original size:17 final size:18
Alignment explanation
Indices: 25853733--25853779 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
25853723 TTCCTCATTT
*
25853733 TTTTCTTTATTATTCTAA
1 TTTTATTTATTATTCTAA
25853751 TCTTTGATTTATTATTCT-A
1 T-TTT-ATTTATTATTCTAA
25853770 TTTTATTTAT
1 TTTTATTTAT
25853780 CTTAGTTATC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.23
18 4 0.15
19 5 0.19
20 11 0.42
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTTATTTATTATTCTAA
Found at i:25863785 original size:43 final size:41
Alignment explanation
Indices: 25863629--25863796 Score: 210
Period size: 41 Copynumber: 4.0 Consensus size: 41
25863619 AAACTCAAAA
**
25863629 GTAAAAGGAAGACTCATGTCTCTTGATGAGAATGAGATTAT
1 GTAAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTAT
*
25863670 GTAAAAGGAAGACTCATGTCTCGGGATCAGAATGAGATTAT
1 GTAAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTAT
* ** * *
25863711 GTAAAAAGAAGACTCATGTCTCGGGGCGAGCATGAGATTAC
1 GTAAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTAT
** * *
25863752 GTATAAATGGAAGACTCATGTCTCGAAATGAGCATGAGACTAT
1 GTA-AAA-GGAAGACTCATGTCTCGGGATGAGAATGAGATTAT
25863795 GT
1 GT
25863797 TTTAAGGAAG
Statistics
Matches: 109, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
41 76 0.70
42 3 0.03
43 30 0.28
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (41 bp):
GTAAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTAT
Found at i:25863826 original size:84 final size:82
Alignment explanation
Indices: 25863660--25863833 Score: 188
Period size: 84 Copynumber: 2.1 Consensus size: 82
25863650 CTTGATGAGA
* ** *
25863660 ATGAGATTATGTAAAAGGAAGACTCATGTCTCGGGATCAGAATGAGATTATGTAAAAAGAAGACT
1 ATGAGATTACGTAAAAGGAAGACTCATGTCTCGAAATCAGAATGAGACTATGTAAAAAGAAGACT
* *
25863725 CATGTCTCGGGGCGAGC
66 CATGACTCAGGGCGAGC
* * ** *
25863742 ATGAGATTACGTATAAATGGAAGACTCATGTCTCGAAATGAGCATGAGACTATGTTTTAAGGAAG
1 ATGAGATTACGTA-AAA-GGAAGACTCATGTCTCGAAATCAGAATGAGACTATG-TAAAAAGAAG
* *
25863807 ACTTATGACTCAGTG-GAGC
63 ACTCATGACTCAGGGCGAGC
*
25863826 ATAAGATT
1 ATGAGATT
25863834 GTTTAAAAAG
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
82 12 0.16
83 3 0.04
84 42 0.56
85 18 0.24
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.26
Consensus pattern (82 bp):
ATGAGATTACGTAAAAGGAAGACTCATGTCTCGAAATCAGAATGAGACTATGTAAAAAGAAGACT
CATGACTCAGGGCGAGC
Found at i:25866978 original size:21 final size:22
Alignment explanation
Indices: 25866954--25867001 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
25866944 TTGAAATACT
25866954 AAAATATATGAAG-GAGTACAA
1 AAAATATATGAAGTGAGTACAA
* * *
25866975 AAAAAATATGAGGTGAGTACTA
1 AAAATATATGAAGTGAGTACAA
25866997 AAAAT
1 AAAAT
25867002 TATAAGAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.21
Consensus pattern (22 bp):
AAAATATATGAAGTGAGTACAA
Found at i:25866979 original size:22 final size:23
Alignment explanation
Indices: 25866954--25867005 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
25866944 TTGAAATACT
25866954 AAAATATATGAAG-GAGTACAAA
1 AAAATATATGAAGTGAGTACAAA
* *
25866976 AAAA-ATATGAGGTGAGTACTAA
1 AAAATATATGAAGTGAGTACAAA
*
25866998 AAATTATA
1 AAAATATA
25867006 AGAGATTACC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 7 0.28
22 15 0.60
23 3 0.12
ACGTcount: A:0.56, C:0.04, G:0.17, T:0.23
Consensus pattern (23 bp):
AAAATATATGAAGTGAGTACAAA
Found at i:25869343 original size:21 final size:20
Alignment explanation
Indices: 25869291--25869344 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
25869281 CATAATTTTT
25869291 GGAATACTAAAAAATATGAG
1 GGAATACTAAAAAATATGAG
25869311 GGAATA-TCAAAAAATATGAG
1 GGAATACT-AAAAAATATGAG
*
25869331 GTGAGTACTAAAAA
1 G-GAATACTAAAAA
25869345 TTATAAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.03
20 19 0.63
21 9 0.30
22 1 0.03
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (20 bp):
GGAATACTAAAAAATATGAG
Found at i:25873086 original size:20 final size:20
Alignment explanation
Indices: 25873042--25873086 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
25873032 GAATGACCAA
*
25873042 TTTAATGAATGTCAAATTTT
1 TTTAATGAATGACAAATTTT
* **
25873062 GTTAATGAATGACACGTTTT
1 TTTAATGAATGACAAATTTT
25873082 TTTAA
1 TTTAA
25873087 GCCTAAAATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (20 bp):
TTTAATGAATGACAAATTTT
Found at i:25873694 original size:20 final size:20
Alignment explanation
Indices: 25873656--25873694 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25873646 CTTTTGTTTT
*
25873656 GTATCGATAAAACTCTTTCG
1 GTATCGATAAAAATCTTTCG
*
25873676 GTATCGATAAAAATGTTTC
1 GTATCGATAAAAATCTTTC
25873695 CAACGGCCAC
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:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (20 bp):
GTATCGATAAAAATCTTTCG
Found at i:25874640 original size:13 final size:13
Alignment explanation
Indices: 25874598--25874649 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
25874588 ATTAGAACTT
25874598 AACTTAAGTTTAG
1 AACTTAAGTTTAG
* * * *
25874611 ACCGTAGGATTAG
1 AACTTAAGTTTAG
25874624 -ACTTAAGTTTAG
1 AACTTAAGTTTAG
*
25874636 AACTTAAGGTTAG
1 AACTTAAGTTTAG
25874649 A
1 A
25874650 TTTATTCTAA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
12 8 0.28
13 21 0.72
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.33
Consensus pattern (13 bp):
AACTTAAGTTTAG
Found at i:25893281 original size:51 final size:51
Alignment explanation
Indices: 25893081--25893268 Score: 197
Period size: 51 Copynumber: 3.8 Consensus size: 51
25893071 AAACGTGATT
* * * * **
25893081 ACAGAACGTTTAAGCTCATCAGCTATTCAG-GATCAGAAT-GATCGTAACAG
1 ACAGAACATTTAAGCTCATCAGCTATACAGAAATCAGAATAG-TCATGTCAG
* * * *
25893131 AC--AACTTTTAAGCTCGTCAGCTATTCAGAAATCAGAATAGTCATGTTAG
1 ACAGAACATTTAAGCTCATCAGCTATACAGAAATCAGAATAGTCATGTCAG
* * *
25893180 ACAGAACATTTAAGCTCATTAGCTATATAGAAATTAGAATAGTCATGTCAG
1 ACAGAACATTTAAGCTCATCAGCTATACAGAAATCAGAATAGTCATGTCAG
* *
25893231 ACAGAACATTTAAGCTCCTCAACTATACAG-AATCAGAA
1 ACAGAACATTTAAGCTCATCAGCTATACAGAAATCAGAA
25893269 AGAATTATGT
Statistics
Matches: 115, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
48 24 0.21
49 15 0.13
50 10 0.09
51 66 0.57
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (51 bp):
ACAGAACATTTAAGCTCATCAGCTATACAGAAATCAGAATAGTCATGTCAG
Found at i:25900464 original size:13 final size:12
Alignment explanation
Indices: 25900426--25900468 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
25900416 TACGGTTTTA
25900426 TATATACAATTT
1 TATATACAATTT
*
25900438 TATTTTACAA-TT
1 TA-TATACAATTT
25900450 TATATACACATTT
1 TATATACA-ATTT
25900463 TATATA
1 TATATA
25900469 TATATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 5 0.19
12 7 0.27
13 14 0.54
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATACAATTT
Found at i:25900726 original size:14 final size:14
Alignment explanation
Indices: 25900707--25900736 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
25900697 ACCCATTACA
25900707 CCCTTTAGTTTAAC
1 CCCTTTAGTTTAAC
25900721 CCCTTTAGTTTAAC
1 CCCTTTAGTTTAAC
25900735 CC
1 CC
25900737 TTCATTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (14 bp):
CCCTTTAGTTTAAC
Found at i:25907854 original size:12 final size:12
Alignment explanation
Indices: 25907837--25907862 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25907827 TGTTATTATG
25907837 ATGAATGCTATT
1 ATGAATGCTATT
25907849 ATGAATGCTATT
1 ATGAATGCTATT
25907861 AT
1 AT
25907863 TTATTTAATT
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:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:25912955 original size:26 final size:26
Alignment explanation
Indices: 25912898--25912955 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
25912888 TTTAGGTGCT
* *
25912898 ATTCTGGACTTGCTCATACAGCAACA
1 ATTCTGGACTTACTCACACAGCAACA
* * * *
25912924 ACTCTGGACTTATTCACACAGCGATA
1 ATTCTGGACTTACTCACACAGCAACA
25912950 ATTCTG
1 ATTCTG
25912956 AACAAGTTCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (26 bp):
ATTCTGGACTTACTCACACAGCAACA
Found at i:25921965 original size:187 final size:187
Alignment explanation
Indices: 25921650--25922026 Score: 754
Period size: 187 Copynumber: 2.0 Consensus size: 187
25921640 TTGTGGGAAA
25921650 GGTAAGGGTATGGATACATTGTTGGTCAGACAGTAGGCATCGAGGTGATAATTTGTGGAGTTTCC
1 GGTAAGGGTATGGATACATTGTTGGTCAGACAGTAGGCATCGAGGTGATAATTTGTGGAGTTTCC
25921715 TTATCTAGTTCATTTACAATTTCTTCAAATACAACTCTCTCACCCTGATTCACTTCACTAGTATC
66 TTATCTAGTTCATTTACAATTTCTTCAAATACAACTCTCTCACCCTGATTCACTTCACTAGTATC
25921780 TATAGGTACTATAGCAGAGTTGGTAGGTGACTCGACAGTTTGTTGACCACTCCGAAG
131 TATAGGTACTATAGCAGAGTTGGTAGGTGACTCGACAGTTTGTTGACCACTCCGAAG
25921837 GGTAAGGGTATGGATACATTGTTGGTCAGACAGTAGGCATCGAGGTGATAATTTGTGGAGTTTCC
1 GGTAAGGGTATGGATACATTGTTGGTCAGACAGTAGGCATCGAGGTGATAATTTGTGGAGTTTCC
25921902 TTATCTAGTTCATTTACAATTTCTTCAAATACAACTCTCTCACCCTGATTCACTTCACTAGTATC
66 TTATCTAGTTCATTTACAATTTCTTCAAATACAACTCTCTCACCCTGATTCACTTCACTAGTATC
25921967 TATAGGTACTATAGCAGAGTTGGTAGGTGACTCGACAGTTTGTTGACCACTCCGAAG
131 TATAGGTACTATAGCAGAGTTGGTAGGTGACTCGACAGTTTGTTGACCACTCCGAAG
25922024 GGT
1 GGT
25922027 GATTGCCTTG
Statistics
Matches: 190, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 190 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (187 bp):
GGTAAGGGTATGGATACATTGTTGGTCAGACAGTAGGCATCGAGGTGATAATTTGTGGAGTTTCC
TTATCTAGTTCATTTACAATTTCTTCAAATACAACTCTCTCACCCTGATTCACTTCACTAGTATC
TATAGGTACTATAGCAGAGTTGGTAGGTGACTCGACAGTTTGTTGACCACTCCGAAG
Found at i:25927512 original size:12 final size:13
Alignment explanation
Indices: 25927485--25927517 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
25927475 TAAGTTTGAT
25927485 AATTCTTAATATTA
1 AATT-TTAATATTA
25927499 AATTTTAA-ATTA
1 AATTTTAATATTA
25927511 AATTTTA
1 AATTTTA
25927518 TGATTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 4 0.21
14 4 0.21
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTTTAATATTA
Found at i:25927772 original size:13 final size:13
Alignment explanation
Indices: 25927754--25927778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25927744 CCAAGTAGTT
25927754 AGCCACCATCGAC
1 AGCCACCATCGAC
25927767 AGCCACCATCGA
1 AGCCACCATCGA
25927779 AAGTCATCGG
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:0.32, C:0.44, G:0.16, T:0.08
Consensus pattern (13 bp):
AGCCACCATCGAC
Found at i:25928157 original size:18 final size:17
Alignment explanation
Indices: 25928118--25928164 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
25928108 TTTATTTTCT
25928118 AATTTTTAAT-TTATTA
1 AATTTTTAATATTATTA
* *
25928134 ACTTTTTAATATATTTTA
1 AATTTTTAATAT-TATTA
25928152 AATTTTTAATATT
1 AATTTTTAATATT
25928165 TTATACTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 15 0.58
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTTAATATTATTA
Found at i:25928163 original size:16 final size:16
Alignment explanation
Indices: 25928118--25928167 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
25928108 TTTATTTTCT
25928118 AATTTTTAAT-TTATTA
1 AATTTTTAATATT-TTA
*
25928134 ACTTTTTAATATATTTTA
1 AATTTTT-A-ATATTTTA
25928152 AATTTTTAATATTTTA
1 AATTTTTAATATTTTA
25928168 TACTAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 14 0.48
17 2 0.07
18 11 0.38
19 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTTTAATATTTTA
Found at i:25931885 original size:12 final size:12
Alignment explanation
Indices: 25931868--25931893 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25931858 TGTTATTATG
25931868 ATGAATGCTATT
1 ATGAATGCTATT
25931880 ATGAATGCTATT
1 ATGAATGCTATT
25931892 AT
1 AT
25931894 TTATTTAATT
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:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:25931977 original size:17 final size:18
Alignment explanation
Indices: 25931942--25931979 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
25931932 GTTGATTGTG
* *
25931942 TTTAATTGCTTGTTTATA
1 TTTAATTGCATGTTCATA
25931960 TTTAATT-CATGTTCATA
1 TTTAATTGCATGTTCATA
25931977 TTT
1 TTT
25931980 TTATAAGCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.61
Consensus pattern (18 bp):
TTTAATTGCATGTTCATA
Found at i:25932477 original size:14 final size:14
Alignment explanation
Indices: 25932458--25932486 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
25932448 TCCCATTTTA
25932458 TCATTTTTTAGCAT
1 TCATTTTTTAGCAT
25932472 TCATTTTTTAGCAT
1 TCATTTTTTAGCAT
25932486 T
1 T
25932487 TTTAACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (14 bp):
TCATTTTTTAGCAT
Found at i:25937829 original size:37 final size:37
Alignment explanation
Indices: 25937743--25937901 Score: 162
Period size: 37 Copynumber: 4.3 Consensus size: 37
25937733 CAGAATTGCG
* ** *
25937743 CCCAAACATCTCGCTACATGAGCACTTCTAGATT-TT
1 CCCAAACATGTCGCCGCATGAGCACTTCTAGATTGTA
*
25937779 CCCAAACATGTCGCCGTATGAGCACTTCTAGATTGTA
1 CCCAAACATGTCGCCGCATGAGCACTTCTAGATTGTA
* **
25937816 CCCAAACATGTCGCCGCATGAGCACCTCTAGATTGCG
1 CCCAAACATGTCGCCGCATGAGCACTTCTAGATTGTA
* * * *
25937853 CTCGAAA-ACTGTTGCCACATGAGCACTTCTAGATTGCA
1 C-CCAAACA-TGTCGCCGCATGAGCACTTCTAGATTGTA
*
25937891 CCAAAAC-TGTC
1 CCCAAACATGTC
25937902 ACTGCATAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
36 33 0.32
37 40 0.39
38 30 0.29
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (37 bp):
CCCAAACATGTCGCCGCATGAGCACTTCTAGATTGTA
Found at i:25938004 original size:26 final size:26
Alignment explanation
Indices: 25937966--25938023 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
25937956 ATTGCACCCA
*
25937966 AGAA-TGTCGCTGCATGAACATGTAC-
1 AGAATTGTCACTGCATGAACATGT-CT
25937991 AGAATTGTCACTGCATGAACATGTCT
1 AGAATTGTCACTGCATGAACATGTCT
25938017 AGAATTG
1 AGAATTG
25938024 CACCCAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (26 bp):
AGAATTGTCACTGCATGAACATGTCT
Found at i:25938034 original size:64 final size:64
Alignment explanation
Indices: 25937955--25938102 Score: 271
Period size: 64 Copynumber: 2.3 Consensus size: 64
25937945 ATAAATATTC
25937955 AATTGCACCCAAGAATGTCGCTGCATGAACATGTACAGAATTGTCACTGCATGAACATGTCTAG
1 AATTGCACCCAAGAATGTCGCTGCATGAACATGTACAGAATTGTCACTGCATGAACATGTCTAG
25938019 AATTGCACCCAAGAATGTCGCTGCATGAACATGTACAGAATTGTCACTGCATGAACATGTCTAG
1 AATTGCACCCAAGAATGTCGCTGCATGAACATGTACAGAATTGTCACTGCATGAACATGTCTAG
*
25938083 AATTGCGCCCAA-AATTGTCG
1 AATTGCACCCAAGAA-TGTCG
25938103 GCGCATCTGA
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
63 2 0.02
64 80 0.98
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (64 bp):
AATTGCACCCAAGAATGTCGCTGCATGAACATGTACAGAATTGTCACTGCATGAACATGTCTAG
Found at i:25938068 original size:26 final size:26
Alignment explanation
Indices: 25938030--25938087 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
25938020 ATTGCACCCA
*
25938030 AGAA-TGTCGCTGCATGAACATGTAC-
1 AGAATTGTCACTGCATGAACATGT-CT
25938055 AGAATTGTCACTGCATGAACATGTCT
1 AGAATTGTCACTGCATGAACATGTCT
25938081 AGAATTG
1 AGAATTG
25938088 CGCCCAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (26 bp):
AGAATTGTCACTGCATGAACATGTCT
Found at i:25938905 original size:16 final size:16
Alignment explanation
Indices: 25938884--25938914 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25938874 TTGTGGATCC
25938884 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
25938900 CATTTTATCTTTATT
1 CATTTTACCTTTATT
25938915 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:25942430 original size:37 final size:37
Alignment explanation
Indices: 25942374--25942547 Score: 136
Period size: 37 Copynumber: 4.7 Consensus size: 37
25942364 GTAAGTTTAA
* *
25942374 TCTAGAATTGCACCCAAACATGTTGA-TACATGAGCACT
1 TCTAG-ATTGCACCCAAACATG-TCACCACATGAGCACT
* * * *
25942412 TTTAGATTGCGCCTAAACATGTCACCGCATGAGCACT
1 TCTAGATTGCACCCAAACATGTCACCACATGAGCACT
* ** * *
25942449 TCTAGATTGCACCCAAACATTTTGCCGCATGAGCACC
1 TCTAGATTGCACCCAAACATGTCACCACATGAGCACT
* ** * * *
25942486 TCTAGACTGGGCCTAAAAACTGTCGCCACATGAGCACT
1 TCTAGATTGCACCCAAACA-TGTCACCACATGAGCACT
* *
25942524 TCTAAATTGCACCAAAAC-TGTCAC
1 TCTAGATTGCACCCAAACATGTCAC
25942548 TGCATAAATA
Statistics
Matches: 105, Mismatches: 29, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
36 7 0.07
37 68 0.65
38 30 0.29
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (37 bp):
TCTAGATTGCACCCAAACATGTCACCACATGAGCACT
Found at i:25942480 original size:74 final size:75
Alignment explanation
Indices: 25942374--25942541 Score: 203
Period size: 74 Copynumber: 2.2 Consensus size: 75
25942364 GTAAGTTTAA
* * * * *
25942374 TCTAGAATTGCACCCAAACATGTTGATACATGAGCACTTTTAGATTGCGCCTAAACA-TGTCACC
1 TCTAG-ATTGCACCCAAACATGTTGACACATGAGCACCTCTAGACTGCGCCTAAAAACTGTCACC
*
25942438 GCATGAGCACT
65 ACATGAGCACT
* * * * *
25942449 TCTAGATTGCACCCAAACATTTTGCCGCATGAGCACCTCTAGACTGGGCCTAAAAACTGTCGCCA
1 TCTAGATTGCACCCAAACATGTTGACACATGAGCACCTCTAGACTGCGCCTAAAAACTGTCACCA
25942514 CATGAGCACT
66 CATGAGCACT
* *
25942524 TCTAAATTGCACCAAAAC
1 TCTAGATTGCACCCAAAC
25942542 TGTCACTGCA
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
74 42 0.53
75 37 0.47
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (75 bp):
TCTAGATTGCACCCAAACATGTTGACACATGAGCACCTCTAGACTGCGCCTAAAAACTGTCACCA
CATGAGCACT
Found at i:25942589 original size:38 final size:38
Alignment explanation
Indices: 25942522--25942598 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
25942512 CACATGAGCA
25942522 CTTCTAAATTGCACCAAAACTGTCACTGCATAAATATT
1 CTTCTAAATTGCACCAAAACTGTCACTGCATAAATATT
* * *
25942560 CTTC-AAATTGCATCCAGAACTGTCGCTGCATAAGTATT
1 CTTCTAAATTGCA-CCAAAACTGTCACTGCATAAATATT
25942598 C
1 C
25942599 AATTGTACCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 8 0.23
38 27 0.77
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (38 bp):
CTTCTAAATTGCACCAAAACTGTCACTGCATAAATATT
Found at i:25964430 original size:18 final size:16
Alignment explanation
Indices: 25964391--25964420 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25964381 AATGCTGAAG
25964391 AAAA-AGGAAGAAGAA
1 AAAAGAGGAAGAAGAA
25964406 AAAAGAGGAAGAAGA
1 AAAAGAGGAAGAAGA
25964421 GAATGAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (16 bp):
AAAAGAGGAAGAAGAA
Found at i:25982426 original size:12 final size:13
Alignment explanation
Indices: 25982409--25982441 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
25982399 GTAAACTGAG
25982409 TTAGTTTTTA-TT
1 TTAGTTTTTAGTT
*
25982421 TTAGTTCTTAGTT
1 TTAGTTTTTAGTT
25982434 TTAGTTTT
1 TTAGTTTT
25982442 CAGGCATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.15, C:0.03, G:0.12, T:0.70
Consensus pattern (13 bp):
TTAGTTTTTAGTT
Found at i:25997189 original size:19 final size:20
Alignment explanation
Indices: 25997165--25997203 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
25997155 CTTTGATTAA
25997165 AATTTTAAGG-CTAAATTGT
1 AATTTTAAGGACTAAATTGT
*
25997184 AATTTTAGGGACTAAATTGT
1 AATTTTAAGGACTAAATTGT
25997204 GTATTAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
AATTTTAAGGACTAAATTGT
Found at i:26000413 original size:26 final size:27
Alignment explanation
Indices: 26000352--26000414 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 27
26000342 CTAGATATGT
*
26000352 TCATGTAGCGATAATTCTGGACAAGTT
1 TCATGTAGCGATAATTCTGGACAAGTC
** * *
26000379 TC-TACAGCGATAATTTTGGACATG-C
1 TCATGTAGCGATAATTCTGGACAAGTC
26000404 TCATGTAGCGA
1 TCATGTAGCGA
26000415 CATTAGTAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
25 2 0.07
26 24 0.86
27 2 0.07
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (27 bp):
TCATGTAGCGATAATTCTGGACAAGTC
Found at i:26000710 original size:51 final size:51
Alignment explanation
Indices: 26000655--26000779 Score: 187
Period size: 51 Copynumber: 2.5 Consensus size: 51
26000645 TAACAGAAAA
* *
26000655 AATGTTTAAGCTCATCAGCTATTCAAAAATCAGAATAGGCATGTCAGATAG
1 AATGTTTAAGCTCATCAGCTATACAAAAATCAGAATAGGCATGTCAGACAG
* * * * *
26000706 AATGTTTAAACTCGTCAGCTATACAGAAATCAGAATAGTCATGTCAGACAT
1 AATGTTTAAGCTCATCAGCTATACAAAAATCAGAATAGGCATGTCAGACAG
26000757 AATGTTTAAGCTCATCAGCTATA
1 AATGTTTAAGCTCATCAGCTATA
26000780 TAGAATCAGA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (51 bp):
AATGTTTAAGCTCATCAGCTATACAAAAATCAGAATAGGCATGTCAGACAG
Found at i:26000802 original size:51 final size:50
Alignment explanation
Indices: 26000648--26000803 Score: 161
Period size: 51 Copynumber: 3.1 Consensus size: 50
26000638 ATGATCGTAA
* **
26000648 CAGAAAAAATGTTTAAGCTCATCAGCTAT-TCAAAAATCAGAATAGGCATGT
1 CAGAAAAAATGTTTAAGCTCATCAGCTATAT--AGAATCAGAATAATCATGT
* * * * * *
26000699 CAGATAGAATGTTTAAACTCGTCAGCTATACAGAAATCAGAATAGTCATGT
1 CAGAAAAAATGTTTAAGCTCATCAGCTATATAG-AATCAGAATAATCATGT
* * *
26000750 CAGACATAATGTTTAAGCTCATCAGCTATATAGAATCAGAATGAATCGTGT
1 CAGAAAAAATGTTTAAGCTCATCAGCTATATAGAATCAGAAT-AATCATGT
26000801 CAG
1 CAG
26000804 GATCTCCTTT
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
50 10 0.11
51 78 0.89
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (50 bp):
CAGAAAAAATGTTTAAGCTCATCAGCTATATAGAATCAGAATAATCATGT
Found at i:26005973 original size:17 final size:17
Alignment explanation
Indices: 26005947--26005997 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
26005937 GACTCGACTC
*
26005947 ATTGATCGACCT-ACCCT
1 ATTGACCGACCTGA-CCT
26005964 ATTGACCGACCTGACCT
1 ATTGACCGACCTGACCT
*
26005981 GTTGACCCGACCTGACC
1 ATTGA-CCGACCTGACC
26005998 AGTTGACCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.24
Consensus pattern (17 bp):
ATTGACCGACCTGACCT
Found at i:26005992 original size:18 final size:18
Alignment explanation
Indices: 26005965--26006005 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
26005955 ACCTACCCTA
*
26005965 TTGA-CCGACCTGACCTG
1 TTGACCCGACCTGACCAG
26005982 TTGACCCGACCTGACCAG
1 TTGACCCGACCTGACCAG
26006000 TTGACC
1 TTGACC
26006006 TAAACTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.20, C:0.37, G:0.22, T:0.22
Consensus pattern (18 bp):
TTGACCCGACCTGACCAG
Found at i:26011336 original size:39 final size:39
Alignment explanation
Indices: 26011282--26011361 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
26011272 TTAGCACTTA
26011282 GTTTAGTTTTCATGCATATCATGTGGTTGTAGTATAATT
1 GTTTAGTTTTCATGCATATCATGTGGTTGTAGTATAATT
26011321 GTTTAGTTTTCATGCATATCATGTGGTTGTAGTATAATT
1 GTTTAGTTTTCATGCATATCATGTGGTTGTAGTATAATT
26011360 GT
1 GT
26011362 CCCTGCATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.23, C:0.07, G:0.21, T:0.49
Consensus pattern (39 bp):
GTTTAGTTTTCATGCATATCATGTGGTTGTAGTATAATT
Found at i:26016462 original size:14 final size:15
Alignment explanation
Indices: 26016443--26016473 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
26016433 CTTTACTTTA
26016443 TTTTATTTTTAT-CT
1 TTTTATTTTTATGCT
26016457 TTTTATTTTTATGCT
1 TTTTATTTTTATGCT
26016472 TT
1 TT
26016474 CAAACAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTATGCT
Found at i:26019755 original size:46 final size:46
Alignment explanation
Indices: 26019658--26019774 Score: 121
Period size: 46 Copynumber: 2.5 Consensus size: 46
26019648 GGTTAGAATT
* * *
26019658 TTTGTATTTTGCCATAATATTGTTTTATTGTCACGACAATTTTGTA
1 TTTGCATTTTGCCATGATATTGTTTTATTGTCACGACAATTTTATA
* *
26019704 GTTGCATTTTGCCATGATATTGTTTCT-TTGTCATGAC-ATTTTCATA
1 TTTGCATTTTGCCATGATATTGTTT-TATTGTCACGACAATTTT-ATA
* * * *
26019750 TTTGCATATTACCATGGTATAGTTT
1 TTTGCATTTTGCCATGATATTGTTT
26019775 GAGAATATGA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
45 5 0.08
46 53 0.90
47 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.50
Consensus pattern (46 bp):
TTTGCATTTTGCCATGATATTGTTTTATTGTCACGACAATTTTATA
Found at i:26035220 original size:3 final size:3
Alignment explanation
Indices: 26035212--26035252 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
26035202 GAGAAGGATC
* * *
26035212 AAG AAG AAG AAG AAG AAG AAG GAG AGG AAG AAG AAA AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
26035253 CCTGCCGAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:26036340 original size:9 final size:9
Alignment explanation
Indices: 26036304--26036340 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
26036294 AACAAAAATG
*
26036304 AGAAAAAGA
1 AGAAAAAAA
*
26036313 AGAAAGAAA
1 AGAAAAAAA
26036322 AGAAAAAAA
1 AGAAAAAAA
26036331 AGAAAAAAA
1 AGAAAAAAA
26036340 A
1 A
26036341 TTGCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:26038710 original size:34 final size:34
Alignment explanation
Indices: 26038649--26038765 Score: 144
Period size: 36 Copynumber: 3.3 Consensus size: 34
26038639 TGCTTACTGT
*
26038649 CTGTTGACCCAAAGGTCATGATGCTCATTTCACTCC
1 CTGTTGACCC-AAGGT-ATGATGCTCATTTTACTCC
* *
26038685 CTGCTGACCCAAGGTATTATGCTCATTTTACTCC
1 CTGTTGACCCAAGGTATGATGCTCATTTTACTCC
* **
26038719 CTATTGATCTAAAGGTTATGATGCTCATTTTACTCC
1 CTGTTGA-CCCAAGG-TATGATGCTCATTTTACTCC
26038755 CTGTTGACCCA
1 CTGTTGACCCA
26038766 TAGCATGGCT
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
34 22 0.32
35 12 0.18
36 34 0.50
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.35
Consensus pattern (34 bp):
CTGTTGACCCAAGGTATGATGCTCATTTTACTCC
Found at i:26046215 original size:23 final size:22
Alignment explanation
Indices: 26046189--26046232 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
26046179 AAAATATTTC
*
26046189 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
26046212 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
26046233 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:26063731 original size:47 final size:47
Alignment explanation
Indices: 26063680--26063796 Score: 155
Period size: 47 Copynumber: 2.5 Consensus size: 47
26063670 CGTTTTTGAT
*
26063680 AATTATGTGGTGGCTTGTCCACGATGTGCTATGTGACC-ATTATCGG
1 AATTATGTGGTGGCTTGTCCACGATGTGCTATGTGACCGATTATCAG
* ** * *
26063726 CAATTATGAGGTGGCTTACCCATGATGTGCTATGTGACCGTTTATCAG
1 -AATTATGTGGTGGCTTGTCCACGATGTGCTATGTGACCGATTATCAG
26063774 AATCTATGTGGTGGCTTGTCCAC
1 AAT-TATGTGGTGGCTTGTCCAC
26063797 AAATGGTGTG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
47 37 0.64
48 21 0.36
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (47 bp):
AATTATGTGGTGGCTTGTCCACGATGTGCTATGTGACCGATTATCAG
Found at i:26064783 original size:15 final size:17
Alignment explanation
Indices: 26064745--26064790 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
26064735 TATTGACTTT
26064745 AAAACTATAGAAATGTG
1 AAAACTATAGAAATGTG
*
26064762 AAAACTATAG-ATTGTG
1 AAAACTATAGAAATGTG
26064778 -AAACTATATGAAA
1 AAAACTATA-GAAA
26064791 CTATAGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 11 0.44
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (17 bp):
AAAACTATAGAAATGTG
Found at i:26070933 original size:27 final size:27
Alignment explanation
Indices: 26070903--26070965 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
26070893 GGTCAAAGGC
* *
26070903 CAAAATGTTTACAAAAGATAGGAATGA
1 CAAAATATTTACAAAAGAAAGGAATGA
* * *
26070930 CAAACTATTTATAAAATAAAGGAATGA
1 CAAAATATTTACAAAAGAAAGGAATGA
*
26070957 CAAACTATT
1 CAAAATATT
26070966 GCCAAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (27 bp):
CAAAATATTTACAAAAGAAAGGAATGA
Found at i:26072002 original size:11 final size:12
Alignment explanation
Indices: 26071978--26072006 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
26071968 AAAACAACAT
26071978 CCAACATAAAAG
1 CCAACATAAAAG
26071990 CCAACAT-AAAG
1 CCAACATAAAAG
26072001 CCAACA
1 CCAACA
26072007 ACAAATAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.55, C:0.31, G:0.07, T:0.07
Consensus pattern (12 bp):
CCAACATAAAAG
Found at i:26072090 original size:20 final size:19
Alignment explanation
Indices: 26072058--26072095 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
26072048 AAATAATATT
26072058 AAAAAACAACATACAAAAA
1 AAAAAACAACATACAAAAA
*
26072077 AAAAGAACATCATACAAAA
1 AAAA-AACAACATACAAAA
26072096 TAATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.74, C:0.16, G:0.03, T:0.08
Consensus pattern (19 bp):
AAAAAACAACATACAAAAA
Found at i:26073883 original size:33 final size:33
Alignment explanation
Indices: 26073846--26073909 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
26073836 ACAAATTACT
26073846 CATCACCATCAGACCAGAAACAAACATTTAATA
1 CATCACCATCAGACCAGAAACAAACATTTAATA
*
26073879 CATCACTATCAGACCAGAAACAAACATTTAA
1 CATCACCATCAGACCAGAAACAAACATTTAA
26073910 CACAACACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.19
Consensus pattern (33 bp):
CATCACCATCAGACCAGAAACAAACATTTAATA
Found at i:26074107 original size:17 final size:17
Alignment explanation
Indices: 26074087--26074123 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
26074077 TATAGAGCAT
*
26074087 ATATATCTGCATAAACA
1 ATATATCTACATAAACA
26074104 ATATATCTACATAAACA
1 ATATATCTACATAAACA
26074121 ATA
1 ATA
26074124 GGCAATTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (17 bp):
ATATATCTACATAAACA
Found at i:26074460 original size:48 final size:47
Alignment explanation
Indices: 26074402--26074493 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 47
26074392 AAACAGTAGC
26074402 AATCAGAATCCAAATCAAAATCGAAAAAAACCCTAAATCAAAAATGAA
1 AATCAGAATCCAAATCAAAATCG-AAAAAACCCTAAATCAAAAATGAA
* * * *
26074450 AATCAGAATCCAAATCAAATTTGAATAAACCCTAACTCAAAAAT
1 AATCAGAATCCAAATCAAAATCGAAAAAACCCTAAATCAAAAAT
26074494 TATAATCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 19 0.47
48 21 0.52
ACGTcount: A:0.57, C:0.20, G:0.05, T:0.18
Consensus pattern (47 bp):
AATCAGAATCCAAATCAAAATCGAAAAAACCCTAAATCAAAAATGAA
Found at i:26074501 original size:47 final size:47
Alignment explanation
Indices: 26074402--26074526 Score: 153
Period size: 47 Copynumber: 2.6 Consensus size: 47
26074392 AAACAGTAGC
* * *
26074402 AATCAGAATCCAAATCAAAATCGAAAAAAACCCTAAATCAAAAATGAA
1 AATCAGAATCCAAATCAAATTTG-AATAAACCCTAAATCAAAAATGAA
* * *
26074450 AATCAGAATCCAAATCAAATTTGAATAAACCCTAACTCAAAAATTAT
1 AATCAGAATCCAAATCAAATTTGAATAAACCCTAAATCAAAAATGAA
* *
26074497 AATCA-ATATCGATATCAAATTTGAATAAAC
1 AATCAGA-ATCCAAATCAAATTTGAATAAAC
26074527 ACAAAATAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
46 1 0.01
47 46 0.68
48 21 0.31
ACGTcount: A:0.54, C:0.18, G:0.06, T:0.22
Consensus pattern (47 bp):
AATCAGAATCCAAATCAAATTTGAATAAACCCTAAATCAAAAATGAA
Found at i:26079388 original size:18 final size:18
Alignment explanation
Indices: 26079365--26079400 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
26079355 CACTACAATG
* *
26079365 TCTTCCTTTTTTTCTTCT
1 TCTTCCTTCTCTTCTTCT
26079383 TCTTCCTTCTCTTCTTCT
1 TCTTCCTTCTCTTCTTCT
26079401 ACATCTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTCCTTCTCTTCTTCT
Found at i:26084075 original size:21 final size:21
Alignment explanation
Indices: 26084051--26084109 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 21
26084041 GGACATTGTC
26084051 TTCAGATGTCACTACATATTA
1 TTCAGATGTCACTACATATTA
** *
26084072 TTCAG--GT-AGGACAT-TGTC
1 TTCAGATGTCACTACATAT-TA
26084090 TTCAGATGTCACTACATATT
1 TTCAGATGTCACTACATATT
26084110 CCTCTGGCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 10
0.65 0.12 0.23
Matches are distributed among these distances:
17 1 0.04
18 11 0.39
19 2 0.07
20 2 0.07
21 11 0.39
22 1 0.04
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (21 bp):
TTCAGATGTCACTACATATTA
Found at i:26084075 original size:39 final size:39
Alignment explanation
Indices: 26084032--26084109 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
26084022 TTATGGTTAC
26084032 ATTCAGGTAGGACATTGTCTTCAGATGTCACTACATATT
1 ATTCAGGTAGGACATTGTCTTCAGATGTCACTACATATT
26084071 ATTCAGGTAGGACATTGTCTTCAGATGTCACTACATATT
1 ATTCAGGTAGGACATTGTCTTCAGATGTCACTACATATT
26084110 CCTCTGGCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (39 bp):
ATTCAGGTAGGACATTGTCTTCAGATGTCACTACATATT
Done.