Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023206.1 Corchorus olitorius cultivar O-4 contig23239, 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: 107221
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:1656 original size:19 final size:20
Alignment explanation
Indices: 1632--1671 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1622 AATTTTTCGA
1632 AAAATT-TTTGAGATTTTTC
1 AAAATTCTTTGAGATTTTTC
**
1651 AAAATTCTTTTTGATTTTTC
1 AAAATTCTTTGAGATTTTTC
1671 A
1 A
1672 TGTATATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (20 bp):
AAAATTCTTTGAGATTTTTC
Found at i:1661 original size:21 final size:19
Alignment explanation
Indices: 1623--1671 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
1613 TTTGAAGAAA
1623 ATTTTTCGAAAAATTTTTGAG
1 ATTTTTC-AAAAATTTTT-AG
* *
1644 ATTTTTCAAAATTCTTTTTG
1 ATTTTTCAAAAAT-TTTTAG
1664 ATTTTTCA
1 ATTTTTCA
1672 TGTATATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (19 bp):
ATTTTTCAAAAATTTTTAG
Found at i:1967 original size:18 final size:18
Alignment explanation
Indices: 1946--1981 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1936 GTATTTACAA
*
1946 AAAAAAAATTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
*
1964 AAAAAGAAGTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
1982 GATAGAGGAG
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:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAAAAAAGTGTTTTCAT
Found at i:21609 original size:25 final size:25
Alignment explanation
Indices: 21581--21633 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
21571 TTTCAATTTT
21581 TTATTTATCTACACTCACAAATTAA
1 TTATTTATCTACACTCACAAATTAA
*
21606 TTATTTATCTACACTCACAAATTTA
1 TTATTTATCTACACTCACAAATTAA
21631 TTA
1 TTA
21634 ATAAACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (25 bp):
TTATTTATCTACACTCACAAATTAA
Found at i:21873 original size:21 final size:21
Alignment explanation
Indices: 21849--21916 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
21839 TTTTGGATTT
21849 TTTTAATCATTCAAATATTGC
1 TTTTAATCATTCAAATATTGC
* ** **
21870 TTTTGATTGTTCTGGAT-TT--
1 TTTTAATCATTC-AAATATTGC
21889 TTTTAATCATTCAAATATTGC
1 TTTTAATCATTCAAATATTGC
21910 TTTTAAT
1 TTTTAAT
21917 GATTTTTTAA
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
18 2 0.06
19 11 0.33
21 18 0.55
22 2 0.06
ACGTcount: A:0.26, C:0.10, G:0.09, T:0.54
Consensus pattern (21 bp):
TTTTAATCATTCAAATATTGC
Found at i:21875 original size:40 final size:40
Alignment explanation
Indices: 21829--21913 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
21819 GCCACAAATA
*
21829 CTTTTGATTCTTTTGGATTTTTTTAATCATTCAAATATTG
1 CTTTTGATTCTTCTGGATTTTTTTAATCATTCAAATATTG
*
21869 CTTTTGATTGTTCTGGATTTTTTTAATCATTCAAATATTG
1 CTTTTGATTCTTCTGGATTTTTTTAATCATTCAAATATTG
21909 CTTTT
1 CTTTT
21914 AATGATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.58
Consensus pattern (40 bp):
CTTTTGATTCTTCTGGATTTTTTTAATCATTCAAATATTG
Found at i:21937 original size:10 final size:11
Alignment explanation
Indices: 21910--21934 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21900 CAAATATTGC
21910 TTTTAATGATT
1 TTTTAATGATT
21921 TTTTAATGATT
1 TTTTAATGATT
21932 TTT
1 TTT
21935 AATCATTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTAATGATT
Found at i:25205 original size:19 final size:18
Alignment explanation
Indices: 25168--25207 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
25158 CTCTTGAAAT
*
25168 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
25186 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
25205 AAT
1 AAT
25208 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:26253 original size:27 final size:27
Alignment explanation
Indices: 26215--26271 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
26205 GGCCCAAAAT
26215 GAAGAAACAATTTTTTTTTTTGTTTGG
1 GAAGAAACAATTTTTTTTTTTGTTTGG
*
26242 GAAGAAACAATTTTTTTTTTTTTTTGG
1 GAAGAAACAATTTTTTTTTTTGTTTGG
26269 GAA
1 GAA
26272 ACAGTTACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.04, G:0.18, T:0.51
Consensus pattern (27 bp):
GAAGAAACAATTTTTTTTTTTGTTTGG
Found at i:29182 original size:13 final size:13
Alignment explanation
Indices: 29137--29186 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
29127 CCACACCATC
* *
29137 CCGTTGACTCTGC
1 CCGTTGACTTTGA
*
29150 CCGTTGATTTTGA
1 CCGTTGACTTTGA
29163 -CGATTGACTTTGA
1 CCG-TTGACTTTGA
29176 CCGTTGACTTT
1 CCGTTGACTTT
29187 TTGGTTGACC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 27 0.87
14 2 0.06
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.40
Consensus pattern (13 bp):
CCGTTGACTTTGA
Found at i:32357 original size:10 final size:10
Alignment explanation
Indices: 32330--32360 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
32320 GAGATGTTAA
*
32330 TGTAATTAAT
1 TGTAATTGAT
32340 TGTAATTGAT
1 TGTAATTGAT
32350 TGTAATTGAT
1 TGTAATTGAT
32360 T
1 T
32361 TTGGTATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (10 bp):
TGTAATTGAT
Found at i:39552 original size:10 final size:10
Alignment explanation
Indices: 39537--39660 Score: 185
Period size: 10 Copynumber: 12.4 Consensus size: 10
39527 GGCGTGGCAT
*
39537 GCGCCGCCAC
1 GCGCCGTCAC
39547 GCGCCGTCAC
1 GCGCCGTCAC
*
39557 GCGTCGTCAC
1 GCGCCGTCAC
*
39567 GCGCCGCCAC
1 GCGCCGTCAC
39577 GCGCCGTCAC
1 GCGCCGTCAC
*
39587 GCGCCGCCAC
1 GCGCCGTCAC
39597 GCGCCGTCAC
1 GCGCCGTCAC
*
39607 GCGTCGTCAC
1 GCGCCGTCAC
*
39617 GCGTCGTCAC
1 GCGCCGTCAC
*
39627 GCGCCGCCAC
1 GCGCCGTCAC
39637 GCGCCGTCAC
1 GCGCCGTCAC
39647 GCGCCGTCAC
1 GCGCCGTCAC
39657 GCGC
1 GCGC
39661 TCACCTCTTC
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 103 1.00
ACGTcount: A:0.10, C:0.51, G:0.31, T:0.09
Consensus pattern (10 bp):
GCGCCGTCAC
Found at i:40023 original size:2 final size:2
Alignment explanation
Indices: 40016--40040 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40006 TACCATTATG
40016 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
40041 AAATCATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40260 original size:58 final size:58
Alignment explanation
Indices: 40161--40295 Score: 198
Period size: 58 Copynumber: 2.3 Consensus size: 58
40151 TGTGGAAAGC
* * * * * *
40161 AAGAACAACCGAGCATTCCTCGGTCACACGACCTAGTGGGCATCCCCCACTTGTGCAAT
1 AAGAA-AAACGAGCATCCCTCGATCACACGACCTAGAGGGCATCCCCCACTCGTGCAAA
*
40220 AAGAAAATCGAGCATCCCTCGATCACACGACCTAGAGGGCATCCCCCACTCGTGCAAA
1 AAGAAAAACGAGCATCCCTCGATCACACGACCTAGAGGGCATCCCCCACTCGTGCAAA
40278 AAGAAAAACGAGCATCCC
1 AAGAAAAACGAGCATCCC
40296 ACAGTCGTAC
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 64 0.93
59 5 0.07
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (58 bp):
AAGAAAAACGAGCATCCCTCGATCACACGACCTAGAGGGCATCCCCCACTCGTGCAAA
Found at i:41137 original size:55 final size:54
Alignment explanation
Indices: 41046--41535 Score: 296
Period size: 55 Copynumber: 8.9 Consensus size: 54
41036 TACAAAAAAA
* * * *
41046 AAATGGTTGTACTCCCTCCAAGCTCTCGAAGA-GGTAGTACGCCTCAAAGTTCTCG
1 AAATGGTAGTAC-CCCTCCAAGTTCGCGAA-ATGGTAGTACGCCTCAAAGCTCTCG
* * ** * ** *
41101 AAATGGTAGTACTCCCTCCAAGATCCCGAGGTGGTAGTACGCTCTCAAGGGACGC-
1 AAATGGTAGTAC-CCCTCCAAGTTCGCGAAATGGTAGTACGC-CTCAAAGCTCTCG
* * * *
41156 AAAGTGGTAGTACGCCTCAAAGTTCGCGAAATGGTAGTACTCCCTCCAAGCTCTCG
1 AAA-TGGTAGTACCCCTCCAAGTTCGCGAAATGGTAGTAC-GCCTCAAAGCTCTCG
* * * *
41212 AAGTGGTAGTACGCCC-CAAAGTTCGCGAAATGGTAGTACTCCTTCTAAGCTCTCG
1 AAATGGTAGTAC-CCCTCCAAGTTCGCGAAATGGTAGTACGCC-TCAAAGCTCTCG
* * * * *
41267 AAGTGGTAGTACGCCTCAAAGTTCGCGAAATGGTAGTACTCCCTCCAAGCTCTCG
1 AAATGGTAGTACCCCTCCAAGTTCGCGAAATGGTAGTAC-GCCTCAAAGCTCTCG
* * * * *
41322 AAGTGGTAGTA-CGCTCCAAAGTTCACGAAATGGTAGTACGCCCTC---GTTCACG
1 AAATGGTAGTACCCCTCC-AAGTTCGCGAAATGGTAGTACG-CCTCAAAGCTCTCG
* * *
41374 AAATGGTAGTACGCCCTCCAAGCTCGC-AAATTGGTAGTACGCCCTCCAAGCTTTCG
1 AAATGGTAGTAC-CCCTCCAAGTTCGCGAAA-TGGTAGTACG-CCTCAAAGCTCTCG
** * ** ** * *
41430 AGGTGGTAGTACGCTCC-CAAAGAGCGCGAAGCGGTAGTACGCTCCCAAAGCTCGCG
1 AAATGGTAGTAC-C-CCTCCAAGTTCGCGAAATGGTAGTACGC-CTCAAAGCTCTCG
* * * * **
41486 AATTGGTAGAACGCCCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAA
1 AAATGGTAGTA---CCCCTCCAAGTTCGCGAAATGGTAGTACGC-CTCAA
41536 GGATCGTAAA
Statistics
Matches: 348, Mismatches: 63, Indels: 45
0.76 0.14 0.10
Matches are distributed among these distances:
52 18 0.05
53 21 0.06
54 12 0.03
55 192 0.55
56 73 0.21
57 6 0.02
58 25 0.07
59 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.22
Consensus pattern (54 bp):
AAATGGTAGTACCCCTCCAAGTTCGCGAAATGGTAGTACGCCTCAAAGCTCTCG
Found at i:41218 original size:83 final size:83
Alignment explanation
Indices: 41046--41416 Score: 371
Period size: 83 Copynumber: 4.5 Consensus size: 83
41036 TACAAAAAAA
* * * * *
41046 AAATGGTTGTACTCCCTCCAAGCTCTCGAAGAGGTAGTACGCCTCAAAGTTCTCGAAATGGTAGT
1 AAATGGTAGTACGCCCTCCAAGCTCGCAAAGTGGTAGTACGCCTCAAAGTTCTCGAAATGGTAGT
* *
41111 ACTCCCTCCAAGATCCCG
66 ACTCCCTCCAAGTTCACG
** * ** *
41129 AGGTGGTAGTACGCTCT-CAAGGGACGCAAAGTGGTAGTACGCCTCAAAGTTCGCGAAATGGTAG
1 AAATGGTAGTACGCCCTCCAA-GCTCGCAAAGTGGTAGTACGCCTCAAAGTTCTCGAAATGGTAG
* *
41193 TACTCCCTCCAAGCTCTCG
65 TACTCCCTCCAAGTTCACG
* * * * * * *
41212 AAGTGGTAGTACGCCC-CAAAGTTCGCGAAA-TGGTAGTACTCCTTCTAAGCTCTCGAAGTGGTA
1 AAATGGTAGTACGCCCTCCAAGCTCGC-AAAGTGGTAGTACGCC-TCAAAGTTCTCGAAATGGTA
* * *
41275 GTAC-GCCTCAAAGTTCGCG
64 GTACTCCCTCCAAGTTCACG
* * * *
41294 AAATGGTAGTACTCCCTCCAAGCTCTCGAAGTGGTAGTACG-CTCCAAAGTTCACGAAATGGTAG
1 AAATGGTAGTACGCCCTCCAAGCTCGCAAAGTGGTAGTACGCCT-CAAAGTTCTCGAAATGGTAG
*
41358 TACGCCCT-C--GTTCACG
65 TACTCCCTCCAAGTTCACG
*
41374 AAATGGTAGTACGCCCTCCAAGCTCGCAAATTGGTAGTACGCC
1 AAATGGTAGTACGCCCTCCAAGCTCGCAAAGTGGTAGTACGCC
41417 CTCCAAGCTT
Statistics
Matches: 234, Mismatches: 45, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
80 43 0.18
81 2 0.01
82 65 0.28
83 124 0.53
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (83 bp):
AAATGGTAGTACGCCCTCCAAGCTCGCAAAGTGGTAGTACGCCTCAAAGTTCTCGAAATGGTAGT
ACTCCCTCCAAGTTCACG
Found at i:41277 original size:110 final size:107
Alignment explanation
Indices: 41157--41471 Score: 425
Period size: 110 Copynumber: 2.9 Consensus size: 107
41147 AAGGGACGCA
41157 AAGTGGTAGTACGCCTCAAAGTTCGCGAAATGGTAGTACTCCCTCCAAGCTCTCGAAGTGGTAGT
1 AAGTGGTAGTACGCCTCAAAGTTCGCGAAATGGTAGTACTCCCTCCAAGCTCTCGAAGTGGTAGT
* *
41222 ACGCCCCAAAGTTCGCGAAATGGTAGTACTCCTTCTAAGCTCTCG
66 ACGCCCCAAAGTTCGCGAAATGGTAGTACGCC--CT-AGCTCACG
41267 AAGTGGTAGTACGCCTCAAAGTTCGCGAAATGGTAGTACTCCCTCCAAGCTCTCGAAGTGGTAGT
1 AAGTGGTAGTACGCCTCAAAGTTCGCGAAATGGTAGTACTCCCTCCAAGCTCTCGAAGTGGTAGT
* * * *
41332 ACGCTCCAAAGTTCACGAAATGGTAGTACGCCCTCGTTCACG
66 ACGCCCCAAAGTTCGCGAAATGGTAGTACGCCCTAGCTCACG
* * * * * *
41374 AAATGGTAGTACGCCCTCCAAGCTCGC-AAATTGGTAGTACGCCCTCCAAGCTTTCGAGGTGGTA
1 AAGTGGTAGTACG-CCTCAAAGTTCGCGAAA-TGGTAGTACTCCCTCCAAGCTCTCGAAGTGGTA
** **
41438 GTACGCTCCCAAAGAGCGCGAAGCGGTAGTACGC
64 GTACGC-CCCAAAGTTCGCGAAATGGTAGTACGC
41472 TCCCAAAGCT
Statistics
Matches: 184, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
107 20 0.11
108 49 0.27
109 21 0.11
110 94 0.51
ACGTcount: A:0.26, C:0.27, G:0.25, T:0.23
Consensus pattern (107 bp):
AAGTGGTAGTACGCCTCAAAGTTCGCGAAATGGTAGTACTCCCTCCAAGCTCTCGAAGTGGTAGT
ACGCCCCAAAGTTCGCGAAATGGTAGTACGCCCTAGCTCACG
Found at i:41573 original size:86 final size:84
Alignment explanation
Indices: 41378--41563 Score: 248
Period size: 86 Copynumber: 2.2 Consensus size: 84
41368 TTCACGAAAT
* * * *
41378 GGTAGTACGC-CCTCCAAGCTCGCAAATTGGTAGTACGCCCTCCAAGCTTTCGAGGTGGTAGTAC
1 GGTAGTACGCTCC-CAAAGCTCGCGAATTGGTAGAACGCCCTCCAAGCTCTCGAGGTGGTAGTAC
* *
41442 GCTCCCAAAGAGCGCGAAGC
65 GCTCCCAAAGAGCGCAAAGA
41462 GGTAGTACGCTCCCAAAGCTCGCGAATTGGTAGAACGCCCCCTCCAAGCTCTCGAGGTGGTAGTA
1 GGTAGTACGCTCCCAAAGCTCGCGAATTGGTAGAACG--CCCTCCAAGCTCTCGAGGTGGTAGTA
* * * *
41527 CGCTCTCAAGGATCGTAAAGA
64 CGCTCCCAAAGAGCGCAAAGA
41548 GGTAGTACGCTCCCAA
1 GGTAGTACGCTCCCAA
41564 CGACGGCGAA
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
84 31 0.35
85 2 0.02
86 56 0.63
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (84 bp):
GGTAGTACGCTCCCAAAGCTCGCGAATTGGTAGAACGCCCTCCAAGCTCTCGAGGTGGTAGTACG
CTCCCAAAGAGCGCAAAGA
Found at i:41580 original size:86 final size:86
Alignment explanation
Indices: 41415--41585 Score: 218
Period size: 86 Copynumber: 2.0 Consensus size: 86
41405 TGGTAGTACG
* * *
41415 CCCTCCAAGCTTTCGAGGTGGTAGTACGCTCCCAAAGAGCGCGAAGCGGTAGTACGCTCCCAAAG
1 CCCTCCAAGCTCTCGAGGTGGTAGTACGCTCCCAAAGAGCGCAAAGAGGTAGTACGCTCCCAAAG
**
41480 CTCGCGAATTGGTAGAACGCC
66 CTCGCGAAGCGGTAGAACGCC
* * * * *
41501 CCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGATCGTAAAGAGGTAGTACGCTCCCAACG
1 CCCTCCAAGCTCTCGAGGTGGTAGTACGCTCCCAAAGAGCGCAAAGAGGTAGTACGCTCCCAAAG
* *
41566 AC-GGCGAAGCGGTAGTACGC
66 -CTCGCGAAGCGGTAGAACGC
41586 TCCCAAAGAT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
86 71 0.99
87 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.18
Consensus pattern (86 bp):
CCCTCCAAGCTCTCGAGGTGGTAGTACGCTCCCAAAGAGCGCAAAGAGGTAGTACGCTCCCAAAG
CTCGCGAAGCGGTAGAACGCC
Found at i:41661 original size:197 final size:197
Alignment explanation
Indices: 41435--41838 Score: 709
Period size: 197 Copynumber: 2.1 Consensus size: 197
41425 TTTCGAGGTG
* *
41435 GTAGTACGCTCCCAAAGAGCGCGAAGCGGTAGTACGCTCCCAAAGCTCGCGAATTGGTAGAACGC
1 GTAGTACGCTCCCAAAGAGCGCGAAGCGGTAGTACGCTCACAAAGCTCGCGAATTGATAGAACGC
*
41500 CCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGATCGTAAAGAGGTAGTACGCTCCCAAC
66 CCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGATCGCAAAGAGGTAGTACGCTCCCAAC
* * * * *
41565 GACGGCGAAGCGGTAGTACGCTCCCAAAGATCGCGAAGAGGTAGTACGCTCTTGAAGACAAAAAT
131 GACCGCAAAGCAGTAATACGCTCCCAAAGATCGCGAAGAGGTAGTACGCTCTCGAAGACAAAAAT
41630 GC
196 GC
41632 GTAGTACGCTCCCAAAGAGCGCGAAGCGGTAGTACGCTCACAAAGCTCGCGAATTGATAGAACGC
1 GTAGTACGCTCCCAAAGAGCGCGAAGCGGTAGTACGCTCACAAAGCTCGCGAATTGATAGAACGC
* *
41697 CCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGATTGCAAAGAGGTGGTACGCTCCCAAC
66 CCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGATCGCAAAGAGGTAGTACGCTCCCAAC
41762 GACCGCAAAGCAGTAATACGCTCCCAAAGATCGCGAAGAGGTAGTACGCTCTCGAAGACAAAAAT
131 GACCGCAAAGCAGTAATACGCTCCCAAAGATCGCGAAGAGGTAGTACGCTCTCGAAGACAAAAAT
41827 GC
196 GC
*
41829 GTAGAACGCT
1 GTAGTACGCT
41839 TGGAGACCCC
Statistics
Matches: 196, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
197 196 1.00
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (197 bp):
GTAGTACGCTCCCAAAGAGCGCGAAGCGGTAGTACGCTCACAAAGCTCGCGAATTGATAGAACGC
CCCCTCCAAGCTCTCGAGGTGGTAGTACGCTCTCAAGGATCGCAAAGAGGTAGTACGCTCCCAAC
GACCGCAAAGCAGTAATACGCTCCCAAAGATCGCGAAGAGGTAGTACGCTCTCGAAGACAAAAAT
GC
Found at i:41819 original size:28 final size:28
Alignment explanation
Indices: 41072--41819 Score: 296
Period size: 28 Copynumber: 26.9 Consensus size: 28
41062 TCCAAGCTCT
* *
41072 CGAAGAGGTAGTACGC-CTCAAAGTTCT
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
* * * *
41099 CGAA-ATGGTAGTACTCCCTCCAAGATCC
1 CGAAGA-GGTAGTACGCTCTCAAAGATCG
* * *
41127 CGAGGTGGTAGTACGCTCTCAAGGGA-CG
1 CGAAGAGGTAGTACGCTCTCAA-AGATCG
* * *
41155 CAAAGTGGTAGTACGC-CTCAAAGTTCG
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
* * * * *
41182 CGAA-ATGGTAGTACTCCCTCCAAGCTCT
1 CGAAGA-GGTAGTACGCTCTCAAAGATCG
* * *
41210 CGAAGTGGTAGTACGC-CCCAAAGTTCG
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
* * * *
41237 CGAA-ATGGTAGTACTC-CTTCTAAGCTCT
1 CGAAGA-GGTAGTACGCTC-TCAAAGATCG
* *
41265 CGAAGTGGTAGTACGC-CTCAAAGTTCG
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
* * * * *
41292 CGAA-ATGGTAGTACTCCCTCCAAGCTCT
1 CGAAGA-GGTAGTACGCTCTCAAAGATCG
* * *
41320 CGAAGTGGTAGTACGCTC-CAAAGTTCA
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
* * *
41347 CGAA-ATGGTAGTACGCCCTC---GTTCA
1 CGAAGA-GGTAGTACGCTCTCAAAGATCG
* * *
41372 CGAA-ATGGTAGTACGCCCTCCAAGCTCG
1 CGAAGA-GGTAGTACGCTCTCAAAGATCG
* ** * * * **
41400 CAAATTGGTAGTACGCCCTCCAAGCTTT
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
* * * *
41428 CGAGGTGGTAGTACGCTCCCAAAGAGCG
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
* * *
41456 CGAAGCGGTAGTACGCTCCCAAAGCTCG
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
** * * * * *
41484 CGAATTGGTAGAACGCCCCCTCCAAGCTCT
1 CGAAGAGGTAGTACG--CTCTCAAAGATCG
* * *
41514 CGAGGTGGTAGTACGCTCTCAAGGATCG
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
** * *
41542 TAAAGAGGTAGTACGCTCCCAACGA-CGG
1 CGAAGAGGTAGTACGCTCTCAAAGATC-G
* *
41570 CGAAGCGGTAGTACGCTCCCAAAGATCG
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
**
41598 CGAAGAGGTAGTACGCTCTTGAAGA---
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
* * * *
41623 CAAAAATGCGTAGTACGCTCCCAAAGAGCG
1 CGAAGA-G-GTAGTACGCTCTCAAAGATCG
* * *
41653 CGAAGCGGTAGTACGCTCACAAAGCTCG
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
** * * * * * *
41681 CGAATTGATAGAACGCCCCCTCCAAGCTCT
1 CGAAGAGGTAGTACG--CTCTCAAAGATCG
* * * *
41711 CGAGGTGGTAGTACGCTCTCAAGGATTG
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
* * * * *
41739 CAAAGAGGTGGTACGCTCCCAACGACCG
1 CGAAGAGGTAGTACGCTCTCAAAGATCG
* * *
41767 CAAAGCA-GTAATACGCTCCCAAAGATCG
1 CGAAG-AGGTAGTACGCTCTCAAAGATCG
*
41795 CGAAGAGGTAGTACGCTCTCGAAGA
1 CGAAGAGGTAGTACGCTCTCAAAGA
41820 CAAAAATGCG
Statistics
Matches: 543, Mismatches: 145, Indels: 65
0.72 0.19 0.09
Matches are distributed among these distances:
25 29 0.05
26 3 0.01
27 111 0.20
28 351 0.65
29 5 0.01
30 44 0.08
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.20
Consensus pattern (28 bp):
CGAAGAGGTAGTACGCTCTCAAAGATCG
Found at i:42094 original size:24 final size:24
Alignment explanation
Indices: 42067--42144 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
42057 GTAGAATGCT
42067 CACCATCAGAAGTGGGAGCGCACC
1 CACCATCAGAAGTGGGAGCGCACC
* ** *
42091 CACCATCGGAAGCAGGAGCACACC
1 CACCATCAGAAGTGGGAGCGCACC
* * * *
42115 CCCCATCCGAAGTGGCAGCGCGCC
1 CACCATCAGAAGTGGGAGCGCACC
42139 CACCAT
1 CACCAT
42145 TAAACGTGGT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.27, C:0.40, G:0.26, T:0.08
Consensus pattern (24 bp):
CACCATCAGAAGTGGGAGCGCACC
Found at i:44057 original size:21 final size:21
Alignment explanation
Indices: 44032--44095 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
44022 TTAATTACTC
44032 AAAAAGCTATAACGGTTATGA
1 AAAAAGCTATAACGGTTATGA
*
44053 AAAAAG-T-TAA---TTACT-C
1 AAAAAGCTATAACGGTTA-TGA
*
44069 AAAAAGCTATAACGGTTACGA
1 AAAAAGCTATAACGGTTATGA
44090 AAAAAG
1 AAAAAG
44096 TTCTATATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 14
0.66 0.06 0.28
Matches are distributed among these distances:
16 9 0.27
17 2 0.06
18 3 0.09
19 3 0.09
20 1 0.03
21 15 0.45
ACGTcount: A:0.52, C:0.11, G:0.16, T:0.22
Consensus pattern (21 bp):
AAAAAGCTATAACGGTTATGA
Found at i:44072 original size:37 final size:37
Alignment explanation
Indices: 44022--44097 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
44012 TTTTCAATAC
*
44022 TTAATTACTCAAAAAGCTATAACGGTTATGAAAAAAG
1 TTAATTACTCAAAAAGCTATAACGGTTACGAAAAAAG
44059 TTAATTACTCAAAAAGCTATAACGGTTACGAAAAAAG
1 TTAATTACTCAAAAAGCTATAACGGTTACGAAAAAAG
44096 TT
1 TT
44098 CTATATGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (37 bp):
TTAATTACTCAAAAAGCTATAACGGTTACGAAAAAAG
Found at i:44697 original size:70 final size:70
Alignment explanation
Indices: 44584--44728 Score: 254
Period size: 70 Copynumber: 2.1 Consensus size: 70
44574 TAACTTCGAA
* *
44584 ACACAACATATAAGCATTGATTATACAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
1 ACACAACATATAAGCATTGATTACAAAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
44649 GTTCT
66 GTTCT
*
44654 ACACAACATATGAGCATTGATTACAAAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
1 ACACAACATATAAGCATTGATTACAAAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
*
44719 GTTTT
66 GTTCT
44724 ACACA
1 ACACA
44729 CAAGCATGCA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.26
Consensus pattern (70 bp):
ACACAACATATAAGCATTGATTACAAAAATAACACATTCGAAATAAACATTTTCTCCAAAACAAC
GTTCT
Found at i:45136 original size:22 final size:18
Alignment explanation
Indices: 45108--45163 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 18
45098 TTGATAATGA
45108 TATGAAAATTTGATAACATC
1 TATGAAAATTTGATAAC--C
45128 ATTATG-AAATTTCGATAACC
1 --TATGAAAATTT-GATAACC
45148 TATGAAAATTTGATAA
1 TATGAAAATTTGATAA
45164 ACACACTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 9 0.28
19 6 0.19
20 1 0.03
21 6 0.19
22 10 0.31
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (18 bp):
TATGAAAATTTGATAACC
Found at i:47905 original size:2 final size:2
Alignment explanation
Indices: 47898--47928 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
47888 ATTCACATTT
47898 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47929 CAAAAATGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:50356 original size:44 final size:44
Alignment explanation
Indices: 50308--50394 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
50298 CTAAGGTCAA
50308 TTTGAATAATTAAGTAAAATTAGTAAGATTTCAAAATTAAAAAG
1 TTTGAATAATTAAGTAAAATTAGTAAGATTTCAAAATTAAAAAG
*
50352 TTTGAATAATTAAGTAAGATTAGTAAGATTTCAAAATTAAAAA
1 TTTGAATAATTAAGTAAAATTAGTAAGATTTCAAAATTAAAAA
50395 TAGGTTTTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.34
Consensus pattern (44 bp):
TTTGAATAATTAAGTAAAATTAGTAAGATTTCAAAATTAAAAAG
Found at i:51852 original size:20 final size:20
Alignment explanation
Indices: 51809--51846 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51799 TGTATTTGGT
* *
51809 TGTTGTTTCTTGTTTATTCA
1 TGTTATTTCATGTTTATTCA
51829 TGTTATTTCATGTTTATT
1 TGTTATTTCATGTTTATT
51847 TGTGTTTACA
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:0.13, C:0.08, G:0.13, T:0.66
Consensus pattern (20 bp):
TGTTATTTCATGTTTATTCA
Found at i:55556 original size:27 final size:28
Alignment explanation
Indices: 55488--55559 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
55478 ATCAACCAGG
* *
55488 GGGCATTTTGGTCATTTTCAAAATCCAG
1 GGGCATTTTGGTCATTTGCAAAATCCAA
* ** *
55516 GGGCATTTTAGTCATTTGC-ACGTCTAA
1 GGGCATTTTGGTCATTTGCAAAATCCAA
55543 GGGCATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
55560 TAGGTTCACT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.39
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTGCAAAATCCAA
Found at i:58499 original size:41 final size:41
Alignment explanation
Indices: 58442--58520 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
58432 GTTCAATATG
* *
58442 GTCCCTAATTTAGGATTCTATTTAATATATGATACAATCTA
1 GTCCCTAATTTAGGATTCTAGTCAATATATGATACAATCTA
* * *
58483 GTCCCTGATTTAGGATTCTAGTCAATATTTGATTCAAT
1 GTCCCTAATTTAGGATTCTAGTCAATATATGATACAAT
58521 TTGGTCCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (41 bp):
GTCCCTAATTTAGGATTCTAGTCAATATATGATACAATCTA
Found at i:61466 original size:6 final size:6
Alignment explanation
Indices: 61450--61491 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
61440 AATAAATATG
* *
61450 CAAAAA AAAAAA CAAAAA -AAAGAA AAAAAA CAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAA-AA CAAAAA CAAAAA CAAAAA
61492 GTGCAAATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
5 3 0.10
6 25 0.81
7 3 0.10
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:61468 original size:9 final size:9
Alignment explanation
Indices: 61454--61485 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
61444 AATATGCAAA
61454 AAAAAAAAC
1 AAAAAAAAC
*
61463 AAAAAAAAG
1 AAAAAAAAC
61472 AAAAAAAAC
1 AAAAAAAAC
61481 AAAAA
1 AAAAA
61486 CAAAAAGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:61513 original size:19 final size:20
Alignment explanation
Indices: 61489--61530 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
61479 ACAAAAACAA
61489 AAAGTGCAAATGGAAAA-TG
1 AAAGTGCAAATGGAAAATTG
* *
61508 AAAGTGGAAATTGAAAATTG
1 AAAGTGCAAATGGAAAATTG
61528 AAA
1 AAA
61531 AAGTATAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (20 bp):
AAAGTGCAAATGGAAAATTG
Found at i:61783 original size:22 final size:22
Alignment explanation
Indices: 61757--61798 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
61747 GTCATTTTCT
*
61757 AATTCACTTTTGGCATTTAGGA
1 AATTCAATTTTGGCATTTAGGA
61779 AATTCAATTTTGGCATTTAG
1 AATTCAATTTTGGCATTTAG
61799 CATAGCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.43
Consensus pattern (22 bp):
AATTCAATTTTGGCATTTAGGA
Found at i:65427 original size:128 final size:129
Alignment explanation
Indices: 65199--65440 Score: 405
Period size: 128 Copynumber: 1.9 Consensus size: 129
65189 TTTTCAATTC
* * * *
65199 CAAAAACACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCTTTTTTGTTTAGTGTTTCCAAA
1 CAAAAACACCCTTTCGGTCGAACGGTCATTTTCGTCGTTTTGCGTTTTAGTTTAGTGTTTCCAAA
65264 AATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTGGTATTTTCTATTTT
66 AATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTGGTATTTTCTATTTT
* * *
65327 CAAAAATACCCTTTTGGTCGAACGGTCATTTTCGTCGTTTTGCGTTTTAGTTTTGTGTTTCCAAA
1 CAAAAACACCCTTTCGGTCGAACGGTCATTTTCGTCGTTTTGCGTTTTAGTTTAGTGTTTCCAAA
*
65392 AATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTTAGTTT
66 AATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTT
65441 TGTGTTTCCA
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
128 90 0.86
129 15 0.14
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (129 bp):
CAAAAACACCCTTTCGGTCGAACGGTCATTTTCGTCGTTTTGCGTTTTAGTTTAGTGTTTCCAAA
AATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTGGTATTTTCTATTTT
Found at i:65488 original size:61 final size:61
Alignment explanation
Indices: 65196--65473 Score: 378
Period size: 61 Copynumber: 4.5 Consensus size: 61
65186 TTATTTTCAA
* * * *
65196 TTCCAAAAACACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCTTTTTTGTTTAGTGT
1 TTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTTAGTTTTGTGT
* * *
65257 TTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTC-TTTTGCATTTAAGTTTGGTATT
1 TTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTTAGTTTTGT-GT
* * * *
65318 TTCTATTTTCAAAAATACCCTTTTGGTCGAACGGTCATTTTCGTCGTTTTGCGTTTTAGTTTTGT
1 TTC------CAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTTAGTTTTGT
65383 GT
60 GT
65385 TTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTTAGTTTTGTGT
1 TTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTTAGTTTTGTGT
*
65446 TTCCAAAAATGCCCTTTCGGTCGAAGGG
1 TTCCAAAAATACCCTTTCGGTCGAAGGG
65474 CTAATTTCAA
Statistics
Matches: 192, Mismatches: 17, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
60 15 0.08
61 123 0.64
67 38 0.20
68 16 0.08
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (61 bp):
TTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTTAGTTTTGTGT
Found at i:68292 original size:22 final size:20
Alignment explanation
Indices: 68258--68298 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
68248 ATTCCCATCA
68258 GAAAAGAAAAAAGAAAAAGT
1 GAAAAGAAAAAAGAAAAAGT
68278 GAAAAGGATAAAAAGAAAAAG
1 GAAAA-GA-AAAAAGAAAAAG
68299 AAAGAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (20 bp):
GAAAAGAAAAAAGAAAAAGT
Found at i:79311 original size:34 final size:35
Alignment explanation
Indices: 79216--79313 Score: 101
Period size: 35 Copynumber: 2.8 Consensus size: 35
79206 TTCAAACAAG
* * *
79216 TTCAATTGATCCAGGACGGTCTTTCTTCAGTTAGT
1 TTCAATAGATCCAGGGCGGTCTTTCTTCAGTTAGC
* * *
79251 TTCAATCGATCCAGGGCGATCATTCTTCAGTTTA-C
1 TTCAATAGATCCAGGGCGGTCTTTCTTCAG-TTAGC
* *
79286 TTCAA-AGATCCAGTGTGGTCTTTCTTCA
1 TTCAATAGATCCAGGGCGGTCTTTCTTCA
79314 ATTTCCATTA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
34 18 0.35
35 31 0.60
36 3 0.06
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.38
Consensus pattern (35 bp):
TTCAATAGATCCAGGGCGGTCTTTCTTCAGTTAGC
Found at i:79491 original size:56 final size:56
Alignment explanation
Indices: 79281--79490 Score: 348
Period size: 56 Copynumber: 3.8 Consensus size: 56
79271 CATTCTTCAG
* *
79281 TTTACTTCAAAGATCCAGTGTGGTCTTTCTTCAATTTCCATTATTCAATGCATCAA
1 TTTACTTCAACGATCCAGTGTGGTCTTTCTTCAATTTCAATTATTCAATGCATCAA
* *
79337 TTTACTTCAACAATCCAGTGTGGTCTATCTTCAATTTCAATTATTCAATGCATCAA
1 TTTACTTCAACGATCCAGTGTGGTCTTTCTTCAATTTCAATTATTCAATGCATCAA
* * *
79393 TTTACTTCAACGATCCAGTGTGGTCTTTCTTCAATTTCAATTCTTCATTGCTTCAA
1 TTTACTTCAACGATCCAGTGTGGTCTTTCTTCAATTTCAATTATTCAATGCATCAA
*
79449 TTTACTTCAACGATCTAGTGTGGTCTTTCTTCAATTTCAATT
1 TTTACTTCAACGATCCAGTGTGGTCTTTCTTCAATTTCAATT
79491 CCAATTTCTC
Statistics
Matches: 144, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 144 1.00
ACGTcount: A:0.25, C:0.21, G:0.10, T:0.43
Consensus pattern (56 bp):
TTTACTTCAACGATCCAGTGTGGTCTTTCTTCAATTTCAATTATTCAATGCATCAA
Found at i:79517 original size:8 final size:8
Alignment explanation
Indices: 79504--79611 Score: 59
Period size: 8 Copynumber: 13.6 Consensus size: 8
79494 ATTTCTCAAA
79504 TTCAATTC
1 TTCAATTC
79512 TTCAATGT-
1 TTCAAT-TC
79520 TTCAA-T-
1 TTCAATTC
79526 TTCAATAT-
1 TTCAAT-TC
*
79534 TTCAATGC
1 TTCAATTC
79542 TTCAATTC
1 TTCAATTC
*
79550 AATTTCAATAC
1 ---TTCAATTC
*
79561 TTCAATGC
1 TTCAATTC
79569 TTCAA-T-
1 TTCAATTC
79575 TTCAATTAC
1 TTCAATT-C
**
79584 -TCAAAAC
1 TTCAATTC
*
79591 TTCAATTT
1 TTCAATTC
79599 TTCAATTC
1 TTCAATTC
79607 TTCAA
1 TTCAA
79612 AACTTCAAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
6 11 0.14
7 2 0.03
8 57 0.73
9 1 0.01
11 7 0.09
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.44
Consensus pattern (8 bp):
TTCAATTC
Found at i:79524 original size:22 final size:22
Alignment explanation
Indices: 79478--79553 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
79468 GTGGTCTTTC
*
79478 TTCAATTTCAATTC--CAAT-T
1 TTCAAATTCAATTCTTCAATGT
79497 TCTCAAATTCAATTCTTCAATGT
1 T-TCAAATTCAATTCTTCAATGT
* *
79520 TTCAATTTCAATAT-TTCAATGC
1 TTCAAATTCAAT-TCTTCAATGT
79542 TTC-AATTCAATT
1 TTCAAATTCAATT
79554 TCAATACTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
19 1 0.02
20 13 0.27
21 7 0.15
22 24 0.50
23 3 0.06
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.46
Consensus pattern (22 bp):
TTCAAATTCAATTCTTCAATGT
Found at i:79558 original size:27 final size:28
Alignment explanation
Indices: 79504--79605 Score: 116
Period size: 30 Copynumber: 3.5 Consensus size: 28
79494 ATTTCTCAAA
* *
79504 TTCAATTCTTCAATGTTTCAATTTCAATAT
1 TTCAATGCTTCAA--TTTCAATTTCAATAC
79534 TTCAATGCTTCAA-TTCAATTTCAATAC
1 TTCAATGCTTCAATTTCAATTTCAATAC
*
79561 TTCAATGCTTCAATTTCAATTACTCAAAAC
1 TTCAATGCTTCAATTTCAATT--TCAATAC
**
79591 TTCAATTTTTCAATT
1 TTCAATGCTTCAATT
79606 CTTCAAAACT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
27 26 0.41
28 7 0.11
30 31 0.48
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (28 bp):
TTCAATGCTTCAATTTCAATTTCAATAC
Found at i:79575 original size:22 final size:22
Alignment explanation
Indices: 79532--79645 Score: 103
Period size: 22 Copynumber: 5.2 Consensus size: 22
79522 CAATTTCAAT
*
79532 ATTTCAATGCTTC--AA-TTCA
1 ATTTCAATACTTCAAAACTTCA
**
79551 ATTTCAATACTTCAATGCTTCA
1 ATTTCAATACTTCAAAACTTCA
79573 ATTTCAATTAC-TCAAAACTTCA
1 ATTTCAA-TACTTCAAAACTTCA
*
79595 ATTTTTCAATTCTTCAAAACTTCAA
1 A--TTTCAATACTTCAAAACTTC-A
*
79620 ATTTCAA-GCATTCAAAACTTCA
1 ATTTCAATAC-TTCAAAACTTCA
79642 ATTT
1 ATTT
79646 TTCAAATATT
Statistics
Matches: 79, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
19 12 0.15
22 27 0.34
23 22 0.28
24 16 0.20
25 2 0.03
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (22 bp):
ATTTCAATACTTCAAAACTTCA
Found at i:79611 original size:24 final size:23
Alignment explanation
Indices: 79584--79650 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
79574 TTTCAATTAC
*
79584 TCAAAACTTCAATTTTTCAATTCT
1 TCAAAACTTCAATTTTTCAA-GCT
*
79608 TCAAAACTTCAA-ATTTCAAGCAT
1 TCAAAACTTCAATTTTTCAAGC-T
79631 TCAAAACTTCAATTTTTCAA
1 TCAAAACTTCAATTTTTCAA
79651 ATATTTAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 1 0.03
23 19 0.50
24 18 0.47
ACGTcount: A:0.39, C:0.21, G:0.01, T:0.39
Consensus pattern (23 bp):
TCAAAACTTCAATTTTTCAAGCT
Found at i:79641 original size:47 final size:46
Alignment explanation
Indices: 79552--79668 Score: 137
Period size: 47 Copynumber: 2.5 Consensus size: 46
79542 TTCAATTCAA
** **
79552 TTTCAATACTTCAATGCTTCAATTTCAATTACTCAAAACTTCAATT
1 TTTCAATACTTCAAAACTTCAATTTCAAGCACTCAAAACTTCAATT
* *
79598 TTTCAATTCTTCAAAACTTCAAATTTCAAGCATTCAAAACTTCAATT
1 TTTCAATACTTCAAAACTTC-AATTTCAAGCACTCAAAACTTCAATT
* *
79645 TTTCAAATA-TTTAAAGCTTCAATT
1 TTTC-AATACTTCAAAACTTCAATT
79669 CTCCAATGCT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
46 21 0.35
47 36 0.60
48 3 0.05
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.41
Consensus pattern (46 bp):
TTTCAATACTTCAAAACTTCAATTTCAAGCACTCAAAACTTCAATT
Found at i:79664 original size:24 final size:24
Alignment explanation
Indices: 79574--79668 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
79564 AATGCTTCAA
* *
79574 TTTCAATTACTCAAAACTTCAATT
1 TTTCAAATATTCAAAACTTCAATT
* * *
79598 TTTCAATTCTTCAAAACTTCAA-A
1 TTTCAAATATTCAAAACTTCAATT
**
79621 TTTCAAGCATTCAAAACTTCAATT
1 TTTCAAATATTCAAAACTTCAATT
* *
79645 TTTCAAATATTTAAAGCTTCAATT
1 TTTCAAATATTCAAAACTTCAATT
79669 CTCCAATGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 19 0.32
24 40 0.68
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTCAAATATTCAAAACTTCAATT
Found at i:79947 original size:53 final size:55
Alignment explanation
Indices: 79725--79978 Score: 297
Period size: 53 Copynumber: 4.7 Consensus size: 55
79715 AAAACATTCA
* * *
79725 AGTGGCTTAAGTTTATCTTCAAAGTAATCCAGTGCGGCCAATCAAGAAAATTTGC
1 AGTGGTTTAAGTTTATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAATTTGC
* * * *
79780 AGTGGTTTAAGTTTTATCTTCAAAGTGATCCAGTGCGATCAAT--TG--AGTTTAC
1 AGTGGTTTAAG-TTTATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAATTTGC
* * *
79832 AATGGTTTAAGTTTATCTTCAAAGTGGTCCAGTGCGGCCAATCAAGAAAATTTGC
1 AGTGGTTTAAGTTTATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAATTTGC
* * ** * *
79887 TGTGGTTTAAGTTTATCTTC-AAGTGATCCAGTGTGGTCGTTC-AGAAAGTTTCC
1 AGTGGTTTAAGTTTATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAATTTGC
*
79940 AGTGGTTTAAATTTATCTTCAAA-TGATCCAGTGCGGTCA
1 AGTGGTTTAAGTTTATCTTCAAAGTGATCCAGTGCGGTCA
79979 GTCAGGGAAG
Statistics
Matches: 166, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
51 28 0.17
52 15 0.09
53 42 0.25
54 20 0.12
55 33 0.20
56 28 0.17
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (55 bp):
AGTGGTTTAAGTTTATCTTCAAAGTGATCCAGTGCGGTCAATCAAGAAAATTTGC
Found at i:79970 original size:107 final size:107
Alignment explanation
Indices: 79725--79975 Score: 348
Period size: 107 Copynumber: 2.3 Consensus size: 107
79715 AAAACATTCA
* *
79725 AGTGGCTTAAGTTTATCTTCAAAGTAATCCAGTGCGGCCAATCAAGAAAATTTGCAGTGGTTTAA
1 AGTGGTTTAAGTTTATCTTCAAAGTGATCCAGTGCGGCCAATCAAGAAAATTTGCAGTGGTTTAA
79790 GTTTTATCTTCAAAGTGATCCAGTGCGATCAATTGAGTTTAC
66 GTTTTATCTTCAAAGTGATCCAGTGCGATCAATTGAGTTTAC
* * *
79832 AATGGTTTAAGTTTATCTTCAAAGTGGTCCAGTGCGGCCAATCAAGAAAATTTGCTGTGGTTTAA
1 AGTGGTTTAAGTTTATCTTCAAAGTGATCCAGTGCGGCCAATCAAGAAAATTTGCAGTGGTTTAA
* * * *
79897 G-TTTATCTTC-AAGTGATCCAGTGTGGTC-GTTCAGAAAGTTTCC
66 GTTTTATCTTCAAAGTGATCCAGTGCGATCAATT--G--AGTTTAC
*
79940 AGTGGTTTAAATTTATCTTCAAA-TGATCCAGTGCGG
1 AGTGGTTTAAGTTTATCTTCAAAGTGATCCAGTGCGG
79976 TCAGTCAGGG
Statistics
Matches: 128, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
104 2 0.02
105 16 0.12
106 10 0.08
107 73 0.57
108 27 0.21
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (107 bp):
AGTGGTTTAAGTTTATCTTCAAAGTGATCCAGTGCGGCCAATCAAGAAAATTTGCAGTGGTTTAA
GTTTTATCTTCAAAGTGATCCAGTGCGATCAATTGAGTTTAC
Found at i:80294 original size:92 final size:92
Alignment explanation
Indices: 80137--80417 Score: 456
Period size: 92 Copynumber: 3.1 Consensus size: 92
80127 TGTTAGACAA
* * *
80137 TTCAAAGTTTGATTCAGTGAATCAAGTTAA-TGTAGTGCAGTATTAATTCAAAGTTTGATTCGGT
1 TTCAAAGTTTGATTCGGTGAATCAAATTAACTG-GGTGCAGTATTAATTCAAAGTTTGATTCGGT
* *
80201 GAATCAAGTTAATGCGATGCAGTATTTC
65 GAATCAAGTTAATGCGGTGCAATATTTC
80229 TTCAAAGTTTGATTCGGTGAATCAAATTAACTGGGTGCAGTATTAATTCAAAGTTTGATTCGGTG
1 TTCAAAGTTTGATTCGGTGAATCAAATTAACTGGGTGCAGTATTAATTCAAAGTTTGATTCGGTG
80294 AATCAAGTTAATGCGGTGCAATATTTC
66 AATCAAGTTAATGCGGTGCAATATTTC
* * *
80321 TTCAAAGTTTGATTCGGTGAATCAAATTAACTCGGTGCAATATTAATTCAAAGTTTGATTTGGTG
1 TTCAAAGTTTGATTCGGTGAATCAAATTAACTGGGTGCAGTATTAATTCAAAGTTTGATTCGGTG
* *
80386 AATCAAGTTGATGCGGTGCATTATTTC
66 AATCAAGTTAATGCGGTGCAATATTTC
80413 TTCAA
1 TTCAA
80418 GATTGGATTC
Statistics
Matches: 178, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
92 176 0.99
93 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.37
Consensus pattern (92 bp):
TTCAAAGTTTGATTCGGTGAATCAAATTAACTGGGTGCAGTATTAATTCAAAGTTTGATTCGGTG
AATCAAGTTAATGCGGTGCAATATTTC
Found at i:80417 original size:46 final size:46
Alignment explanation
Indices: 80135--80410 Score: 385
Period size: 46 Copynumber: 6.0 Consensus size: 46
80125 CTTGTTAGAC
* **
80135 AATTCAAAGTTTGATTCAGTGAATCAAGTTAATGTAGTGCAGTATT
1 AATTCAAAGTTTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATT
*
80181 AATTCAAAGTTTGATTCGGTGAATCAAGTTAATGCGATGCAGTATT
1 AATTCAAAGTTTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATT
** *
80227 TCTTCAAAGTTTGATTCGGTGAATCAAATTAACTG-GGTGCAGTATT
1 AATTCAAAGTTTGATTCGGTGAATCAAGTTAA-TGCGGTGCAGTATT
*
80273 AATTCAAAGTTTGATTCGGTGAATCAAGTTAATGCGGTGCAATATT
1 AATTCAAAGTTTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATT
** * *
80319 TCTTCAAAGTTTGATTCGGTGAATCAAATTAACT-CGGTGCAATATT
1 AATTCAAAGTTTGATTCGGTGAATCAAGTTAA-TGCGGTGCAGTATT
* * *
80365 AATTCAAAGTTTGATTTGGTGAATCAAGTTGATGCGGTGCATTATT
1 AATTCAAAGTTTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATT
80411 TCTTCAAGAT
Statistics
Matches: 205, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
45 3 0.01
46 199 0.97
47 3 0.01
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (46 bp):
AATTCAAAGTTTGATTCGGTGAATCAAGTTAATGCGGTGCAGTATT
Found at i:81003 original size:22 final size:22
Alignment explanation
Indices: 80977--81018 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
80967 GTCATTTTCT
*
80977 AATTCACTTTTGGCATTTAGGA
1 AATTCAATTTTGGCATTTAGGA
80999 AATTCAATTTTGGCATTTAG
1 AATTCAATTTTGGCATTTAG
81019 CATAGCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.43
Consensus pattern (22 bp):
AATTCAATTTTGGCATTTAGGA
Found at i:86353 original size:145 final size:141
Alignment explanation
Indices: 85985--86372 Score: 560
Period size: 141 Copynumber: 2.7 Consensus size: 141
85975 GCAAACAGGT
* * *
85985 GTTTAAGTTTTAATAAACCTTGCTCAAGGTGGAGTTTGCATTTGTAAGACCTCCGGGCACAATTT
1 GTTTAAATTTCAATAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTT
* * * * *
86050 CAGAAACTTCCAGGTATTAATTCTGATAAATCCTCTGGGTATCATTTCATTTAATCATGTTGTTA
66 CAGAAACCTCCAGGTATTAATTCTGATAAATCCTCCGGGTATCATTTAATTTAATCAAGTTATTA
**
86115 ATCAAATTTGC
131 ATCAAAGCTGC
*
86126 GTTTGAATTTCAATAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTT
1 GTTTAAATTTCAATAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTT
* * *
86191 CAGAAACCTCCGGGTATTAATTCTGATAAATCCTCCGTGTATCATTTAATTTCATCAAGTTATTA
66 CAGAAACCTCCAGGTATTAATTCTGATAAATCCTCCGGGTATCATTTAATTTAATCAAGTTATTA
86256 ATCAAAGCTGC
131 ATCAAAGCTGC
* * * *
86267 GTTTAAATTTCAAAATCAAAGCCTTGCTCAAGGTCGAGTGTGCCTCTGTAAGACCTCCGGGTACA
1 GTTTAAATTTC--AAT-AAA-CCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACA
* *
86332 ATTTCAGAAACCTCTAGGTATTAATTCTGATAAGTCCTCCG
62 ATTTCAGAAACCTCCAGGTATTAATTCTGATAAATCCTCCG
86373 AGCATTCCAT
Statistics
Matches: 221, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
141 137 0.62
143 3 0.01
144 3 0.01
145 78 0.35
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (141 bp):
GTTTAAATTTCAATAAACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACAATTT
CAGAAACCTCCAGGTATTAATTCTGATAAATCCTCCGGGTATCATTTAATTTAATCAAGTTATTA
ATCAAAGCTGC
Found at i:86540 original size:40 final size:40
Alignment explanation
Indices: 86432--86917 Score: 574
Period size: 40 Copynumber: 12.3 Consensus size: 40
86422 TTATTCATGC
* *
86432 TCATTGCTTTATC-AA-TCATTTCAGAATCCTGCTCAGGA
1 TCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
* * *** *
86470 TCATTTCTTTAT-TAGCCAA-TTCAAAATCCTACTCAGGA
1 TCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
* *
86508 TCATTGCTTTGTCAAATTAATTTCAAAATCCTACTCAGGA
1 TCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
*
86548 TCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGA
1 TCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
* * *
86588 TCATTGCTTTATCAAATTAATTTTACAATCCTGCTCAGGA
1 TCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
* *
86628 TCATTGCTTTATCAAATTAACTTT-ACAATCCTGCTCAGGA
1 TCATTGCTTTATCAAATTAA-TTTCAGAATCCTACTCAGGA
* * * *
86668 TCATTGCTTTATCAAATTAATTTTACAATCCTGCTCAAGA
1 TCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
* *
86708 TCATTGCTTTATCAAATTAATTTTAGAATCCTACTCAAGA
1 TCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
*
86748 TAATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
1 TCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
* * *
86788 TCATTGCTTTATCAAGTGAATTTCAGAATCCTATTCAGGA
1 TCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
* * * * *
86828 TCATTTCTTAATC-AGTCAATTTCAGAATCCTATTCAGGA
1 TCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
* * * *
86867 TCA-TCCTTTTATC-AGTCAATTTCAGAATCCTATTCAGGA
1 TCATTGC-TTTATCAAATTAATTTCAGAATCCTACTCAGGA
*
86906 TCCTTGCTTTAT
1 TCATTGCTTTAT
86918 TAGTCAATTT
Statistics
Matches: 406, Mismatches: 34, Indels: 15
0.89 0.07 0.03
Matches are distributed among these distances:
38 41 0.10
39 73 0.18
40 289 0.71
41 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (40 bp):
TCATTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGA
Found at i:86968 original size:118 final size:118
Alignment explanation
Indices: 86432--86986 Score: 315
Period size: 120 Copynumber: 4.7 Consensus size: 118
86422 TTATTCATGC
* ** * ** * * *
86432 TCATTGCTTTATCAA-TC-ATTTCAGAATCCTGCTCAGGATCATTTCTTTATTAGCCAA-TTCAA
1 TCATTGCTTTATCAAGTCAATTTCAAAATCCTATTCAGGACCATGGCTTAATCAGTCAATTTCAA
* * * * * * *
86494 AATCCTACTCAGGATCATTGC-TTTGTCAAATTAATTTCAAAATCCTACTCAGGA
66 CATCCAACTCAGGATCA-TCCTTTTATC-AGTCAATTTCAGAATCCTACTCAGGA
* * * ** * * * * * *
86548 TCATTGCTTTATCAAATTAATTTCAGAATCCTGCTCAGGATCATTGCTTTATCAAATTAATTT-T
1 TCATTGCTTTATCAAGTCAATTTCAAAATCCTATTCAGGACCATGGCTTAATC-AGTCAATTTCA
** * * * * *
86612 ACAATCCTGCTCAGGATCATTGC-TTTATCAAATTAACTTT-ACAATCCTGCTCAGGA
65 AC-ATCCAACTCAGGATCA-TCCTTTTATC-AGTCAA-TTTCAGAATCCTACTCAGGA
* * * * ** * * * * * * *
86668 TCATTGCTTTATCAAATTAATTTTACAATCCTGCTCAAGATCATTGCTTTATCAAATTAATTTTA
1 TCATTGCTTTATCAAGTCAATTTCAAAATCCTATTCAGGACCATGGCTTAATC-AGTCAATTTCA
* * * * * *
86733 GA-ATCCTACTCAAGATAATTGC-TTTATCAAATTAATTTCAGAATCCTACTCAGGA
65 -ACATCCAACTCAGGATCA-TCCTTTTATC-AGTCAATTTCAGAATCCTACTCAGGA
* * * **
86788 TCATTGCTTTATCAAGTGAATTTCAGAATCCTATTCAGGATCATTTCTTAATCAGTCAATTTCAG
1 TCATTGCTTTATCAAGTCAATTTCAAAATCCTATTCAGGACCATGGCTTAATCAGTCAATTTCA-
* * *
86853 A-ATCCTATTCAGGATCATCCTTTTATCAGTCAATTTCAGAATCCTATTCAGGA
65 ACATCCAACTCAGGATCATCCTTTTATCAGTCAATTTCAGAATCCTACTCAGGA
* * **
86906 TCCTTGCTTTAT-TAGTCAATTTCAAAAATCCTATTCAGGACCAGTGGCTT-ATCAGTTGATTTC
1 TCATTGCTTTATCAAGTCAATTTC-AAAATCCTATTCAGGACCA-TGGCTTAATCAGTCAATTTC
86969 AACATCCAACTCAGGATC
64 AACATCCAACTCAGGATC
86987 CTGATTTAGG
Statistics
Matches: 375, Mismatches: 51, Indels: 24
0.83 0.11 0.05
Matches are distributed among these distances:
116 15 0.04
117 11 0.03
118 110 0.29
119 40 0.11
120 195 0.52
121 3 0.01
122 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (118 bp):
TCATTGCTTTATCAAGTCAATTTCAAAATCCTATTCAGGACCATGGCTTAATCAGTCAATTTCAA
CATCCAACTCAGGATCATCCTTTTATCAGTCAATTTCAGAATCCTACTCAGGA
Found at i:86984 original size:79 final size:77
Alignment explanation
Indices: 86435--86988 Score: 209
Period size: 80 Copynumber: 7.0 Consensus size: 77
86425 TTCATGCTCA
* * * ** * * * * *
86435 TTGCTTTATCAATC-ATTTCAGAATCCTGCTCAGGATCATTTCTTTATTAGCCAA-TTCAAAATC
1 TTGCTTAATCAGTCAATTTCAAAATCCTATTCAGGACCA-TCCTTTATCAGTCAATTTCAGAATC
* *
86498 CTACTCAGGATCA
65 CAACTCAGGATCC
** * * * * * * *
86511 TTGCTTTGTCAAATTAATTTCAAAATCCTACTCAGGATCATTGCTTTATCAAATTAATTTCAGAA
1 TTGCTTAATC-AGTCAATTTCAAAATCCTATTCAGGACCA-TCCTTTATC-AGTCAATTTCAGAA
** *
86576 TCCTGCTCAGGATCA
63 TCCAACTCAGGATCC
* * * * * ** * * * * *
86591 TTGCTTTATCAAATTAATTTTACAATCCTGCTCAGGATCATTGCTTTATCAAATTAACTTT-ACA
1 TTGCTTAATC-AGTCAATTTCAAAATCCTATTCAGGACCA-TCCTTTATC-AGTCAA-TTTCAGA
** *
86655 ATCCTGCTCAGGATCA
62 ATCCAACTCAGGATCC
* * * * * ** * * * * * *
86671 TTGCTTTATCAAATTAATTTTACAATCCTGCTCAAGATCATTGCTTTATCAAATTAATTTTAGAA
1 TTGCTTAATC-AGTCAATTTCAAAATCCTATTCAGGACCA-TCCTTTATC-AGTCAATTTCAGAA
* * **
86736 TCCTACTCAAGATAA
63 TCCAACTCAGGATCC
* * * * * * * *
86751 TTGCTTTATCAAATTAATTTCAGAATCCTACTCAGGATCATTGCTTTATCAAGTGAATTTCAGAA
1 TTGCTTAATC-AGTCAATTTCAAAATCCTATTCAGGACCA-TCCTTTATC-AGTCAATTTCAGAA
* * *
86816 TCCTATTCAGGATCA
63 TCCAACTCAGGATCC
* * *
86831 TTTCTTAATCAGTCAATTTCAGAATCCTATTCAGGATCATCCTTTTATCAGTCAATTTCAGAATC
1 TTGCTTAATCAGTCAATTTCAAAATCCTATTCAGGACCATCC-TTTATCAGTCAATTTCAGAATC
* *
86896 CTATTCAGGATCC
65 CAACTCAGGATCC
* * * **
86909 TTGCTTTATTAGTCAATTTCAAAAATCCTATTCAGGACCAGTGGC-TTATCAGTTGATTTCA-AC
1 TTGCTTAATCAGTCAATTTC-AAAATCCTATTCAGGACCA-T-CCTTTATCAGTCAATTTCAGA-
86972 ATCCAACTCAGGATCC
62 ATCCAACTCAGGATCC
86988 T
1 T
86989 GATTTAGGAT
Statistics
Matches: 418, Mismatches: 49, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
76 9 0.02
77 3 0.01
78 77 0.18
79 84 0.20
80 241 0.58
81 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.38
Consensus pattern (77 bp):
TTGCTTAATCAGTCAATTTCAAAATCCTATTCAGGACCATCCTTTATCAGTCAATTTCAGAATCC
AACTCAGGATCC
Found at i:87309 original size:11 final size:9
Alignment explanation
Indices: 87275--87309 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
87265 CACTCATGGG
87275 CATTTTGGT
1 CATTTTGGT
87284 CATTTTGGT
1 CATTTTGGT
87293 CATTTTAGGT
1 CATTTT-GGT
87303 ACATTTT
1 -CATTTT
87310 TAACATTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 3 0.12
11 6 0.25
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.54
Consensus pattern (9 bp):
CATTTTGGT
Found at i:89776 original size:61 final size:61
Alignment explanation
Indices: 89681--89803 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
89671 GAAGCGTCGG
*
89681 GTATCGTTTGGTTTGAAGATTGGGGAATCTCTATGAAGGAAATAAGTCGAGGTTCAAGAGA
1 GTATCGTTGGGTTTGAAGATTGGGGAATCTCTATGAAGGAAATAAGTCGAGGTTCAAGAGA
89742 GTATCGTTGGGTTTGAAGATTGGGGAATCTCTATGAAGGAAATAAGTCGAGGTTCAAGAGA
1 GTATCGTTGGGTTTGAAGATTGGGGAATCTCTATGAAGGAAATAAGTCGAGGTTCAAGAGA
89803 G
1 G
89804 AGAAAAGAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.31, C:0.08, G:0.33, T:0.28
Consensus pattern (61 bp):
GTATCGTTGGGTTTGAAGATTGGGGAATCTCTATGAAGGAAATAAGTCGAGGTTCAAGAGA
Found at i:90314 original size:44 final size:44
Alignment explanation
Indices: 90266--90353 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
90256 AACTAAGGTC
*
90266 AGTTTGAATAATTAAGTAAAATTAGTAAGATTTCAAAGTTAAAA
1 AGTTTGAATAATTAAGTAAAATTAGTAAGATTTCAAAATTAAAA
*
90310 AGTTTGAATAATTAAGTAAGATTAGTAAGATTTCAAAATTAAAA
1 AGTTTGAATAATTAAGTAAAATTAGTAAGATTTCAAAATTAAAA
90354 TTAGGTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (44 bp):
AGTTTGAATAATTAAGTAAAATTAGTAAGATTTCAAAATTAAAA
Found at i:91880 original size:21 final size:21
Alignment explanation
Indices: 91854--91894 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
91844 TTTAAACCCT
91854 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
91875 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
91895 GGGTTTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:97211 original size:65 final size:65
Alignment explanation
Indices: 97107--97236 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 65
97097 GCTTGCTATT
* * ** *
97107 GATTCCAATTTTCTGCAATAGCCCTTGCATGAGTAGGCCAAGGGTACCCCATGCATGGGTTGGAC
1 GATTCAAACTTTCTGCAATAGCCCAGGCATGAGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
* * *
97172 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
1 GATTCAAACTTTCTGCAATAGCCCAGGCATGAGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
97237 CAGTTTTTCC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (65 bp):
GATTCAAACTTTCTGCAATAGCCCAGGCATGAGTAGGCCAAGGGTACCCCATGCATGGGTAGGAC
Found at i:98813 original size:2 final size:2
Alignment explanation
Indices: 98806--98831 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
98796 CATAGTTCTG
98806 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
98832 TACAATCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101216 original size:11 final size:11
Alignment explanation
Indices: 101200--101247 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
101190 GAAGTTCGTG
101200 TTTGAAGACCA
1 TTTGAAGACCA
**
101211 TTTGAAGATAA
1 TTTGAAGACCA
101222 TTTGAAGA-C-
1 TTTGAAGACCA
101231 -TTGAAGACCA
1 TTTGAAGACCA
101241 -TTGAAGA
1 TTTGAAGA
101248 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:104899 original size:2 final size:2
Alignment explanation
Indices: 104892--104923 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
104882 CATAGTTCTG
104892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
104924 TACAACATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.