Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002407.1 Hibiscus syriacus cultivar Beakdansim tig00004925_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 161894
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:17840 original size:30 final size:30
Alignment explanation
Indices: 17804--17861 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
17794 ACTAAATTTT
*
17804 ATCTGTGCTCACTTTTGTTTTGCCAGAGAC
1 ATCTGTGCTCACTTTTGCTTTGCCAGAGAC
17834 ATCTGTGCTCACTTTTGCTTTGCCAGAG
1 ATCTGTGCTCACTTTTGCTTTGCCAGAG
17862 GTATAAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.40
Consensus pattern (30 bp):
ATCTGTGCTCACTTTTGCTTTGCCAGAGAC
Found at i:18782 original size:24 final size:24
Alignment explanation
Indices: 18750--18799 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
18740 AGTACCCTTG
*
18750 GTTCGGCGGCATATCTCCCATGTT
1 GTTCGGCGGCATACCTCCCATGTT
*
18774 GTTCGGCGGCATCCCTCCCATGTT
1 GTTCGGCGGCATACCTCCCATGTT
18798 GT
1 GT
18800 CAGGTGGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.10, C:0.32, G:0.26, T:0.32
Consensus pattern (24 bp):
GTTCGGCGGCATACCTCCCATGTT
Found at i:18808 original size:24 final size:25
Alignment explanation
Indices: 18750--18814 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
18740 AGTACCCTTG
**
18750 GTTCGGCGGCAT-ATCTCCCATGTT
1 GTTCGGCGGCATGCCCTCCCATGTT
18774 GTTCGGCGGCAT-CCCTCCCATGTT
1 GTTCGGCGGCATGCCCTCCCATGTT
*
18798 G-TCAGGTGGCATGCCCT
1 GTTC-GGCGGCATGCCCT
18815 GATTAGGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.06
24 30 0.83
25 4 0.11
ACGTcount: A:0.11, C:0.32, G:0.28, T:0.29
Consensus pattern (25 bp):
GTTCGGCGGCATGCCCTCCCATGTT
Found at i:22028 original size:11 final size:11
Alignment explanation
Indices: 22008--22066 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
21998 GTTAGATGAG
22008 AAATAATAAAT
1 AAATAATAAAT
*
22019 AAATATTAAAT
1 AAATAATAAAT
*
22030 AAATCAA-AGAAA
1 AAAT-AATA-AAT
22042 AAATAAT-AAT
1 AAATAATAAAT
*
22052 AAAATAAAAAAT
1 -AAATAATAAAT
22064 AAA
1 AAA
22067 AGAATATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
10 2 0.05
11 26 0.68
12 10 0.26
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:22046 original size:34 final size:30
Alignment explanation
Indices: 22008--22070 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
21998 GTTAGATGAG
*
22008 AAATAATAAATAAATATTAAATAAATCAAAGAAA
1 AAATAAT-AATAAA-A-TAAA-AAATAAAAGAAA
22042 AAATAATAATAAAATAAAAAATAAAAGAA
1 AAATAATAATAAAATAAAAAATAAAAGAA
22071 TATTAAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 10 0.36
31 4 0.14
32 1 0.04
33 6 0.21
34 7 0.25
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.21
Consensus pattern (30 bp):
AAATAATAATAAAATAAAAAATAAAAGAAA
Found at i:22067 original size:23 final size:23
Alignment explanation
Indices: 22008--22077 Score: 56
Period size: 23 Copynumber: 3.1 Consensus size: 23
21998 GTTAGATGAG
* *
22008 AAATAATAAAT-AAATATTAA-A
1 AAATAAAAAATAAAATAATAATA
*
22029 TAAATCAAAGAA-AAAATAATAATA
1 -AAAT-AAAAAATAAAATAATAATA
* *
22053 AAATAAAAAATAAAAGAATATTA
1 AAATAAAAAATAAAATAATAATA
22076 AA
1 AA
22078 CTTTGGAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
22 9 0.24
23 28 0.74
24 1 0.03
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (23 bp):
AAATAAAAAATAAAATAATAATA
Found at i:24002 original size:84 final size:86
Alignment explanation
Indices: 23822--24005 Score: 270
Period size: 84 Copynumber: 2.2 Consensus size: 86
23812 TCTGAGTTGA
* *
23822 ATGTAATCGAACTCGAAGGTATTTGGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGTTGCAAA
1 ATGTAATCGAACTCGAAGGTATTTGATTGGCAAATAGCCCTTCTCGCCTTGAGCTATGTTGCAAA
23887 TGATGTGCCTTGGAGCTGAGC
66 TGATGTGCCTTGGAGCTGAGC
* * * *
23908 ATAGT--T-GAACTCTAAGGTCTTTTATTGGCAAATAGCCCTTCTCGGCTTGAGCTATGTTGCAA
1 AT-GTAATCGAACTCGAAGGTATTTGATTGGCAAATAGCCCTTCTCGCCTTGAGCTATGTTGCAA
23970 ATGATGTGCCTTGGAGCTG-G-
65 ATGATGTGCCTTGGAGCTGAGC
23990 ATGTAATCGAACTCGA
1 ATGTAATCGAACTCGA
24006 TGGTTTGGTG
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
81 2 0.02
82 2 0.02
83 2 0.02
84 76 0.87
85 1 0.01
86 2 0.02
87 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (86 bp):
ATGTAATCGAACTCGAAGGTATTTGATTGGCAAATAGCCCTTCTCGCCTTGAGCTATGTTGCAAA
TGATGTGCCTTGGAGCTGAGC
Found at i:24092 original size:37 final size:37
Alignment explanation
Indices: 24051--24202 Score: 135
Period size: 37 Copynumber: 4.3 Consensus size: 37
24041 TTTTTTTTTG
* *
24051 TGTTTCAAGAGAAACTATCTCAAGGGAGGCAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
*
24088 TGTTTCAAGAGAAACATAT-TC-------A-AAAATTGG
1 TGTTTCAAGAGAAAC-TATCTCAAGAGAGACAAAATT-T
* * *
24118 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* * *
24155 TGTTTCAAGGGAAACTGTATCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
24191 TGTTTCAAGAGA
1 TGTTTCAAGAGA
24203 GACAACTTTG
Statistics
Matches: 95, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
29 8 0.08
30 17 0.18
36 13 0.14
37 49 0.52
38 8 0.08
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:24200 original size:21 final size:20
Alignment explanation
Indices: 24174--24215 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
24164 GGAAACTGTA
24174 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGAC-AAATTTGTT
*
24195 TCAAGAGAGACAACTTTGTT
1 TCAAGAGAGACAAATTTGTT
24215 T
1 T
24216 TGAGTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (20 bp):
TCAAGAGAGACAAATTTGTT
Found at i:24505 original size:116 final size:116
Alignment explanation
Indices: 24322--24650 Score: 509
Period size: 116 Copynumber: 2.8 Consensus size: 116
24312 TAGGTGGTAC
** * *
24322 GATTCCCTTTGTCGTGAAGTTGAAACCGTGGATGATCCTTTCATCGTGAAGTTGAGCCTTGAATT
1 GATTCCCTTTGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTCGTGAAGTTGAGCCTTGAATT
* *
24387 GGATATCATTCATCGTGAAGTTGAAATCCAATGAATGTTGCTGGTGAGCAT
66 GGATATCCTTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTGAGCAT
24438 GATTCCCTTTGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTCGTGAAGTTGAGCCTTGAATT
1 GATTCCCTTTGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTCGTGAAGTTGAGCCTTGAATT
*
24503 GGATATCCTTGGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTGAGCAT
66 GGATATCCTTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTGAGCAT
* * * *
24554 GATT-CTTTTCGTCGTAAAGTTGAAACCGTGGATGGCTCATTCGTTGTGAAGTTGAGCCTT-AAC
1 GATTCCCTTT-GTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTCGTGAAGTTGAGCCTTGAA-
* *
24617 TTGAATATCCTTCGTCGTAAAGTTGAAATCCAAT
64 TTGGATATCCTTCGTCGTGAAGTTGAAATCCAAT
24651 CTTGCATTGT
Statistics
Matches: 197, Mismatches: 14, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
115 6 0.03
116 191 0.97
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (116 bp):
GATTCCCTTTGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTCGTGAAGTTGAGCCTTGAATT
GGATATCCTTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTGAGCAT
Found at i:25388 original size:32 final size:32
Alignment explanation
Indices: 25352--25425 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
25342 TTCACATCAG
*
25352 GATGTGGAATC-CCCAAATATGCCCCAATATTC
1 GATGTTGAATCTCCCAAA-ATGCCCCAATATTC
* * * *
25384 GATGTTAAATCTCCGAAAATGCCTCAATATTT
1 GATGTTGAATCTCCCAAAATGCCCCAATATTC
25416 GATGTTGAAT
1 GATGTTGAAT
25426 ATTCAAAGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 30 0.86
33 5 0.14
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCTCCCAAAATGCCCCAATATTC
Found at i:25438 original size:32 final size:31
Alignment explanation
Indices: 25364--25439 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
25354 TGTGGAATCC
*
25364 CCAAATATGCCCCAATATTCGATGTTAAATCT
1 CCAAA-ATGCCCCAATATTCGATGTTAAATAT
* * *
25396 CCGAAAATGCCTCAATATTTGATGTTGAATAT
1 CC-AAAATGCCCCAATATTCGATGTTAAATAT
*
25428 TCAAAGATGCCC
1 CCAAA-ATGCCC
25440 TCATTGTTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 3 0.08
32 30 0.83
33 3 0.08
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.30
Consensus pattern (31 bp):
CCAAAATGCCCCAATATTCGATGTTAAATAT
Found at i:31479 original size:12 final size:13
Alignment explanation
Indices: 31462--31491 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
31452 TACGATCGTA
31462 ATGAGAGAAAG-G
1 ATGAGAGAAAGCG
31474 ATGAGAGAAAGCG
1 ATGAGAGAAAGCG
31487 ATGAG
1 ATGAG
31492 GATGGAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.47, C:0.03, G:0.40, T:0.10
Consensus pattern (13 bp):
ATGAGAGAAAGCG
Found at i:34672 original size:3 final size:3
Alignment explanation
Indices: 34666--34731 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
34656 AATAATTATT
*
34666 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TATT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA
**
34710 TAA TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
34732 TTAAGTAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 6 0.12
3 41 0.79
4 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:34977 original size:76 final size:76
Alignment explanation
Indices: 34885--35521 Score: 1204
Period size: 76 Copynumber: 8.4 Consensus size: 76
34875 GAGGTCTTAA
*
34885 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATAAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
34950 AGGCTTTTTGG
66 AGGCTTTTTGG
34961 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
35026 AGGCTTTTTGG
66 AGGCTTTTTGG
*
35037 AAACATCATGCACTGCAGGACTTACAGATGACCCCAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
35102 AGGCTTTTTGG
66 AGGCTTTTTGG
*
35113 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
35178 AGGCTTTTTGG
66 AGGCTTTTTGG
35189 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
35254 AGGATTTTTGG
66 AGGCTTTTTGG
*
35265 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
35330 AGGCTTTTTGG
66 AGGCTTTTTGG
*
35341 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
35405 AGGCTTTTTGG
66 AGGCTTTTTGG
35416 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
35481 AGGCTTTTTGG
66 AGGCTTTTTGG
*
35492 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
35522 TGGGAAATAG
Statistics
Matches: 548, Mismatches: 12, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
75 74 0.14
76 474 0.86
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:36392 original size:22 final size:22
Alignment explanation
Indices: 36367--36421 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
36357 AATAAAGCTT
36367 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
36389 TCATCTTTTAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
36411 TCATCTTTGAA
1 TCATCTTTGAA
36422 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:39269 original size:114 final size:114
Alignment explanation
Indices: 39069--39288 Score: 395
Period size: 114 Copynumber: 1.9 Consensus size: 114
39059 GATCATGCAG
*
39069 TTCATCTTCCTAATCCAATGATTGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTCCAAATCCAATGATTGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
39134 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAGCAAA
* * *
39183 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAATA
1 TTCATCTTCCAAATCCAATGATTGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
39248 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTTTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTA
39289 CGAGAACGTG
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 101 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTCCAAATCCAATGATTGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTATACTATGAGCAAA
Found at i:43587 original size:27 final size:27
Alignment explanation
Indices: 43528--43587 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
43518 AAATGTAATT
*
43528 ATGT-AAAAATGAAAATGTAAATACAA
1 ATGTAAAAAATGAAAATGCAAATACAA
** * *
43554 ACATAAAAAATGCAAATGCAAATGCAA
1 ATGTAAAAAATGAAAATGCAAATACAA
43581 ATGTAAA
1 ATGTAAA
43588 TATATGAATG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (27 bp):
ATGTAAAAAATGAAAATGCAAATACAA
Found at i:43681 original size:7 final size:7
Alignment explanation
Indices: 43647--43688 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
43637 ATAAAAGTAT
43647 AAATGCA
1 AAATGCA
* *
43654 CAATGAA
1 AAATGCA
43661 AAATGCA
1 AAATGCA
43668 AAGATGCA
1 AA-ATGCA
43676 AAATGC-
1 AAATGCA
43682 AAATGCA
1 AAATGCA
43689 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:46123 original size:2 final size:2
Alignment explanation
Indices: 46118--46171 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
46108 AAACACACAC
46118 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
46160 AT AT AT TT AT AT
1 AT AT AT AT AT AT
46172 GACTGATATA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:47552 original size:3 final size:3
Alignment explanation
Indices: 47546--47614 Score: 72
Period size: 3 Copynumber: 23.3 Consensus size: 3
47536 AATAATTATT
*
47546 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TATT TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA
**
47590 TAA TAA TAA TAA TTT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
47615 TTAAGTAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
2 6 0.11
3 44 0.80
4 5 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:47573 original size:22 final size:24
Alignment explanation
Indices: 47537--47602 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 24
47527 TGGGCTTGTA
*
47537 ATAATTATTTAATAATAAT-ATAAT
1 ATAA-TATATAATAATAATAATAAT
47561 AT-ATATA-ATATAATAATAAT-AT
1 ATAATATATA-ATAATAATAATAAT
*
47583 TTAATA-ATAATAATAATAAT
1 ATAATATATAATAATAATAAT
47603 TTTAATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
21 1 0.03
22 26 0.72
23 7 0.19
24 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATAATATATAATAATAATAATAAT
Found at i:47580 original size:25 final size:22
Alignment explanation
Indices: 47535--47614 Score: 102
Period size: 21 Copynumber: 3.9 Consensus size: 22
47525 TTTGGGCTTG
47535 TAATAATTATTTAATAATAAT-A
1 TAATAA-TATTTAATAATAATAA
47557 TAAT-ATA--T-ATAAT-ATAA
1 TAATAATATTTAATAATAATAA
47574 TAATAATATTTAATAATAATAA
1 TAATAATATTTAATAATAATAA
47596 TAATAAT-TTTAATAATAAT
1 TAATAATATTTAATAATAAT
47615 TTAAGTAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.04
17 10 0.19
18 4 0.08
20 3 0.06
21 18 0.35
22 15 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATAATATTTAATAATAATAA
Found at i:47626 original size:11 final size:11
Alignment explanation
Indices: 47535--47618 Score: 76
Period size: 9 Copynumber: 8.3 Consensus size: 11
47525 TTTGGGCTTG
*
47535 TAATAATTATT
1 TAATAATAATT
*
47546 TAATAATAATA
1 TAATAATAATT
*
47557 TAAT-AT-ATA
1 TAATAATAATT
47566 TAAT-ATAA--
1 TAATAATAATT
47574 TAATAAT-ATT
1 TAATAATAATT
47584 TAATAATAA--
1 TAATAATAATT
47593 TAATAATAATTT
1 TAATAATAA-TT
47605 TAATAATAATT
1 TAATAATAATT
47616 TAA
1 TAA
47619 GTAAAATTAA
Statistics
Matches: 63, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
8 5 0.08
9 20 0.32
10 10 0.16
11 19 0.30
12 9 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAATAATAATT
Found at i:48232 original size:39 final size:40
Alignment explanation
Indices: 48188--48289 Score: 102
Period size: 39 Copynumber: 2.6 Consensus size: 40
48178 TATTACGAGG
* * *
48188 TAACATTTTCAGTTCAACCTAAAAAATTATATGAA-TTTA
1 TAACATTTTCAGTTCAACCTAAAAAATGATATGAAGATGA
* * *
48227 TAACATTTTCATTTGCAA--TAAAAAATGCTATGAAGATGG
1 TAACATTTTCAGTT-CAACCTAAAAAATGATATGAAGATGA
* *
48266 TAATATTTTCGGTTCAACCTAAAA
1 TAACATTTTCAGTTCAACCTAAAA
48290 GGTTACGCTC
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
38 17 0.34
39 25 0.50
40 8 0.16
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (40 bp):
TAACATTTTCAGTTCAACCTAAAAAATGATATGAAGATGA
Found at i:48252 original size:74 final size:76
Alignment explanation
Indices: 48147--48289 Score: 175
Period size: 74 Copynumber: 1.9 Consensus size: 76
48137 AAAATATACA
** * *
48147 AATTTATAACATTTTCGATTGCAACCGAAAA-TATTACGA-GGTAACATTTTCAGTTCAACCTAA
1 AATTTATAACATTTTCGATTGCAACAAAAAACTATGAAGATGGTAACATTTTCAGTTCAACCTAA
48210 AAAATTATATG
66 AAAATTATATG
* * *
48221 AATTTATAACATTTTC-ATTTGCAATAAAAAATGCTATGAAGATGGTAATATTTTCGGTTCAACC
1 AATTTATAACATTTTCGA-TTGCAACAAAAAA--CTATGAAGATGGTAACATTTTCAGTTCAACC
48285 TAAAA
63 TAAAA
48290 GGTTACGCTC
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
73 1 0.02
74 26 0.46
77 6 0.11
78 24 0.42
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (76 bp):
AATTTATAACATTTTCGATTGCAACAAAAAACTATGAAGATGGTAACATTTTCAGTTCAACCTAA
AAAATTATATG
Found at i:48313 original size:38 final size:38
Alignment explanation
Indices: 48270--48347 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
48260 AGATGGTAAT
* * *
48270 ATTTTCGGTTCAACCTAAAAGGTTACGCTCTTGATAAC
1 ATTTTCGATTCAACCTAAAAAGTTACGATCTTGATAAC
*
48308 ATTTTCGATTCAACCTAAAAAGTTACGATTTTGATAAC
1 ATTTTCGATTCAACCTAAAAAGTTACGATCTTGATAAC
48346 AT
1 AT
48348 ATTTGTTTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (38 bp):
ATTTTCGATTCAACCTAAAAAGTTACGATCTTGATAAC
Found at i:48970 original size:17 final size:17
Alignment explanation
Indices: 48948--48997 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
48938 TGAAGCAAAC
48948 TTATATTAATACTTATG
1 TTATATTAATACTTATG
* * * *
48965 TTATATTACTAATTTTT
1 TTATATTAATACTTATG
48982 TTATATTAATACTTAT
1 TTATATTAATACTTAT
48998 ATAATAAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (17 bp):
TTATATTAATACTTATG
Found at i:54617 original size:60 final size:60
Alignment explanation
Indices: 54491--54656 Score: 163
Period size: 60 Copynumber: 2.8 Consensus size: 60
54481 TCTCTTATTT
* * * * * *
54491 TAAATTAGTTCTTAAACTTTTAAATATTTTAATTTTATCCCTAAATCATGTCTCTCATTC
1 TAAATTAGTTCTTAAATTTTTGAATATTCTAATTTCATCCCTAAATCATGACCCTCATTC
* * * * *
54551 TGAATTAATTCTTAAATTTTTGAACATTCTAATTTCATCCTTAAA-CTATGACCCTCTTTC
1 TAAATTAGTTCTTAAATTTTTGAATATTCTAATTTCATCCCTAAATC-ATGACCCTCATTC
* ** * * *
54611 TAAATTAGTCCCCAAATTTTTGAATGTTCCAATTTCATCCCCAAAT
1 TAAATTAGTTCTTAAATTTTTGAATATTCTAATTTCATCCCTAAAT
54657 TCATCCAAAT
Statistics
Matches: 83, Mismatches: 21, Indels: 3
0.78 0.20 0.03
Matches are distributed among these distances:
59 1 0.01
60 82 0.99
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (60 bp):
TAAATTAGTTCTTAAATTTTTGAATATTCTAATTTCATCCCTAAATCATGACCCTCATTC
Found at i:54860 original size:22 final size:22
Alignment explanation
Indices: 54833--54874 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54823 TTTCGTGTAT
54833 TTTTTTTAATATTTTGTTTTAA
1 TTTTTTTAATATTTTGTTTTAA
* *
54855 TTTTTTTAATTTTTTTTTTT
1 TTTTTTTAATATTTTGTTTT
54875 GAAAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTTTTAATATTTTGTTTTAA
Found at i:61972 original size:14 final size:14
Alignment explanation
Indices: 61953--61980 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
61943 CTCGCTCTAC
61953 TACCAGTAGACATT
1 TACCAGTAGACATT
61967 TACCAGTAGACATT
1 TACCAGTAGACATT
61981 GAAATGTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
TACCAGTAGACATT
Found at i:63678 original size:31 final size:30
Alignment explanation
Indices: 63592--63682 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 30
63582 TAGAATCAAG
* * * * *
63592 GGTCAATTTGATATTTTATCTAAAATTCAGT
1 GGTCAAATTAATA-TTTATCTAAAGTTTAGA
63623 GGTCAAATTAATACTTTATCTAAAGTTTAGA
1 GGTCAAATTAATA-TTTATCTAAAGTTTAGA
63654 GGTCAAATTAATATTCTATCTAAAGTTTA
1 GGTCAAATTAATATT-TATCTAAAGTTTA
63683 TGGATAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 2 0.04
31 51 0.96
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (30 bp):
GGTCAAATTAATATTTATCTAAAGTTTAGA
Found at i:72682 original size:76 final size:77
Alignment explanation
Indices: 72523--72732 Score: 273
Period size: 76 Copynumber: 2.8 Consensus size: 77
72513 CAAAGCCAAA
* * * * **
72523 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATCGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAATCA
72587 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
72600 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAA-CAT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAATCAT
* *
72664 TTTTGCTCCGAG
66 TTTGGCCCCGAG
* * * *
72676 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
72733 TGTACAACGG
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
75 19 0.16
76 65 0.55
77 34 0.29
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAATCAT
TTTGGCCCCGAG
Found at i:75535 original size:2 final size:2
Alignment explanation
Indices: 75530--75556 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
75520 AAAAATTAAG
75530 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
75557 CTAAAATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:75917 original size:18 final size:19
Alignment explanation
Indices: 75882--75919 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
75872 AAACCAACTC
* *
75882 AATAATTCGAGTTGAATCA
1 AATAATTCGAGATAAATCA
75901 AATAATTCGA-ATAAATCA
1 AATAATTCGAGATAAATCA
75919 A
1 A
75920 CTCGAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (19 bp):
AATAATTCGAGATAAATCA
Found at i:76306 original size:41 final size:41
Alignment explanation
Indices: 76227--76319 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 41
76217 AATATTAAGA
* * ** *
76227 TCAATGTATATATCATAAGTTTAGCAGGCGTAAGATTTATT
1 TCAATATATATATCATAAGTTGAGCAGGAATAAAATTTATT
* **
76268 TCAATTTATATATCATAAGTTGAGTGGGAATAAAATTTATT
1 TCAATATATATATCATAAGTTGAGCAGGAATAAAATTTATT
76309 TCAATATATAT
1 TCAATATATAT
76320 TATAAATTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (41 bp):
TCAATATATATATCATAAGTTGAGCAGGAATAAAATTTATT
Found at i:79132 original size:23 final size:23
Alignment explanation
Indices: 79102--79148 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
79092 AATATTTTTG
* *
79102 TATGACACGTTTTCATCTGTCTT
1 TATGACACATTTACATCTGTCTT
*
79125 TATGACACATTTACTTCTGTCTT
1 TATGACACATTTACATCTGTCTT
79148 T
1 T
79149 TGGTATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (23 bp):
TATGACACATTTACATCTGTCTT
Found at i:81173 original size:21 final size:21
Alignment explanation
Indices: 81143--81202 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
81133 TGCAGGAATA
81143 CTGCTGTGTTAATACTGTATG
1 CTGCTGTGTTAATACTGTATG
* *
81164 CTGTTGTGTTAATATTGTATG
1 CTGCTGTGTTAATACTGTATG
81185 CTGCTGTGTTAATACTGT
1 CTGCTGTGTTAATACTGT
81203 CCGAGTGGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.18, C:0.12, G:0.23, T:0.47
Consensus pattern (21 bp):
CTGCTGTGTTAATACTGTATG
Found at i:82244 original size:30 final size:31
Alignment explanation
Indices: 82204--82279 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
82194 GATTTATAAT
* *
82204 TATATTTTAATTATAATAAA-AATATAAGAA
1 TATATATTAATTATAATAAATAATATAAAAA
* *
82234 TATATATTAATT-TTATAAATTATATAAAAA
1 TATATATTAATTATAATAAATAATATAAAAA
*
82264 TATATAATAATATATA
1 TATATATTAAT-TATA
82280 GGTTTAGAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
29 6 0.16
30 29 0.78
31 1 0.03
32 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (31 bp):
TATATATTAATTATAATAAATAATATAAAAA
Found at i:82403 original size:30 final size:30
Alignment explanation
Indices: 82354--82417 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
82344 ATAATATAAT
82354 AAATGACAAAATATAAAATAAAATAGCACA
1 AAATGACAAAATATAAAATAAAATAGCACA
* *
82384 AAAT-ACAATAATATGAAATATAATAGCACA
1 AAATGACAA-AATATAAAATAAAATAGCACA
82414 AAAT
1 AAAT
82418 TATGGTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.64, C:0.09, G:0.06, T:0.20
Consensus pattern (30 bp):
AAATGACAAAATATAAAATAAAATAGCACA
Found at i:83275 original size:17 final size:18
Alignment explanation
Indices: 83242--83275 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
83232 AAAAATATAT
83242 ATATTATTGATAAATTTA
1 ATATTATTGATAAATTTA
*
83260 ATATTA-TGATATATTT
1 ATATTATTGATAAATTT
83276 TTAACCTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATATTATTGATAAATTTA
Found at i:83701 original size:30 final size:30
Alignment explanation
Indices: 83654--83716 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
83644 CAGTGGACGA
83654 TAATTAATAATTTATCTAAAATTTAAGAGT
1 TAATTAATAATTTATCTAAAATTTAAGAGT
*
83684 TAATTGAT-ATTTCATCTAAAATTTAAGAGT
1 TAATTAATAATTT-ATCTAAAATTTAAGAGT
83714 TAA
1 TAA
83717 ATTAGTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (30 bp):
TAATTAATAATTTATCTAAAATTTAAGAGT
Found at i:83976 original size:32 final size:32
Alignment explanation
Indices: 83933--84013 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
83923 ACGTACTACC
*
83933 TCATTACCTTAAGTGATGT-ATTACATATCA-T
1 TCATTATCTTAAGTGATGTGA-TACATATCACT
* *
83964 ATCATTATCTTAAATGATGTGATACTTATCACT
1 -TCATTATCTTAAGTGATGTGATACATATCACT
* *
83997 TTATCATCTTAAGTGAT
1 TCATTATCTTAAGTGAT
84014 TTAGCATATG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 39 0.95
33 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (32 bp):
TCATTATCTTAAGTGATGTGATACATATCACT
Found at i:87089 original size:26 final size:26
Alignment explanation
Indices: 87054--87114 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
87044 ATATCTACAC
*
87054 TACTATTTATACAATTAGATATAGAT
1 TACTATTTATACAATTAGATATAAAT
** *
87080 TACTATTTATACTGTTAGATGTAAAT
1 TACTATTTATACAATTAGATATAAAT
87106 TACTATTTA
1 TACTATTTA
87115 AAGTATAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (26 bp):
TACTATTTATACAATTAGATATAAAT
Found at i:91851 original size:16 final size:16
Alignment explanation
Indices: 91830--91890 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
91820 TAATAAATAA
*
91830 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
91846 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* * *
91862 ACAAACATAAATGAAT
1 ACGAACATAAACGAAC
91878 ACGAACATAAACG
1 ACGAACATAAACG
91891 TTGGAGACCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.59, C:0.21, G:0.10, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:92989 original size:14 final size:14
Alignment explanation
Indices: 92963--93003 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
92953 GATTGGGTTA
*
92963 AACATAAATGAACG
1 AACATAAACGAACG
* *
92977 AAGATAACCGAACG
1 AACATAAACGAACG
92991 AACATAAACGAAC
1 AACATAAACGAAC
93004 ATAACCGAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.20, G:0.15, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:93024 original size:24 final size:24
Alignment explanation
Indices: 92972--93024 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
92962 AAACATAAAT
* *
92972 GAACGAAGATAACCGAACGAACAT
1 GAACGAACATAACCGAACGAACAC
* **
92996 AAACGAACATAACCGAACGTTCAC
1 GAACGAACATAACCGAACGAACAC
93020 GAACG
1 GAACG
93025 TAAATGAACG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.09
Consensus pattern (24 bp):
GAACGAACATAACCGAACGAACAC
Found at i:97587 original size:19 final size:18
Alignment explanation
Indices: 97547--97582 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
97537 TTGCTTTTAA
97547 TAAAAAATAATACTTTTT
1 TAAAAAATAATACTTTTT
*
97565 TAAAAAATCATA-TTTTT
1 TAAAAAATAATACTTTTT
97582 T
1 T
97583 TTAAATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAAAAATAATACTTTTT
Found at i:97590 original size:31 final size:33
Alignment explanation
Indices: 97555--97617 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 33
97545 AATAAAAAAT
97555 AATACTTTTTTAAAAAATCATAT-T-TTTTTTA
1 AATACTTTTTTAAAAAATCATATATCTTTTTTA
97586 AATACTTTTTTAAAAAATCATATATCTTTTTT
1 AATACTTTTTTAAAAAATCATATATCTTTTTT
97618 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 23 0.77
32 1 0.03
33 6 0.20
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (33 bp):
AATACTTTTTTAAAAAATCATATATCTTTTTTA
Found at i:97782 original size:14 final size:15
Alignment explanation
Indices: 97763--97797 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
97753 TACACATTGA
97763 ATTTAGGG-TTAGAG
1 ATTTAGGGTTTAGAG
97777 ATTTAGGGTTTAGAG
1 ATTTAGGGTTTAGAG
97792 -TTTAGG
1 ATTTAGG
97798 ATAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (15 bp):
ATTTAGGGTTTAGAG
Found at i:98073 original size:30 final size:30
Alignment explanation
Indices: 98039--98112 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
98029 GTTACAGCTC
*
98039 AGACACCTAAAATATAAC-GTCA-AAAATGTT
1 AGACACCTAAAATATAACAG--AGAAAACGTT
*
98069 AGACACCTAAAAATGTAACAGAGAAAACGTT
1 AGACACCT-AAAATATAACAGAGAAAACGTT
98100 AGACACCTAAAAT
1 AGACACCTAAAAT
98113 GAAACGAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 14 0.36
31 24 0.62
32 1 0.03
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (30 bp):
AGACACCTAAAATATAACAGAGAAAACGTT
Found at i:98124 original size:30 final size:30
Alignment explanation
Indices: 98039--98125 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
98029 GTTACAGCTC
* *
98039 AGACACCTAAAAT-ATAACGTCA-AAAATGTT
1 AGACACCTAAAATGA-AACG-AAGAAAACGTT
*
98069 AGACACCTAAAAATGTAAC-AGAGAAAACGTT
1 AGACACCT-AAAATGAAACGA-AGAAAACGTT
98100 AGACACCTAAAATGAAACGAAGAAAA
1 AGACACCTAAAATGAAACGAAGAAAA
98126 TGTTTTGTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
30 24 0.50
31 24 0.50
ACGTcount: A:0.54, C:0.16, G:0.14, T:0.16
Consensus pattern (30 bp):
AGACACCTAAAATGAAACGAAGAAAACGTT
Found at i:103997 original size:20 final size:20
Alignment explanation
Indices: 103923--104331 Score: 522
Period size: 20 Copynumber: 20.4 Consensus size: 20
103913 GATTTTCCAT
* ** *
103923 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
103943 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
103963 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
103983 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104003 AATTGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104023 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104043 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
104063 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
104083 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
104103 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104123 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
104143 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104163 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
104183 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104203 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
104223 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
104243 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
104263 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
104283 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
104303 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
104323 AATCACAAC
1 AATCGCAAC
104332 ACTGAAATTT
Statistics
Matches: 343, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.01
20 335 0.98
21 4 0.01
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:105051 original size:24 final size:24
Alignment explanation
Indices: 105012--105058 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
105002 AAATTTGGTC
**
105012 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATAAACGGACTTTGATA
*
105036 TTGGTCAATAAACGGATTTTGAT
1 TTGGTCAATAAACGGACTTTGAT
105059 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATAAACGGACTTTGATA
Found at i:105250 original size:12 final size:12
Alignment explanation
Indices: 105233--105257 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
105223 ATATAATCCT
105233 GAAGAAGAAAAA
1 GAAGAAGAAAAA
105245 GAAGAAGAAAAA
1 GAAGAAGAAAAA
105257 G
1 G
105258 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:107558 original size:19 final size:19
Alignment explanation
Indices: 107536--107789 Score: 316
Period size: 19 Copynumber: 14.4 Consensus size: 19
107526 CGGAAAATAC
*
107536 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
107555 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
107569 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
107589 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
107603 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
107622 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
107641 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
107655 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
107674 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
107693 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
107711 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
107730 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
107749 AATCGCAA--CGAAAT---
1 AATCGCAATGCGAAATGAA
107763 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
107782 AATCGCAA
1 AATCGCAA
107790 CGAGAGAATC
Statistics
Matches: 207, Mismatches: 6, Indels: 44
0.81 0.02 0.17
Matches are distributed among these distances:
14 40 0.19
15 2 0.01
16 11 0.05
17 10 0.05
18 21 0.10
19 110 0.53
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:107623 original size:33 final size:33
Alignment explanation
Indices: 107536--107737 Score: 173
Period size: 33 Copynumber: 5.8 Consensus size: 33
107526 CGGAAAATAC
* *
107536 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
107569 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
107603 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
107641 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
107674 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAGA--A
107711 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
107738 TGCGAAATGA
Statistics
Matches: 148, Mismatches: 7, Indels: 24
0.83 0.04 0.13
Matches are distributed among these distances:
33 55 0.37
34 30 0.20
35 6 0.04
36 3 0.02
37 30 0.20
38 24 0.16
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:107651 original size:52 final size:52
Alignment explanation
Indices: 107564--107789 Score: 380
Period size: 52 Copynumber: 4.2 Consensus size: 52
107554 AAATCCCAAC
*
107564 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
107617 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
107669 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G-AATCGCAATGCGAA
*
107725 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
107777 ATGAAAATCGCAA
1 ATGAAAATCGCAA
107790 CGAGAGAATC
Statistics
Matches: 167, Mismatches: 2, Indels: 9
0.94 0.01 0.05
Matches are distributed among these distances:
52 95 0.57
53 16 0.10
54 9 0.05
55 1 0.01
56 46 0.28
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:107772 original size:33 final size:33
Alignment explanation
Indices: 107622--107811 Score: 247
Period size: 33 Copynumber: 5.5 Consensus size: 33
107612 GCGAAATGAA
* *
107622 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAT
107655 AATCGCAATGCGAAATGAAAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAAT
107690 GAAAATCGCAATGCGAAATG-AAATCGCAATGCGAAAT
1 ---AATCGCAATGCGAAATGAAAATCGCAA--CGAAAT
107727 GAAAATCGCAATGCGAAATGAAAATCGCAACGAAAT
1 ---AATCGCAATGCGAAATGAAAATCGCAACGAAAT
* *
107763 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAT
107796 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
107812 TATAAACGCA
Statistics
Matches: 147, Mismatches: 4, Indels: 12
0.90 0.02 0.07
Matches are distributed among these distances:
33 74 0.50
35 4 0.03
36 6 0.04
37 37 0.25
38 26 0.18
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAT
Found at i:107907 original size:19 final size:19
Alignment explanation
Indices: 107818--107899 Score: 120
Period size: 19 Copynumber: 4.6 Consensus size: 19
107808 AAATTATAAA
107818 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
*
107837 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
107853 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
107870 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
107889 CGCATTGCGAT
1 CGCATTGCGAT
107900 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 36 0.64
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:108025 original size:14 final size:14
Alignment explanation
Indices: 108006--108042 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
107996 CATCAATTAC
108006 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
108020 ACAAATCATCTTTT
1 ACAAATCAACTTTT
108034 ACAAATCAA
1 ACAAATCAA
108043 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:108658 original size:19 final size:19
Alignment explanation
Indices: 108631--108765 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
108621 TTTAGCCAAA
*
108631 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
108650 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
**
108666 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
108683 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
108699 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
108716 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
108735 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
108755 TCGTGTTGCGA
1 TCGCGTTGCGA
108766 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 16 0.17
16 10 0.11
17 10 0.11
19 47 0.49
20 12 0.13
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:108672 original size:14 final size:14
Alignment explanation
Indices: 108653--108709 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
108643 TTTCATTTCG
108653 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
108667 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
108684 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
108700 CGTTGCGATT
1 CGTTGCGATT
108710 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:108678 original size:33 final size:33
Alignment explanation
Indices: 108636--108728 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
108626 CCAAATCGCA
*
108636 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
**
108669 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
108702 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
108729 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:108968 original size:93 final size:93
Alignment explanation
Indices: 108809--109467 Score: 1293
Period size: 93 Copynumber: 7.1 Consensus size: 93
108799 TTGAATGGAT
108809 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
108874 AGTTTAGCAGAATTGGCAACAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
108902 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
108967 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
108995 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
109060 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
109088 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
109152 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
109180 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
109245 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
109273 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
109338 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
109366 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
109431 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
109459 AAATTTACT
1 AAATTTACT
109468 AAGCAATCTA
Statistics
Matches: 563, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 92 0.16
93 471 0.84
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:111187 original size:14 final size:14
Alignment explanation
Indices: 111168--111257 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
111158 TTGAAATGAA
111168 AATCGCAACGAGAG
1 AATCGCAACGAGAG
111182 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
111199 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
111215 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
111234 AATCGCAACGAGAG
1 AATCGCAACGAGAG
111248 AATCGCAACG
1 AATCGCAACG
111258 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:111205 original size:33 final size:33
Alignment explanation
Indices: 111160--111274 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
111150 TCTTTTGGTT
111160 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
111193 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
111226 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
111259 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
111275 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:111206 original size:19 final size:18
Alignment explanation
Indices: 111167--111279 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
111157 GTTGAAATGA
111167 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
111182 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
111199 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
111215 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
111232 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
111248 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
111265 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
111280 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:111310 original size:14 final size:14
Alignment explanation
Indices: 111291--111345 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
111281 TTTGGTTTCG
111291 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
111305 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
111324 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
111338 CGTTGCGA
1 CGTTGCGA
111346 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:111323 original size:33 final size:33
Alignment explanation
Indices: 111275--111345 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
111265 AAAATCGCAA
**
111275 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
111308 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
111341 TGCGA
1 TGCGA
111346 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:111353 original size:33 final size:33
Alignment explanation
Indices: 111286--111367 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
111276 GCGATTTTGG
***
111286 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
111319 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
111352 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
111368 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:111372 original size:20 final size:20
Alignment explanation
Indices: 111298--111386 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
111288 TCGCGTTGCG
111298 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
111318 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
111331 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
111351 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
111371 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
111387 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:111508 original size:33 final size:33
Alignment explanation
Indices: 111466--111536 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
111456 AATACTAACT
*
111466 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
111499 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
111532 TGAAA
1 TGAAA
111537 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:111770 original size:22 final size:22
Alignment explanation
Indices: 111718--111772 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
111708 TGGTTGTGAG
**
111718 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
111740 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
111762 GGATTTCTTCG
1 GGATTTCTTCG
111773 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:111943 original size:20 final size:20
Alignment explanation
Indices: 111918--112091 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
111908 CTTTAAATAT
111918 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
111938 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
111960 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
111979 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
111999 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
112019 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
112039 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
112059 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
112079 CGCGTTGCGATTT
1 CGCGTTGCGATTT
112092 TTCATATTCG
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 113 0.86
21 15 0.11
22 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:112083 original size:60 final size:60
Alignment explanation
Indices: 111920--112091 Score: 245
Period size: 60 Copynumber: 2.9 Consensus size: 60
111910 TTAAATATCG
** *
111920 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
111981 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
112041 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
112092 TTCATATTCG
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:112103 original size:21 final size:20
Alignment explanation
Indices: 111917--112111 Score: 75
Period size: 20 Copynumber: 9.7 Consensus size: 20
111907 GCTTTAAATA
***
111917 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* *
111937 ACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGA-TTTATATAT
** ***
111958 TATCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
111978 ACGCGTTGCGATATACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
111998 ACGCATTGCGATTTACCCAT
1 TCGCGTTGCGATTTATATAT
* ***
112018 ACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
112038 ACACGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * *
112058 ACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTATATAT
*
112078 TCGCGTTGCGATTTTTCATAT
1 TCGCGTTGCGATTTAT-ATAT
112099 TCGCGTTGCGATT
1 TCGCGTTGCGATT
112112 ATGGAAAATC
Statistics
Matches: 145, Mismatches: 28, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
20 115 0.79
21 30 0.21
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGATTTATATAT
Found at i:112192 original size:20 final size:20
Alignment explanation
Indices: 112167--112218 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
112157 AAGAATCGCG
*
112167 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
112187 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
112207 TTGCGATTCTGG
1 TTGCGATTCTGG
112219 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:125054 original size:36 final size:36
Alignment explanation
Indices: 125007--125077 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
124997 TTATCGACAT
*
125007 CTGATGCAGTAAGGTAACTTACCTCTTTCATCATAC
1 CTGATGCAGTAAGGTAACTTACCACTTTCATCATAC
*
125043 CTGATGCAGTAAGGTAACTTATCACTTTCATCATA
1 CTGATGCAGTAAGGTAACTTACCACTTTCATCATA
125078 GCAGAACGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (36 bp):
CTGATGCAGTAAGGTAACTTACCACTTTCATCATAC
Found at i:134609 original size:24 final size:23
Alignment explanation
Indices: 134542--134614 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 23
134532 AATTGTATAC
* *
134542 ATTTATAAAAATTAAATTAATTTAT
1 ATTTATAATATTTAAATT-ATTT-T
**
134567 ATTTATAATATGAAGAATTATTTT
1 ATTTATAATATTTA-AATTATTTT
134591 ATTTATAATATTTTAAATT-TTTT
1 ATTTATAATA-TTTAAATTATTTT
134614 A
1 A
134615 AACAGTTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
23 5 0.12
24 15 0.38
25 16 0.40
26 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (23 bp):
ATTTATAATATTTAAATTATTTT
Found at i:141987 original size:2 final size:2
Alignment explanation
Indices: 141980--142009 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
141970 GTTTAATTTG
141980 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
142010 TTTAGAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:144637 original size:46 final size:44
Alignment explanation
Indices: 144584--144672 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 44
144574 AATAATATAA
144584 AAAATCTTTAATTTCAAAAAT-TGTACCTATTTCAATCATATAAAAC
1 AAAATCTTTAATTTCAAAAATCTGTA---ATTTCAATCATATAAAAC
*
144630 AAAATCTTTAATTTCAAAAATCTTTAATTTCAATCATATAAAA
1 AAAATCTTTAATTTCAAAAATCTGTAATTTCAATCATATAAAA
144673 GATCTTCATT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
44 17 0.41
46 21 0.51
47 3 0.07
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.38
Consensus pattern (44 bp):
AAAATCTTTAATTTCAAAAATCTGTAATTTCAATCATATAAAAC
Found at i:144651 original size:16 final size:16
Alignment explanation
Indices: 144630--144662 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
144620 CATATAAAAC
144630 AAAATCTTTAATTTCA
1 AAAATCTTTAATTTCA
144646 AAAATCTTTAATTTCA
1 AAAATCTTTAATTTCA
144662 A
1 A
144663 TCATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATCTTTAATTTCA
Found at i:145499 original size:15 final size:15
Alignment explanation
Indices: 145479--145516 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
145469 ACTGAAATAT
145479 AAATAAATTATTTTA
1 AAATAAATTATTTTA
145494 AAATAAATTATTTTA
1 AAATAAATTATTTTA
145509 AAATAAAT
1 AAATAAAT
145517 AACATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATAAATTATTTTA
Found at i:155351 original size:59 final size:58
Alignment explanation
Indices: 155224--155351 Score: 134
Period size: 59 Copynumber: 2.2 Consensus size: 58
155214 GAAATGAATG
* * * *
155224 TTTCTTAATGTATTAAAATTGAAACCATTTATGATCATCGGTTTTTCGGTTTTATCTGTTG
1 TTTC-TAATGTATTAAAATTGAAACCATTTATGATCATCGGTTTTT--GTTTGACCGGTTC
* * *
155285 ATT-TAATGTATTAAAATTGAAACCATTTATGATCATTGGTATTTT-TTTGCCCGGTATC
1 TTTCTAATGTATTAAAATTGAAACCATTTATGATCATCGGT-TTTTGTTTGACCGGT-TC
155343 TTTCTAATG
1 TTTCTAATG
155352 CATTTCTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
57 6 0.11
58 3 0.05
59 41 0.73
60 4 0.07
61 2 0.04
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.48
Consensus pattern (58 bp):
TTTCTAATGTATTAAAATTGAAACCATTTATGATCATCGGTTTTTGTTTGACCGGTTC
Done.