Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011592.1 Corchorus capsularis cultivar CVL-1 contig11613, 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: 75245
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2911 original size:11 final size:11
Alignment explanation
Indices: 2895--2924 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2885 GAAGTTCGTG
*
2895 TTTGAAGATTA
1 TTTGAAGATAA
2906 TTTGAAGATAA
1 TTTGAAGATAA
2917 TTTGAAGA
1 TTTGAAGA
2925 CTTGAAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:2931 original size:19 final size:18
Alignment explanation
Indices: 2907--2942 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2897 TGAAGATTAT
2907 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
2926 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
2943 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:4301 original size:6 final size:6
Alignment explanation
Indices: 4290--4320 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
4280 ATAATTGCTA
4290 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
4321 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:4638 original size:20 final size:19
Alignment explanation
Indices: 4612--4659 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
4602 TCCTTTTTAA
4612 AAAAAAAAAATTTGCGTCG
1 AAAAAAAAAATTTGCGTCG
*
4631 AGAAAAAAAAATTTGTGTCG
1 A-AAAAAAAAATTTGCGTCG
4651 AAAAAAAAA
1 AAAAAAAAA
4660 TTAGGGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (19 bp):
AAAAAAAAAATTTGCGTCG
Found at i:8664 original size:11 final size:11
Alignment explanation
Indices: 8648--8677 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
8638 GAAGTTCGTG
*
8648 TTTGAAGATTA
1 TTTGAAGATAA
8659 TTTGAAGATAA
1 TTTGAAGATAA
8670 TTTGAAGA
1 TTTGAAGA
8678 CTTGAAGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (11 bp):
TTTGAAGATAA
Found at i:8684 original size:19 final size:18
Alignment explanation
Indices: 8660--8695 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8650 TGAAGATTAT
8660 TTGAAGATAATTTGAAGAC
1 TTGAAGATAA-TTGAAGAC
*
8679 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
8696 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.31
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAC
Found at i:8790 original size:8 final size:8
Alignment explanation
Indices: 8779--8806 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
8769 CTGAAGTTGA
8779 GGATTTTT
1 GGATTTTT
8787 GGATTTTT
1 GGATTTTT
8795 GGATTTTT
1 GGATTTTT
8803 GGAT
1 GGAT
8807 CTATGGCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (8 bp):
GGATTTTT
Found at i:9227 original size:6 final size:6
Alignment explanation
Indices: 9216--9270 Score: 103
Period size: 6 Copynumber: 9.3 Consensus size: 6
9206 ATAATTGCTA
9216 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT TAGATT
9264 TAG-TT TA
1 TAGATT TA
9271 CTTTGCTTAG
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 4 0.08
6 45 0.92
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TAGATT
Found at i:20161 original size:27 final size:27
Alignment explanation
Indices: 20131--20230 Score: 94
Period size: 27 Copynumber: 3.6 Consensus size: 27
20121 TCGAATTAGC
*
20131 ATTTTGGTCTTTTTTGCATTTAGGGGT
1 ATTTTGGTCTTTTTTGCATTCAGGGGT
* * *
20158 ATTTTGGTCATTCTGGCATTCAGGGGT
1 ATTTTGGTCTTTTTTGCATTCAGGGGT
* * *
20185 ATTTTGGTC-ATTTTGACACTCAGGGGGC
1 ATTTTGGTCTTTTTTG-CATTCA-GGGGT
*
20213 ATTTTGGTCATTCTTTGC
1 ATTTTGGTC-TTTTTTGC
20231 GTTTAAGGGT
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
26 3 0.05
27 37 0.64
28 13 0.22
29 1 0.02
30 4 0.07
ACGTcount: A:0.14, C:0.14, G:0.26, T:0.46
Consensus pattern (27 bp):
ATTTTGGTCTTTTTTGCATTCAGGGGT
Found at i:20220 original size:28 final size:27
Alignment explanation
Indices: 20152--20226 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
20142 TTTTGCATTT
* *
20152 AGGGGTATTTTGGTCATTCTGGCATTC
1 AGGGGTATTTTGGTCATTCTGACACTC
*
20179 AGGGGTATTTTGGTCATTTTGACACTC
1 AGGGGTATTTTGGTCATTCTGACACTC
*
20206 AGGGGGCATTTTGGTCATTCT
1 A-GGGGTATTTTGGTCATTCT
20227 TTGCGTTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.16, C:0.15, G:0.29, T:0.40
Consensus pattern (27 bp):
AGGGGTATTTTGGTCATTCTGACACTC
Found at i:20357 original size:23 final size:23
Alignment explanation
Indices: 20331--20374 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
20321 TTTGCATATT
*
20331 TGCATTTAGTAACTTGGTATTAC
1 TGCATTTAGTAACTTAGTATTAC
*
20354 TGCATTTAGTAATTTAGTATT
1 TGCATTTAGTAACTTAGTATT
20375 GTTGCATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.48
Consensus pattern (23 bp):
TGCATTTAGTAACTTAGTATTAC
Found at i:20380 original size:23 final size:23
Alignment explanation
Indices: 20330--20381 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
20320 TTTTGCATAT
*
20330 TTGCATTTAGTAACTTGGTATTA
1 TTGCATTTAGTAACTTAGTATTA
* * *
20353 CTGCATTTAGTAATTTAGTATTG
1 TTGCATTTAGTAACTTAGTATTA
20376 TTGCAT
1 TTGCAT
20382 CTCCATTTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (23 bp):
TTGCATTTAGTAACTTAGTATTA
Found at i:24275 original size:17 final size:17
Alignment explanation
Indices: 24253--24305 Score: 97
Period size: 17 Copynumber: 3.1 Consensus size: 17
24243 AAAGGTCTAC
24253 AATACAAGGGTATCAGT
1 AATACAAGGGTATCAGT
24270 AATACAAGGGTATCAGT
1 AATACAAGGGTATCAGT
*
24287 AATACAAGGTTATCAGT
1 AATACAAGGGTATCAGT
24304 AA
1 AA
24306 ATTAAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (17 bp):
AATACAAGGGTATCAGT
Found at i:24412 original size:20 final size:20
Alignment explanation
Indices: 24389--24502 Score: 96
Period size: 20 Copynumber: 6.0 Consensus size: 20
24379 AATAAACATA
* *
24389 AAGAGTAAAAGATGATTAGT
1 AAGAGTAAAAGATAATCAGT
*
24409 AAGAGTAAAAGGTAATCAGT
1 AAGAGTAAAAGATAATCAGT
* *
24429 AAGAGTAAGAGGTAATCAGT
1 AAGAGTAAAAGATAATCAGT
24449 -A-AG---AAGATAATCAGT
1 AAGAGTAAAAGATAATCAGT
* *
24464 AAGGGCAAAA-AGTAATCAGT
1 AAGAGTAAAAGA-TAATCAGT
* *
24484 AAAAGTAAAAGGTAATCAG
1 AAGAGTAAAAGATAATCAG
24503 CTAGTGGGTA
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
15 10 0.13
16 1 0.01
17 1 0.01
18 2 0.03
19 2 0.03
20 60 0.79
ACGTcount: A:0.51, C:0.05, G:0.25, T:0.19
Consensus pattern (20 bp):
AAGAGTAAAAGATAATCAGT
Found at i:24461 original size:15 final size:14
Alignment explanation
Indices: 24432--24466 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
24422 AATCAGTAAG
*
24432 AGTAAGAGGTAATC
1 AGTAAGAGATAATC
24446 AGTAAGAAGATAATC
1 AGTAAG-AGATAATC
24461 AGTAAG
1 AGTAAG
24467 GGCAAAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.49, C:0.06, G:0.26, T:0.20
Consensus pattern (14 bp):
AGTAAGAGATAATC
Found at i:24464 original size:35 final size:34
Alignment explanation
Indices: 24412--24488 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 34
24402 GATTAGTAAG
* * * *
24412 AGTAAAAGGTAATCAGTAAGAGTAAGAGGTAATC
1 AGTAAAAGATAATCAGTAAGAGCAAAAAGTAATC
*
24446 AGTAAGAAGATAATCAGTAAGGGCAAAAAGTAATC
1 AGTAA-AAGATAATCAGTAAGAGCAAAAAGTAATC
24481 AGTAAAAG
1 AGTAAAAG
24489 TAAAAGGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 8 0.22
35 29 0.78
ACGTcount: A:0.51, C:0.06, G:0.25, T:0.18
Consensus pattern (34 bp):
AGTAAAAGATAATCAGTAAGAGCAAAAAGTAATC
Found at i:24465 original size:55 final size:55
Alignment explanation
Indices: 24392--24683 Score: 180
Period size: 55 Copynumber: 5.4 Consensus size: 55
24382 AAACATAAAG
* * * *
24392 AGTAA-AAGATGATTAGTAAGAGTAAAAGGTAATCAGTAAGAGTAAGAGGTAATC
1 AGTAAGAAGATAATCAGTAAGAGTAAAAGGTAATCAGTAAAAGTAAAAGGTAATC
* * *
24446 AGTAAGAAGATAATCAGTAAGGGCAAAAAGTAATCAGTAAAAGTAAAAGGTAATC
1 AGTAAGAAGATAATCAGTAAGAGTAAAAGGTAATCAGTAAAAGTAAAAGGTAATC
** * * * *
24501 AGCT-AGTGGGTAATCAATAAAAGTAAAAGGTAATCAGCT---AGT---GGGTAATC
1 AG-TAAGAAGATAATCAGTAAGAGTAAAAGGTAATCAG-TAAAAGTAAAAGGTAATC
* * * * * *
24551 AATAAG-AG-TAA-AAGGTAATCAGTAAGAGGGTAATCAGTAAAAGCAAAAGGGTAATT
1 AGTAAGAAGATAATCA-GTAA-GAGTAA-AAGGTAATCAGTAAAAGTAAAA-GGTAATC
* * * *
24607 AGCAA-AA-ATAATCAGTAAGAGTGAAAGGTGATCAGTAAGAGT-AAAGGATAATC
1 AGTAAGAAGATAATCAGTAAGAGTAAAAGGTAATCAGTAAAAGTAAAAGG-TAATC
24660 AGTAAAGTAAAAGATAATCAGTAA
1 AGT-AAG---AAGATAATCAGTAA
24684 AATAGTAATC
Statistics
Matches: 178, Mismatches: 36, Indels: 43
0.69 0.14 0.17
Matches are distributed among these distances:
47 1 0.01
48 6 0.03
49 8 0.04
50 20 0.11
52 4 0.02
53 12 0.07
54 21 0.12
55 73 0.41
56 19 0.11
57 1 0.01
58 2 0.01
59 11 0.06
ACGTcount: A:0.49, C:0.07, G:0.24, T:0.21
Consensus pattern (55 bp):
AGTAAGAAGATAATCAGTAAGAGTAAAAGGTAATCAGTAAAAGTAAAAGGTAATC
Found at i:24514 original size:35 final size:35
Alignment explanation
Indices: 24475--24605 Score: 192
Period size: 35 Copynumber: 3.7 Consensus size: 35
24465 AGGGCAAAAA
*
24475 GTAATCAGTAAAAGTAAAAGGTAATCAGCTAGTGG
1 GTAATCAATAAAAGTAAAAGGTAATCAGCTAGTGG
24510 GTAATCAATAAAAGTAAAAGGTAATCAGCTAGTGG
1 GTAATCAATAAAAGTAAAAGGTAATCAGCTAGTGG
* *
24545 GTAATCAATAAGAGTAAAAGGTAATCAG-TAAGAGG
1 GTAATCAATAAAAGTAAAAGGTAATCAGCT-AGTGG
* *
24580 GTAATCAGTAAAAGCAAAAGGGTAAT
1 GTAATCAATAAAAGTAAAA-GGTAAT
24606 TAGCAAAAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
34 1 0.01
35 81 0.92
36 6 0.07
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.21
Consensus pattern (35 bp):
GTAATCAATAAAAGTAAAAGGTAATCAGCTAGTGG
Found at i:24640 original size:20 final size:19
Alignment explanation
Indices: 24615--24900 Score: 104
Period size: 22 Copynumber: 13.9 Consensus size: 19
24605 TTAGCAAAAA
24615 TAATCAGTAAGAGTGAAAGG
1 TAATCAGTAAGAGT-AAAGG
*
24635 TGATCAGTAAGAGTAAAGG
1 TAATCAGTAAGAGTAAAGG
*
24654 ATAATCAGTAA-AGTAAAAGA
1 -TAATCAGTAAGAGT-AAAGG
*
24674 TAATCAGTAA-A--ATA-G
1 TAATCAGTAAGAGTAAAGG
* * * *
24689 TAATCCGTAAAAAAAATAATA-A
1 TAATCAGT---AAGAGTAA-AGG
*
24711 TAATCAGTAAAAGGTAAAATGG
1 TAATCAGTAAGA-GT-AAA-GG
* *
24733 TAATTAGTAAAGAGCAATATGG
1 TAATCAGT-AAGAGTAA-A-GG
*
24755 TAATCAGTAAAGAGTAATA-A
1 TAATCAGT-AAGAGTAA-AGG
*
24775 TAATCAGTAAGAAGTAATGG
1 TAATCAGTAAG-AGTAAAGG
*
24795 TAATCAGTAAAAAAAGTAAAAAGG
1 TAATCAGT---AAGAGT--AAAGG
*
24819 TAGTCAGTAATTG-GTACAATGG
1 TAATCAGTAA--GAGTA-AA-GG
*
24841 TAATTAGTAAAGAGTAAAGTG
1 TAATCAGT-AAGAGTAAAG-G
24862 ATAATCAGTAAAGAGTAATAGG
1 -TAATCAGT-AAGAGTAA-AGG
24884 -AATCAGTAAGAGTAAAG
1 TAATCAGTAAGAGTAAAG
24901 TAGTAATTAA
Statistics
Matches: 209, Mismatches: 26, Indels: 64
0.70 0.09 0.21
Matches are distributed among these distances:
15 7 0.03
16 2 0.01
18 4 0.02
19 35 0.17
20 58 0.28
21 13 0.06
22 70 0.33
23 9 0.04
24 11 0.05
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.23
Consensus pattern (19 bp):
TAATCAGTAAGAGTAAAGG
Found at i:24668 original size:19 final size:20
Alignment explanation
Indices: 24614--24683 Score: 99
Period size: 19 Copynumber: 3.5 Consensus size: 20
24604 ATTAGCAAAA
24614 ATAATCAGTAAGAGTGAAAGG
1 ATAATCAGTAAGAGT-AAAGG
*
24635 -TGATCAGTAAGAGTAAAGG
1 ATAATCAGTAAGAGTAAAGG
*
24654 ATAATCAGTAA-AGTAAAAG
1 ATAATCAGTAAGAGTAAAGG
24673 ATAATCAGTAA
1 ATAATCAGTAA
24684 AATAGTAATC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 23 0.51
20 22 0.49
ACGTcount: A:0.50, C:0.06, G:0.23, T:0.21
Consensus pattern (20 bp):
ATAATCAGTAAGAGTAAAGG
Found at i:24684 original size:19 final size:20
Alignment explanation
Indices: 24610--24683 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
24600 GGTAATTAGC
24610 AAAA-ATAATCAGTAAGAGT
1 AAAAGATAATCAGTAAGAGT
* * *
24629 GAAAGGTGATCAGTAAGAGT
1 AAAAGATAATCAGTAAGAGT
*
24649 AAAGGATAATCAGTAA-AGT
1 AAAAGATAATCAGTAAGAGT
24668 AAAAGATAATCAGTAA
1 AAAAGATAATCAGTAA
24684 AATAGTAATC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 21 0.46
20 25 0.54
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAAGATAATCAGTAAGAGT
Found at i:24791 original size:108 final size:108
Alignment explanation
Indices: 24679--24958 Score: 293
Period size: 108 Copynumber: 2.6 Consensus size: 108
24669 AAAGATAATC
* *
24679 AGTAAAATAGTAATCCGTAAAAAAAATAATAA-TAATCAGTAAAAGGTAAAATGGTAATTAGTAA
1 AGTAAAATAGTAATCAGTAAAAAAAATAAAAAGTAATCAGTAAAAGGTAAAATGGTAATTAGTAA
* *
24743 AGAGCAATA-TGGTAATCAGTAAAGAGTAATAATAATCAGTAAG
66 AGAGCAA-AGTGATAATCAGTAAAGAGTAATAAGAATCAGTAAG
* * * ** *
24786 AAGT--AATGGTAATCAGTAAAAAAAGTAAAAAGGTAGTCAGTAATTGGTACAATGGTAATTAGT
1 -AGTAAAATAGTAATCAGTAAAAAAAATAAAAA-GTAATCAGTAAAAGGTAAAATGGTAATTAGT
* *
24849 AAAGAGTAAAGTGATAATCAGTAAAGAGTAATAGGAATCAGTAAG
64 AAAGAGCAAAGTGATAATCAGTAAAGAGTAATAAGAATCAGTAAG
* * * * * * * *
24894 AGTAAAGTAGTAATTAAT-AAAAAAGTAAAGAAATAATTAGT-AAAGAGTAAAATGATAGTTAGT
1 AGTAAAATAGTAATCAGTAAAAAAAATAAA-AAGTAATCAGTAAAAG-GTAAAATGGTAATTAGT
24957 AA
64 AA
24959 TTAAGTTCAA
Statistics
Matches: 141, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
106 23 0.16
107 6 0.04
108 101 0.72
109 11 0.08
ACGTcount: A:0.52, C:0.04, G:0.19, T:0.25
Consensus pattern (108 bp):
AGTAAAATAGTAATCAGTAAAAAAAATAAAAAGTAATCAGTAAAAGGTAAAATGGTAATTAGTAA
AGAGCAAAGTGATAATCAGTAAAGAGTAATAAGAATCAGTAAG
Found at i:24826 original size:64 final size:63
Alignment explanation
Indices: 24705--24828 Score: 144
Period size: 64 Copynumber: 1.9 Consensus size: 63
24695 GTAAAAAAAA
* * * *
24705 TAATAATAATCAGTAAAAGGTAAAATGGTAATTAGTAAAGAGCAATATGGTAATCAGTAAAGAG
1 TAATAATAATCAGTAAAAGGT-AAATGGTAATCAGTAAAAAGCAAAAAGGTAATCAGTAAAGAG
* *
24769 TAATAATAATCAGTAAGAA-GT-AATGGTAATCAGTAAAAAAAGTAAAAAGGTAGTCAGTAA
1 TAATAATAATCAGTAA-AAGGTAAATGGTAATCAGT--AAAAAGCAAAAAGGTAATCAGTAA
24829 TTGGTACAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
62 12 0.24
64 37 0.73
65 2 0.04
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (63 bp):
TAATAATAATCAGTAAAAGGTAAATGGTAATCAGTAAAAAGCAAAAAGGTAATCAGTAAAGAG
Found at i:24923 original size:23 final size:23
Alignment explanation
Indices: 24894--24937 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
24884 AATCAGTAAG
* *
24894 AGTAAAGTAGTAATTAATAAAAA
1 AGTAAAGAAATAATTAATAAAAA
*
24917 AGTAAAGAAATAATTAGTAAA
1 AGTAAAGAAATAATTAATAAA
24938 GAGTAAAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (23 bp):
AGTAAAGAAATAATTAATAAAAA
Found at i:25074 original size:167 final size:169
Alignment explanation
Indices: 24875--25197 Score: 521
Period size: 167 Copynumber: 1.9 Consensus size: 169
24865 ATCAGTAAAG
* * *
24875 AGTAATAGGAATCAGTAAGAGTAAAGTAGTAATTAATAAAAAAGTAAAGAAATAATTAGTAAAGA
1 AGTAATAGGAATCAGTAAGAGTAAAGTAGTAATCAATAAAAAAGTAAAAAAATAATCAGTAAAGA
* *
24940 GTAAAATGATAGTTAGTAATTAAGTTCAAAGAGTAAAATGGTAGTCAGTAAAAGAGAAAAAGAAG
66 GTAAAATGATAGTCAGTAATTAAATTCAAAGAGTAAAATGGTAGTCAGTAAAAGAGAAAAAGAAG
25005 AA-AAGTA-AAAAAG-GGTAATCAGTGTTCAAGTTCAAAA
131 AAGAAG-AGAAAAAGTGGTAATCAGTGTTCAAGTTCAAAA
25042 AGTAAT-GGTAATCAGTAAGAGTGAAA-TAGTAATCAATAAAAAAGTAAAAAAATAATCAGTAAA
1 AGTAATAGG-AATCAGTAAGAGT-AAAGTAGTAATCAATAAAAAAGTAAAAAAATAATCAGTAAA
*
25105 GAGTAAAATGATAGTCAGTAATTAAATTCAAAGAGTAAAATGGTAGTCAGTAAAAGAGAAGAAGA
64 GAGTAAAATGATAGTCAGTAATTAAATTCAAAGAGTAAAATGGTAGTCAGTAAAAGAGAAAAAGA
25170 AGAAGAAGAGTAAAAAGTGGTAATCAGT
129 AGAAGAAGAG-AAAAAGTGGTAATCAGT
25198 AAAAAAGAGT
Statistics
Matches: 144, Mismatches: 6, Indels: 9
0.91 0.04 0.06
Matches are distributed among these distances:
166 2 0.01
167 120 0.83
168 6 0.04
169 6 0.04
170 10 0.07
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.22
Consensus pattern (169 bp):
AGTAATAGGAATCAGTAAGAGTAAAGTAGTAATCAATAAAAAAGTAAAAAAATAATCAGTAAAGA
GTAAAATGATAGTCAGTAATTAAATTCAAAGAGTAAAATGGTAGTCAGTAAAAGAGAAAAAGAAG
AAGAAGAGAAAAAGTGGTAATCAGTGTTCAAGTTCAAAA
Found at i:25208 original size:27 final size:26
Alignment explanation
Indices: 25175--25236 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
25165 GAAGAAGAAG
25175 AAGAGTAAAAAGTGGTAATCAGTAAAA
1 AAGAGTAAAAAGTGGTAATCAGT-AAA
*
25202 AAGAGTAAGAAAAG-AGTAATCAGTAAA
1 AAGAGT-A-AAAAGTGGTAATCAGTAAA
25229 AAGAGTAA
1 AAGAGTAA
25237 GAAATGGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 1 0.03
26 1 0.03
27 15 0.47
28 10 0.31
29 5 0.16
ACGTcount: A:0.58, C:0.03, G:0.23, T:0.16
Consensus pattern (26 bp):
AAGAGTAAAAAGTGGTAATCAGTAAA
Found at i:25212 original size:42 final size:39
Alignment explanation
Indices: 25135--25216 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 39
25125 ATTAAATTCA
* *
25135 AAGAGTAAAATGGTAGTCAGTAAAAGAGAAGAAGAAGAAG
1 AAGAGTAAAATGGTAATCAGTAAAAAAGAAGAAGAA-AAG
25175 AAGAGTAAAAAGTGGTAATCAGTAAAAAAG-AGTAAGAAAAG
1 AAGAGT-AAAA-TGGTAATCAGTAAAAAAGAAG-AAGAAAAG
25216 A
1 A
25217 GTAATCAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
40 6 0.16
41 10 0.27
42 21 0.57
ACGTcount: A:0.57, C:0.02, G:0.27, T:0.13
Consensus pattern (39 bp):
AAGAGTAAAATGGTAATCAGTAAAAAAGAAGAAGAAAAG
Found at i:25302 original size:64 final size:65
Alignment explanation
Indices: 25169--25311 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 65
25159 AGAGAAGAAG
* * *
25169 AAGAAGAAGAGTAAAAAGTGGTAATCAGTAAAAAAGAGTAAGAAAAGAGTAATCAGTAAAAAGAG
1 AAGAA-AAGGGTAAAAAGTGGTAATAAGTAAAAAAGAGTAAGAAAAGAGTAATCAGTAAAAACAG
25234 T
65 T
* * *
25235 AAGAAATGGGTAAGAAA-TGGTAATTAAGTAAAAAA-AGT-A-AAAAGTGGTATTCAGTAAAAAC
1 AAGAAAAGGGTAA-AAAGTGGTAA-TAAGTAAAAAAGAGTAAGAAAAG-AGTAATCAGTAAAAAC
25296 AGT
63 AGT
25299 AAGAAAAGGGTAA
1 AAGAAAAGGGTAA
25312 TCAGTAAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
63 5 0.07
64 29 0.43
65 15 0.22
66 18 0.27
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.17
Consensus pattern (65 bp):
AAGAAAAGGGTAAAAAGTGGTAATAAGTAAAAAAGAGTAAGAAAAGAGTAATCAGTAAAAACAGT
Found at i:25311 original size:54 final size:54
Alignment explanation
Indices: 25244--25373 Score: 158
Period size: 54 Copynumber: 2.4 Consensus size: 54
25234 TAAGAAATGG
*
25244 GTAAG-AAATGGTAATTAAGTAAAAAA-AGTAAAA-AGTGGTATTCAGTAAAAACA
1 GTAAGAAAATGGTAATT-AGTAAAAAAGAGTAAAATA-TGGTAATCAGTAAAAACA
* * * *
25297 GTAAGAAAAGGGTAATCAGTAAAAAAGAGTAAAATATGGTAATCAGTACAAAGA
1 GTAAGAAAATGGTAATTAGTAAAAAAGAGTAAAATATGGTAATCAGTAAAAACA
*
25351 GTAAAAAAAATGGTAATTAGTAA
1 GT-AAGAAAATGGTAATTAGTAA
25374 TCAAGAAATA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
53 14 0.22
54 33 0.51
55 18 0.28
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.22
Consensus pattern (54 bp):
GTAAGAAAATGGTAATTAGTAAAAAAGAGTAAAATATGGTAATCAGTAAAAACA
Found at i:25328 original size:17 final size:18
Alignment explanation
Indices: 25295--25328 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25285 TCAGTAAAAA
*
25295 CAGTAAGAAAAGGGTAAT
1 CAGTAAGAAAAGAGTAAT
25313 CAGTAA-AAAAGAGTAA
1 CAGTAAGAAAAGAGTAA
25329 AATATGGTAA
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:0.56, C:0.06, G:0.24, T:0.15
Consensus pattern (18 bp):
CAGTAAGAAAAGAGTAAT
Found at i:25360 original size:92 final size:91
Alignment explanation
Indices: 25134--25360 Score: 225
Period size: 92 Copynumber: 2.4 Consensus size: 91
25124 AATTAAATTC
* *
25134 AAAGAGT-AAAATGGTAGTCAGTAAAAGAGAAGAAGAAGAAGAAGAGTAAAAAGTGGTAATCAGT
1 AAAGAGTAAAAATGGTAATCAGTAAAAGAGTA-AA-AA-AA-AAGAGTAAAAAGTGGTAATCAGT
*
25198 AAAAAAGAGTAAGAAAAGAGTAATCAGTAA
62 AAAAAACAGTAAGAAAAGAGTAATCAGTAA
* * *
25228 AAAGAGTAAGAAATGGGT-A--AG-AAATG-GTAATTAAGTAAAAAAAGTAAAAAGTGGTATTCA
1 AAAGAGTAA-AAAT-GGTAATCAGTAAAAGAGTAA--AA--AAAAAGAGTAAAAAGTGGTAATCA
*
25288 GT-AAAAACAGTAAGAAAAGGGTAATCAGTAAA
60 GTAAAAAACAGTAAGAAAAGAGTAATCAGT-AA
25320 AAAGAGTAAAATATGGTAATCAGTACAAAGAGTAAAAAAAA
1 AAAGAGTAAAA-ATGGTAATCAGTA-AAAGAGTAAAAAAAA
25361 TGGTAATTAG
Statistics
Matches: 110, Mismatches: 8, Indels: 31
0.74 0.05 0.21
Matches are distributed among these distances:
91 31 0.28
92 38 0.35
93 11 0.10
94 12 0.11
95 4 0.04
96 7 0.06
97 7 0.06
ACGTcount: A:0.56, C:0.04, G:0.23, T:0.17
Consensus pattern (91 bp):
AAAGAGTAAAAATGGTAATCAGTAAAAGAGTAAAAAAAAAGAGTAAAAAGTGGTAATCAGTAAAA
AACAGTAAGAAAAGAGTAATCAGTAA
Found at i:25367 original size:28 final size:27
Alignment explanation
Indices: 25249--25373 Score: 119
Period size: 27 Copynumber: 4.6 Consensus size: 27
25239 AATGGGTAAG
* *
25249 AAATGGTAATTAAGTAAAAAAAGT-AAA
1 AAATGGTAA-TCAGTAAAAAGAGTAAAA
* * * *
25276 AAGTGGTATTCAGTAAAAACAGTAAGA
1 AAATGGTAATCAGTAAAAAGAGTAAAA
*
25303 AAAGGGTAATCAGTAAAAAAGAGT-AAA
1 AAATGGTAATCAGT-AAAAAGAGTAAAA
* *
25330 ATATGGTAATCAGTACAAAGAGTAAAAA
1 AAATGGTAATCAGTAAAAAGAGT-AAAA
*
25358 AAATGGTAATTAGTAA
1 AAATGGTAATCAGTAA
25374 TCAAGAAATA
Statistics
Matches: 78, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
26 20 0.26
27 34 0.44
28 24 0.31
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.22
Consensus pattern (27 bp):
AAATGGTAATCAGTAAAAAGAGTAAAA
Found at i:29320 original size:23 final size:23
Alignment explanation
Indices: 29290--29346 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
29280 CAAAAAATGA
29290 CACGTGGCATGTATCCTTTTGTG
1 CACGTGGCATGTATCCTTTTGTG
29313 CACGTGGCATGTATCCTTTTGTG
1 CACGTGGCATGTATCCTTTTGTG
*
29336 CTCGTGGCATG
1 CACGTGGCATG
29347 CCACGTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.28, T:0.37
Consensus pattern (23 bp):
CACGTGGCATGTATCCTTTTGTG
Found at i:29375 original size:31 final size:31
Alignment explanation
Indices: 29338--29476 Score: 152
Period size: 31 Copynumber: 4.5 Consensus size: 31
29328 CTTTTGTGCT
* * * *
29338 CGTGGCATGCCACGTGCCATTTTTTGAAACA
1 CGTGGCGTGCCACGTGTCACTTTTTGATACA
* * * * *
29369 TGTGGCATGCCACGTGTAATTTTTTGGTACA
1 CGTGGCGTGCCACGTGTCACTTTTTGATACA
* * *
29400 CGTGGCGTGACATGTGTCACTTTTTGGTACA
1 CGTGGCGTGCCACGTGTCACTTTTTGATACA
* *
29431 TGTGGCGTGCCACATGTCACTTTTTGATACA
1 CGTGGCGTGCCACGTGTCACTTTTTGATACA
29462 CGTGGCGTGCCACGT
1 CGTGGCGTGCCACGT
29477 CGGACATCGT
Statistics
Matches: 90, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 90 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (31 bp):
CGTGGCGTGCCACGTGTCACTTTTTGATACA
Found at i:29405 original size:62 final size:62
Alignment explanation
Indices: 29338--29476 Score: 170
Period size: 62 Copynumber: 2.2 Consensus size: 62
29328 CTTTTGTGCT
* * * * *
29338 CGTGGCATGCCACGTGCCATTTTTTGAAACATGTGGCATGCCACGTGTAATTTTTTGGTACA
1 CGTGGCGTGCCACGTGCCACTTTTTGAAACATGTGGCATGCCACATGTAACTTTTTGATACA
* * * ** * *
29400 CGTGGCGTGACATGTGTCACTTTTTGGTACATGTGGCGTGCCACATGTCACTTTTTGATACA
1 CGTGGCGTGCCACGTGCCACTTTTTGAAACATGTGGCATGCCACATGTAACTTTTTGATACA
29462 CGTGGCGTGCCACGT
1 CGTGGCGTGCCACGT
29477 CGGACATCGT
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (62 bp):
CGTGGCGTGCCACGTGCCACTTTTTGAAACATGTGGCATGCCACATGTAACTTTTTGATACA
Found at i:35288 original size:3 final size:3
Alignment explanation
Indices: 35280--35332 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
35270 AACTACATAG
35280 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35328 TAA TA
1 TAA TA
35333 TATAGTACAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:41890 original size:24 final size:24
Alignment explanation
Indices: 41863--41912 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
41853 AAAAGTTTTA
*
41863 CCGTTTCAAAACCCCTTTCTAAAC
1 CCGTTTCAAAACCCCTTGCTAAAC
41887 CCGTTTCAAAACCCCTTGCTAAAC
1 CCGTTTCAAAACCCCTTGCTAAAC
41911 CC
1 CC
41913 AGCAACGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.40, G:0.06, T:0.26
Consensus pattern (24 bp):
CCGTTTCAAAACCCCTTGCTAAAC
Found at i:41910 original size:12 final size:12
Alignment explanation
Indices: 41866--41912 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
41856 AGTTTTACCG
*
41866 TTTCAAAACCCC
1 TTTCTAAACCCC
*
41878 TTTCTAAACCCG
1 TTTCTAAACCCC
*
41890 TTTCAAAACCCC
1 TTTCTAAACCCC
*
41902 TTGCTAAACCC
1 TTTCTAAACCC
41913 AGCAACGGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.28
Consensus pattern (12 bp):
TTTCTAAACCCC
Found at i:46099 original size:2 final size:2
Alignment explanation
Indices: 46092--46116 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46082 ACTCTATTAT
46092 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
46117 GTTTCTAAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57227 original size:2 final size:2
Alignment explanation
Indices: 57220--57244 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57210 ACTTATAGTA
57220 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
57245 AGTCATTAGC
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:58144 original size:3 final size:3
Alignment explanation
Indices: 58136--58187 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
58126 ATATATATAT
58136 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
58184 ATA A
1 ATA A
58188 GATAGACAGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:59192 original size:20 final size:20
Alignment explanation
Indices: 59164--59202 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59154 ACCTGAATTC
*
59164 AATACTAATATTTGAAAATA
1 AATAATAATATTTGAAAATA
*
59184 AATAATAATTTTTGAAAAT
1 AATAATAATATTTGAAAAT
59203 TTCATTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
AATAATAATATTTGAAAATA
Found at i:59381 original size:32 final size:32
Alignment explanation
Indices: 59337--59436 Score: 141
Period size: 32 Copynumber: 3.2 Consensus size: 32
59327 GCGAAAACCC
59337 AACCCG-ACCCGAAAT-AACCTGACCCAAATTT
1 AACCCGAACCCG-AATCAACCTGACCCAAATTT
*
59368 AACCCGAACCCGAATCGACCTGACCCAAATTT
1 AACCCGAACCCGAATCAACCTGACCCAAATTT
** *
59400 AACCCGAACCCGAATCAGTCTAACCCAAATTT
1 AACCCGAACCCGAATCAACCTGACCCAAATTT
59432 AACCC
1 AACCC
59437 AATCTGACTC
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
31 9 0.15
32 53 0.85
ACGTcount: A:0.37, C:0.37, G:0.10, T:0.16
Consensus pattern (32 bp):
AACCCGAACCCGAATCAACCTGACCCAAATTT
Found at i:60267 original size:13 final size:13
Alignment explanation
Indices: 60249--60275 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
60239 GCCATTGCAA
60249 ACCCTATTTATAC
1 ACCCTATTTATAC
60262 ACCCTATTTATAC
1 ACCCTATTTATAC
60275 A
1 A
60276 GTATAACCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (13 bp):
ACCCTATTTATAC
Found at i:61650 original size:21 final size:21
Alignment explanation
Indices: 61624--61666 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
61614 GATAAACAGG
61624 GTATGAATCGAAGCCATGGAT
1 GTATGAATCGAAGCCATGGAT
61645 GTATGAATCGAAGCCATGGAT
1 GTATGAATCGAAGCCATGGAT
61666 G
1 G
61667 AATAAATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (21 bp):
GTATGAATCGAAGCCATGGAT
Found at i:64751 original size:6 final size:6
Alignment explanation
Indices: 64740--64781 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
64730 CCACATATAT
* *
64740 GGAACC GGAACC GGAATC -GAACC GGAACC GTAACC GGAACC G
1 GGAACC GGAACC GGAACC GGAACC GGAACC GGAACC GGAACC G
64782 TCCATATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.33, C:0.31, G:0.31, T:0.05
Consensus pattern (6 bp):
GGAACC
Found at i:71470 original size:44 final size:44
Alignment explanation
Indices: 71373--71522 Score: 128
Period size: 44 Copynumber: 3.4 Consensus size: 44
71363 ACATAGTCCT
* * * *
71373 ACTATGAAATTTTGATAAT-TTCGCTAT-ATTATTTTGATAACCTC
1 ACTATGAAATTGTGATAATCATC-CTATGA-AATTTTGATAACCAC
* * * *
71417 CCTAAGAAATAGTGATAGA-C-TCTCTGTGAAATTTTGATAACCAC
1 ACTATGAAATTGTGATA-ATCATC-CTATGAAATTTTGATAACCAC
* * *
71461 GCTATGAAATTTTGATAATCATCCTATGTAATTTTGATAACCAC
1 ACTATGAAATTGTGATAATCATCCTATGAAATTTTGATAACCAC
*
71505 ACTATAAAATTGTGATAA
1 ACTATGAAATTGTGATAA
71523 CCTCTATATG
Statistics
Matches: 84, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
43 1 0.01
44 79 0.94
45 4 0.05
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (44 bp):
ACTATGAAATTGTGATAATCATCCTATGAAATTTTGATAACCAC
Found at i:71536 original size:22 final size:21
Alignment explanation
Indices: 71374--71537 Score: 107
Period size: 22 Copynumber: 7.5 Consensus size: 21
71364 CATAGTCCTA
**
71374 CTATGAAATTTTGATAATTTC
1 CTATGAAATTTTGATAACCTC
*
71395 GCTAT-ATTATTTTGATAACCTCC
1 -CTATGA-AATTTTGATAACCT-C
* **
71418 CTAAGAAATAGTGATAGA-CTC
1 CTATGAAATTTTGATA-ACCTC
* *
71439 TCTGTGAAATTTTGATAACCAC
1 -CTATGAAATTTTGATAACCTC
*
71461 GCTATGAAATTTTGATAATCATC
1 -CTATGAAATTTTGATAA-CCTC
* *
71484 CTATGTAATTTTGATAACCAC
1 CTATGAAATTTTGATAACCTC
* *
71505 ACTATAAAATTGTGATAACCTC
1 -CTATGAAATTTTGATAACCTC
*
71527 TATATGAAATT
1 -CTATGAAATT
71538 AATTTTGATG
Statistics
Matches: 108, Mismatches: 26, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
21 5 0.05
22 98 0.91
23 5 0.05
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCTC
Found at i:71677 original size:22 final size:22
Alignment explanation
Indices: 71635--71677 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
71625 TTATGAAATT
*
71635 TTGATAACCTCCCTACGGAATG
1 TTGATAACCTCCCTACAGAATG
* *
71657 TTGATAACTTCCCTATAGAAT
1 TTGATAACCTCCCTACAGAAT
71678 TTCGTTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (22 bp):
TTGATAACCTCCCTACAGAATG
Found at i:72194 original size:15 final size:16
Alignment explanation
Indices: 72146--72200 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
72136 GCTTTTGTAA
*
72146 GTGAGTATCTCACCAG
1 GTGAGTATCTTACCAG
72162 GTGAGTATCTTACCAG
1 GTGAGTATCTTACCAG
*
72178 GTGAGTAT-TTACTAG
1 GTGAGTATCTTACCAG
72193 GTGAGTAT
1 GTGAGTAT
72201 GGTATTGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
15 14 0.38
16 23 0.62
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAGTATCTTACCAG
Found at i:72665 original size:23 final size:23
Alignment explanation
Indices: 72593--72675 Score: 62
Period size: 23 Copynumber: 3.6 Consensus size: 23
72583 TTGGGGAGAG
*
72593 CTCCGCGCAAGAGCT-GGATTAGC
1 CTCCGCGCAAGAGCTAGG-TGAGC
** * * *
72616 CTATGCGCGAGAGC-AGGGGAGTG
1 CTCCGCGCAAGAGCTAGGTGAG-C
72639 CTCCGCGCAAGAGCTAGGTGAGC
1 CTCCGCGCAAGAGCTAGGTGAGC
**
72662 CTCCGTTCAAGAGC
1 CTCCGCGCAAGAGC
72676 AAGGGAGTTC
Statistics
Matches: 44, Mismatches: 13, Indels: 6
0.70 0.21 0.10
Matches are distributed among these distances:
22 2 0.05
23 36 0.82
24 6 0.14
ACGTcount: A:0.22, C:0.28, G:0.35, T:0.16
Consensus pattern (23 bp):
CTCCGCGCAAGAGCTAGGTGAGC
Found at i:72675 original size:46 final size:46
Alignment explanation
Indices: 72585--72697 Score: 111
Period size: 46 Copynumber: 2.5 Consensus size: 46
72575 ATGGCTACTT
* * * *
72585 GGGGAGAGCTCCGCGCAAGAGCTGGATTAGCCTATGCGCGAGAGCA
1 GGGGAGTGCTCCGCGCAAGAGCTGGATGAGCCTACGCGCAAGAGCA
* **
72631 GGGGAGTGCTCCGCGCAAGAGCTAGG-TGAGCCTCCGTTCAAGAGCA
1 GGGGAGTGCTCCGCGCAAGAGCT-GGATGAGCCTACGCGCAAGAGCA
* * * *
72677 AGGGAGTTCTCTGCACAAGAG
1 GGGGAGTGCTCCGCGCAAGAG
72698 TAAGGGAGTA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 53 0.96
47 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.37, T:0.15
Consensus pattern (46 bp):
GGGGAGTGCTCCGCGCAAGAGCTGGATGAGCCTACGCGCAAGAGCA
Found at i:72929 original size:17 final size:18
Alignment explanation
Indices: 72898--72941 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
72888 AAATCTGACC
72898 CGAACCCGATAACCCGCT
1 CGAACCCGATAACCCGCT
72916 CGAACCCG-TAACCCGC-
1 CGAACCCGATAACCCGCT
*
72932 CCAACCCGAT
1 CGAACCCGAT
72942 TTGACCAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 9 0.38
18 8 0.33
ACGTcount: A:0.27, C:0.48, G:0.16, T:0.09
Consensus pattern (18 bp):
CGAACCCGATAACCCGCT
Found at i:73011 original size:16 final size:16
Alignment explanation
Indices: 72975--73109 Score: 112
Period size: 16 Copynumber: 8.4 Consensus size: 16
72965 GAATCCGCCC
* *
72975 GACCCGAGACCCGACT
1 GACCCGAAACCCGAAT
* **
72991 AACCCGTGACCCGAAT
1 GACCCGAAACCCGAAT
* *
73007 GACCCGCAACCC-AGCT
1 GACCCGAAACCCGA-AT
* *
73023 GACCCGAGACCTGAAT
1 GACCCGAAACCCGAAT
* *
73039 GACCTGTAACCC-AGAT
1 GACCCGAAACCCGA-AT
73055 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
* *
73071 GACCCGAGACCCGTAT
1 GACCCGAAACCCGAAT
73087 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
*
73103 AACCCGA
1 GACCCGA
73110 GACATTAACC
Statistics
Matches: 93, Mismatches: 22, Indels: 8
0.76 0.18 0.07
Matches are distributed among these distances:
15 2 0.02
16 89 0.96
17 2 0.02
ACGTcount: A:0.31, C:0.39, G:0.21, T:0.10
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:73011 original size:32 final size:31
Alignment explanation
Indices: 72975--73112 Score: 136
Period size: 32 Copynumber: 4.3 Consensus size: 31
72965 GAATCCGCCC
* **
72975 GACCCGAGACCCGACTAACCCGTGACCCGAAT
1 GACCCGAGACCCGA-TGACCCGAAACCCGAAT
* * *
73007 GACCCGCA-ACCCAGCTGACCCGAGACCTGAAT
1 GACCCG-AGACCC-GATGACCCGAAACCCGAAT
*
73039 GACCTGTA-ACCCAGATGACCCGAAACCCGAAT
1 GACCCG-AGACCC-GATGACCCGAAACCCGAAT
73071 GACCCGAGACCCGTATGACCCGAAACCCGAAT
1 GACCCGAGACCCG-ATGACCCGAAACCCGAAT
*
73103 AACCCGAGAC
1 GACCCGAGAC
73113 ATTAACCCGA
Statistics
Matches: 91, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.02
32 87 0.96
33 2 0.02
ACGTcount: A:0.31, C:0.38, G:0.21, T:0.09
Consensus pattern (31 bp):
GACCCGAGACCCGATGACCCGAAACCCGAAT
Found at i:73108 original size:48 final size:47
Alignment explanation
Indices: 72975--73109 Score: 139
Period size: 48 Copynumber: 2.8 Consensus size: 47
72965 GAATCCGCCC
* * * *
72975 GACCCGAGACCCGACTAACCCGTGACCCGAATGACCCGCAACCCAGCT
1 GACCCGAGACCCGA-TGACCCGTAACCCGAATGACCCGAAACCCAGAT
* *
73023 GACCCGAGACCTGAATGACCTGTAACCC-AGATGACCCGAAACCC-GAAT
1 GACCCGAGACCCG-ATGACCCGTAACCCGA-ATGACCCGAAACCCAG-AT
* *
73071 GACCCGAGACCCGTATGACCCGAAACCCGAATAACCCGA
1 GACCCGAGACCCG-ATGACCCGTAACCCGAATGACCCGA
73110 GACATTAACC
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
47 2 0.03
48 68 0.94
49 2 0.03
ACGTcount: A:0.31, C:0.39, G:0.21, T:0.10
Consensus pattern (47 bp):
GACCCGAGACCCGATGACCCGTAACCCGAATGACCCGAAACCCAGAT
Found at i:73168 original size:20 final size:20
Alignment explanation
Indices: 73145--73214 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
73135 TATTATAAAT
73145 TAAAATTATCTTTTATTCAA
1 TAAAATTATCTTTTATTCAA
*
73165 TAAAATTTATAATTTTACTT-AA
1 TAAAA-TTAT-CTTTTA-TTCAA
* *
73187 TCTAAATCATCTTTTATTCAA
1 T-AAAATTATCTTTTATTCAA
*
73208 TACAATT
1 TAAAATT
73215 TATATTATTG
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
20 10 0.26
21 12 0.32
22 11 0.29
23 5 0.13
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATTATCTTTTATTCAA
Found at i:73243 original size:21 final size:21
Alignment explanation
Indices: 73218--73264 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
73208 TACAATTTAT
73218 ATTATTGTTATAATTTTACCA
1 ATTATTGTTATAATTTTACCA
* *
73239 ATTATTGTTATGATTTTACCT
1 ATTATTGTTATAATTTTACCA
73260 ATTAT
1 ATTAT
73265 GAATCGACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTATTGTTATAATTTTACCA
Found at i:73719 original size:16 final size:16
Alignment explanation
Indices: 73692--73736 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
73682 CCCGAAGTCA
73692 AAACCCGA-ACCCGCC
1 AAACCCGAGACCCGCC
**
73707 AAACCCGAGACCCGGT
1 AAACCCGAGACCCGCC
*
73723 AGACCCGAGACCCG
1 AAACCCGAGACCCG
73737 AATGACCCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.31, C:0.44, G:0.22, T:0.02
Consensus pattern (16 bp):
AAACCCGAGACCCGCC
Found at i:73743 original size:16 final size:16
Alignment explanation
Indices: 73709--73823 Score: 173
Period size: 16 Copynumber: 7.2 Consensus size: 16
73699 AACCCGCCAA
*
73709 ACCCGAGACCCG-GTAG
1 ACCCGAGACCCGAAT-G
73725 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
*
73741 ACCCGAGACCCGTATG
1 ACCCGAGACCCGAATG
73757 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
73773 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
73789 ACCC-AGACCCGAATG
1 ACCCGAGACCCGAATG
73804 ACCCGTA-ACCCGAATG
1 ACCCG-AGACCCGAATG
73820 ACCC
1 ACCC
73824 AAAAAAACTG
Statistics
Matches: 93, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
15 15 0.16
16 76 0.82
17 2 0.02
ACGTcount: A:0.30, C:0.39, G:0.23, T:0.08
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Done.