Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021032.1 Corchorus olitorius cultivar O-4 contig21065, 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: 143401
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:120 original size:73 final size:72
Alignment explanation
Indices: 1--144 Score: 252
Period size: 73 Copynumber: 2.0 Consensus size: 72
*
1 TTTGTTATTTGAGTTAATTTAAAAGTTGATTTGGTGATTGAGGCATGTAAAATGTTCTAAATTTA
1 TTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGAGGCATGT-AAATGTTCTAAATTTA
66 GCTAATTG
65 GCTAATTG
* *
74 TTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGATGCATGTAAATGTTCTAAATTTAT
1 TTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGAGGCATGTAAATGTTCTAAATTTAG
139 CTAATT
66 CTAATT
145 TATGAATACA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
72 22 0.32
73 46 0.68
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.47
Consensus pattern (72 bp):
TTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGAGGCATGTAAATGTTCTAAATTTAG
CTAATTG
Found at i:1626 original size:40 final size:40
Alignment explanation
Indices: 1571--1882 Score: 419
Period size: 40 Copynumber: 7.8 Consensus size: 40
1561 CCCAAATTCC
1571 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACT
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACT
1611 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACT
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACT
* * *
1651 CGGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATACC
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACT
* *
1691 CAGTTTACCCTTCCCCACCGGAAGGTGTTGTTTAAATACC
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACT
* * *
1731 CAGTTTGCCCTTTCCCACCGGAAGGTGTTGTTTAAATTCC
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACT
* * * * *
1771 CAGTTTGCCTTTCCCTACCGGAAAGTGTTGTCTAAATTCT
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACT
* * *
1811 CAGTTTGCCTTTCCCCACCGGAAAGTGTT-TTCTAAATTCT
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT-TAAATACT
* * * * *
1851 CAATTTGCCCTTCCTCATCGGGAGGAGTTGTT
1 CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTT
1883 CCTATTCCCC
Statistics
Matches: 246, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
39 1 0.00
40 243 0.99
41 2 0.01
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.33
Consensus pattern (40 bp):
CAGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACT
Found at i:11221 original size:163 final size:163
Alignment explanation
Indices: 10951--11275 Score: 614
Period size: 163 Copynumber: 2.0 Consensus size: 163
10941 GCAAACAATT
*
10951 AGGTAGTGATTACTTGGTTGTTTGTGAATCTTATGATCTTAGGTTGTCAATTGTAGGTCTAATTG
1 AGGTAGTGATTACTTGGTTGTTTGTGAATCTTATGATCATAGGTTGTCAATTGTAGGTCTAATTG
* *
11016 ATCTTCTAAGGCCGACGAACGAAGAAGAGAGCTTGGTTAGATTCAATCGATTCAACAAGTCTAGA
66 ATCATCTAAGGACGACGAACGAAGAAGAGAGCTTGGTTAGATTCAATCGATTCAACAAGTCTAGA
11081 AGTTGGTGTTTTCAAGTTTGATCTTTGGAGGAA
131 AGTTGGTGTTTTCAAGTTTGATCTTTGGAGGAA
11114 AGGTAGTGATTACTTGGTTGTTTGTGAATCTTATGATCATAGGTTGTCAATTGTAGGTCTAATTG
1 AGGTAGTGATTACTTGGTTGTTTGTGAATCTTATGATCATAGGTTGTCAATTGTAGGTCTAATTG
*
11179 ATCATCTAAGGACGACGAACGAAGAAGAGAGCTTGGTTAGATTCAATCGTTTCAACAAGTCTAGA
66 ATCATCTAAGGACGACGAACGAAGAAGAGAGCTTGGTTAGATTCAATCGATTCAACAAGTCTAGA
11244 AGTTGGTGTTTTCAAGTTTGATCTTTGGAGGA
131 AGTTGGTGTTTTCAAGTTTGATCTTTGGAGGA
11276 TTTCAAAGGT
Statistics
Matches: 158, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 158 1.00
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.35
Consensus pattern (163 bp):
AGGTAGTGATTACTTGGTTGTTTGTGAATCTTATGATCATAGGTTGTCAATTGTAGGTCTAATTG
ATCATCTAAGGACGACGAACGAAGAAGAGAGCTTGGTTAGATTCAATCGATTCAACAAGTCTAGA
AGTTGGTGTTTTCAAGTTTGATCTTTGGAGGAA
Found at i:16900 original size:23 final size:23
Alignment explanation
Indices: 16794--16904 Score: 95
Period size: 22 Copynumber: 4.8 Consensus size: 23
16784 TTGTTTTGTG
16794 TTTTGCGTCGA-AAAAAAAATA-T
1 TTTTGCGTC-ATAAAAAAAATAGT
*** *
16816 TTTTGCGTCATAAAAATTTTTGT
1 TTTTGCGTCATAAAAAAAATAGT
*
16839 TTCTGCGTCATAAAAAAAA-AGT
1 TTTTGCGTCATAAAAAAAATAGT
*
16861 TTTTGCGTTTTTC-TAAAAAAAAGAGT
1 TTTTGCG----TCATAAAAAAAATAGT
16887 TTTTGCGTCATAAAAAAA
1 TTTTGCGTCATAAAAAAA
16905 GAAAAAAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
21 1 0.01
22 25 0.35
23 24 0.34
25 9 0.13
26 12 0.17
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (23 bp):
TTTTGCGTCATAAAAAAAATAGT
Found at i:20132 original size:21 final size:21
Alignment explanation
Indices: 20089--20143 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
20079 CACCCATTCA
***
20089 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGACCAAGC
*
20110 CCGTGCCACCACCGACCATGC
1 CCGTGCCACCACCGACCAAGC
*
20131 CCGTGCCATCACC
1 CCGTGCCACCACC
20144 ATTCCATGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.49, G:0.20, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGACCAAGC
Found at i:25600 original size:21 final size:21
Alignment explanation
Indices: 25570--25625 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
25560 GTTTCTGCAC
*
25570 AACTTACAATCGATTAAAACT
1 AACTTTCAATCGATTAAAACT
* *
25591 AACTTTCAATTGATTGAAACT
1 AACTTTCAATCGATTAAAACT
***
25612 GTTTTTCAATCGAT
1 AACTTTCAATCGAT
25626 GGAAACCTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
AACTTTCAATCGATTAAAACT
Found at i:26146 original size:25 final size:25
Alignment explanation
Indices: 26118--26168 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
26108 ATGTTGATAA
26118 CAATCTAGTTGTTATATGATCAAAT
1 CAATCTAGTTGTTATATGATCAAAT
26143 CAATCTAGTTGTTATATGATCAAAT
1 CAATCTAGTTGTTATATGATCAAAT
26168 C
1 C
26169 TACCATCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (25 bp):
CAATCTAGTTGTTATATGATCAAAT
Found at i:26170 original size:21 final size:23
Alignment explanation
Indices: 26112--26165 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 23
26102 TGACACATGT
26112 TGAT-AACAATCTAGTTGTTATA
1 TGATCAACAATCTAGTTGTTATA
26134 TGATCAAATCAATCTAGTTGTTATA
1 TGATC-AA-CAATCTAGTTGTTATA
26159 TGATCAA
1 TGATCAA
26166 ATCTACCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.14
24 4 0.14
25 21 0.72
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (23 bp):
TGATCAACAATCTAGTTGTTATA
Found at i:27007 original size:24 final size:24
Alignment explanation
Indices: 26970--27015 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
26960 ATCTTCATGC
26970 CTCCATGCAATCCATGCTCATCCT
1 CTCCATGCAATCCATGCTCATCCT
** *
26994 CTCCATGCTCTCCATGGTCATC
1 CTCCATGCAATCCATGCTCATC
27016 TTCAAGTCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.41, G:0.11, T:0.30
Consensus pattern (24 bp):
CTCCATGCAATCCATGCTCATCCT
Found at i:31247 original size:23 final size:23
Alignment explanation
Indices: 31221--31264 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
31211 TTAATGTATA
*
31221 TTTTTGTAT-TTTTTGT-ATTAT
1 TTTTTTTATATTTTTGTGATTAT
31242 TTTTTTTATATTTTTGTGATTAT
1 TTTTTTTATATTTTTGTGATTAT
31265 GAATGTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 7 0.35
23 5 0.25
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.75
Consensus pattern (23 bp):
TTTTTTTATATTTTTGTGATTAT
Found at i:36908 original size:22 final size:22
Alignment explanation
Indices: 36866--36913 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
36856 CGACCGTTTG
* *
36866 CTTCCTCTTGAGTTGAAAATTT
1 CTTCCTCTTGAGTCGAAAATTC
*
36888 CTTCCTCTT-AGTCGATTAATTC
1 CTTCCTCTTGAGTCGA-AAATTC
36910 CTTC
1 CTTC
36914 ACTTGAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.19, C:0.25, G:0.10, T:0.46
Consensus pattern (22 bp):
CTTCCTCTTGAGTCGAAAATTC
Found at i:48743 original size:3 final size:3
Alignment explanation
Indices: 48735--48768 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
48725 CCCCTCAAAA
48735 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
48769 AAAGAGCTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:49625 original size:30 final size:28
Alignment explanation
Indices: 49572--49627 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
49562 GACTTCAATA
* *
49572 AATAGATGATAAATAATGGAAATAGATG
1 AATAGATAATAAATAAGGGAAATAGATG
49600 AATAGATAATAGAATTAAGGGAAATAGA
1 AATAGATAATA-AA-TAAGGGAAATAGA
49628 ATAAATTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.42
29 2 0.08
30 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.23
Consensus pattern (28 bp):
AATAGATAATAAATAAGGGAAATAGATG
Found at i:50047 original size:25 final size:25
Alignment explanation
Indices: 50013--50144 Score: 212
Period size: 25 Copynumber: 5.3 Consensus size: 25
50003 CGGTCACCAA
*
50013 TGTATTGCCACGTAGGTGTGGGCTT
1 TGTATTGCCACATAGGTGTGGGCTT
*
50038 TGTATTGCCACATGGGTGTGGGCTT
1 TGTATTGCCACATAGGTGTGGGCTT
*
50063 TGTAGTGCCACAT-GGATGTGGGCTT
1 TGTATTGCCACATAGG-TGTGGGCTT
50088 TGTATTGCCACATAGGTGTGGGCTT
1 TGTATTGCCACATAGGTGTGGGCTT
*
50113 TGTATTGCCACATACGTGTGGGCTT
1 TGTATTGCCACATAGGTGTGGGCTT
50138 TGTATTG
1 TGTATTG
50145 AACCATGGAG
Statistics
Matches: 100, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
24 2 0.02
25 96 0.96
26 2 0.02
ACGTcount: A:0.14, C:0.16, G:0.33, T:0.36
Consensus pattern (25 bp):
TGTATTGCCACATAGGTGTGGGCTT
Found at i:50751 original size:18 final size:19
Alignment explanation
Indices: 50728--50766 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
50718 TGGGTATTTT
50728 GTGTTT-GATTTAGGCTAA
1 GTGTTTGGATTTAGGCTAA
*
50746 GTGTTTGGGATTTGGGCTAA
1 GTGTTT-GGATTTAGGCTAA
50766 G
1 G
50767 AGAGGTTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.18, C:0.05, G:0.36, T:0.41
Consensus pattern (19 bp):
GTGTTTGGATTTAGGCTAA
Found at i:51652 original size:3 final size:3
Alignment explanation
Indices: 51646--51712 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
51636 CAAATAATAT
51646 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
51694 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
51713 AGTATATAGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54449 original size:17 final size:18
Alignment explanation
Indices: 54429--54471 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
54419 TAATTTTTAG
54429 ATTTTTTCC-ACTTTTTC
1 ATTTTTTCCTACTTTTTC
*
54446 ATTTTTTCCTTCTTTTTC
1 ATTTTTTCCTACTTTTTC
54464 ATTTTTTC
1 ATTTTTTC
54472 TTCAACTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTTCCTACTTTTTC
Found at i:57609 original size:21 final size:21
Alignment explanation
Indices: 57583--57626 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
57573 ATCTAGATGC
**
57583 AAATGTGAGATTAATATGCAA
1 AAATGTGAGACAAATATGCAA
*
57604 AAATGTGATACAAATATGCAA
1 AAATGTGAGACAAATATGCAA
57625 AA
1 AA
57627 GAACACAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (21 bp):
AAATGTGAGACAAATATGCAA
Found at i:57784 original size:27 final size:26
Alignment explanation
Indices: 57743--57796 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
57733 CACAATGCCC
**
57743 CCCCTGAAGTACAAATGACCAAAATG
1 CCCCTGAAGTACAAACCACCAAAATG
*
57769 CCCCTGAACGTGCAAACCACCAAAATG
1 CCCCTGAA-GTACAAACCACCAAAATG
57796 C
1 C
57797 TAAATAAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.39, C:0.33, G:0.15, T:0.13
Consensus pattern (26 bp):
CCCCTGAAGTACAAACCACCAAAATG
Found at i:60654 original size:21 final size:21
Alignment explanation
Indices: 60629--60674 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
60619 CTAGAGATAG
*
60629 AAAAAGATAAAAAAAAAAAAA
1 AAAAAGAGAAAAAAAAAAAAA
** *
60650 AAAAAGAGAAATCAAAAAATA
1 AAAAAGAGAAAAAAAAAAAAA
60671 AAAA
1 AAAA
60675 GACGCAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAAAGAGAAAAAAAAAAAAA
Found at i:60849 original size:38 final size:38
Alignment explanation
Indices: 60807--60908 Score: 204
Period size: 38 Copynumber: 2.7 Consensus size: 38
60797 TTTAAGCAAC
60807 TCCAAAAGAAGATTTTGGAAAATAAAAGTTTGGGTAAT
1 TCCAAAAGAAGATTTTGGAAAATAAAAGTTTGGGTAAT
60845 TCCAAAAGAAGATTTTGGAAAATAAAAGTTTGGGTAAT
1 TCCAAAAGAAGATTTTGGAAAATAAAAGTTTGGGTAAT
60883 TCCAAAAGAAGATTTTGGAAAATAAA
1 TCCAAAAGAAGATTTTGGAAAATAAA
60909 GAAATCCAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (38 bp):
TCCAAAAGAAGATTTTGGAAAATAAAAGTTTGGGTAAT
Found at i:61920 original size:27 final size:26
Alignment explanation
Indices: 61890--61967 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 26
61880 GCTTTAGGAT
*
61890 CACCCATGGGCATTTTGGTCATTTGGG
1 CACCCA-GGGCATTTTGGTCATTTGGA
* *
61917 CACCAAAGGGCATTTTGGTCATTTGTA
1 CACC-CAGGGCATTTTGGTCATTTGGA
**
61944 CATTCAGGAGCATTTTGGTCATTT
1 CACCCAGG-GCATTTTGGTCATTT
61968 TACGTCCACT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.07
27 39 0.91
28 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (26 bp):
CACCCAGGGCATTTTGGTCATTTGGA
Found at i:64737 original size:30 final size:30
Alignment explanation
Indices: 64703--64765 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
64693 TTGTTTTCTG
*
64703 GTTCGTTTAAAGACTCAACA-TTGTTTCCGT
1 GTTCGTTTAAAGACTCAA-ATTTGTTTCCAT
**
64733 GTTCGTTTAGGGACTCAAATTTGTTTCCAT
1 GTTCGTTTAAAGACTCAAATTTGTTTCCAT
64763 GTT
1 GTT
64766 TGCATGGTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (30 bp):
GTTCGTTTAAAGACTCAAATTTGTTTCCAT
Found at i:64899 original size:40 final size:41
Alignment explanation
Indices: 64855--64946 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 41
64845 TGCGGCTTAG
*
64855 TCCCTGATTTAAGA-TTTATTTACTATTTGATGCAATCTGA
1 TCCCTGATTTAAGATTTTACTTACTATTTGATGCAATCTGA
* * * *
64895 TCCCTGATTTAGGATTTTACTTGCTTTTTGATGCAATTTGA
1 TCCCTGATTTAAGATTTTACTTACTATTTGATGCAATCTGA
*
64936 CCCCTGATTTA
1 TCCCTGATTTA
64947 TATTATTGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 13 0.29
41 32 0.71
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.46
Consensus pattern (41 bp):
TCCCTGATTTAAGATTTTACTTACTATTTGATGCAATCTGA
Found at i:65728 original size:74 final size:73
Alignment explanation
Indices: 65598--65734 Score: 168
Period size: 74 Copynumber: 1.9 Consensus size: 73
65588 CTGGTCATAA
* * * ** *
65598 AAAAAATAAATTCTTTGAATTAAATGTTCGATTTTGGATTAAAATTAGTTTTGAAATCGATTAAT
1 AAAAAATAAAGTCTTTGAATTAAATGTTCGATTTTAGATTAAAATTAATTCAGAAATAGATTAAT
65663 CTTAATTT
66 CTTAATTT
* * *
65671 AAAAAATCAAGTCTTTGATTTAAA-GATTTGACTTTTAGATTAAAATTAATTCAGAAATAGATTA
1 AAAAAATAAAGTCTTTGAATTAAATG-TTCGA-TTTTAGATTAAAATTAATTCAGAAATAGATTA
65735 TCGAATCTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
72 1 0.02
73 25 0.47
74 27 0.51
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (73 bp):
AAAAAATAAAGTCTTTGAATTAAATGTTCGATTTTAGATTAAAATTAATTCAGAAATAGATTAAT
CTTAATTT
Found at i:86062 original size:40 final size:40
Alignment explanation
Indices: 86018--86103 Score: 120
Period size: 43 Copynumber: 2.1 Consensus size: 40
86008 AGTGCATTAC
* *
86018 CTAAATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAG
1 CTAAATTCTACCTCCATCTCTAGATAATTCATC-AAATAAA
86058 CTAAATTCTACTCCTCCATCTCTAGATAATTCATCAAATAAA
1 CTAAATTCTA--CCTCCATCTCTAGATAATTCATCAAATAAA
86100 CTAA
1 CTAA
86104 TATTAATTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 10 0.24
42 10 0.24
43 21 0.51
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (40 bp):
CTAAATTCTACCTCCATCTCTAGATAATTCATCAAATAAA
Found at i:90764 original size:38 final size:38
Alignment explanation
Indices: 90721--90918 Score: 256
Period size: 38 Copynumber: 5.1 Consensus size: 38
90711 AATGATTCTC
*
90721 AAAGTTTTCAAATTGGGGAAGATCCCATCAAGTTTTCA
1 AAAGTTTTCAAATTGGGAAAGATCCCATCAAGTTTTCA
*
90759 AAAGTTTTCAAATTGGGAAAGATCCCATCAAGTCTTCA
1 AAAGTTTTCAAATTGGGAAAGATCCCATCAAGTTTTCA
* *
90797 AAAGTTTTCAAATTGTGAAAGATCCCATCCAGTTTTTC-
1 AAAGTTTTCAAATTGGGAAAGATCCCATCAAG-TTTTCA
*
90835 AAAGTTTTCAAATTGGGAAAGATCCCATCCAGTTTTGTTTTTC-
1 AAAGTTTTCAAATTGGGAAAGATCCCAT-CA----AG-TTTTCA
*
90878 AAAGTTTTCAATTTGGGGAAAGATCCCATCAAGTTTTCA
1 AAAGTTTTCAAATT-GGGAAAGATCCCATCAAGTTTTCA
90917 AA
1 AA
90919 GTAATTCAAA
Statistics
Matches: 142, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
38 98 0.69
39 8 0.06
43 22 0.15
44 14 0.10
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (38 bp):
AAAGTTTTCAAATTGGGAAAGATCCCATCAAGTTTTCA
Found at i:90969 original size:21 final size:21
Alignment explanation
Indices: 90944--91021 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
90934 AAGTAAAATG
90944 GTAATCAGTAAAGAATAAAAA
1 GTAATCAGTAAAGAATAAAAA
* * * **
90965 GTAATCTGTAAAAAAATGGTAATG
1 GTAATCAGT-AAAGAAT--AAAAA
* * *
90989 GTAATCAATAAAGAGTAAAGA
1 GTAATCAGTAAAGAATAAAAA
91010 GTAATCAGTAAA
1 GTAATCAGTAAA
91022 ATGGTAATGG
Statistics
Matches: 41, Mismatches: 13, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
21 21 0.51
22 6 0.15
23 5 0.12
24 9 0.22
ACGTcount: A:0.54, C:0.05, G:0.18, T:0.23
Consensus pattern (21 bp):
GTAATCAGTAAAGAATAAAAA
Found at i:91034 original size:21 final size:22
Alignment explanation
Indices: 91010--91069 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
91000 AGAGTAAAGA
*
91010 GTAATCAGTAAAATGGTAATG-
1 GTAATCAGTAAAATGGTAAAGA
91031 GTAATCAGT-AAA-GAGTAAAGA
1 GTAATCAGTAAAATG-GTAAAGA
*
91052 GTAATTAGTAAAATGGTA
1 GTAATCAGTAAAATGGTA
91070 TTTGGTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 1 0.03
20 8 0.24
21 17 0.52
22 6 0.18
23 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.23, T:0.27
Consensus pattern (22 bp):
GTAATCAGTAAAATGGTAAAGA
Found at i:91036 original size:42 final size:42
Alignment explanation
Indices: 90940--91108 Score: 193
Period size: 42 Copynumber: 4.0 Consensus size: 42
90930 CAAAAAGTAA
* * *
90940 AATGGTAATCAGTAAAGAATAAAAAGTAATCTGTAAAAAAATGGT
1 AATGGTAATCAGTAAAGAGTAAAGAGTAATCAGT---AAAATGGT
*
90985 AATGGTAATCAATAAAGAGTAAAGAGTAATCAGTAAAATGGT
1 AATGGTAATCAGTAAAGAGTAAAGAGTAATCAGTAAAATGGT
*
91027 AATGGTAATCAGTAAAGAGTAAAGAGTAATTAGTAAAATGGT
1 AATGGTAATCAGTAAAGAGTAAAGAGTAATCAGTAAAATGGT
* ** *
91069 ATTTGGTAAAAAGT--TGA--AAAGAGTAATCAGTAAAATGGT
1 A-ATGGTAATCAGTAAAGAGTAAAGAGTAATCAGTAAAATGGT
91108 A
1 A
91109 TTTGGTAAAA
Statistics
Matches: 112, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
39 22 0.20
41 2 0.02
42 49 0.44
43 9 0.08
45 30 0.27
ACGTcount: A:0.50, C:0.04, G:0.21, T:0.25
Consensus pattern (42 bp):
AATGGTAATCAGTAAAGAGTAAAGAGTAATCAGTAAAATGGT
Found at i:91101 original size:39 final size:39
Alignment explanation
Indices: 91005--91166 Score: 185
Period size: 39 Copynumber: 4.2 Consensus size: 39
90995 AATAAAGAGT
* ** *
91005 AAAGAGTAATCAGTAAAATGGTA-ATGGTAATCAGTAAAGA
1 AAAGAGTAATCAGTAAAATGGTATTTGGTAAAAAGT--TGA
*
91045 GTAAAGAGTAATTAGTAAAATGGTATTTGGTAAAAAGTTGA
1 --AAAGAGTAATCAGTAAAATGGTATTTGGTAAAAAGTTGA
91086 AAAGAGTAATCAGTAAAATGGTATTTGGTAAAAAGTTGA
1 AAAGAGTAATCAGTAAAATGGTATTTGGTAAAAAGTTGA
*
91125 AAAGAG---T-A--AAAATGGCATTTGGTAAAAAGTTGA
1 AAAGAGTAATCAGTAAAATGGTATTTGGTAAAAAGTTGA
91158 AAAGAGTAA
1 AAAGAGTAA
91167 AAATGGTATT
Statistics
Matches: 109, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
33 30 0.28
35 1 0.01
36 1 0.01
39 44 0.40
41 2 0.02
42 22 0.20
43 9 0.08
ACGTcount: A:0.48, C:0.02, G:0.23, T:0.26
Consensus pattern (39 bp):
AAAGAGTAATCAGTAAAATGGTATTTGGTAAAAAGTTGA
Found at i:91135 original size:17 final size:17
Alignment explanation
Indices: 91113--91169 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
91103 ATGGTATTTG
91113 GTAAAAAGTTGAAAAGA
1 GTAAAAAGTTGAAAAGA
* ***
91130 GTAAAAA-TGGCATTTG-
1 GTAAAAAGTTG-AAAAGA
91146 GTAAAAAGTTGAAAAGA
1 GTAAAAAGTTGAAAAGA
91163 GTAAAAA
1 GTAAAAA
91170 TGGTATTTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
16 11 0.38
17 18 0.62
ACGTcount: A:0.54, C:0.02, G:0.23, T:0.21
Consensus pattern (17 bp):
GTAAAAAGTTGAAAAGA
Found at i:91190 original size:34 final size:33
Alignment explanation
Indices: 91100--91222 Score: 192
Period size: 33 Copynumber: 3.6 Consensus size: 33
91090 AGTAATCAGT
91100 AAAATGGTATTTGGTAAAAAGTTGAAAAGAGTA
1 AAAATGGTATTTGGTAAAAAGTTGAAAAGAGTA
*
91133 AAAATGGCATTTGGTAAAAAGTTGAAAAGAGTA
1 AAAATGGTATTTGGTAAAAAGTTGAAAAGAGTA
**
91166 AAAATGGTATTTAATTAAAAAGTTGAAAAGAGTA
1 AAAATGGTATTT-GGTAAAAAGTTGAAAAGAGTA
91200 AAAATGGTATTTGGAGTAAAAAG
1 AAAATGGTATTT-G-GTAAAAAG
91223 GTATTTAGTA
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
33 43 0.53
34 31 0.38
35 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.23, T:0.27
Consensus pattern (33 bp):
AAAATGGTATTTGGTAAAAAGTTGAAAAGAGTA
Found at i:91216 original size:18 final size:17
Alignment explanation
Indices: 91195--91228 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
91185 AAGTTGAAAA
91195 GAGTAAAAATGGTATTTG
1 GAGTAAAAA-GGTATTTG
91213 GAGTAAAAAGGTATTT
1 GAGTAAAAAGGTATTT
91229 AGTAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.32
Consensus pattern (17 bp):
GAGTAAAAAGGTATTTG
Found at i:91220 original size:17 final size:18
Alignment explanation
Indices: 91195--91228 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
91185 AAGTTGAAAA
*
91195 GAGTAAAAATGGTATTTG
1 GAGTAAAAAAGGTATTTG
91213 GAGT-AAAAAGGTATTT
1 GAGTAAAAAAGGTATTT
91229 AGTAATTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.32
Consensus pattern (18 bp):
GAGTAAAAAAGGTATTTG
Found at i:91240 original size:51 final size:54
Alignment explanation
Indices: 91161--91264 Score: 126
Period size: 53 Copynumber: 2.0 Consensus size: 54
91151 AAGTTGAAAA
* * * *
91161 GAGTAAAAATGGTATTTAATTAAAAAG-TT-GAAAAGAGTAAAAATGGTATTTG
1 GAGTAAAAATGGTATTTAAGTAAAAAGTTTAAAAAAGACTAAAAAAGGTATTTG
*
91213 GAGTAAAAA-GGTATTT-AGTAATTAAGTTTAAAAAAGACTAAAAAAGGTATTT
1 GAGTAAAAATGGTATTTAAGTAA-AAAGTTTAAAAAAGACTAAAAAAGGTATTT
91265 AATAATTAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 4 0.09
51 10 0.23
52 11 0.25
53 19 0.43
ACGTcount: A:0.49, C:0.01, G:0.19, T:0.31
Consensus pattern (54 bp):
GAGTAAAAATGGTATTTAAGTAAAAAGTTTAAAAAAGACTAAAAAAGGTATTTG
Found at i:91255 original size:35 final size:34
Alignment explanation
Indices: 91216--91308 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 34
91206 GTATTTGGAG
91216 TAAAAAGGTATTTAGTAATTAAGTTTAAAAAAGAC
1 TAAAAAGGTATTTAGTAATTAAGTTT-AAAAAGAC
* *
91251 TAAAAAAGGTATTTAATAATTAAGTTTAAAAAGAG
1 T-AAAAAGGTATTTAGTAATTAAGTTTAAAAAGAC
* *
91286 TAAAAATGGGATTCAGTAATTAA
1 TAAAAA-GGTATTTAGTAATTAA
91309 AGTAAAAAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
34 5 0.10
35 22 0.43
36 24 0.47
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.31
Consensus pattern (34 bp):
TAAAAAGGTATTTAGTAATTAAGTTTAAAAAGAC
Found at i:91258 original size:36 final size:35
Alignment explanation
Indices: 91217--91308 Score: 130
Period size: 35 Copynumber: 2.6 Consensus size: 35
91207 TATTTGGAGT
91217 AAAAAGGTATTTAGTAATTAAGTTTAAAAAAGACTA
1 AAAAAGGTATTTAGTAATTAAGTTT-AAAAAGACTA
* *
91253 AAAAAGGTATTTAATAATTAAGTTTAAAAAGAGTA
1 AAAAAGGTATTTAGTAATTAAGTTTAAAAAGACTA
* * *
91288 AAAATGGGATTCAGTAATTAA
1 AAAAAGGTATTTAGTAATTAA
91309 AGTAAAAAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
35 26 0.52
36 24 0.48
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.30
Consensus pattern (35 bp):
AAAAAGGTATTTAGTAATTAAGTTTAAAAAGACTA
Found at i:91317 original size:35 final size:34
Alignment explanation
Indices: 91213--91318 Score: 124
Period size: 35 Copynumber: 3.0 Consensus size: 34
91203 ATGGTATTTG
91213 GAGTAAAAAGGTATTTAGTAATTAAGTTTAAAAAA
1 GAGTAAAAAGGTATTTAGTAATTAAG-TTAAAAAA
* * *
91248 GACTAAAAAAGGTATTTAATAATTAAGTTTAAAAA
1 GAGT-AAAAAGGTATTTAGTAATTAAGTTAAAAAA
* *
91283 GAGTAAAAATGGGATTCAGTAATTAAAG-TAAAAAA
1 GAGTAAAAA-GGTATTTAGTAATT-AAGTTAAAAAA
91318 G
1 G
91319 GTTAAATTGG
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
34 5 0.08
35 31 0.52
36 24 0.40
ACGTcount: A:0.53, C:0.02, G:0.17, T:0.28
Consensus pattern (34 bp):
GAGTAAAAAGGTATTTAGTAATTAAGTTAAAAAA
Found at i:91386 original size:33 final size:34
Alignment explanation
Indices: 91349--91425 Score: 97
Period size: 33 Copynumber: 2.3 Consensus size: 34
91339 AAAGGGTGAG
*
91349 AAATGGTAATAAGTAATTCAAGTT-A-AAAGAGTA
1 AAATGGTAATAAGTAA-TCAAATTCAGAAAGAGTA
*
91382 AAATGGTAATCAGTAATCAAATTCAGTAAAGAGTA
1 AAATGGTAATAAGTAATCAAATTCAG-AAAGAGTA
91417 AAA-GGTAAT
1 AAATGGTAAT
91426 GGTAAAGAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 6 0.15
33 16 0.41
34 6 0.15
35 11 0.28
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.26
Consensus pattern (34 bp):
AAATGGTAATAAGTAATCAAATTCAGAAAGAGTA
Found at i:93960 original size:11 final size:11
Alignment explanation
Indices: 93944--93969 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
93934 AGATAATTTC
93944 TTTTCTTCTAG
1 TTTTCTTCTAG
93955 TTTTCTTCTAG
1 TTTTCTTCTAG
93966 TTTT
1 TTTT
93970 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:94760 original size:15 final size:15
Alignment explanation
Indices: 94730--94771 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
94720 TTACTCTGCT
94730 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
94746 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
94761 TTGCTTTCTGT
1 TTGTTTTCTGT
94772 CAATCTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:95247 original size:26 final size:27
Alignment explanation
Indices: 95218--95284 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
95208 TTTTTCGTCG
*
95218 AAAAAAAAATATTGTTTCTGCG-TCAT
1 AAAAAAAAATATTGTTCCTGCGTTCAT
* * **
95244 AAAAAAAATTCTTGTTCCTGCGTTTTT
1 AAAAAAAAATATTGTTCCTGCGTTCAT
95271 AGAAAAAAAATATT
1 A-AAAAAAAATATT
95285 TTCTTTTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 19 0.59
27 3 0.09
28 10 0.31
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (27 bp):
AAAAAAAAATATTGTTCCTGCGTTCAT
Found at i:95821 original size:15 final size:15
Alignment explanation
Indices: 95791--95832 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
95781 TTACTCTGCT
95791 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
95807 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
95822 TTGCTTTCTGT
1 TTGTTTTCTGT
95833 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:103081 original size:2 final size:2
Alignment explanation
Indices: 103068--103104 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
103058 TGCTTTCCAT
*
103068 TA TA TG TA TA TA 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 TA TA TA TA TA TA T
103105 TCTACTGTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:103533 original size:16 final size:15
Alignment explanation
Indices: 103512--103551 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
103502 TTTCAAACGA
103512 TTTTTCAAAAAAATG
1 TTTTTCAAAAAAATG
103527 TTTTTTC-AAAAAATG
1 -TTTTTCAAAAAAATG
*
103542 GTTTTCAAAA
1 TTTTTCAAAA
103552 TTTGTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 11 0.50
16 6 0.27
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (15 bp):
TTTTTCAAAAAAATG
Found at i:103537 original size:15 final size:14
Alignment explanation
Indices: 103512--103551 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
103502 TTTCAAACGA
103512 TTTTTCAAAAAAATG
1 TTTTTC-AAAAAATG
103527 TTTTTTCAAAAAATG
1 -TTTTTCAAAAAATG
*
103542 GTTTTCAAAA
1 TTTTTCAAAA
103552 TTTGTTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.39
15 8 0.35
16 6 0.26
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (14 bp):
TTTTTCAAAAAATG
Found at i:105194 original size:36 final size:36
Alignment explanation
Indices: 105084--105559 Score: 559
Period size: 36 Copynumber: 13.2 Consensus size: 36
105074 TCGGTTTTTA
* ** * *
105084 TTCAGTTTATTT-TAGTTGATTCAGGGCGATCTGTTCC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCT-TT-C
* * *
105121 TTCAGTTTATTTCAA-CTGATCCA-GGTCGATCTCTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGT-GGTCT-TTC
* *
105157 TTCAGTTTATATCAAGTTGACCTAGGGTGGTCTTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTC
* *
105193 TTCAGTTTATTTCAAGTTGAACTAGGGTGGTCTTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTC
* * *
105229 TTCAATTTATTTCAAGTTGACCTAGGGTGATCTTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTC
*
105265 TTCAGTTTACTTC-AGTTGACCCAGGGTGGTCTTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTC
* * * * *
105300 CTCAGTTTATTTCAAGTTGATCAAGGGCGATCTCTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCT-TTC
105337 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTC
*
105373 TTCAGTTTATTTCAAGTTGACCCAGGGTGTTCTTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTC
* *
105409 TTCAGTTTACTTC-AGTTGACCCAGGGTAGTCTTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTC
* *
105444 TTCAGTTTATTTCAGGTTGACCCATGGTGGTCTTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTC
* * *
105480 TTCAGTTTATTTC-AGTTGATCCAGGGCGATCTCTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCT-TTC
* * *
105516 TTCAGTTTATTTCAAGTTGATCCAGGGCGATCCTTTC
1 TTCAGTTTATTTCAAGTTGACCCAGGGTGGT-CTTTC
105553 TTCAGTT
1 TTCAGTT
105560 AGCTTCAGTT
Statistics
Matches: 386, Mismatches: 43, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
35 77 0.20
36 211 0.55
37 92 0.24
38 6 0.02
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (36 bp):
TTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTC
Found at i:105366 original size:180 final size:179
Alignment explanation
Indices: 105084--105559 Score: 679
Period size: 180 Copynumber: 2.6 Consensus size: 179
105074 TCGGTTTTTA
* ** * * * *
105084 TTCAGTTTATTTTAGTTGATTCAGGGCGATCTGTTCCTTCAGTTTATTTCAA-CTGATCCAGGTC
1 TTCAGTTTATTTCAGTTGACCCAGGGTGGTCT-TTCC-TCAGTTTATTTCAAGTTGATCCAGGGC
* *
105148 GATCTCTTCTTCAGTTTATATCAAGTTGACCTAGGGTGGTCTTTCTTCAGTTTATTTCAAGTTGA
64 GATCTCTTCTTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAAGTTGA
* * *
105213 ACTAGGGTGGTCTTTCTTCAATTTATTTCAAGTTGACCTAGGGT-GATCTTTC
129 ACCAGGGTGGTCTTTCTTCAATTTACTTC-AGTTGACCCAGGGTAG-TCTTTC
* *
105265 TTCAGTTTACTTCAGTTGACCCAGGGTGGTCTTTCCTCAGTTTATTTCAAGTTGATCAAGGGCGA
1 TTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCCTCAGTTTATTTCAAGTTGATCCAGGGCGA
*
105330 TCTCTTCTTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAAGTTGACC
66 TCTCTTCTTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAAGTTGAAC
* *
105395 CAGGGTGTTCTTTCTTCAGTTTACTTCAGTTGACCCAGGGTAGTCTTTC
131 CAGGGTGGTCTTTCTTCAATTTACTTCAGTTGACCCAGGGTAGTCTTTC
* *
105444 TTCAGTTTATTTCAGGTTGACCCATGGTGGTCTTTCTTCAGTTTATTTC-AGTTGATCCAGGGCG
1 TTCAGTTTATTTCA-GTTGACCCAGGGTGGTCTTTCCTCAGTTTATTTCAAGTTGATCCAGGGCG
* * *
105508 ATCTCTTCTTCAGTTTATTTCAAGTTGATCCAGGGCGATCCTTTCTTCAGTT
65 ATCTCTTCTTCAGTTTATTTCAAGTTGACCCAGGGTGGT-CTTTCTTCAGTT
105560 AGCTTCAGTT
Statistics
Matches: 267, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
179 96 0.36
180 145 0.54
181 26 0.10
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (179 bp):
TTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCCTCAGTTTATTTCAAGTTGATCCAGGGCGA
TCTCTTCTTCAGTTTATTTCAAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCAAGTTGAAC
CAGGGTGGTCTTTCTTCAATTTACTTCAGTTGACCCAGGGTAGTCTTTC
Found at i:105592 original size:33 final size:32
Alignment explanation
Indices: 105475--105608 Score: 76
Period size: 36 Copynumber: 3.9 Consensus size: 32
105465 CCATGGTGGT
* *
105475 CTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGAT-
1 CTTTCTGCAGTTTACTTCAGTTGA-CC---GCGATC
* *
105510 CTCTTCTTCAGTTTATTTCAAGTTGATCCAGGGCGATC
1 CT-TTCTGCAGTTTACTTC-AGTTGA-CC---GCGATC
*
105548 CTTTCTTCAG-TTAGCTTCAGTTGATCCGCGAT-
1 CTTTCTGCAGTTTA-CTTCAGTTGA-CCGCGATC
*
105580 CTTCTCTGCAGTTTATTTCAGTTGACCGC
1 CTT-TCTGCAGTTTACTTCAGTTGACCGC
105609 AAATTGGTCC
Statistics
Matches: 90, Mismatches: 3, Indels: 15
0.83 0.03 0.14
Matches are distributed among these distances:
32 7 0.08
33 20 0.22
34 3 0.03
35 2 0.02
36 28 0.31
37 28 0.31
38 2 0.02
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (32 bp):
CTTTCTGCAGTTTACTTCAGTTGACCGCGATC
Found at i:105891 original size:30 final size:30
Alignment explanation
Indices: 105855--106444 Score: 934
Period size: 30 Copynumber: 19.8 Consensus size: 30
105845 TTGAGGATCG
105855 TTATTTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
105885 TTATTTTAATCTTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
105915 TTATTTTAAACCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
105945 TTATTTTAATCCTGTTTGAGGATCATGGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
105975 TTATTTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
106005 TTATTTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* *
106035 TCATTTTAATCTTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
106065 TTATTTTAATCATGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* *
106095 TTA-TTAAATCCTATTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
106124 TTATTTTAATCCTGGTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* * *
106154 TTATTTTAATCCTGGTTGAGGATCGTCGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
106184 TTATTTTAATCCTGTTTTAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* *
106214 TTA-TTAAATCCTGTTTGAGGATCATTGTT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
106243 TTATTTTAATCCTGGTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* * *
106273 TTA-TTAAATCTTGTTTGAGGATCATTACT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
106302 TTATTTTAATCCTGGTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
* *
106332 TCATTTTAATCCTGTTTGAGGATCATTACT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
106362 TTATTTTAATCCTGGTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
106392 TCATTTTAATCCTGTTTGAGGATCATTGCT
1 TTATTTTAATCCTGTTTGAGGATCATTGCT
*
106422 TTATTTTAATCCTGGTTGAGGAT
1 TTATTTTAATCCTGTTTGAGGAT
106445 ATTTGCATGA
Statistics
Matches: 511, Mismatches: 46, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
29 77 0.15
30 434 0.85
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.48
Consensus pattern (30 bp):
TTATTTTAATCCTGTTTGAGGATCATTGCT
Found at i:106760 original size:22 final size:22
Alignment explanation
Indices: 106732--106862 Score: 217
Period size: 22 Copynumber: 5.9 Consensus size: 22
106722 TGGAAACATT
*
106732 TTTGCAGAGCATTATTTACCAC
1 TTTGCAGAGCATTATTTTCCAC
*
106754 TTTGCAGAGCATTATTTTCTAC
1 TTTGCAGAGCATTATTTTCCAC
106776 TTTGCAGAGCATTATTTTCCAC
1 TTTGCAGAGCATTATTTTCCAC
*
106798 TTTGCAGAGCATTATTTTCTAC
1 TTTGCAGAGCATTATTTTCCAC
106820 TTTGCAGAGCATTATTTTCCAC
1 TTTGCAGAGCATTATTTTCCAC
106842 TTTGCAGAGTGCATTATTTTC
1 TTTGCAGA--GCATTATTTTC
106863 TTCAACTTCA
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
22 91 0.89
24 11 0.11
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.43
Consensus pattern (22 bp):
TTTGCAGAGCATTATTTTCCAC
Found at i:110737 original size:2 final size:2
Alignment explanation
Indices: 110726--110755 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
110716 ATATCTTTTG
110726 AT AT -T 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 AT AT A
110756 AAAGAATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110789 original size:19 final size:19
Alignment explanation
Indices: 110765--110801 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
110755 AAAAGAATTG
110765 AAGTACTTTGAATTTATCC
1 AAGTACTTTGAATTTATCC
110784 AAGTACTTTGAATTTATC
1 AAGTACTTTGAATTTATC
110802 ATTTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (19 bp):
AAGTACTTTGAATTTATCC
Found at i:123090 original size:16 final size:15
Alignment explanation
Indices: 123069--123116 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 15
123059 AGGAATAAGC
123069 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
123084 TAATCAATCAAAGCAA
1 -AATCAATCAAAGCAA
123100 AA-CAATGCAAAG-AA
1 AATCAAT-CAAAGCAA
123114 AAT
1 AAT
123117 AAATAGATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.27
15 7 0.23
16 15 0.50
ACGTcount: A:0.60, C:0.17, G:0.08, T:0.15
Consensus pattern (15 bp):
AATCAATCAAAGCAA
Found at i:123289 original size:6 final size:6
Alignment explanation
Indices: 123273--123310 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
123263 ATGAAACCCT
123273 AAAAG- AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA
123311 CTAGAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:125408 original size:18 final size:20
Alignment explanation
Indices: 125378--125414 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
125368 GCACCCTAGC
125378 CTAAAACCTAGAA-GAAAAA
1 CTAAAACCTAGAAGGAAAAA
125397 CTAAAA-CTAGAAGGAAAA
1 CTAAAACCTAGAAGGAAAA
125415 TAGATGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.11
Consensus pattern (20 bp):
CTAAAACCTAGAAGGAAAAA
Found at i:132215 original size:19 final size:18
Alignment explanation
Indices: 132182--132217 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
132172 TTGAGATAAT
132182 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
132200 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
132218 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:132814 original size:127 final size:127
Alignment explanation
Indices: 132586--132829 Score: 285
Period size: 127 Copynumber: 1.9 Consensus size: 127
132576 GAAGAATTCT
* * *
132586 GAATTTTGTGATTTTTGTTCTACATTCATTATTGCTTCGATTGGCTTGAAATTTGAGATTTAGAG
1 GAATTTTGTGATTTTTCTTCTACATTCATTAGTGCTGCGATTGGCTTGAAATTTGAGATTTAGAG
* * ** *
132651 TTCTTATACAACAAGGTTTTATCGAAAAATACTGAAAAATTAAAAAAA-AAAATTCGCAGGGA
66 TTCTTACACAACAAGCTTCCATAGAAAAATACTG-AAAATTAAAAAAATAAAATTCGCAGGGA
* * * * *
132713 GAATTTTCG-GATTTTTCTTCTGCATTCATTAGTGGTGCGATTTGCTTGAAATTTTAGATTTAGG
1 GAATTTT-GTGATTTTTCTTCTACATTCATTAGTGCTGCGATTGGCTTGAAATTTGAGATTTAGA
* ** * * *
132777 GTTCTTACACTATTATCTTCCATAGAAAAATAGTGAAAGTTAAAAAAATAAAA
65 GTTCTTACACAACAAGCTTCCATAGAAAAATACTGAAAATTAAAAAAATAAAA
132830 AAAAGTTTGT
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
126 12 0.12
127 83 0.86
128 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (127 bp):
GAATTTTGTGATTTTTCTTCTACATTCATTAGTGCTGCGATTGGCTTGAAATTTGAGATTTAGAG
TTCTTACACAACAAGCTTCCATAGAAAAATACTGAAAATTAAAAAAATAAAATTCGCAGGGA
Found at i:133402 original size:2 final size:2
Alignment explanation
Indices: 133395--133426 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
133385 TAAACAAGTC
*
133395 TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
133427 AGGATTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
TG
Found at i:141507 original size:27 final size:27
Alignment explanation
Indices: 141477--141550 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
141467 TTGGTCACCT
*
141477 AGGGGCATTTTGGTCATTTTTGCACTA
1 AGGGGCATTTTGGTCATTTTTACACTA
* * *
141504 AGGGGCATTTTGGTCATTTGTACATTC
1 AGGGGCATTTTGGTCATTTTTACACTA
141531 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
141551 AAGTCCACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.42
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTTACACTA
Found at i:143203 original size:2 final size:2
Alignment explanation
Indices: 143198--143229 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
143188 CTCTCTCGGA
143198 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
143230 GATCTTGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.