Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016460.1 Corchorus capsularis cultivar CVL-1 contig16481, 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: 127322
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3663 original size:40 final size:40
Alignment explanation
Indices: 3590--3694 Score: 138
Period size: 40 Copynumber: 2.6 Consensus size: 40
3580 ATCAGTAATT
* **
3590 AAGTAAAAAGAGATTAATCAGTAATTTGATAATTAAAAGTAG
1 AAGT-AAAAGA-AGTAATCAGTAAAATGATAATTAAAAGTAG
* *
3632 AAGTAAAAGAAGTAATCAGTAAAATGGTAATTAAGAGTAG
1 AAGTAAAAGAAGTAATCAGTAAAATGATAATTAAAAGTAG
*
3672 GAGTAAAAGAAGTAATCAGTAAA
1 AAGTAAAAGAAGTAATCAGTAAA
3695 TCGGTAAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 47 0.82
41 6 0.11
42 4 0.07
ACGTcount: A:0.53, C:0.03, G:0.20, T:0.24
Consensus pattern (40 bp):
AAGTAAAAGAAGTAATCAGTAAAATGATAATTAAAAGTAG
Found at i:3731 original size:15 final size:16
Alignment explanation
Indices: 3692--3732 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3682 AGTAATCAGT
3692 AAATCGGTAAAGAGCAA
1 AAAT-GGTAAAGAGCAA
*
3709 AAATGGTAAAGAGTAA
1 AAATGGTAAAGAGCAA
3725 AAA-GGTAA
1 AAATGGTAA
3733 TCAATGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.22
16 14 0.61
17 4 0.17
ACGTcount: A:0.56, C:0.05, G:0.24, T:0.15
Consensus pattern (16 bp):
AAATGGTAAAGAGCAA
Found at i:3837 original size:21 final size:21
Alignment explanation
Indices: 3813--3894 Score: 103
Period size: 21 Copynumber: 3.9 Consensus size: 21
3803 CAGTAAAGGG
*
3813 TAATCAGTAAGAGTAAAACAA
1 TAATCAGTAAGAGTAAAATAA
* * *
3834 TAATCAGTAAGAGCAAAGTGA
1 TAATCAGTAAGAGTAAAATAA
3855 TAATTC-GTAAGAGTAAAATAA
1 TAA-TCAGTAAGAGTAAAATAA
3876 TAATCAGTAAAGAGTAAAA
1 TAATCAGT-AAGAGTAAAA
3895 GGGTGATCAG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.04
21 37 0.73
22 12 0.24
ACGTcount: A:0.54, C:0.07, G:0.17, T:0.22
Consensus pattern (21 bp):
TAATCAGTAAGAGTAAAATAA
Found at i:3984 original size:13 final size:13
Alignment explanation
Indices: 3968--4015 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
3958 GGTAATAAAT
3968 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
* *
3981 AAAAGAGTAATTAG
1 AAAAGAG-AGTAAG
3995 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
4008 AAAAGAGA
1 AAAAGAGA
4016 AAAAAATGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 4 0.14
13 14 0.50
14 6 0.21
15 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (13 bp):
AAAAGAGAGTAAG
Found at i:3984 original size:29 final size:28
Alignment explanation
Indices: 3959--4014 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
3949 GTAAAAAGTG
3959 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
* *
3987 GTAATTAGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
4014 G
1 G
4015 AAAAAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:18760 original size:155 final size:153
Alignment explanation
Indices: 18420--18838 Score: 420
Period size: 155 Copynumber: 2.7 Consensus size: 153
18410 TGTAAGTCAT
*** *
18420 CTTGGCTAAATTTCATCTCAAACAAACTTACGGTGAAAAACTTATGCAAGTTTTTCAATTAAGGA
1 CTTGGC-AAATTTCATCTCAAAC-AACTTAAAATGAAAAACTTATACAAGTTTTTCAATTAAGGA
* * * *
18485 CAGTTTGGGATGTGAAACCAACTTCACTATGATA-GGGAGTTCGGTTTTACTTAGAATTTTTTCC
64 CAGTTTGGGA-GTGAAACCAAGTTCACCATGA-AGGGGAGCTCGGTTTCACTTAGAATTTTTTCC
* *
18549 ATAGATTTATGGAAATAATCTAAGCCTA
127 ATAGATTTATGGAAAGAACCTAAGCC-A
* * *** * *
18577 CTGGTGG-AAA-ATCAACTTCATTGAACTTAAAATGAAAAAC-TATACAAGTTTTTCATTTAAAG
1 CT--TGGCAAATTTCATC-TCAAACAACTTAAAATGAAAAACTTATACAAGTTTTTCAATTAAGG
*
18639 ACAGTTTAGGGAGTGAAACCAAGTTCACCATCAAGGGGAGCTCGGTTTCACTTAGAATTTTTTCC
63 ACAGTTT-GGGAGTGAAACCAAGTTCACCATGAAGGGGAGCTCGGTTTCACTTAGAATTTTTTCC
* *
18704 ATAG-TCTTGTGGAGAGAACCTAAGTCC-
127 ATAGAT-TTATGGAAAGAACCTAAG-CCA
** * *
18731 CTTGGCAAAGTTTCATCTCAAACAGACTTAGTATGAAAAACTTATACATGTTTTTCAGTTAAGGA
1 CTTGGCAAA-TTTCATCTCAAACA-ACTTAAAATGAAAAACTTATACAAGTTTTTCAATTAAGGA
* *
18796 CAGTTTGGAGTGTGAAACCTAGTTCACCATGAAGGAGG-GCTCG
64 CAGTTTGG-GAGTGAAACCAAGTTCACCATGAAGG-GGAGCTCG
18839 AACCAAGCCA
Statistics
Matches: 215, Mismatches: 33, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
152 3 0.01
153 3 0.01
154 8 0.04
155 110 0.51
156 78 0.36
157 10 0.05
159 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (153 bp):
CTTGGCAAATTTCATCTCAAACAACTTAAAATGAAAAACTTATACAAGTTTTTCAATTAAGGACA
GTTTGGGAGTGAAACCAAGTTCACCATGAAGGGGAGCTCGGTTTCACTTAGAATTTTTTCCATAG
ATTTATGGAAAGAACCTAAGCCA
Found at i:19167 original size:17 final size:17
Alignment explanation
Indices: 19145--19196 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
19135 GATACAGCAG
19145 ATGCTACCTGGTACCAC
1 ATGCTACCTGGTACCAC
*
19162 ATGCTACCTAGTACCAC
1 ATGCTACCTGGTACCAC
* *
19179 GTGATACCTGGTACCAC
1 ATGCTACCTGGTACCAC
19196 A
1 A
19197 AGGAGAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (17 bp):
ATGCTACCTGGTACCAC
Found at i:26210 original size:26 final size:26
Alignment explanation
Indices: 26174--26240 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
26164 CACTTGCTTG
26174 AGCTTGGGGAAAGCTCTGTGTTGTCA
1 AGCTTGGGGAAAGCTCTGTGTTGTCA
26200 AGCTTGGGGAAAGCTCTGTGTTGTCA
1 AGCTTGGGGAAAGCTCTGTGTTGTCA
*
26226 GGCTTGGGGAAAGCT
1 AGCTTGGGGAAAGCT
26241 TGGTTGCTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.19, C:0.15, G:0.37, T:0.28
Consensus pattern (26 bp):
AGCTTGGGGAAAGCTCTGTGTTGTCA
Found at i:27635 original size:21 final size:21
Alignment explanation
Indices: 27602--27641 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27592 ACCATGGACG
*
27602 AGACAGATACAGAAATGAAAA
1 AGACAAATACAGAAATGAAAA
*
27623 AGACAAATTCAGAAATGAA
1 AGACAAATACAGAAATGAA
27642 GAAGTTCAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.10, G:0.17, T:0.12
Consensus pattern (21 bp):
AGACAAATACAGAAATGAAAA
Found at i:37637 original size:20 final size:21
Alignment explanation
Indices: 37598--37637 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
37588 GCTTGGTCCC
* *
37598 TTTGCTTCCAAATTTCAATTT
1 TTTGCTACCAAATCTCAATTT
37619 TTTGCTACCAAA-CTCAATT
1 TTTGCTACCAAATCTCAATT
37638 CCAACTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.45
Consensus pattern (21 bp):
TTTGCTACCAAATCTCAATTT
Found at i:39007 original size:110 final size:110
Alignment explanation
Indices: 38814--39033 Score: 440
Period size: 110 Copynumber: 2.0 Consensus size: 110
38804 GCCTTCCTAA
38814 CAAAAGAGGGCATTGATCCTTTGTAATTTCTCCTTCCATTTCCATAACAAAAATGTCAACAGGAA
1 CAAAAGAGGGCATTGATCCTTTGTAATTTCTCCTTCCATTTCCATAACAAAAATGTCAACAGGAA
38879 AAATTAAATGTTGAACTTTAATCAAAATGTTCTCTAGCACACCTT
66 AAATTAAATGTTGAACTTTAATCAAAATGTTCTCTAGCACACCTT
38924 CAAAAGAGGGCATTGATCCTTTGTAATTTCTCCTTCCATTTCCATAACAAAAATGTCAACAGGAA
1 CAAAAGAGGGCATTGATCCTTTGTAATTTCTCCTTCCATTTCCATAACAAAAATGTCAACAGGAA
38989 AAATTAAATGTTGAACTTTAATCAAAATGTTCTCTAGCACACCTT
66 AAATTAAATGTTGAACTTTAATCAAAATGTTCTCTAGCACACCTT
39034 TGGAATGTAC
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (110 bp):
CAAAAGAGGGCATTGATCCTTTGTAATTTCTCCTTCCATTTCCATAACAAAAATGTCAACAGGAA
AAATTAAATGTTGAACTTTAATCAAAATGTTCTCTAGCACACCTT
Found at i:44321 original size:17 final size:17
Alignment explanation
Indices: 44280--44321 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
44270 GATTAAATTG
*
44280 ATTTTTGCTTGCATGTT
1 ATTTTTGCTTGAATGTT
*
44297 ATTATTGCTTGAAT-TT
1 ATTTTTGCTTGAATGTT
44313 AGTTTTTGC
1 A-TTTTTGC
44322 ATTTAGTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.57
Consensus pattern (17 bp):
ATTTTTGCTTGAATGTT
Found at i:46586 original size:30 final size:31
Alignment explanation
Indices: 46551--46615 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
46541 CTTTCAATAG
*
46551 TTGATTTGAATTGCCA-TATCTTGCTA-TTGA
1 TTGATTTGAATTGCAATTAT-TTGCTAGTTGA
*
46581 TTGA-TTGAATTGCAATTATTTGTTAGTTGA
1 TTGATTTGAATTGCAATTATTTGCTAGTTGA
46611 TTGAT
1 TTGAT
46616 AGATTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (31 bp):
TTGATTTGAATTGCAATTATTTGCTAGTTGA
Found at i:50730 original size:21 final size:20
Alignment explanation
Indices: 50700--50755 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
50690 TCTTTTTAAA
50700 AATAATCTTATAAGATCTTTT
1 AATAA-CTTATAAGATCTTTT
*
50721 AATAAGCTTAGT-AGATTTTTT
1 AATAA-CTTA-TAAGATCTTTT
*
50742 AGTAACTTTATAAG
1 AATAAC-TTATAAG
50756 TTTTTTTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (20 bp):
AATAACTTATAAGATCTTTT
Found at i:51206 original size:41 final size:40
Alignment explanation
Indices: 51160--51341 Score: 179
Period size: 41 Copynumber: 4.5 Consensus size: 40
51150 AAATTACCTT
*
51160 TGACACCAAAAGTTGTCACGTTGGTAAATTAAAATTACTGC
1 TGACACCAGAAGTTGTCAC-TTGGTAAATTAAAATTACTGC
* * **
51201 TGACACTAGAAGTTGTCACCTTGGTAAATTGAAATTACTTT
1 TGACACCAGAAGTTGTCA-CTTGGTAAATTAAAATTACTGC
*
51242 TGACACCAGAAGTTGTCACTCTGGTAAATTAAAATTACCT-T
1 TGACACCAGAAGTTGTCACT-TGGTAAATTAAAATTA-CTGC
* * ** * **
51283 TGACACCATAAG-TGTTACTCTAATAAATTATAATTACTAT
1 TGACACCAGAAGTTGTCACT-TGGTAAATTAAAATTACTGC
*
51323 TGACACCAGAAATTGTCAC
1 TGACACCAGAAGTTGTCAC
51342 CTTTGAATTA
Statistics
Matches: 121, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 2 0.02
40 33 0.27
41 83 0.69
42 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (40 bp):
TGACACCAGAAGTTGTCACTTGGTAAATTAAAATTACTGC
Found at i:51287 original size:82 final size:81
Alignment explanation
Indices: 51139--51341 Score: 225
Period size: 82 Copynumber: 2.5 Consensus size: 81
51129 CCTTATAGTA
* *
51139 AATAATATTGAAAATTACCTTTGACACCAAAAGTTGTCACGTTGGTAAATTAAAATTACTGCTGA
1 AATAA-ATTG-AAATTACTTTTGACACCAGAAGTTGTCACGTTGGTAAATTAAAATTACTGCTGA
*
51204 CACTAGAAGTTGTCAC-CTT
64 CACCAGAAG-TGTCACTC-T
** *
51223 GGTAAATTGAAATTACTTTTGACACCAGAAGTTGTCAC-TCTGGTAAATTAAAATTACCT-TTGA
1 AATAAATTGAAATTACTTTTGACACCAGAAGTTGTCACGT-TGGTAAATTAAAATTA-CTGCTGA
* *
51286 CACCATAAGTGTTACTCT
64 CACCAGAAGTGTCACTCT
* *
51304 AATAAATT-ATAATTACTATTGACACCAGAAATTGTCAC
1 AATAAATTGA-AATTACTTTTGACACCAGAAGTTGTCAC
51342 CTTTGAATTA
Statistics
Matches: 103, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
80 1 0.01
81 39 0.38
82 54 0.52
83 6 0.06
84 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (81 bp):
AATAAATTGAAATTACTTTTGACACCAGAAGTTGTCACGTTGGTAAATTAAAATTACTGCTGACA
CCAGAAGTGTCACTCT
Found at i:56104 original size:13 final size:13
Alignment explanation
Indices: 56082--56121 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
56072 CAGAGAATAT
56082 TATCAACAGAAGA
1 TATCAACAGAAGA
*
56095 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
56108 TTTCAACTGAAGA
1 TATCAACAGAAGA
56121 T
1 T
56122 TATCTGGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:56886 original size:3 final size:3
Alignment explanation
Indices: 56872--56923 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
56862 ATATATTAAT
56872 TAA TAA -AA 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
56919 TAA TA
1 TAA TA
56924 TACTCCCTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:66883 original size:8 final size:8
Alignment explanation
Indices: 66870--66907 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
66860 TCTAGTATTA
66870 GTGAAATT
1 GTGAAATT
66878 GTGAAATT
1 GTGAAATT
66886 GTGAAATT
1 GTGAAATT
66894 GTGAAATT
1 GTGAAATT
66902 GTGAAA
1 GTGAAA
66908 GTGCTGTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.34
Consensus pattern (8 bp):
GTGAAATT
Found at i:77400 original size:27 final size:27
Alignment explanation
Indices: 77363--77419 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
77353 AATAGTTCAC
*
77363 ATCATGGCAAGGTTTATCATAATTTAT
1 ATCATGCCAAGGTTTATCATAATTTAT
77390 ATCATGCCAAGGTTTATCATAATTTAT
1 ATCATGCCAAGGTTTATCATAATTTAT
77417 ATC
1 ATC
77420 GGATGGCAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (27 bp):
ATCATGCCAAGGTTTATCATAATTTAT
Found at i:79715 original size:3 final size:3
Alignment explanation
Indices: 79707--79734 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
79697 CCTCAAGGTA
79707 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
79735 TTTTTCACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:87654 original size:3 final size:3
Alignment explanation
Indices: 87648--87679 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
87638 AGAAGAGGTT
87648 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
87680 TCAAGATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:91881 original size:3 final size:3
Alignment explanation
Indices: 91864--91967 Score: 68
Period size: 3 Copynumber: 34.7 Consensus size: 3
91854 ATTACTATCA
* * * *
91864 TCT TCAT TC- TCT TCT TCT TCT TCC TCC TCT TCC TCT TTT TCT TCT
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * * *
91909 TCT TCT TCC TCC TCC TCC TCC TCC TCT T-T CTCT TCT TCT TCT ACT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT
*
91954 TCT TCT TCC TCT TC
1 TCT TCT TCT TCT TC
91968 CTCCTCATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
2 3 0.04
3 78 0.92
4 4 0.05
ACGTcount: A:0.02, C:0.42, G:0.00, T:0.56
Consensus pattern (3 bp):
TCT
Found at i:92050 original size:12 final size:12
Alignment explanation
Indices: 92031--92086 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
92021 ACGATTCTGA
*
92031 TTCTTCTTCTTC
1 TTCTTCTTCCTC
*
92043 TTCCTCTTCCTC
1 TTCTTCTTCCTC
92055 TTCCTTC-TCCTC
1 TT-CTTCTTCCTC
* *
92067 ATTCTTGTTCCTT
1 -TTCTTCTTCCTC
92080 TTCTTCT
1 TTCTTCT
92087 GTTTACTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 26 0.74
13 9 0.26
ACGTcount: A:0.02, C:0.38, G:0.02, T:0.59
Consensus pattern (12 bp):
TTCTTCTTCCTC
Found at i:92121 original size:93 final size:90
Alignment explanation
Indices: 91941--92109 Score: 259
Period size: 93 Copynumber: 1.8 Consensus size: 90
91931 CCTCTTTCTC
* *
91941 TTCTTCTTCTACTTCTTCTTCCTCTTCCTCCTCATTCTTGTCACTTTTCTTTTGTTTACTTTTAC
1 TTCTTCTTCTACTTCCTCTTCCTCTTCCTCCTCATTCTTGTCACTTTTCTTCTGTTTACTTTTAC
*
92006 CTCCCTTCTTACTAGACGATTCTGA
66 CTCCATTCTTACTAGACGATTCTGA
*
92031 TTCTTCTTCTTCTTCCTCTTCCTCTTCCTTCTCCTCATTCTTGTTC-CTTTTCTTCTGTTTACTT
1 TTCTTCTTCTACTTCCTCTTCCTCTT-C--CTCCTCATTCTTG-TCACTTTTCTTCTGTTTACTT
92095 TTACCTCCATTCTTA
62 TTACCTCCATTCTTA
92110 ACAGATGATT
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
90 24 0.34
91 1 0.01
93 44 0.62
94 2 0.03
ACGTcount: A:0.09, C:0.33, G:0.04, T:0.54
Consensus pattern (90 bp):
TTCTTCTTCTACTTCCTCTTCCTCTTCCTCCTCATTCTTGTCACTTTTCTTCTGTTTACTTTTAC
CTCCATTCTTACTAGACGATTCTGA
Found at i:94334 original size:20 final size:20
Alignment explanation
Indices: 94296--94333 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
94286 GAATTTATAA
*
94296 ATAACCTTATTATTGTTTTG
1 ATAACCTTATAATTGTTTTG
94316 ATAACC-TATAATTGTTTT
1 ATAACCTTATAATTGTTTT
94334 TTAGTAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (20 bp):
ATAACCTTATAATTGTTTTG
Found at i:98350 original size:7 final size:7
Alignment explanation
Indices: 98338--98362 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
98328 TCGTCCAAGA
98338 TTTGATG
1 TTTGATG
98345 TTTGATG
1 TTTGATG
98352 TTTGATG
1 TTTGATG
98359 TTTG
1 TTTG
98363 CTGTCGGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (7 bp):
TTTGATG
Found at i:99462 original size:3 final size:3
Alignment explanation
Indices: 99454--99496 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
99444 ATATAAGAAG
99454 TAT TAT TAT TAT ATAT ATAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
99497 ATAATCAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 29 0.76
4 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:99477 original size:20 final size:20
Alignment explanation
Indices: 99454--99496 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
99444 ATATAAGAAG
99454 TATTATTATTA-TATATATAT
1 TATTATTATTATTAT-TATAT
99474 TATTATTATTATTATTATAT
1 TATTATTATTATTATTATAT
99494 TAT
1 TAT
99497 ATAATCAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTATTATTATTATTATAT
Found at i:99514 original size:29 final size:26
Alignment explanation
Indices: 99454--99520 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
99444 ATATAAGAAG
* *
99454 TATTATTATTATATATATATTATTAT
1 TATTATTATTATATATATATCATCAT
99480 TATTATTATTATATTATATAATCAGTCAT
1 TATTATTATTATA-TATAT-ATCA-TCAT
* *
99509 TTTTATTTTTAT
1 TATTATTATTAT
99521 TAAATGCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 13 0.38
27 5 0.15
28 3 0.09
29 13 0.38
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (26 bp):
TATTATTATTATATATATATCATCAT
Found at i:100662 original size:37 final size:38
Alignment explanation
Indices: 100612--100691 Score: 126
Period size: 37 Copynumber: 2.1 Consensus size: 38
100602 AAGCATATAA
100612 AATGTAAACAAAAATTATATTT-GTAAGCTCAATATTG
1 AATGTAAACAAAAATTATATTTCGTAAGCTCAATATTG
* * *
100649 AATGTAAACAAAAATTATATTTCTTTAGCTCCATATTG
1 AATGTAAACAAAAATTATATTTCGTAAGCTCAATATTG
100687 AATGT
1 AATGT
100692 TGATATTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 22 0.56
38 17 0.44
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (38 bp):
AATGTAAACAAAAATTATATTTCGTAAGCTCAATATTG
Found at i:101408 original size:7 final size:7
Alignment explanation
Indices: 101398--101427 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
101388 TAGTCCAAGA
101398 TTTGATG
1 TTTGATG
101405 TTTGATG
1 TTTGATG
101412 TTTGATG
1 TTTGATG
*
101419 TTTGTTG
1 TTTGATG
101426 TT
1 TT
101428 GGTAGGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.27, T:0.63
Consensus pattern (7 bp):
TTTGATG
Found at i:103128 original size:19 final size:20
Alignment explanation
Indices: 103104--103154 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
103094 ATTTACTCTT
103104 ACTAATTTTTAATAAT-ATA
1 ACTAATTTTTAATAATAATA
*
103123 ACTAATTTTAAATAATAATA
1 ACTAATTTTTAATAATAATA
*
103143 ACTAATTATTAA
1 ACTAATTTTTAA
103155 ATTTTTTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (20 bp):
ACTAATTTTTAATAATAATA
Found at i:104483 original size:3 final size:3
Alignment explanation
Indices: 104475--104517 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
104465 TAAGAATAAG
104475 TAT TAT TAT TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
104518 ATAATCAGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:105348 original size:66 final size:66
Alignment explanation
Indices: 105242--105375 Score: 225
Period size: 66 Copynumber: 2.0 Consensus size: 66
105232 ATTAGACTTT
*
105242 TTGGTCATTTCTCAATTGACTTTAATAGAATAGTTGAATTACTAAAAGATCCCTATC-AAGACTT
1 TTGGTCATTTCTCAATTGACTTTAATAGAATAGTGGAATTACTAAAAGATCCCT-TCTAAGACTT
105306 GC
65 GC
* *
105308 TTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTTCTAAGGCTTG
1 TTGGTCATTTCTCAATTGACTTTAATAGAATAGTGGAATTACTAAAAGATCCCTTCTAAGACTTG
105373 C
66 C
105374 TT
1 TT
105376 TTGGAGCTAG
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
65 2 0.03
66 62 0.97
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (66 bp):
TTGGTCATTTCTCAATTGACTTTAATAGAATAGTGGAATTACTAAAAGATCCCTTCTAAGACTTG
C
Found at i:105582 original size:165 final size:167
Alignment explanation
Indices: 105308--105653 Score: 500
Period size: 165 Copynumber: 2.1 Consensus size: 167
105298 CAAGACTTGC
* * * *
105308 TTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTTCTAAGGCTTG
1 TTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTACTAAAAGATCCCATCTAAGGATTG
* ** * * * * *
105373 CTTTTGGAGCTAGAGAACTTATTTTTTTCGTCTTTTCTTACTTGGCAGATTACTTAAATGTCCTA
66 ATGATGGAGCTAGAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATATCCTA
* * * * * *
105438 ATTTTTTATTCTTGAGGGGATTAAATTAGTAATCTTT
131 ACTTTTGATTCTTGAGGAGATTAAATAACTAAACTTT
105475 TTGGTCATTTCTCAATGGAC-TGAATAGAGTAGTGGAATTACTAAAAGATCACCATC-AAGGATT
1 TTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTACTAAAAGATC-CCATCTAAGGATT
105538 GATGAT-GAGCTAGAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATATCCT
65 GATGATGGAGCTAGAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATATCCT
105602 AACTTTTGATTCTTGAGGAGATTAAATAACTAAACTTT
130 AACTTTTGATTCTTGAGGAGATTAAATAACTAAACTTT
105640 TTGGTCATTTCTCA
1 TTGGTCATTTCTCA
105654 TTTCTCAATT
Statistics
Matches: 160, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
165 99 0.62
166 38 0.24
167 23 0.14
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.40
Consensus pattern (167 bp):
TTGGTCATTTCTCAATGGACTTGAATAGAGTAGTGGAATTACTAAAAGATCCCATCTAAGGATTG
ATGATGGAGCTAGAGAACTAATCTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATATCCTA
ACTTTTGATTCTTGAGGAGATTAAATAACTAAACTTT
Found at i:107862 original size:2 final size:2
Alignment explanation
Indices: 107855--107897 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
107845 ACCCAATGTG
107855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
107898 GGGTCTTTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:108521 original size:24 final size:24
Alignment explanation
Indices: 108494--108540 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
108484 TCTTAGATAT
108494 AATATATATT-AATAAATAAATAAA
1 AATATATATTAAAT-AATAAATAAA
*
108518 AATATATTTTAAATAATAAATAA
1 AATATATATTAAATAATAAATAA
108541 TGAGTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AATATATATTAAATAATAAATAAA
Found at i:110141 original size:17 final size:17
Alignment explanation
Indices: 110119--110157 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
110109 AAATATATTC
* *
110119 TTATATATCTATTTATA
1 TTATATATATATATATA
110136 TTATATATATATATATA
1 TTATATATATATATATA
110153 TTATA
1 TTATA
110158 AATTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATATATATATATA
Found at i:111640 original size:16 final size:16
Alignment explanation
Indices: 111564--111683 Score: 91
Period size: 17 Copynumber: 7.3 Consensus size: 16
111554 TCGTGCCATC
* *
111564 GGGTTCGGGCTATTTT
1 GGGTTCGGGTTAATTT
* *
111580 CGGGTTCGGGTCATTTTT
1 -GGGTTCGGGTTA-ATTT
*
111598 GGGCTCGGGTTGAATTT
1 GGGTTCGGGTT-AATTT
*
111615 GGG-TCAGGTTAATTT
1 GGGTTCGGGTTAATTT
111630 GGGTTCGGGTTGAATTT
1 GGGTTCGGGTT-AATTT
* *
111647 GGGTT-AGGTTTATTT
1 GGGTTCGGGTTAATTT
* *
111662 GGGTTTGGGTTTAGTTT
1 GGGTTCGGG-TTAATTT
111679 GGGTT
1 GGGTT
111684 TTGACCAGAT
Statistics
Matches: 85, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
15 17 0.20
16 18 0.21
17 45 0.53
18 5 0.06
ACGTcount: A:0.10, C:0.07, G:0.38, T:0.44
Consensus pattern (16 bp):
GGGTTCGGGTTAATTT
Found at i:111683 original size:32 final size:32
Alignment explanation
Indices: 111595--111683 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
111585 TCGGGTCATT
* *
111595 TTTGGGCTCGGGTTGAATTTGGGTCAGGTTAA
1 TTTGGGTTCGGGTTGAATTTGGGTTAGGTTAA
*
111627 TTTGGGTTCGGGTTGAATTTGGGTTAGGTTTA
1 TTTGGGTTCGGGTTGAATTTGGGTTAGGTTAA
* * *
111659 TTTGGGTTTGGGTTTAGTTTGGGTT
1 TTTGGGTTCGGGTTGAATTTGGGTT
111684 TTGACCAGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.11, C:0.04, G:0.38, T:0.46
Consensus pattern (32 bp):
TTTGGGTTCGGGTTGAATTTGGGTTAGGTTAA
Found at i:111891 original size:16 final size:16
Alignment explanation
Indices: 111827--111904 Score: 52
Period size: 16 Copynumber: 4.9 Consensus size: 16
111817 ATTTTTTGGA
* *
111827 TTCGGGTTCGGGTTTT
1 TTCGGGTTCAGATTTT
* *
111843 TTTGGGTTCTA-ACTTT
1 TTCGGGTTC-AGATTTT
* *
111859 TTCGGGTT-TGAGCTTT
1 TTCGGGTTCAGA-TTTT
111875 TTCGGGTTCAGATTTT
1 TTCGGGTTCAGATTTT
* *
111891 TTCGAGTTCGGATT
1 TTCGGGTTCAGATT
111905 CAGACGGGTT
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
15 1 0.02
16 45 0.94
17 2 0.04
ACGTcount: A:0.09, C:0.13, G:0.28, T:0.50
Consensus pattern (16 bp):
TTCGGGTTCAGATTTT
Found at i:115431 original size:3 final size:3
Alignment explanation
Indices: 115423--115457 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
115413 CTTATTTGAA
115423 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
115458 ATATATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:115467 original size:3 final size:3
Alignment explanation
Indices: 115461--115490 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
115451 ATAATAAATA
115461 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
115491 GAACATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:120655 original size:31 final size:30
Alignment explanation
Indices: 120605--120737 Score: 102
Period size: 31 Copynumber: 4.6 Consensus size: 30
120595 ACAATTTCCG
* *
120605 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
1 ACGT-GCACGCCACATGTACCAAAAAGTGAC
*
120636 ATGTGACACGCCACATGTACCAAAAAGT---
1 ACGTG-CACGCCACATGTACCAAAAAGTGAC
120664 -CGT----GCCACATGTACCAAAAAGTGAC
1 ACGTGCACGCCACATGTACCAAAAAGTGAC
* * * *
120689 ACATGTCACACTACGTGTACCAAAAAGTGAC
1 ACGTG-CACGCCACATGTACCAAAAAGTGAC
*
120720 ACGTGGCATGCCACATGT
1 ACGT-GCACGCCACATGT
120738 TTCAAAAAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
22 19 0.24
26 2 0.03
27 2 0.03
30 1 0.01
31 53 0.68
32 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (30 bp):
ACGTGCACGCCACATGTACCAAAAAGTGAC
Found at i:120693 original size:19 final size:20
Alignment explanation
Indices: 120647--120694 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
120637 TGTGACACGC
*
120647 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
120669 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
120688 CACATGT
1 CACATGT
120695 CACACTACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:120708 original size:53 final size:53
Alignment explanation
Indices: 120613--120716 Score: 145
Period size: 53 Copynumber: 2.0 Consensus size: 53
120603 CGACGTGGCA
* ** *
120613 TGCCACGTGTACCAAAAAGTGACATGTGACACGCCACATGTACCAAAAAGTCG
1 TGCCACATGTACCAAAAAGTGACACATGACACACCACATGTACCAAAAAGTCG
* * *
120666 TGCCACATGTACCAAAAAGTGACACATGTCACACTACGTGTACCAAAAAGT
1 TGCCACATGTACCAAAAAGTGACACATGACACACCACATGTACCAAAAAGT
120717 GACACGTGGC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (53 bp):
TGCCACATGTACCAAAAAGTGACACATGACACACCACATGTACCAAAAAGTCG
Found at i:121151 original size:11 final size:11
Alignment explanation
Indices: 121135--121159 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
121125 AATCATGTAC
121135 AAAAAATTAAA
1 AAAAAATTAAA
121146 AAAAAATTAAA
1 AAAAAATTAAA
121157 AAA
1 AAA
121160 GATTAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAATTAAA
Found at i:126425 original size:16 final size:15
Alignment explanation
Indices: 126404--126450 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
126394 TTGAGGTTGG
126404 TTTGCTACTTGCTTCT
1 TTTGCTACTT-CTTCT
*
126420 TTTGCTTCTTCTTCT
1 TTTGCTACTTCTTCT
*
126435 TCTT-CTTCTTCTTCT
1 T-TTGCTACTTCTTCT
126450 T
1 T
126451 AATATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.02, C:0.28, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTGCTACTTCTTCT
Found at i:126432 original size:3 final size:3
Alignment explanation
Indices: 126415--126450 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
126405 TTGCTACTTG
126415 CTT CTT -TT GCTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT -CTT CTT CTT CTT CTT CTT CTT CTT CTT
126451 AATATATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.67
Consensus pattern (3 bp):
CTT
Done.