Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018950.1 Corchorus olitorius cultivar O-4 contig18983, 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: 60903
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:3853 original size:17 final size:17
Alignment explanation
Indices: 3831--3865 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3821 TCTTATGGCG
3831 CAAACTAACTTTTGGAT
1 CAAACTAACTTTTGGAT
3848 CAAACTAACTTTTGGAT
1 CAAACTAACTTTTGGAT
3865 C
1 C
3866 GCTTTTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (17 bp):
CAAACTAACTTTTGGAT
Found at i:6851 original size:9 final size:9
Alignment explanation
Indices: 6837--6864 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6827 CCTCTACCAA
6837 CTCCACAAC
1 CTCCACAAC
6846 CTCCACAAC
1 CTCCACAAC
6855 CTCCACAAC
1 CTCCACAAC
6864 C
1 C
6865 ACTTCCAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.57, G:0.00, T:0.11
Consensus pattern (9 bp):
CTCCACAAC
Found at i:10924 original size:72 final size:71
Alignment explanation
Indices: 10801--11070 Score: 245
Period size: 72 Copynumber: 3.8 Consensus size: 71
10791 ATTCTTGTAC
* * * * * * *
10801 GGTGGAGGCGCCTGCTCTGGTTGAGACTAATTTTGAATGTGAAGCAGAGCCTTCTCTGGATAAGT
1 GGTGGAGGCACCTGCTATGGTTGAGAATAATTCTGAATGTGAAACAAAGCCTTCTC-AGATAAGT
*
10866 CAGGCTT
65 CAGGCAT
* * **
10873 GGTGGAGGCACCTGCTATGGTTGAGAATAGTTCTGAATGTGAAACAAAGCCTTGTCCAGACGAGT
1 GGTGGAGGCACCTGCTATGGTTGAGAATAATTCTGAATGTGAAACAAAGCCTTCT-CAGATAAGT
* * *
10938 CTGTCGT
65 CAGGCAT
* * * * * *
10945 GTTGGAGGTACCTGCCATGGTTGAGATTAATTCTGAATGTGAAAAAAAGCCTTGTGCAGATAAGT
1 GGTGGAGGCACCTGCTATGGTTGAGAATAATTCTGAATGTGAAACAAAGCCTTCT-CAGATAAGT
*
11010 CCGGCAT
65 CAGGCAT
* * * * * *
11017 GGTCGAAGCTCCTGCTGTGGTTGAG-ATAAATTCTGAATGTGAAGCAGAGCCTTC
1 GGTGGAGGCACCTGCTATGGTTGAGAAT-AATTCTGAATGTGAAACAAAGCCTTC
11071 AATGAAGTCA
Statistics
Matches: 158, Mismatches: 38, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
71 1 0.01
72 156 0.99
73 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (71 bp):
GGTGGAGGCACCTGCTATGGTTGAGAATAATTCTGAATGTGAAACAAAGCCTTCTCAGATAAGTC
AGGCAT
Found at i:13678 original size:31 final size:31
Alignment explanation
Indices: 13643--13701 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
13633 CCTTCAAGGG
13643 GAGGGCCTCCTCCGCCACCCTCTCTATTAAA
1 GAGGGCCTCCTCCGCCACCCTCTCTATTAAA
13674 GAGGGCCTCCTCCGCCACCCTCTCTATT
1 GAGGGCCTCCTCCGCCACCCTCTCTATT
13702 GCTTGTAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.15, C:0.44, G:0.17, T:0.24
Consensus pattern (31 bp):
GAGGGCCTCCTCCGCCACCCTCTCTATTAAA
Found at i:14832 original size:117 final size:117
Alignment explanation
Indices: 14626--14854 Score: 415
Period size: 117 Copynumber: 2.0 Consensus size: 117
14616 TGGAAGAACA
* *
14626 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTCAGTTTTCCACTTCAAACCAA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
14691 CTCTTCCAATAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAACGC
66 CTCTTCCAATAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAACGC
*
14743 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAGCC-A
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
14807 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCA
66 CTCTTCCAAT-AAAATAGTATAAATTACTCCTTAATTCTTAGATCCCA
14855 GGTTAACAAT
Statistics
Matches: 108, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
116 11 0.10
117 97 0.90
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (117 bp):
TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
CTCTTCCAATAAAATAGTATAAATTACTCCTTAATTCTTAGATCCCAAACGC
Found at i:16612 original size:22 final size:21
Alignment explanation
Indices: 16541--16839 Score: 104
Period size: 22 Copynumber: 13.3 Consensus size: 21
16531 TCAATCGAAC
*
16541 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGG-AGGTTAT
* *
16563 CAAATTTTTCATAGTGTGGTTAAT
1 CAAA-ATTTCATAG-GAGGTT-AT
16587 -AAAATTTCATATGGAGGTTAT
1 CAAAATTTCATA-GGAGGTTAT
**
16608 CAAAACGTCATAGTGTA-GTTAT
1 CAAAATTTCATAG-G-AGGTTAT
* * ** *
16630 CAAAATTCCATACAGACATTAC
1 CAAAATTTCATA-GGAGGTTAT
**
16652 CAAAATTTCATAAAAAGGTTAT
1 CAAAATTTCAT-AGGAGGTTAT
* * * * *
16674 CACATTTTCTTAGAGTGTCGTTAA
1 CAAAATTTCATAG-GAG--GTTAT
* * *
16698 CAAAATTTTATACGAAAGTTAT
1 CAAAATTTCATA-GGAGGTTAT
*
16720 CAAAATTT-ATAGTGTGGTTAT
1 CAAAATTTCATAG-GAGGTTAT
16741 CAAAATTTCATAGGGAGTGAGGTTAT
1 CAAAATTTCAT----AG-GAGGTTAT
** * *
16767 CAAAGCTTCCTAGGGAGGTTAA
1 CAAAATTTCATA-GGAGGTTAT
*
16789 CAAAATTTCATTGGAAGGTTA-
1 CAAAATTTCATAGG-AGGTTAT
*
16810 CAAAAATTTTAT-GGAGATGTTAT
1 C-AAAATTTCATAGGAG--GTTAT
16833 CAAAATT
1 CAAAATT
16840 AAATAAAGAG
Statistics
Matches: 205, Mismatches: 46, Indels: 52
0.68 0.15 0.17
Matches are distributed among these distances:
20 3 0.01
21 26 0.13
22 123 0.60
23 19 0.09
24 15 0.07
25 1 0.00
26 18 0.09
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (21 bp):
CAAAATTTCATAGGAGGTTAT
Found at i:16733 original size:111 final size:111
Alignment explanation
Indices: 16539--16752 Score: 268
Period size: 111 Copynumber: 1.9 Consensus size: 111
16529 AATCAATCGA
** * * * * * *
16539 ACCAAAATTACATAGGAAGGTTATCAAATTTTTCATAGTGTGGTTAATAAAATTTCATATGGAGG
1 ACCAAAATTACATAAAAAGGTTATCAAATTTTTCAGAGTGTCGTTAACAAAATTTCATACGAAAG
16604 TTATCAAAACGTCATAGTGTAGTTATCAAAATTCCATACAGACATT
66 TTATCAAAACGTCATAGTGTAGTTATCAAAATTCCATACAGACATT
* * * *
16650 ACCAAAATTTCATAAAAAGGTTATCACATTTTCTTAGAGTGTCGTTAACAAAATTTTATACGAAA
1 ACCAAAATTACATAAAAAGGTTATCAAATTTT-TCAGAGTGTCGTTAACAAAATTTCATACGAAA
* * * *
16715 GTTATCAAAA-TTTATAGTGTGGTTATCAAAATTTCATA
65 GTTATCAAAACGTCATAGTGTAGTTATCAAAATTCCATA
16753 GGGAGTGAGG
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
111 52 0.60
112 34 0.40
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (111 bp):
ACCAAAATTACATAAAAAGGTTATCAAATTTTTCAGAGTGTCGTTAACAAAATTTCATACGAAAG
TTATCAAAACGTCATAGTGTAGTTATCAAAATTCCATACAGACATT
Found at i:16780 original size:26 final size:26
Alignment explanation
Indices: 16730--16783 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
16720 CAAAATTTAT
* *
16730 AGTGTGGTTATCAAAATTTCATAGGG
1 AGTGAGGTTATCAAAACTTCATAGGG
* *
16756 AGTGAGGTTATCAAAGCTTCCTAGGG
1 AGTGAGGTTATCAAAACTTCATAGGG
16782 AG
1 AG
16784 GTTAACAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (26 bp):
AGTGAGGTTATCAAAACTTCATAGGG
Found at i:16947 original size:23 final size:23
Alignment explanation
Indices: 16920--17024 Score: 69
Period size: 22 Copynumber: 4.8 Consensus size: 23
16910 TTTATGAAGA
*
16920 GATTATCAAAATTTTCATAGTGC
1 GATTATCAAAATTTTCATAATGC
* *
16943 GATTA-C-CAATTTT-ATAATGT
1 GATTATCAAAATTTTCATAATGC
* * *
16963 AATTATCAAAA-TTTCATAAGGA
1 GATTATCAAAATTTTCATAATGC
* * * *
16985 AATTATTAAAA-TTTCACAATGT
1 GATTATCAAAATTTTCATAATGC
*
17007 GGTTATCAAAA-TTTCATA
1 GATTATCAAAATTTTCATA
17025 GGTTATCGAA
Statistics
Matches: 64, Mismatches: 15, Indels: 7
0.74 0.17 0.08
Matches are distributed among these distances:
20 9 0.14
21 10 0.16
22 40 0.62
23 5 0.08
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (23 bp):
GATTATCAAAATTTTCATAATGC
Found at i:16976 original size:22 final size:22
Alignment explanation
Indices: 16950--17024 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
16940 TGCGATTACC
*
16950 AATTTTATAATGTAATTATCAA
1 AATTTCATAATGTAATTATCAA
* * *
16972 AATTTCATAAGGAAATTATTAA
1 AATTTCATAATGTAATTATCAA
* **
16994 AATTTCACAATGTGGTTATCAA
1 AATTTCATAATGTAATTATCAA
17016 AATTTCATA
1 AATTTCATA
17025 GGTTATCGAA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (22 bp):
AATTTCATAATGTAATTATCAA
Found at i:17030 original size:18 final size:18
Alignment explanation
Indices: 17007--17042 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16997 TTCACAATGT
17007 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
*
17025 GGTTATCGAAATTTCATA
1 GGTTATCAAAATTTCATA
17043 ACAATGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (18 bp):
GGTTATCAAAATTTCATA
Found at i:20106 original size:84 final size:84
Alignment explanation
Indices: 19943--20093 Score: 191
Period size: 84 Copynumber: 1.8 Consensus size: 84
19933 TTCATAATTA
* * **
19943 TGTTTAAAAGGACTGGTTTGAATGTGATATGCTGGGTATTGAAGAATTCATTATGTATCTTAATG
1 TGTTTAAAAGCACTGGTTTGAATCTGATATGCTGGGTATCAAAGAATTCATTATGTATCTTAATG
*
20008 CAATGTACCCTCAGCATTT
66 CAATATACCCTCAGCATTT
* * * *
20027 TGTTTATAAGCACTGGTTTGACTCTGGTATGCT-GGTGTCAAAGAATTCA-T-TGTATCTTAATG
1 TGTTTAAAAGCACTGGTTTGAATCTGATATGCTGGGTATCAAAGAATTCATTATGTATCTTAATG
*
20089 TAATA
66 CAATA
20094 ATACTCCCTC
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
81 15 0.26
82 1 0.02
83 13 0.23
84 28 0.49
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (84 bp):
TGTTTAAAAGCACTGGTTTGAATCTGATATGCTGGGTATCAAAGAATTCATTATGTATCTTAATG
CAATATACCCTCAGCATTT
Found at i:26294 original size:13 final size:13
Alignment explanation
Indices: 26276--26302 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
26266 GAGATTTTGG
26276 TGGTGGAAAAATC
1 TGGTGGAAAAATC
26289 TGGTGGAAAAATC
1 TGGTGGAAAAATC
26302 T
1 T
26303 TGATGCAGGC
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:0.37, C:0.07, G:0.30, T:0.26
Consensus pattern (13 bp):
TGGTGGAAAAATC
Found at i:30197 original size:21 final size:24
Alignment explanation
Indices: 30168--30218 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
30158 TTTTGAACTC
30168 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
30191 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
30214 ATTAT
1 ATTAT
30219 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:30213 original size:25 final size:25
Alignment explanation
Indices: 30168--30216 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
30158 TTTTGAACTC
*
30168 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
30193 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
30217 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:30677 original size:32 final size:32
Alignment explanation
Indices: 30636--30732 Score: 185
Period size: 32 Copynumber: 3.0 Consensus size: 32
30626 ATTCCTTCAA
30636 TTCAAATCCATTAAGCCCTTTGCCATAAACTC
1 TTCAAATCCATTAAGCCCTTTGCCATAAACTC
30668 TTCAAATCCATTAAGCCCTTTGCCATAAACTC
1 TTCAAATCCATTAAGCCCTTTGCCATAAACTC
*
30700 TTCAAATCCATTAAGCCCTTTGCCATGAACTC
1 TTCAAATCCATTAAGCCCTTTGCCATAAACTC
30732 T
1 T
30733 AACTTAAAAG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.32
Consensus pattern (32 bp):
TTCAAATCCATTAAGCCCTTTGCCATAAACTC
Found at i:38278 original size:3 final size:3
Alignment explanation
Indices: 38270--38298 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38260 ACAGGCACTC
38270 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
38299 ACCAACGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:42944 original size:77 final size:75
Alignment explanation
Indices: 42801--42948 Score: 215
Period size: 77 Copynumber: 1.9 Consensus size: 75
42791 TCGAGTCTAG
42801 CCAACAGTTAACCCCCTGAGGCACGAGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
1 CCAACAGTTAACCCCCTGAGGCACGAGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
42866 TCCACTCTTA
66 TCCACTCTTA
* * * * * * *
42876 CCAACAGTTTAACCCCCTGTGGTATGAGTCCACTCTTTACCATCAGTTTAACCCCTTGAGGTATG
1 CCAACAG-TTAACCCCCTGAGGCACGAGTCCACTC-TTACCAACAGTTTAACCCCCTGAGGCACG
42941 GGTCCACT
64 GGTCCACT
42949 ATGCACAGCC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
75 7 0.11
76 24 0.38
77 33 0.52
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.25
Consensus pattern (75 bp):
CCAACAGTTAACCCCCTGAGGCACGAGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
TCCACTCTTA
Found at i:42948 original size:39 final size:38
Alignment explanation
Indices: 42801--42936 Score: 202
Period size: 38 Copynumber: 3.6 Consensus size: 38
42791 TCGAGTCTAG
42801 CCAACAG-TTAACCCCCTGAGGCACGAGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGAGTCCACTCTTA
*
42838 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGAGTCCACTCTTA
* * *
42876 CCAACAGTTTAACCCCCTGTGGTATGAGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGAGTCCACTC-TTA
* *
42915 CCATCAGTTTAACCCCTTGAGG
1 CCAACAGTTTAACCCCCTGAGG
42937 TATGGGTCCA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
37 7 0.08
38 60 0.67
39 22 0.25
ACGTcount: A:0.24, C:0.35, G:0.17, T:0.24
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGAGTCCACTCTTA
Found at i:46392 original size:21 final size:21
Alignment explanation
Indices: 46368--46413 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
46358 AAGATAACCA
*
46368 AAAATTAAGAGGATTTCTTTG
1 AAAATCAAGAGGATTTCTTTG
* *
46389 AAAATCAGGGGGATTTCTTTG
1 AAAATCAAGAGGATTTCTTTG
46410 AAAA
1 AAAA
46414 AAATTTAGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (21 bp):
AAAATCAAGAGGATTTCTTTG
Found at i:47932 original size:1 final size:1
Alignment explanation
Indices: 47921--47954 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
47911 GAAATCTTCA
*
47921 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
47955 GTTGTTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:50337 original size:19 final size:19
Alignment explanation
Indices: 50313--50354 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
50303 ACTCTTGTTT
*
50313 ATCCCCATTTTGTGTTAAG
1 ATCCCCATCTTGTGTTAAG
50332 ATCCCCATCTTGTGTTAAG
1 ATCCCCATCTTGTGTTAAG
50351 ATCC
1 ATCC
50355 ACTCTTGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (19 bp):
ATCCCCATCTTGTGTTAAG
Found at i:54187 original size:27 final size:26
Alignment explanation
Indices: 54140--54195 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
54130 ATTAAATGAT
*
54140 AATACTTAGGAATCAATAGATTCAAA
1 AATACTTAAGAATCAATAGATTCAAA
* *
54166 AATACTTAATAATACAATAGATTCAGA
1 AATACTTAAGAAT-CAATAGATTCAAA
54193 AAT
1 AAT
54196 GTGATTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.29
Consensus pattern (26 bp):
AATACTTAAGAATCAATAGATTCAAA
Found at i:54202 original size:40 final size:40
Alignment explanation
Indices: 54158--54237 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
54148 GGAATCAATA
54158 GATTCAAAAATACTTAATAATACAATAGATTCAGAAATGT
1 GATTCAAAAATACTTAATAATACAATAGATTCAGAAATGT
54198 GATTCAAAAATACTTAATAATACAATAGATTCAGAAATGT
1 GATTCAAAAATACTTAATAATACAATAGATTCAGAAATGT
54238 CTTTTTCGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (40 bp):
GATTCAAAAATACTTAATAATACAATAGATTCAGAAATGT
Found at i:55675 original size:3 final size:3
Alignment explanation
Indices: 55667--55721 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
55657 CTATTTACTT
*
55667 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
55715 TTT TTA T
1 TTA TTA T
55722 CTTGATACCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:59883 original size:22 final size:22
Alignment explanation
Indices: 59840--59915 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
59830 TTGGAAACAT
*
59840 CTTTGCAGAG-ATT-CCTTCTA
1 CTTTGCAGAGCATTATCTTCTA
*
59860 CTTTGCAGAGCATTATTTTCTA
1 CTTTGCAGAGCATTATCTTCTA
59882 CTTTGCAGAGCATTATCTTCTA
1 CTTTGCAGAGCATTATCTTCTA
*
59904 TTTTGCAGAGCA
1 CTTTGCAGAGCA
59916 CTTCTTGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.20
21 3 0.06
22 37 0.74
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (22 bp):
CTTTGCAGAGCATTATCTTCTA
Found at i:59950 original size:22 final size:22
Alignment explanation
Indices: 59925--60090 Score: 124
Period size: 22 Copynumber: 7.1 Consensus size: 22
59915 ACTTCTTGTT
59925 GCATTATTTTCTACTTTGCAGA
1 GCATTATTTTCTACTTTGCAGA
*
59947 GCATTATTTTCCACTTTGCAGA
1 GCATTATTTTCTACTTTGCAGA
*
59969 GTGCATTATTTTCTTCAAC-TT-CAGTTTT
1 --GCATTATTTTC-T--ACTTTGCAG---A
**
59997 GCATTATTGGAAAC-ATCTTTGCAGA
1 GCATTATT---TTCTA-CTTTGCAGA
60022 GCATTATTTTCTACTTTGCAGA
1 GCATTATTTTCTACTTTGCAGA
60044 GCATTATTTT-TCACTTTGCAGA
1 GCATTATTTTCT-ACTTTGCAGA
* * *
60066 GCATTATCTTCCATTTTGCAGA
1 GCATTATTTTCTACTTTGCAGA
60088 GCA
1 GCA
60091 CTTCTTGTTG
Statistics
Matches: 116, Mismatches: 11, Indels: 34
0.72 0.07 0.21
Matches are distributed among these distances:
21 1 0.01
22 72 0.62
23 1 0.01
24 11 0.09
25 12 0.10
26 11 0.09
27 4 0.03
28 3 0.03
29 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.43
Consensus pattern (22 bp):
GCATTATTTTCTACTTTGCAGA
Done.