Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018384.1 Corchorus olitorius cultivar O-4 contig18417, 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: 84439
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:10593 original size:27 final size:27
Alignment explanation
Indices: 10555--10609 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
10545 GAAGCACTGG
10555 TTAGATATAATTCTCCTAGGAAAATTT
1 TTAGATATAATTCTCCTAGGAAAATTT
*
10582 TTAGATTTAATTCTCCTAGGAAAATTT
1 TTAGATATAATTCTCCTAGGAAAATTT
10609 T
1 T
10610 AAAATGAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (27 bp):
TTAGATATAATTCTCCTAGGAAAATTT
Found at i:12335 original size:17 final size:16
Alignment explanation
Indices: 12313--12344 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12303 GTTGAAGAAA
12313 AAAACAAAAGCATAAGC
1 AAAACAAAAG-ATAAGC
12330 AAAACAAAAGATAAG
1 AAAACAAAAGATAAG
12345 ATAACAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.69, C:0.12, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAACAAAAGATAAGC
Found at i:13959 original size:10 final size:10
Alignment explanation
Indices: 13939--14096 Score: 307
Period size: 10 Copynumber: 15.7 Consensus size: 10
13929 ATGAAAGAGG
13939 GGTCAGGGTTC
1 GGTC-GGGTTC
13950 GGTCGGGTTC
1 GGTCGGGTTC
13960 GGTCGGGTTC
1 GGTCGGGTTC
13970 GGTCGGGTTC
1 GGTCGGGTTC
13980 GGTCGGGTTC
1 GGTCGGGTTC
13990 GGTCGGGTTC
1 GGTCGGGTTC
14000 GGTCGGGTTC
1 GGTCGGGTTC
14010 GGTCGGGTTC
1 GGTCGGGTTC
14020 GGTCGGGTTC
1 GGTCGGGTTC
14030 GGTCGGGTTC
1 GGTCGGGTTC
14040 GGTCGGGTTC
1 GGTCGGGTTC
14050 GGTCGGGTTC
1 GGTCGGGTTC
14060 GGTCGGGTTC
1 GGTCGGGTTC
14070 GGTCGGGTTC
1 GGTCGGGTTC
14080 GGTCGGGTTC
1 GGTCGGGTTC
14090 GGTCGGG
1 GGTCGGG
14097 AACCGCCAGC
Statistics
Matches: 147, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
10 143 0.97
11 4 0.03
ACGTcount: A:0.01, C:0.20, G:0.51, T:0.29
Consensus pattern (10 bp):
GGTCGGGTTC
Found at i:14254 original size:24 final size:24
Alignment explanation
Indices: 14222--14325 Score: 145
Period size: 24 Copynumber: 4.1 Consensus size: 24
14212 CTCTTCAATG
14222 CAAAACAGAGATACAACAAAATCC
1 CAAAACAGAGATACAACAAAATCC
14246 CAAAACAGAGATACATACAGCAAAATCC
1 CAAAACAGAGATAC--A-A-CAAAATCC
*
14274 CAAAAACAGAGATACAGCAAAATCC
1 C-AAAACAGAGATACAACAAAATCC
*
14299 CAAAACAGAGATACAGCAAAATCC
1 CAAAACAGAGATACAACAAAATCC
14323 CAA
1 CAA
14326 TCATTTATGG
Statistics
Matches: 74, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
24 40 0.54
25 9 0.12
26 1 0.01
27 2 0.03
28 9 0.12
29 13 0.18
ACGTcount: A:0.56, C:0.25, G:0.11, T:0.09
Consensus pattern (24 bp):
CAAAACAGAGATACAACAAAATCC
Found at i:14440 original size:29 final size:29
Alignment explanation
Indices: 14398--14457 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
14388 AAAGCTTCTA
14398 CTTAATTTAACAGAGCGCTTACCTTGGCT
1 CTTAATTTAACAGAGCGCTTACCTTGGCT
14427 CTTAATTTAACAGAGCGCTTACCTTGGCT
1 CTTAATTTAACAGAGCGCTTACCTTGGCT
14456 CT
1 CT
14458 GGCTCTCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (29 bp):
CTTAATTTAACAGAGCGCTTACCTTGGCT
Found at i:14781 original size:18 final size:17
Alignment explanation
Indices: 14758--14832 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 17
14748 TAGGGTTTTA
14758 ATATAAAATATATAT-T
1 ATATAAAATATATATAT
*
14774 ATATATAATACTAATATTAAT
1 ATATAAAATA-T-ATA-T-AT
*
14795 ATATATAATGATATATAT
1 ATATAAAAT-ATATATAT
14813 A-A-AAAATATA-ATAT
1 ATATAAAATATATATAT
14827 ATATAA
1 ATATAA
14833 TTTGTCGGTC
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
14 5 0.10
15 4 0.08
16 15 0.31
17 2 0.04
18 6 0.12
19 2 0.04
20 3 0.06
21 11 0.22
22 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (17 bp):
ATATAAAATATATATAT
Found at i:14830 original size:9 final size:9
Alignment explanation
Indices: 14758--14833 Score: 62
Period size: 9 Copynumber: 7.8 Consensus size: 9
14748 TAGGGTTTTA
*
14758 ATATAAAAT
1 ATATAATAT
*
14767 ATATATTAT
1 ATATAATAT
14776 ATATAATACT
1 ATATAATA-T
14786 AATATTAATAT
1 -ATA-TAATAT
14797 ATATAATGATAT
1 ATAT-A--ATAT
* *
14809 ATATAAAAA
1 ATATAATAT
14818 ATATAATAT
1 ATATAATAT
14827 ATATAAT
1 ATATAAT
14834 TTGTCGGTCG
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
9 31 0.57
10 5 0.09
11 5 0.09
12 13 0.24
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (9 bp):
ATATAATAT
Found at i:16618 original size:27 final size:27
Alignment explanation
Indices: 16588--16641 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
16578 CTACTTGTTT
*
16588 TTTTATAAGTTAAGGTAGAGTTATTTA
1 TTTTATAAGTTAAGGCAGAGTTATTTA
* *
16615 TTTTCTAAGTTGAGGCAGAGTTATTTA
1 TTTTATAAGTTAAGGCAGAGTTATTTA
16642 GATCACAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (27 bp):
TTTTATAAGTTAAGGCAGAGTTATTTA
Found at i:19642 original size:6 final size:6
Alignment explanation
Indices: 19610--19641 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
19600 CAGGCTGCAC
*
19610 CACAAT CACAAT CACAAT CACAAT CATAAT CA
1 CACAAT CACAAT CACAAT CACAAT CACAAT CA
19642 TCCGTTAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (6 bp):
CACAAT
Found at i:19797 original size:39 final size:38
Alignment explanation
Indices: 19671--19818 Score: 226
Period size: 38 Copynumber: 3.9 Consensus size: 38
19661 TCGAGTCTAG
*
19671 CCAACAG-TTAACCCCCTGAGGCATGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
19708 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
19746 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA
* *
19785 CCATCAGTTTAACCCCCTGAGGTACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
19819 ATGCACAGCC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
37 7 0.07
38 61 0.60
39 34 0.33
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.24
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:19812 original size:77 final size:75
Alignment explanation
Indices: 19671--19818 Score: 242
Period size: 77 Copynumber: 1.9 Consensus size: 75
19661 TCGAGTCTAG
19671 CCAACAGTTAACCCCCTGAGGCATGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
1 CCAACAGTTAACCCCCTGAGGCATGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
19736 TCCACTCTTA
66 TCCACTCTTA
* * * *
19746 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTACCATCAGTTTAACCCCCTGAGGTACG
1 CCAACAG-TTAACCCCCTGAGGCATGGGTCCACTC-TTACCAACAGTTTAACCCCCTGAGGCACG
19811 GGTCCACT
64 GGTCCACT
19819 ATGCACAGCC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
75 7 0.10
76 25 0.37
77 35 0.52
ACGTcount: A:0.22, C:0.34, G:0.19, T:0.24
Consensus pattern (75 bp):
CCAACAGTTAACCCCCTGAGGCATGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
TCCACTCTTA
Found at i:23813 original size:104 final size:104
Alignment explanation
Indices: 23653--23906 Score: 440
Period size: 104 Copynumber: 2.5 Consensus size: 104
23643 AATTTTTCTA
* **
23653 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTGAATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAATTAGTTATATATTTTAT
*
23717 TTCTAAAACCCTATAACAATATTATTAATAATGGAATTT
66 TTCTAAAACCCTATAACAATATTATTAATAATGAAATTT
23756 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAATTAGTTATATATTTTAT
23821 TTCTAAAACCCTATAACAATATTATTAATAATGAAATTT
66 TTCTAAAACCCTATAACAATATTATTAATAATGAAATTT
* *
23860 ACCCTTCAAATAAAAA-AAAATTTTAATCTGGGGCTAAACTTAGTGAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAA
23907 ATTAAGGCTA
Statistics
Matches: 144, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
103 57 0.40
104 87 0.60
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAATTAGTTATATATTTTAT
TTCTAAAACCCTATAACAATATTATTAATAATGAAATTT
Found at i:25934 original size:51 final size:50
Alignment explanation
Indices: 25833--25934 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
25823 GTTCTTCATA
* **
25833 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
25883 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
25934 T
1 T
25935 CTTCATTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 7 0.16
51 36 0.82
52 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:41177 original size:13 final size:13
Alignment explanation
Indices: 41159--41184 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41149 CTTGGCATGA
41159 GTGATGATTTTTG
1 GTGATGATTTTTG
41172 GTGATGATTTTTG
1 GTGATGATTTTTG
41185 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:41560 original size:19 final size:19
Alignment explanation
Indices: 41538--41588 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
41528 GGGCTGAAAT
41538 TAATTAATTATTAATTAAA
1 TAATTAATTATTAATTAAA
* *
41557 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAATTAAA
41576 TAATT-ATTATTAA
1 TAATTAATTATTAA
41589 AAATCTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TAATTAATTATTAATTAAA
Found at i:43041 original size:51 final size:50
Alignment explanation
Indices: 42940--43041 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 50
42930 GTTCTTCATA
* **
42940 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTTTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTTGTACAGTGT
* *
42990 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACA-TTGTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTTGTACA-GTGT
43041 T
1 T
43042 CTTTATTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
50 9 0.20
51 34 0.77
52 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.43
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTTGTACAGTGT
Found at i:43908 original size:22 final size:22
Alignment explanation
Indices: 43878--43996 Score: 102
Period size: 22 Copynumber: 5.4 Consensus size: 22
43868 TTGAATATTT
43878 TTATGAAATTTTGATAACTATC-
1 TTATGAAATTTTGATAACTA-CA
*
43900 TTATTAAATTTTGATAACTACA
1 TTATGAAATTTTGATAACTACA
* *
43922 CTATGAAATTTTGATAATTTAC-
1 TTATGAAATTTTGATAA-CTACA
* * *
43944 CTATGAAATTGTGATAAACTCCA
1 TTATGAAATTTTGAT-AACTACA
*
43967 -TATGAAACTTTGATAACCTA-A
1 TTATGAAATTTTGATAA-CTACA
*
43988 CTATGAAAT
1 TTATGAAAT
43997 ATTAATAAAC
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
21 4 0.05
22 71 0.89
23 5 0.06
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (22 bp):
TTATGAAATTTTGATAACTACA
Found at i:44036 original size:44 final size:43
Alignment explanation
Indices: 43879--44074 Score: 145
Period size: 44 Copynumber: 4.5 Consensus size: 43
43869 TGAATATTTT
* * * *
43879 TATGAAATTTTGATAACTATCTTATTAAATTTTGAT-AA-CTACAC
1 TATGAAATTTTGATAA-TTTCCTATGAAA-TTTGATAAACCTTC-C
43923 TATGAAATTTTGATAATTTACCTATGAAATTGTGATAAA-C-TCC
1 TATGAAATTTTGATAATTT-CCTATGAAATT-TGATAAACCTTCC
* * ** *
43966 ATATGAAACTTTGATAACCTAACTATGAAATATTAATAAACCTTCC
1 -TATGAAATTTTGATAA-TTTCCTATGAAAT-TTGATAAACCTTCC
**
44012 TATGAAATTTTG-TAATCTTCCTATGATTTTTGAT-AACCTTCC
1 TATGAAATTTTGATAAT-TTCCTATGAAATTTGATAAACCTTCC
*
44054 TAT-AAGATTTTGTTAATTTCC
1 TATGAA-ATTTTGATAATTTCC
44075 CTATAATTTT
Statistics
Matches: 125, Mismatches: 16, Indels: 24
0.76 0.10 0.15
Matches are distributed among these distances:
41 2 0.02
42 21 0.17
43 13 0.10
44 69 0.55
45 17 0.14
46 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.42
Consensus pattern (43 bp):
TATGAAATTTTGATAATTTCCTATGAAATTTGATAAACCTTCC
Found at i:44037 original size:66 final size:66
Alignment explanation
Indices: 43879--44050 Score: 176
Period size: 66 Copynumber: 2.6 Consensus size: 66
43869 TGAATATTTT
* * * * *
43879 TATGAAATTTTGATAACTATCTTATTAAATTTTGATAA-CTACACTATGAAATTTTGATAATTTA
1 TATGAAATTTTGATAACT-TCCTATGAAATTTTGATAACCTACACTATGAAATATTAATAACTTA
43943 CC
65 CC
* *
43945 TATGAAATTGTGATAAAC-TCCATATGAAACTTTGATAACCTA-ACTATGAAATATTAATAAACC
1 TATGAAATTTTGAT-AACTTCC-TATGAAATTTTGATAACCTACACTATGAAATATTAAT-AA-C
44008 TT-CC
62 TTACC
*
44012 TATGAAATTTTG-TAATCTTCCTATG-ATTTTTGATAACCT
1 TATGAAATTTTGATAA-CTTCCTATGAAATTTTGATAACCT
44051 TCCTATAAGA
Statistics
Matches: 89, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
65 16 0.18
66 47 0.53
67 24 0.27
68 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (66 bp):
TATGAAATTTTGATAACTTCCTATGAAATTTTGATAACCTACACTATGAAATATTAATAACTTAC
C
Found at i:44085 original size:21 final size:19
Alignment explanation
Indices: 44008--44084 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 19
43998 TTAATAAACC
44008 TTCCTATGAAATTTTGTAAT
1 TTCCTAT-AAATTTTGTAAT
* * *
44028 CTTCCTATGATTTTTGATAACC
1 -TTCCTATAAATTTTG-TAA-T
44050 TTCCTATAAGATTTTGTTAAT
1 TTCCTATAA-ATTTTG-TAAT
44071 TTCCCTAT-AATTTT
1 TT-CCTATAAATTTT
44085 TTGATACTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 11 0.24
21 21 0.47
22 13 0.29
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.51
Consensus pattern (19 bp):
TTCCTATAAATTTTGTAAT
Found at i:44876 original size:25 final size:24
Alignment explanation
Indices: 44848--44904 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
44838 GTGGATTGTA
*
44848 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
*
44873 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTGAAGAATTAAACATT
44897 AAA-AAATT
1 AAATAAATT
44905 CAAGGCTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.32
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Found at i:48622 original size:22 final size:22
Alignment explanation
Indices: 48594--48663 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
48584 ATATATACTA
*
48594 TTAAATAAATAATTAATATATT
1 TTAAATAAATAAATAATATATT
*
48616 TTAAAT-AATAAATAATGA-GTT
1 TTAAATAAATAAATAAT-ATATT
*
48637 TAAAATAAATAAATAATATATAT
1 TTAAATAAATAAATAATATAT-T
48660 TTAA
1 TTAA
48664 TTACGGGTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 17 0.44
22 18 0.46
23 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TTAAATAAATAAATAATATATT
Found at i:58429 original size:85 final size:85
Alignment explanation
Indices: 58286--58451 Score: 305
Period size: 85 Copynumber: 2.0 Consensus size: 85
58276 TTCCTCGATC
*
58286 CATGAAGTGATTGTCTTTCTTAAGCTTTCCCGTGGTCAGAGCTTTTGATTTCATGGAAGTATTGT
1 CATGAAGTGATTGTCTTTCTTAAGCTTTCCCGTGGTCAGAGCTTTTGATTTCATGGAAGGATTGT
58351 TAATTCCACCTTTTGTAATT
66 TAATTCCACCTTTTGTAATT
*
58371 CATGAAGTGATTGTCTTTCTTAAGCTTTCCCGTGGTCAGAGGTTTTGATTTCATGGAAGGATTGT
1 CATGAAGTGATTGTCTTTCTTAAGCTTTCCCGTGGTCAGAGCTTTTGATTTCATGGAAGGATTGT
*
58436 TAATTCCTCCTTTTGT
66 TAATTCCACCTTTTGT
58452 CTTCCCGATG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 78 1.00
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (85 bp):
CATGAAGTGATTGTCTTTCTTAAGCTTTCCCGTGGTCAGAGCTTTTGATTTCATGGAAGGATTGT
TAATTCCACCTTTTGTAATT
Found at i:62680 original size:36 final size:36
Alignment explanation
Indices: 62633--62702 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
62623 TTCAATAACC
*
62633 TTACATCTTTTGTGATTTTGATTACCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTACCATATTTCTTA
* *
62669 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTACCATATTTCT
62703 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.59
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTACCATATTTCTTA
Found at i:74741 original size:2 final size:2
Alignment explanation
Indices: 74728--74793 Score: 75
Period size: 2 Copynumber: 33.0 Consensus size: 2
74718 ACTAAAAATA
*
74728 AT AT AT AGT AT AT AT AT A- AT AT AT AT AT -T AT AT CT AT A- ACT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
74769 AT AT AT AT AT AT AGT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT
74794 TTTTTGAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
1 3 0.05
2 48 0.86
3 5 0.09
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:74744 original size:11 final size:10
Alignment explanation
Indices: 74728--74793 Score: 75
Period size: 9 Copynumber: 6.6 Consensus size: 10
74718 ACTAAAAATA
74728 ATATATAGTAT
1 ATATATA-TAT
74739 ATATATA-AT
1 ATATATATAT
74748 ATATATAT-T
1 ATATATATAT
*
74757 ATATCTATA-
1 ATATATATAT
74766 ACTATATATAT
1 A-TATATATAT
74777 ATATAGTATAT
1 ATATA-TATAT
74788 ATATAT
1 ATATAT
74794 TTTTTGAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
9 18 0.38
10 12 0.25
11 18 0.38
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (10 bp):
ATATATATAT
Found at i:81984 original size:28 final size:27
Alignment explanation
Indices: 81930--81985 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
81920 CACACACAAC
* *
81930 ACCTGGAGCTTCTTTGAGCCTCTCCTA
1 ACCTAGAGCTTCTTTGAGCCTCACCTA
*
81957 ACCTAGAGCTTTCTTTGAGTCTCACCTA
1 ACCTAGAGC-TTCTTTGAGCCTCACCTA
81985 A
1 A
81986 AACCCTAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (27 bp):
ACCTAGAGCTTCTTTGAGCCTCACCTA
Found at i:82712 original size:75 final size:75
Alignment explanation
Indices: 82582--82722 Score: 194
Period size: 75 Copynumber: 1.9 Consensus size: 75
82572 ACCCATCAAG
* * * * *
82582 ATCAATTTTTGATAATCTAAAAATTTCAGTAGAGAATTTTGCATCCAAACCAGAATCCCACAAAC
1 ATCAATTTTTGACAATCTAAAAACTTCAGTAGAAAACTTTGCATCAAAACCAGAATCCCACAAAC
82647 CTTCAAAGTC
66 CTTCAAAGTC
* * *
82657 ATCAATTTTTGACAATCTCAAGACTTCAGCTA-AAAACTTTGCATCAAAACTAGAATCCCACAAA
1 ATCAATTTTTGACAATCTAAAAACTTCAG-TAGAAAACTTTGCATCAAAACCAGAATCCCACAAA
82721 CC
65 CC
82723 AAGATCTTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 55 0.96
76 2 0.04
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (75 bp):
ATCAATTTTTGACAATCTAAAAACTTCAGTAGAAAACTTTGCATCAAAACCAGAATCCCACAAAC
CTTCAAAGTC
Found at i:83466 original size:28 final size:27
Alignment explanation
Indices: 83418--83473 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
83408 CACACACAAC
*
83418 ACCTGGAGCTTCTTTGAGCCTCTCCTA
1 ACCTGGAGCTTCTTTGAGCCTCACCTA
*
83445 ACCTGGAGCTTTCTTTTAGCCTCACCTA
1 ACCTGGAGC-TTCTTTGAGCCTCACCTA
83473 A
1 A
83474 AACCTTAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (27 bp):
ACCTGGAGCTTCTTTGAGCCTCACCTA
Found at i:84309 original size:2 final size:2
Alignment explanation
Indices: 84302--84330 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
84292 AATCAACTTT
84302 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 T
84331 CTAAATAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.