Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020584.1 Corchorus olitorius cultivar O-4 contig20617, 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: 69257
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:8771 original size:22 final size:22
Alignment explanation
Indices: 8746--8790 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
8736 AAATAACCCT
* *
8746 TTTCTTAGTCTTTTTAGGATTC
1 TTTCTTAGTCTTGTTAAGATTC
8768 TTTCTTAGTCTTGTTAAGATTC
1 TTTCTTAGTCTTGTTAAGATTC
8790 T
1 T
8791 AAACCTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (22 bp):
TTTCTTAGTCTTGTTAAGATTC
Found at i:12653 original size:27 final size:30
Alignment explanation
Indices: 12617--12687 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
12607 AAGCCCACTC
*
12617 TTTTCTTTTCTTCTC-C-TCTTCTTGC-T-T
1 TTTTTTTTTCTTCTCTCTTCTTCTT-CTTCT
12644 TTTTTTTTTCTCTCTCTCTTCTTCTTCTTCT
1 TTTTTTTTTCT-TCTCTCTTCTTCTTCTTCT
12675 TTTTTTTTTCTTC
1 TTTTTTTTTCTTC
12688 CGGTTAGCAG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 10 0.26
28 4 0.11
29 2 0.05
30 10 0.26
31 12 0.32
ACGTcount: A:0.00, C:0.27, G:0.01, T:0.72
Consensus pattern (30 bp):
TTTTTTTTTCTTCTCTCTTCTTCTTCTTCT
Found at i:12663 original size:24 final size:25
Alignment explanation
Indices: 12616--12677 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
12606 CAAGCCCACT
12616 CTTTTCTTTTCTTCTCCTCTTCTTG
1 CTTTTCTTTTCTTCTCCTCTTCTTG
* *
12641 CTTTTTTTTTTTCTCTCTCTCTTCTT-
1 CTTTTCTTTTCT-TCTC-CTCTTCTTG
12667 CTTCTTCTTTT
1 CTT-TTCTTTT
12678 TTTTTTCTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 10 0.32
26 7 0.23
27 14 0.45
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (25 bp):
CTTTTCTTTTCTTCTCCTCTTCTTG
Found at i:14421 original size:19 final size:19
Alignment explanation
Indices: 14397--14442 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
14387 CAGTTCATAA
14397 TTAAAATTTAAATGAAA-AT
1 TTAAAATTTAAAT-AAATAT
14416 TTAAAATTTAAATAAATAT
1 TTAAAATTTAAATAAATAT
14435 TTAAAATT
1 TTAAAATT
14443 AACTATGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TTAAAATTTAAATAAATAT
Found at i:16719 original size:16 final size:15
Alignment explanation
Indices: 16698--16727 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16688 GTCTCCTTTA
16698 ATTATATATAATTATT
1 ATTATATA-AATTATT
16714 ATTATATAAATTAT
1 ATTATATAAATTAT
16728 AAATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTATATAAATTATT
Found at i:18521 original size:31 final size:28
Alignment explanation
Indices: 18477--18540 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
18467 GCTTAATACC
*
18477 CAAATTAGTCCCTTAACTATCCATTTTGGGA
1 CAAATTAGCCCCTTAACT-T--ATTTTGGGA
* *
18508 CAAATTGGCCCCTTAACTTTTTTTGGGA
1 CAAATTAGCCCCTTAACTTATTTTGGGA
18536 CAAAT
1 CAAAT
18541 AAATCCCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 13 0.43
30 1 0.03
31 16 0.53
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (28 bp):
CAAATTAGCCCCTTAACTTATTTTGGGA
Found at i:20731 original size:24 final size:22
Alignment explanation
Indices: 20671--20838 Score: 90
Period size: 22 Copynumber: 7.5 Consensus size: 22
20661 TGAATATTTT
*
20671 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACCACCC
* *
20693 TATTAAATTTTGATAACCACGC
1 TATGAAATTTTGATAACCACCC
**
20715 TATGAAAAGTTTTGATAATTA-CC
1 TATG-AAA-TTTTGATAACCACCC
* **** *
20738 TATGAAATTGTGATAAATTTCA
1 TATGAAATTTTGATAACCACCC
** *
20760 TATGAAACATTGATAACCTA-AC
1 TATGAAATTTTGATAACC-ACCC
* * **
20782 TATGAAATTTTAATAAATCTTCC
1 TATGAAATTTTGAT-AACCACCC
*
20805 TATGAAATTTTG-TAACCTTCCC
1 TATGAAATTTTGATAACC-ACCC
*
20827 TATGAGATTTTG
1 TATGAAATTTTG
20839 TTAATCTTCC
Statistics
Matches: 110, Mismatches: 29, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
21 12 0.11
22 65 0.59
23 23 0.21
24 10 0.09
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACCC
Found at i:20831 original size:22 final size:22
Alignment explanation
Indices: 20781--20848 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
20771 GATAACCTAA
*
20781 CTATGAAATTTTAATAAATCTT-C
1 CTATGAAATTTT-GT-AATCTTCC
*
20804 CTATGAAATTTTGTAACCTTCC
1 CTATGAAATTTTGTAATCTTCC
*
20826 CTATGAGATTTTGTTAATCTTCC
1 CTATGAAATTTTG-TAATCTTCC
20849 TATAATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.13
22 14 0.36
23 20 0.51
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (22 bp):
CTATGAAATTTTGTAATCTTCC
Found at i:20850 original size:22 final size:21
Alignment explanation
Indices: 20781--20851 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 21
20771 GATAACCTAA
*
20781 CTATGAAATTTTAATAAATCTTC
1 CTATGAAATTTT-GT-AATCTTC
*
20804 CTATGAAATTTTGTAACCTTCC
1 CTATGAAATTTTGTAATCTT-C
*
20826 CTATGAGATTTTGTTAATCTTC
1 CTATGAAATTTTG-TAATCTTC
20848 CTAT
1 CTAT
20852 AATTTTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
21 5 0.12
22 19 0.45
23 18 0.43
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (21 bp):
CTATGAAATTTTGTAATCTTC
Found at i:24929 original size:2 final size:2
Alignment explanation
Indices: 24922--24950 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24912 ACAACCAATT
24922 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
24951 CTGTAATTTA
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
Found at i:25340 original size:57 final size:57
Alignment explanation
Indices: 25271--25386 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
25261 AAGCAATTTA
*
25271 AAACAGGCATCATAAATCACTCATGAAAACAATCAAATCGGCAATTTGGACAACTTG
1 AAACAGGCATCATAAATCACTCATGAAAACAATCAAATAGGCAATTTGGACAACTTG
25328 AAACAGGCATCATAAATCACTCATGAAAACAATCAAATAGGCAATTTGGACAACTTG
1 AAACAGGCATCATAAATCACTCATGAAAACAATCAAATAGGCAATTTGGACAACTTG
25385 AA
1 AA
25387 GAGATTTTAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.21
Consensus pattern (57 bp):
AAACAGGCATCATAAATCACTCATGAAAACAATCAAATAGGCAATTTGGACAACTTG
Found at i:33796 original size:22 final size:23
Alignment explanation
Indices: 33771--33817 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
33761 AATATTGAAT
*
33771 AATTA-CATTATAATCTCGATTA
1 AATTACCAATATAATCTCGATTA
*
33793 AATTATCCAATATAATCTTGATTA
1 AATTA-CCAATATAATCTCGATTA
33817 A
1 A
33818 TTCAAAGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
24 16 0.76
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.40
Consensus pattern (23 bp):
AATTACCAATATAATCTCGATTA
Found at i:34148 original size:71 final size:70
Alignment explanation
Indices: 34035--34175 Score: 255
Period size: 71 Copynumber: 2.0 Consensus size: 70
34025 CAACACACAC
*
34035 AAAAAAATTATAGGAGGACTTTTTTTTCTGAGATTATTCATAGGAGTACTTTAACATGCTAAGAT
1 AAAAAAATTATAGGAGGACTTTTTTTTCTAAGATTATTCATAGGAGTACTTTAACATGCTAAGAT
34100 AATAA
66 AATAA
*
34105 AAAAAAATTATAGGAGGACCTTTTTTTTCTAAGATTATTCATAGGAGTATTTTAACATGCTAAGA
1 AAAAAAATTATAGGAGGA-CTTTTTTTTCTAAGATTATTCATAGGAGTACTTTAACATGCTAAGA
34170 TAATAA
65 TAATAA
34176 TCATTAAACA
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 18 0.26
71 50 0.74
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (70 bp):
AAAAAAATTATAGGAGGACTTTTTTTTCTAAGATTATTCATAGGAGTACTTTAACATGCTAAGAT
AATAA
Found at i:35333 original size:18 final size:18
Alignment explanation
Indices: 35310--35345 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35300 ACATTGTCAA
35310 AATTGATTTCCAAACAAC
1 AATTGATTTCCAAACAAC
35328 AATTGATTTCCAAACAAC
1 AATTGATTTCCAAACAAC
35346 TCACCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (18 bp):
AATTGATTTCCAAACAAC
Found at i:36453 original size:308 final size:308
Alignment explanation
Indices: 35895--36512 Score: 1236
Period size: 308 Copynumber: 2.0 Consensus size: 308
35885 TTGTTGTTTG
35895 GCTATACTTCCGTGGTTGAATATTTGATGCATCTTCATGTTAATATTGGAGTTAAGTTCAGTCGT
1 GCTATACTTCCGTGGTTGAATATTTGATGCATCTTCATGTTAATATTGGAGTTAAGTTCAGTCGT
35960 CCAATGGATATCTGCAATTTAATGAAGTTTTACCTCCTAGGATTCTTGAAGTCATGTTATCCAGA
66 CCAATGGATATCTGCAATTTAATGAAGTTTTACCTCCTAGGATTCTTGAAGTCATGTTATCCAGA
36025 TTTTATATGATGCATTTATCCTGTATTGAGGATCAATTTGACTCCAGAATTTTTACTCAGCAATT
131 TTTTATATGATGCATTTATCCTGTATTGAGGATCAATTTGACTCCAGAATTTTTACTCAGCAATT
36090 AGTTGGTCTACTTTGACTTTTGATTGTGGCTTATATGTAATGATGTTTTCCTTCTCACTTTGTTG
196 AGTTGGTCTACTTTGACTTTTGATTGTGGCTTATATGTAATGATGTTTTCCTTCTCACTTTGTTG
36155 CCTGCTGAAAATCTTGTGTTCACCTAATAGATGATTTCTCGATTTGTC
261 CCTGCTGAAAATCTTGTGTTCACCTAATAGATGATTTCTCGATTTGTC
36203 GCTATACTTCCGTGGTTGAATATTTGATGCATCTTCATGTTAATATTGGAGTTAAGTTCAGTCGT
1 GCTATACTTCCGTGGTTGAATATTTGATGCATCTTCATGTTAATATTGGAGTTAAGTTCAGTCGT
36268 CCAATGGATATCTGCAATTTAATGAAGTTTTACCTCCTAGGATTCTTGAAGTCATGTTATCCAGA
66 CCAATGGATATCTGCAATTTAATGAAGTTTTACCTCCTAGGATTCTTGAAGTCATGTTATCCAGA
36333 TTTTATATGATGCATTTATCCTGTATTGAGGATCAATTTGACTCCAGAATTTTTACTCAGCAATT
131 TTTTATATGATGCATTTATCCTGTATTGAGGATCAATTTGACTCCAGAATTTTTACTCAGCAATT
36398 AGTTGGTCTACTTTGACTTTTGATTGTGGCTTATATGTAATGATGTTTTCCTTCTCACTTTGTTG
196 AGTTGGTCTACTTTGACTTTTGATTGTGGCTTATATGTAATGATGTTTTCCTTCTCACTTTGTTG
36463 CCTGCTGAAAATCTTGTGTTCACCTAATAGATGATTTCTCGATTTGTC
261 CCTGCTGAAAATCTTGTGTTCACCTAATAGATGATTTCTCGATTTGTC
36511 GC
1 GC
36513 AGGGGTCCAA
Statistics
Matches: 310, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
308 310 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (308 bp):
GCTATACTTCCGTGGTTGAATATTTGATGCATCTTCATGTTAATATTGGAGTTAAGTTCAGTCGT
CCAATGGATATCTGCAATTTAATGAAGTTTTACCTCCTAGGATTCTTGAAGTCATGTTATCCAGA
TTTTATATGATGCATTTATCCTGTATTGAGGATCAATTTGACTCCAGAATTTTTACTCAGCAATT
AGTTGGTCTACTTTGACTTTTGATTGTGGCTTATATGTAATGATGTTTTCCTTCTCACTTTGTTG
CCTGCTGAAAATCTTGTGTTCACCTAATAGATGATTTCTCGATTTGTC
Found at i:38791 original size:42 final size:44
Alignment explanation
Indices: 38740--38833 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
38730 AGTGCATTAT
*
38740 CTAA-ATTCTA-T-TCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
* *
38781 CTAATATTCTACTCCTCCATGTCTAGATAATTTATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
38826 CTAATATT
1 CTAATATT
38834 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
43 1 0.02
45 35 0.76
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:43847 original size:6 final size:6
Alignment explanation
Indices: 43836--43888 Score: 56
Period size: 6 Copynumber: 8.7 Consensus size: 6
43826 TTATTTCTTT
*
43836 ATATTA ATATTA ATATTA AT-TTT ATGGATTA ATA-TA TATATTA ATATTA
1 ATATTA ATATTA ATATTA ATATTA AT--ATTA ATATTA -ATATTA ATATTA
43885 ATAT
1 ATAT
43889 ATATATTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
5 6 0.15
6 28 0.70
7 2 0.05
8 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:44777 original size:21 final size:22
Alignment explanation
Indices: 44746--44787 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
44736 TTTGGCGTGC
44746 GAAATTTCAAAATTCGAATTTT
1 GAAATTTCAAAATTCGAATTTT
*
44768 GAAA-TTCAAAATTTGAATTT
1 GAAATTTCAAAATTCGAATTT
44788 CGGAAGTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (22 bp):
GAAATTTCAAAATTCGAATTTT
Found at i:48213 original size:2 final size:2
Alignment explanation
Indices: 48206--48239 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
48196 TGAACAAACA
*
48206 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48240 TTATTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:48244 original size:10 final size:10
Alignment explanation
Indices: 48206--48247 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
48196 TGAACAAACA
*
48206 ATATATATAT
1 ATATATATTT
*
48216 ATATATATAT
1 ATATATATTT
48226 ATATATATTT
1 ATATATATTT
*
48236 ATATTTATTT
1 ATATATATTT
48246 AT
1 AT
48248 TTTATACGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATATATTT
Found at i:48648 original size:76 final size:76
Alignment explanation
Indices: 48438--48753 Score: 440
Period size: 76 Copynumber: 4.2 Consensus size: 76
48428 AACATGGGTG
* * *
48438 GACGAACGGGGGTG-CTAGTTTAGGCACTTAGCCGTTGAGTGAGCGGCGTCTGCGTGGATGCTCT
1 GACGAACGGGGGCGTC-AGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCT
48502 GTCTCACTAGTA
65 GTCTCACTAGTA
* * *
48514 GACGAACGGGGGCGCCAG-TCAGGCACTGAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
1 GACGAACGGGGGCGTCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
*
48578 TCTCACTAATA
66 TCTCACTAGTA
* * *
48589 GACGAACGGGGGCGTCAGTTTAAGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGGGGACGCTCCG
1 GACGAACGGGGGCGTCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
48654 TCTCA-TAGGTA
66 TCTCACTA-GTA
* * * *
48665 GACGAACGGGGGTGTCAGTCTAGGCACTCAGCCGTTTAGTCAGCGGCGTCTGCGTGGACGCTCTG
1 GACGAACGGGGGCGTCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
* *
48730 TCTCACTGGTG
66 TCTCACTAGTA
*
48741 GGCGAACGGGGGC
1 GACGAACGGGGGC
48754 ACTATTCTGG
Statistics
Matches: 213, Mismatches: 23, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
75 72 0.34
76 139 0.65
77 2 0.01
ACGTcount: A:0.17, C:0.25, G:0.37, T:0.21
Consensus pattern (76 bp):
GACGAACGGGGGCGTCAGTTTAGGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGTGGACGCTCTG
TCTCACTAGTA
Found at i:48776 original size:152 final size:151
Alignment explanation
Indices: 48438--48736 Score: 449
Period size: 151 Copynumber: 2.0 Consensus size: 151
48428 AACATGGGTG
* * * * * *
48438 GACGAACGGGGGTGCT-AGTTTAGGCACTTAGCCGTTGAGTGAGCGGCGTCTGCGTGGATGCTCT
1 GACGAACGGGGG-CCTCAGTTTAAGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGGGGACGCTCC
* *
48502 GTCTCACTAGTAGACGAACGGGGGCGCCAGTCAGGCACTGAGCCGTTGAGTGAGCGGCGTCTGCG
65 GTCTCACTAGTAGACGAACGGGGGCGCCAGTCAGGCACTCAGCCGTTGAGTCAGCGGCGTCTGCG
48567 TGGACGCTCTGTCTCACTAATA
130 TGGACGCTCTGTCTCACTAATA
*
48589 GACGAACGGGGGCGTCAGTTTAAGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGGGGACGCTCCG
1 GACGAACGGGGGCCTCAGTTTAAGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGGGGACGCTCCG
* * *
48654 TCTCA-TAGGTAGACGAACGGGGGTGTCAGTCTAGGCACTCAGCCGTTTAGTCAGCGGCGTCTGC
66 TCTCACTA-GTAGACGAACGGGGGCGCCAGTC-AGGCACTCAGCCGTTGAGTCAGCGGCGTCTGC
48718 GTGGACGCTCTGTCTCACT
129 GTGGACGCTCTGTCTCACT
48737 GGTGGGCGAA
Statistics
Matches: 133, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
150 3 0.02
151 82 0.62
152 48 0.36
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.22
Consensus pattern (151 bp):
GACGAACGGGGGCCTCAGTTTAAGCACTCAGCCGTTGAGTGAGCGGCGTCTGCGGGGACGCTCCG
TCTCACTAGTAGACGAACGGGGGCGCCAGTCAGGCACTCAGCCGTTGAGTCAGCGGCGTCTGCGT
GGACGCTCTGTCTCACTAATA
Found at i:56094 original size:16 final size:16
Alignment explanation
Indices: 56073--56106 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
56063 TGTAACACAC
56073 GTGAAAGTGATAACTA
1 GTGAAAGTGATAACTA
56089 GTGAAAGTGATAACTA
1 GTGAAAGTGATAACTA
56105 GT
1 GT
56107 TACCATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
GTGAAAGTGATAACTA
Found at i:57316 original size:2 final size:2
Alignment explanation
Indices: 57311--57351 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
57301 TTGTTTTTGC
*
57311 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57352 GCTAAATAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64010 original size:29 final size:28
Alignment explanation
Indices: 63966--64023 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 28
63956 TTTTTCAAAC
*
63966 TTTCTAATTTCAAGAACGCTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
63994 TTTCTAATCTTCAAGAACGCTAAAGAACA
1 TTTCTAAT-TTCAAGAACGCTAAAGAACA
64023 T
1 T
64024 GGAATAACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Found at i:67586 original size:18 final size:18
Alignment explanation
Indices: 67563--67605 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
67553 TATGCCGAAA
67563 ATTATTAAATAAATAATT
1 ATTATTAAATAAATAATT
* * *
67581 ATTATTTATTTAATAATT
1 ATTATTAAATAAATAATT
67599 ATTATTA
1 ATTATTA
67606 TTTCCCCATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATTAAATAAATAATT
Found at i:68644 original size:10 final size:10
Alignment explanation
Indices: 68629--68657 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
68619 CCATATTAAC
68629 AATTTTATTT
1 AATTTTATTT
68639 AATTTTATTT
1 AATTTTATTT
68649 AA-TTTATTT
1 AATTTTATTT
68658 CCTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
AATTTTATTT
Done.