Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022474.1 Corchorus olitorius cultivar O-4 contig22507, 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: 50216
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:8543 original size:13 final size:13
Alignment explanation
Indices: 8525--8551 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8515 TGGAGATCTT
8525 TGATCTTTTCCTA
1 TGATCTTTTCCTA
8538 TGATCTTTTCCTA
1 TGATCTTTTCCTA
8551 T
1 T
8552 TTGGGTCACT
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:0.15, C:0.22, G:0.07, T:0.56
Consensus pattern (13 bp):
TGATCTTTTCCTA
Found at i:16113 original size:56 final size:57
Alignment explanation
Indices: 16005--16118 Score: 151
Period size: 56 Copynumber: 2.0 Consensus size: 57
15995 ATAGTCGTAT
* * *
16005 AATGGCTTAATGGAAAAAAAGACCATTGAACCTTCTGGTTAACGGTCAAATAAGTCC
1 AATGGCTTAATGGAAAAAAAGACCACTAAACCTTCTGGTTAACGATCAAATAAGTCC
* * *
16062 AATGGCTTAATGG-AAAAAAGACCCCTAAACTTTCTGGTTAATGAT-AGAATAAGTCC
1 AATGGCTTAATGGAAAAAAAGACCACTAAACCTTCTGGTTAACGATCA-AATAAGTCC
16118 A
1 A
16119 TGTACTTCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
55 1 0.02
56 36 0.72
57 13 0.26
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (57 bp):
AATGGCTTAATGGAAAAAAAGACCACTAAACCTTCTGGTTAACGATCAAATAAGTCC
Found at i:16892 original size:54 final size:54
Alignment explanation
Indices: 16828--16940 Score: 217
Period size: 54 Copynumber: 2.1 Consensus size: 54
16818 CTAATAGTGC
*
16828 AAACTAATTCATTAAATGCATGCCGAAAAAAACTAATTCATTAAATAAGATCTG
1 AAACGAATTCATTAAATGCATGCCGAAAAAAACTAATTCATTAAATAAGATCTG
16882 AAACGAATTCATTAAATGCATGCCGAAAAAAACTAATTCATTAAATAAGATCTG
1 AAACGAATTCATTAAATGCATGCCGAAAAAAACTAATTCATTAAATAAGATCTG
16936 AAACG
1 AAACG
16941 TGTATATGTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (54 bp):
AAACGAATTCATTAAATGCATGCCGAAAAAAACTAATTCATTAAATAAGATCTG
Found at i:16938 original size:29 final size:29
Alignment explanation
Indices: 16828--16927 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
16818 CTAATAGTGC
16828 AAACTAATTCATTAAATGCATGCCGAAAA
1 AAACTAATTCATTAAATGCATGCCGAAAA
*
16857 AAACTAATTCATTAAATAAG-AT-CTG----
1 AAACTAATTCATTAAAT--GCATGCCGAAAA
*
16882 AAACGAATTCATTAAATGCATGCCGAAAA
1 AAACTAATTCATTAAATGCATGCCGAAAA
16911 AAACTAATTCATTAAAT
1 AAACTAATTCATTAAAT
16928 AAGATCTGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
23 1 0.02
24 2 0.03
25 18 0.31
29 35 0.59
30 2 0.03
31 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (29 bp):
AAACTAATTCATTAAATGCATGCCGAAAA
Found at i:18591 original size:58 final size:56
Alignment explanation
Indices: 18472--18583 Score: 154
Period size: 58 Copynumber: 2.0 Consensus size: 56
18462 AGGTAATTAC
* * *
18472 AAAAAAGGTAGCAGGAAAAGAAAGGGGGGAAACTCATAGAGGGGCTTTTTAGTCATA
1 AAAAAAGGTAGCAGAAAAAGAAAGGGGAGAAACTCATAGA-GCGCTTTTTAGTCATA
* *
18529 AAAAAAGGGTAGCAGAAAAAGGAAGGGGAGAAACTCATAGA-CGTTTTTTAGTCAT
1 AAAAAA-GGTAGCAGAAAAAGAAAGGGGAGAAACTCATAGAGCGCTTTTTAGTCAT
18584 CCGAAAAATG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
56 12 0.24
57 6 0.12
58 31 0.63
ACGTcount: A:0.43, C:0.09, G:0.29, T:0.19
Consensus pattern (56 bp):
AAAAAAGGTAGCAGAAAAAGAAAGGGGAGAAACTCATAGAGCGCTTTTTAGTCATA
Found at i:18725 original size:54 final size:53
Alignment explanation
Indices: 18627--18734 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 53
18617 ACGTGGCAAC
*
18627 ACATTAATCCTCAATTTGACTTTTTAGTAATTTCACTGATAACTAAAAATAAT
1 ACATTAATCCTCAATTTGACTTTTTAATAATTTCACTGATAACTAAAAATAAT
* * *
18680 ACATTAATTCTCAATTTGGCCTTTTTAATCATTTTC-CTGATAACTAAAAATAAT
1 ACATTAATCCTCAATTT-GACTTTTTAAT-AATTTCACTGATAACTAAAAATAAT
18734 A
1 A
18735 TATAATATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
53 16 0.33
54 28 0.57
55 5 0.10
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (53 bp):
ACATTAATCCTCAATTTGACTTTTTAATAATTTCACTGATAACTAAAAATAAT
Found at i:19717 original size:2 final size:2
Alignment explanation
Indices: 19712--19742 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19702 AGTGTTTACG
19712 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 T
19743 TTGTTTTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20406 original size:20 final size:20
Alignment explanation
Indices: 20367--20406 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20357 TTAGTCTAAT
*
20367 AAATAAAAAAAGAATCAAAA
1 AAATAAAAAAAGAATAAAAA
20387 AAATAAAAAATA-AATAAAAA
1 AAATAAAAAA-AGAATAAAAA
20407 CATACTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (20 bp):
AAATAAAAAAAGAATAAAAA
Found at i:21797 original size:13 final size:15
Alignment explanation
Indices: 21764--21802 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
21754 GCCTTTATTG
21764 ATATATGGGGTGAAA
1 ATATATGGGGTGAAA
21779 ATATATGGGGTGAAA
1 ATATATGGGGTGAAA
21794 ATATATGGG
1 ATATATGGG
21803 AGGTCCCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.28
Consensus pattern (15 bp):
ATATATGGGGTGAAA
Found at i:23082 original size:22 final size:21
Alignment explanation
Indices: 23035--23082 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
23025 TTACCCTTCT
*
23035 TCTCT-CTCCCCCACTAACTT
1 TCTCTCCTCCCCCACTAACTA
* *
23055 TTTCTCCTCCTCCCACTCACTA
1 TCTCTCCTCC-CCCACTAACTA
23077 TCTCTC
1 TCTCTC
23083 TTCGTAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
22 14 0.64
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (21 bp):
TCTCTCCTCCCCCACTAACTA
Found at i:23637 original size:17 final size:18
Alignment explanation
Indices: 23617--23656 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
23607 AACTTAGATT
**
23617 AAAAAT-AAATTATCCCC
1 AAAAATAAAATTAAACCC
23634 AAAAATAAAATTAAACCC
1 AAAAATAAAATTAAACCC
23652 AAAAA
1 AAAAA
23657 AGAAAAGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.65, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAATAAAATTAAACCC
Found at i:31440 original size:22 final size:22
Alignment explanation
Indices: 31415--31461 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
31405 CTCGTTTAAT
** *
31415 TTTTCATTTTTTACCTAATATA
1 TTTTCATTTCATACATAATATA
31437 TTTTCATTTCATACATAATATA
1 TTTTCATTTCATACATAATATA
31459 TTT
1 TTT
31462 AAATTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTCATTTCATACATAATATA
Found at i:31820 original size:2 final size:2
Alignment explanation
Indices: 31813--31842 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31803 TTTGCAGCCT
31813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31843 AAGGTGACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34850 original size:19 final size:19
Alignment explanation
Indices: 34826--34864 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
34816 TTTGAGTCCA
*
34826 AAACGATGATGAAACGGTT
1 AAACGATAATGAAACGGTT
*
34845 AAACGATAATGAAATGGTT
1 AAACGATAATGAAACGGTT
34864 A
1 A
34865 CGTATAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (19 bp):
AAACGATAATGAAACGGTT
Found at i:37902 original size:20 final size:19
Alignment explanation
Indices: 37877--37914 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
37867 CTTACTTTGA
37877 AGCAATTTAAATTGATAATT
1 AGCAA-TTAAATTGATAATT
*
37897 AGCAATTGAATTGATAAT
1 AGCAATTAAATTGATAAT
37915 CGCTTTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (19 bp):
AGCAATTAAATTGATAATT
Found at i:38034 original size:17 final size:17
Alignment explanation
Indices: 38012--38045 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38002 TGATGAGTAT
38012 GGCACAACACTTCGTAA
1 GGCACAACACTTCGTAA
**
38029 GGCACATGACTTCGTAA
1 GGCACAACACTTCGTAA
38046 AAGCTTCACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (17 bp):
GGCACAACACTTCGTAA
Found at i:40754 original size:22 final size:23
Alignment explanation
Indices: 40687--40761 Score: 91
Period size: 22 Copynumber: 3.3 Consensus size: 23
40677 TGAATATCTT
*
40687 AAATTTCATATATAAAGGTTATCA
1 AAATTTCATAGA-AAAGGTTATCA
* *
40711 AAATTTCACAGTAAA-GTTATCA
1 AAATTTCATAGAAAAGGTTATCA
*
40733 AAATTTCATA-AAAAGGTCATCA
1 AAATTTCATAGAAAAGGTTATCA
40755 AAATTTC
1 AAATTTC
40762 TTAGGGAGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
21 3 0.07
22 29 0.66
23 3 0.07
24 9 0.20
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (23 bp):
AAATTTCATAGAAAAGGTTATCA
Found at i:40778 original size:22 final size:22
Alignment explanation
Indices: 40702--40930 Score: 106
Period size: 22 Copynumber: 10.3 Consensus size: 22
40692 TCATATATAA
* * **
40702 AGGTTATCAAAATTTCACAGTA
1 AGGTTAACAAAATTTCATAGGG
* * ***
40724 AAGTTATCAAAATTTCATAAAA
1 AGGTTAACAAAATTTCATAGGG
* * *
40746 AGGTCATCAAAATTTCTTAGGG
1 AGGTTAACAAAATTTCATAGGG
* *
40768 AGGTTAACAAAAGTTCATACGG
1 AGGTTAACAAAATTTCATAGGG
* * **
40790 A-GTTATCGAAATTGT-ATAATG
1 AGGTTAACAAAATT-TCATAGGG
* ** * *
40811 TGGTTATTAAAATTTCATATGA
1 AGGTTAACAAAATTTCATAGGG
40833 AGGTTAACAAAATTTCATAAGGAGGG
1 AGGTTAACAAAATTTCAT----AGGG
* *
40859 AGGTTATCAAAATTTCATATGG
1 AGGTTAACAAAATTTCATAGGG
*
40881 AGGTTAACAAAATTAT-ATAGGA
1 AGGTTAACAAAATT-TCATAGGG
** *
40903 AGGTTATGAAAATTTTAT-GGAG
1 AGGTTAACAAAATTTCATAGG-G
40925 AGGTTA
1 AGGTTA
40931 TCGAGAATAC
Statistics
Matches: 158, Mismatches: 39, Indels: 20
0.73 0.18 0.09
Matches are distributed among these distances:
21 17 0.11
22 121 0.77
23 1 0.01
26 19 0.12
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (22 bp):
AGGTTAACAAAATTTCATAGGG
Found at i:40779 original size:44 final size:46
Alignment explanation
Indices: 40687--40786 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 46
40677 TGAATATCTT
* * *
40687 AAATTTCATATATAAAGGTTATCAAAATTTCACAGTAAAGTTATCA
1 AAATTTCATATATAAAGGTCATCAAAATTTCACAGGAAAGTTAACA
** * *
40733 AAATTTCATA-A-AAAGGTCATCAAAATTTCTTAGGGAGGTTAACA
1 AAATTTCATATATAAAGGTCATCAAAATTTCACAGGAAAGTTAACA
*
40777 AAAGTTCATA
1 AAATTTCATA
40787 CGGAGTTATC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 35 0.76
45 1 0.02
46 10 0.22
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (46 bp):
AAATTTCATATATAAAGGTCATCAAAATTTCACAGGAAAGTTAACA
Found at i:40802 original size:65 final size:65
Alignment explanation
Indices: 40725--40856 Score: 149
Period size: 65 Copynumber: 2.0 Consensus size: 65
40715 TTCACAGTAA
* * *
40725 AGTTATCAAAATT-TCATAAAAAGGTCATCAAAATTTCTTAGGGAGGTTAACAAAAGTTCATACG
1 AGTTATCAAAATTGT-ATAAAAAGGTCATCAAAATTTCATAGGAAGGTTAACAAAAGTTCATAAG
40789 G
65 G
* *** * * * *
40790 AGTTATCGAAATTGTATAATGTGGTTATTAAAATTTCATATGAAGGTTAACAAAATTTCATAAGG
1 AGTTATCAAAATTGTATAAAAAGGTCATCAAAATTTCATAGGAAGGTTAACAAAAGTTCATAAGG
40855 AG
1 AG
40857 GGAGGTTATC
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
65 54 0.98
66 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (65 bp):
AGTTATCAAAATTGTATAAAAAGGTCATCAAAATTTCATAGGAAGGTTAACAAAAGTTCATAAGG
Found at i:40869 original size:26 final size:26
Alignment explanation
Indices: 40833--40883 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
40823 TTTCATATGA
40833 AGGTTAACAAAATTTCATAAGGAGGG
1 AGGTTAACAAAATTTCATAAGGAGGG
* *
40859 AGGTTATCAAAATTTCATATGGAGG
1 AGGTTAACAAAATTTCATAAGGAGG
40884 TTAACAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.27
Consensus pattern (26 bp):
AGGTTAACAAAATTTCATAAGGAGGG
Found at i:41115 original size:22 final size:22
Alignment explanation
Indices: 41087--41144 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
41077 AGGGAGATTA
41087 TTATCAAAATTTCACACTAAGG
1 TTATCAAAATTTCACACTAAGG
* * * **
41109 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCACACTAAGG
41131 TTATCAAAATTTCA
1 TTATCAAAATTTCA
41145 ATGCAGTTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCACACTAAGG
Found at i:41198 original size:22 final size:23
Alignment explanation
Indices: 41173--41228 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 23
41163 CATAAGGAAA
* *
41173 TTATTGAAA-TTTCATAATGGGG
1 TTATTCAAATTTTCACAATGGGG
*
41195 TTA-TCAAATTTTCACAATGTGG
1 TTATTCAAATTTTCACAATGGGG
41217 TTA-TCAATATTT
1 TTATTCAA-ATTT
41229 CTACCAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.14
22 21 0.72
23 4 0.14
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (23 bp):
TTATTCAAATTTTCACAATGGGG
Found at i:41229 original size:22 final size:21
Alignment explanation
Indices: 41179--41229 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
41169 GAAATTATTG
*
41179 AAATTTCATAATGGGGTTATC
1 AAATTTCACAATGGGGTTATC
*
41200 AAATTTTCACAATGTGGTTATC
1 AAA-TTTCACAATGGGGTTATC
41222 AATATTTC
1 AA-ATTTC
41230 TACCAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 3 0.12
22 22 0.85
23 1 0.04
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATTTCACAATGGGGTTATC
Found at i:43776 original size:2 final size:2
Alignment explanation
Indices: 43763--43807 Score: 56
Period size: 2 Copynumber: 22.0 Consensus size: 2
43753 ACTAAAAATA
*
43763 AT AT AT AGT AT AT AT TT CAT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
43806 AT
1 AT
43808 GTATGTGTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 1 0.03
2 34 0.89
3 3 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46729 original size:23 final size:23
Alignment explanation
Indices: 46702--46748 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
46692 CGACATATAA
*
46702 AGATTTATTCATATTATAATGAG
1 AGATTTATTCAGATTATAATGAG
46725 AGATTTATTCAGATTATAATGAG
1 AGATTTATTCAGATTATAATGAG
46748 A
1 A
46749 TTTCACATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.40
Consensus pattern (23 bp):
AGATTTATTCAGATTATAATGAG
Found at i:49848 original size:2 final size:2
Alignment explanation
Indices: 49841--49878 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
49831 CTTGGATTTG
49841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49879 GTACTCATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50010 original size:22 final size:21
Alignment explanation
Indices: 49980--50026 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
49970 GATGGTGAGG
*
49980 TTTTCTTTTTCAAATAGGTAGT
1 TTTTATTTTT-AAATAGGTAGT
**
50002 TTTTATTTTTTTATAGGTAGT
1 TTTTATTTTTAAATAGGTAGT
50023 TTTT
1 TTTT
50027 TACTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.19, C:0.04, G:0.13, T:0.64
Consensus pattern (21 bp):
TTTTATTTTTAAATAGGTAGT
Found at i:50027 original size:23 final size:22
Alignment explanation
Indices: 49993--50037 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 22
49983 TCTTTTTCAA
49993 ATAGGTAGTTTTTA-TTTTTTT
1 ATAGGTAGTTTTTACTTTTTTT
50014 ATAGGTAGTTTTTTACTTTTTTT
1 ATAGGTAG-TTTTTACTTTTTTT
50037 A
1 A
50038 ATGATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.36
22 6 0.27
23 8 0.36
ACGTcount: A:0.20, C:0.02, G:0.13, T:0.64
Consensus pattern (22 bp):
ATAGGTAGTTTTTACTTTTTTT
Done.