Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011377.1 Corchorus capsularis cultivar CVL-1 contig11398, 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: 28506
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1228 original size:34 final size:32
Alignment explanation
Indices: 1190--1257 Score: 82
Period size: 34 Copynumber: 2.1 Consensus size: 32
1180 CCTAAGATGC
1190 TTAAAAATAAAATCCTAAATCTAGAAAACATAAA
1 TTAAAAATAAAATCCT-AATCT-GAAAACATAAA
** * *
1224 TTAAACTTAAAATCCTAATCTTAAAACCTAAA
1 TTAAAAATAAAATCCTAATCTGAAAACATAAA
1256 TT
1 TT
1258 GGTTTAGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 11 0.37
33 5 0.17
34 14 0.47
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.29
Consensus pattern (32 bp):
TTAAAAATAAAATCCTAATCTGAAAACATAAA
Found at i:2229 original size:33 final size:32
Alignment explanation
Indices: 2191--2252 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
2181 TTTGCTTCCA
* * *
2191 AAAGTCGCCTTGTGTAGTCGATTTGCTCCTTGT
1 AAAGTCGACTTGTATAGTCGACTT-CTCCTTGT
2224 AAAGTCGACTTGTATAGTCGACTTCTCCT
1 AAAGTCGACTTGTATAGTCGACTTCTCCT
2253 CTAATCGACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 5 0.19
33 21 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (32 bp):
AAAGTCGACTTGTATAGTCGACTTCTCCTTGT
Found at i:2546 original size:22 final size:22
Alignment explanation
Indices: 2518--2561 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2508 CCTAATCTTC
*
2518 CTTGCATGTAGCTGGCGCGGCA
1 CTTGCATGGAGCTGGCGCGGCA
**
2540 CTTGCATGGATTTGGCGCGGCA
1 CTTGCATGGAGCTGGCGCGGCA
2562 TTCCCCTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (22 bp):
CTTGCATGGAGCTGGCGCGGCA
Found at i:8144 original size:15 final size:16
Alignment explanation
Indices: 8112--8145 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8102 AAAGAAGAAT
*
8112 TAAAATTAAATCTAAC
1 TAAAAATAAATCTAAC
8128 TAAAAATAAAT-TAAC
1 TAAAAATAAATCTAAC
8143 TAA
1 TAA
8146 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAATAAATCTAAC
Found at i:9458 original size:19 final size:18
Alignment explanation
Indices: 9425--9460 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9415 TTGAAATAAT
9425 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
9443 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
9461 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:21820 original size:9 final size:9
Alignment explanation
Indices: 21767--21838 Score: 57
Period size: 9 Copynumber: 8.7 Consensus size: 9
21757 TGAAATGGCC
*
21767 ATTAATATA
1 ATTAATATG
*
21776 ACTAATATG
1 ATTAATATG
*
21785 ATTAACA--
1 ATTAATATG
*
21792 AGTAATATG
1 ATTAATATG
21801 ATTAATA--
1 ATTAATATG
21808 ATTAATATG
1 ATTAATATG
21817 ATT-A-ATG
1 ATTAATATG
*
21824 ACTAATATG
1 ATTAATATG
21833 ATTAAT
1 ATTAAT
21839 GAGAAAGTGA
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
7 17 0.35
8 2 0.04
9 29 0.60
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (9 bp):
ATTAATATG
Found at i:21840 original size:16 final size:16
Alignment explanation
Indices: 21773--21838 Score: 96
Period size: 16 Copynumber: 4.1 Consensus size: 16
21763 GGCCATTAAT
21773 ATAACTAATATGATTA
1 ATAACTAATATGATTA
* *
21789 ACAAGTAATATGATTA
1 ATAACTAATATGATTA
*
21805 ATAATTAATATGATTA
1 ATAACTAATATGATTA
*
21821 ATGACTAATATGATTA
1 ATAACTAATATGATTA
21837 AT
1 AT
21839 GAGAAAGTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (16 bp):
ATAACTAATATGATTA
Found at i:22128 original size:27 final size:28
Alignment explanation
Indices: 22096--22171 Score: 100
Period size: 29 Copynumber: 2.7 Consensus size: 28
22086 AAGTGAACTT
22096 AAAATGACCAAAATGCCCCTAAAT-GAA
1 AAAATGACCAAAATGCCCCTAAATCGAA
* * * *
22123 AGAATGACAAAAATGCCCCCTGAATCTAA
1 AAAATGACCAAAATG-CCCCTAAATCGAA
22152 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
22172 GGGTGACCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 13 0.32
28 13 0.32
29 15 0.37
ACGTcount: A:0.47, C:0.25, G:0.12, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTAAATCGAA
Found at i:22688 original size:23 final size:24
Alignment explanation
Indices: 22642--22688 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
22632 TTTAGTCATA
* *
22642 ATTTGGGTCTTGCTTATTCCATTT
1 ATTTGGGTCTTGCTAATTACATTT
*
22666 ATTTGGGT-TTGCTAATTAGATTT
1 ATTTGGGTCTTGCTAATTACATTT
22689 GGACTAGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.17, C:0.11, G:0.19, T:0.53
Consensus pattern (24 bp):
ATTTGGGTCTTGCTAATTACATTT
Found at i:23413 original size:38 final size:38
Alignment explanation
Indices: 23371--23596 Score: 231
Period size: 39 Copynumber: 6.1 Consensus size: 38
23361 AATCAAAATG
* *
23371 AAGTTTTTAAAGTTTTCAATTTAGTGAAAGATCCCATC
1 AAGTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC
*
23409 AAGTTTTCCAAAGTTTTCAATTTAGGAAAAGATCCCATC
1 AAGTTTT-CAAAGTTTTCAATTTAGGGAAAGATCCCATC
* *
23448 AAGTTTTCCAATA-TTTTCAATTTAAGGAAAGATCCCACC
1 AAGTTTT-CAA-AGTTTTCAATTTAGGGAAAGATCCCATC
23487 AAGTTTTCAAAGTTTT-AGATTTAGGGAAAGATCCCA-C
1 AAGTTTTCAAAGTTTTCA-ATTTAGGGAAAGATCCCATC
*
23524 -------C-ATGTTTTCAATTTAGGGAAAGATCCCATC
1 AAGTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC
* * *
23554 CAGTTTTTTAAAAGGTTTTCAATTTAGGGAAAGATCCCGTC
1 AAG--TTTTCAAA-GTTTTCAATTTAGGGAAAGATCCCATC
23595 AA
1 AA
23597 AAGGCATTTT
Statistics
Matches: 159, Mismatches: 12, Indels: 31
0.79 0.06 0.15
Matches are distributed among these distances:
29 24 0.15
30 3 0.02
37 3 0.02
38 31 0.19
39 69 0.43
40 2 0.01
41 27 0.17
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (38 bp):
AAGTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC
Found at i:23471 original size:78 final size:77
Alignment explanation
Indices: 23383--23532 Score: 223
Period size: 77 Copynumber: 1.9 Consensus size: 77
23373 GTTTTTAAAG
*
23383 TTTTCAATTT-AGTGAAAGATCCCATCAAGTTTTCCAAAGTTTTCA-ATTTAGGAAAAGATCCCA
1 TTTTCAATTTAAG-GAAAGATCCCACCAAGTTTT-CAAAGTTTT-AGATTTAGGAAAAGATCCCA
*
23446 TCAAGTTTTCCAATA
63 CCAAGTTTTCCAATA
*
23461 TTTTCAATTTAAGGAAAGATCCCACCAAGTTTTCAAAGTTTTAGATTTAGGGAAAGATCCCACCA
1 TTTTCAATTTAAGGAAAGATCCCACCAAGTTTTCAAAGTTTTAGATTTAGGAAAAGATCCCACCA
*
23526 TGTTTTC
66 AGTTTTC
23533 AATTTAGGGA
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
76 1 0.02
77 34 0.52
78 29 0.44
79 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.35
Consensus pattern (77 bp):
TTTTCAATTTAAGGAAAGATCCCACCAAGTTTTCAAAGTTTTAGATTTAGGAAAAGATCCCACCA
AGTTTTCCAATA
Found at i:23531 original size:29 final size:29
Alignment explanation
Indices: 23497--23560 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
23487 AAGTTTTCAA
23497 AGTTTT-AGATTTAGGGAAAGATCCCA-CC
1 AGTTTTCA-ATTTAGGGAAAGATCCCATCC
23525 ATGTTTTCAATTTAGGGAAAGATCCCATCC
1 A-GTTTTCAATTTAGGGAAAGATCCCATCC
23555 AGTTTT
1 AGTTTT
23561 TTAAAAGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 1 0.03
29 28 0.85
30 4 0.12
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (29 bp):
AGTTTTCAATTTAGGGAAAGATCCCATCC
Found at i:23537 original size:67 final size:69
Alignment explanation
Indices: 23461--23591 Score: 189
Period size: 67 Copynumber: 1.9 Consensus size: 69
23451 TTTTCCAATA
*
23461 TTTTCAATTTAAGGAAAGATCCCA-CCAAG-TTTTCAAA-GTTTT-AGATTTAGGGAAAGATCCC
1 TTTTCAATTTAAGGAAAGATCCCATCC-AGTTTTTAAAAGGTTTTCA-ATTTAGGGAAAGATCCC
23522 ACCATG
64 ACCATG
*
23528 TTTTCAATTTAGGGAAAGATCCCATCCAGTTTTTTAAAAGGTTTTCAATTTAGGGAAAGATCCC
1 TTTTCAATTTAAGGAAAGATCCCATCCAG-TTTTTAAAAGGTTTTCAATTTAGGGAAAGATCCC
23592 GTCAAAAGGC
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
67 25 0.44
68 2 0.04
69 7 0.12
70 22 0.39
71 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (69 bp):
TTTTCAATTTAAGGAAAGATCCCATCCAGTTTTTAAAAGGTTTTCAATTTAGGGAAAGATCCCAC
CATG
Found at i:27187 original size:66 final size:66
Alignment explanation
Indices: 27069--27250 Score: 260
Period size: 66 Copynumber: 2.7 Consensus size: 66
27059 AGAAAAAGTT
* *
27069 TTTTAAGAGTTAATCGGAAGACGATCTTAGTAAGAAATTCACCGGAAAACAGTTTGCTAGAAAGA
1 TTTTAAGAGTTAATCGGAAGACGATCTTAGTAAGAAATTAACCAGAAAACAGTTTGCTAGAAAGA
27134 A
66 A
*
27135 TTTTAAGAGTTAATCGGAAGACGATCTTAGTAAGAAATTAACCAGAAGACAGTTTGCTAGAAAGA
1 TTTTAAGAGTTAATCGGAAGACGATCTTAGTAAGAAATTAACCAGAAAACAGTTTGCTAGAAAGA
27200 A
66 A
* * * *
27201 TTTTCAAAAGTTGATCGGAAGATGATCTT-GTCAAG-AAGTACACCAGAAAA
1 TTTT-AAGAGTTAATCGGAAGACGATCTTAGT-AAGAAATTA-ACCAGAAAA
27251 TGGTTTATCA
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
66 73 0.70
67 32 0.30
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (66 bp):
TTTTAAGAGTTAATCGGAAGACGATCTTAGTAAGAAATTAACCAGAAAACAGTTTGCTAGAAAGA
A
Found at i:27297 original size:64 final size:64
Alignment explanation
Indices: 27133--27423 Score: 259
Period size: 64 Copynumber: 4.5 Consensus size: 64
27123 TGCTAGAAAG
* * * * ** *
27133 AATTTTAAG-AGTTAATCGGAAGACGATCTTAGT-AAGAAATTA-ACCAGAAGACAGTTTGCTAG
1 AATTTTCAGAAGTTGATCGGAAAACGATCTT-GTCAAG-AAGTACACCAGAAGATGGTTT-CT-C
27195 AAA
62 AAA
* * * * * *
27198 GAATTTTCAAAAGTTGATCGGAAGATGATCTTGTCAAGAAGTACACCAGAAAATGGTTTATCAAG
1 -AATTTTCAGAAGTTGATCGGAAAACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * *
27263 AGTTTTCAGAAGTTTATCGGAAAACGATCGTGTCAAGAAGTACACCGGAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAAACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
** ** * *
27327 AATTTTCAGAAGTTGATTAGAAGTCGATCTTGTTAA-AAGTACACCAGAAGATAGTTTCTCGAAA
1 AATTTTCAGAAGTTGATCGGAAAACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAA
**
27391 AGGTTTCAGAAGTTGATC-GAAAGACGATCTTGT
1 AATTTTCAGAAGTTGATCGGAAA-ACGATCTTGT
27424 TAAAAGATGC
Statistics
Matches: 184, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
63 25 0.14
64 109 0.59
65 2 0.01
66 14 0.08
67 34 0.18
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAAACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
Found at i:27358 original size:128 final size:128
Alignment explanation
Indices: 27199--27442 Score: 307
Period size: 128 Copynumber: 1.9 Consensus size: 128
27189 TGCTAGAAAG
* * *
27199 AATTTTCAAAAGTTGATCGGAAGATGATCTTGTCAAGAAGTACACCAGAAAATGGTTTATC-AAG
1 AATTTTCAAAAGTTGATCAGAAGATGATCTTGTCAA-AAGTACACCAGAAAATAGTTTATCGAAA
* *
27263 AGTTTTCAGAAGTTTATCGGAAA-ACGATCGTGTCAAGAAG-TACACCGGAAGATGGTTTCTCAA
65 AGGTTTCAGAAGTTGATC-GAAAGACGATCGTGTCAA-AAGATACACCGGAAGATGGTTTCTCAA
27326 A
128 A
* * * * *
27327 AATTTTCAGAAGTTGATTAGAAG-TCGATCTTGTTAAAAGTACACCAGAAGATAGTTTCTCGAAA
1 AATTTTCAAAAGTTGATCAGAAGAT-GATCTTGTCAAAAGTACACCAGAAAATAGTTTATCGAAA
* * *
27391 AGGTTTCAGAAGTTGATCGAAAGACGATCTTGTTAAAAGATGCACCGGAAGA
65 AGGTTTCAGAAGTTGATCGAAAGACGATCGTGTCAAAAGATACACCGGAAGA
27443 CTGTTATTTA
Statistics
Matches: 99, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
127 29 0.29
128 70 0.71
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (128 bp):
AATTTTCAAAAGTTGATCAGAAGATGATCTTGTCAAAAGTACACCAGAAAATAGTTTATCGAAAA
GGTTTCAGAAGTTGATCGAAAGACGATCGTGTCAAAAGATACACCGGAAGATGGTTTCTCAAA
Found at i:27731 original size:58 final size:60
Alignment explanation
Indices: 27659--27793 Score: 157
Period size: 62 Copynumber: 2.2 Consensus size: 60
27649 GATGGAATTG
* * * *
27659 GAAGACAATCCTTTT-T-TGAATGGGGAGACAGGTCACGAAAGATTTTGAATGATGGATC
1 GAAGACGATCCTTTTGTATGAATCGGAAGACAGATCACGAAAGATTTTGAATGATGGATC
* * * * *
27717 GAAGACGATCCTTTTGAGTATGAGTCTGAAGACAGATCATGAAATATTTTGAATGATGGATT
1 GAAGACGATCCTTTT--GTATGAATCGGAAGACAGATCACGAAAGATTTTGAATGATGGATC
27779 GAAGACGATCCTTTT
1 GAAGACGATCCTTTT
27794 AAGTATGAGA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 14 0.22
61 1 0.02
62 49 0.77
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (60 bp):
GAAGACGATCCTTTTGTATGAATCGGAAGACAGATCACGAAAGATTTTGAATGATGGATC
Found at i:27769 original size:62 final size:62
Alignment explanation
Indices: 27684--27819 Score: 202
Period size: 62 Copynumber: 2.2 Consensus size: 62
27674 TTGAATGGGG
* * *
27684 AGACAGGTCACGAAAGATTTTGAATGATGGATCGAAGACGATCCTTTTGAGTATGAG-TCTGA
1 AGACAGATCATGAAAGATTTTGAATGATGGATCGAAGACGATCCTTTTAAGTATGAGAT-TGA
* *
27746 AGACAGATCATGAAATATTTTGAATGATGGATTGAAGACGATCCTTTTAAGTATGAGATTGA
1 AGACAGATCATGAAAGATTTTGAATGATGGATCGAAGACGATCCTTTTAAGTATGAGATTGA
*
27808 AGACAGCTCATG
1 AGACAGATCATG
27820 GATGAATCTG
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 66 0.99
63 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.29
Consensus pattern (62 bp):
AGACAGATCATGAAAGATTTTGAATGATGGATCGAAGACGATCCTTTTAAGTATGAGATTGA
Found at i:27834 original size:85 final size:85
Alignment explanation
Indices: 27736--27916 Score: 274
Period size: 85 Copynumber: 2.1 Consensus size: 85
27726 CCTTTTGAGT
* **
27736 ATGAGTCTGAAGACAGATCATGAAATATTTTGAATGATGGATTGAAGACGATCCTTTTAAGTA-T
1 ATGAATCTGAAGACAGATCACAAAATATTTTGAATGATGGATTGAAGACGATCCTTTTAAG-AGT
* **
27800 GAGATTGAAGACAGCTCATGG
65 GAGACTGAAGACAGCTCACAG
27821 ATGAATCTGAAGACAGATCACAAAATATTTTGAATGATGGATTGAAGACGATCCTTTTAAGAGTG
1 ATGAATCTGAAGACAGATCACAAAATATTTTGAATGATGGATTGAAGACGATCCTTTTAAGAGTG
*
27886 AGGCTGAAGACAGCTCACAG
66 AGACTGAAGACAGCTCACAG
*
27906 ATGGATCTGAA
1 ATGAATCTGAA
27917 TACATTTCCT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 1 0.01
85 86 0.99
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (85 bp):
ATGAATCTGAAGACAGATCACAAAATATTTTGAATGATGGATTGAAGACGATCCTTTTAAGAGTG
AGACTGAAGACAGCTCACAG
Found at i:27960 original size:58 final size:58
Alignment explanation
Indices: 27884--28053 Score: 241
Period size: 58 Copynumber: 2.9 Consensus size: 58
27874 CTTTTAAGAG
* *
27884 TGAGGCTGAAGACAGCTCACAGATGGATCTGAATACATTTCCTAAAAGATTTGAAAAT
1 TGAGGCTGAAGACAGCTCACAGATGGATCTGAAGACAGTTCCTAAAAGATTTGAAAAT
* *
27942 TGAGGCTGAAGACAGCTCACAGGTAGATCTGAAGACAGTTCCTAAAAGATTTGAAAAT
1 TGAGGCTGAAGACAGCTCACAGATGGATCTGAAGACAGTTCCTAAAAGATTTGAAAAT
* * * * *
28000 TGAGACTGAAGATAGCTCACAAATGGGTTCTGAAGACAGATCCTAAAAGTATTT
1 TGAGGCTGAAGACAGCTCACAGAT-GGATCTGAAGACAGTTCCTAAAAG-ATTT
28054 AAGAGTAAAT
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
58 74 0.75
59 21 0.21
60 4 0.04
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (58 bp):
TGAGGCTGAAGACAGCTCACAGATGGATCTGAAGACAGTTCCTAAAAGATTTGAAAAT
Found at i:28150 original size:36 final size:36
Alignment explanation
Indices: 28028--28152 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 36
28018 ACAAATGGGT
* * *
28028 TCTGAAGACAGATCCTAAAA-GTATTTAAGAGTAAA
1 TCTGAAGACAGTTCCTAAAAGGTATTTAAGAATGAA
** * *
28063 TCTGAAGACAGTTCACT-AAAGACAGTTCACAGAGATAGAT
1 TCTGAAGACAGTTC-CTAAAAGGTA-TTTA-AGA-AT-GAA
*
28103 TCTGAAGACAGTTCCTAAAAGGTATTTAAGAATGAG
1 TCTGAAGACAGTTCCTAAAAGGTATTTAAGAATGAA
28139 TCTGAAGACAGTTC
1 TCTGAAGACAGTTC
28153 ACAAAGATGG
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
35 16 0.22
36 19 0.26
37 5 0.07
38 6 0.08
39 6 0.08
40 20 0.28
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TCTGAAGACAGTTCCTAAAAGGTATTTAAGAATGAA
Found at i:28178 original size:62 final size:61
Alignment explanation
Indices: 28081--28272 Score: 260
Period size: 62 Copynumber: 3.1 Consensus size: 61
28071 CAGTTCACTA
* * *
28081 AAGACAGTTCACAGAGATAGATTCTGAAGACAGTTCCTAAAAGGTATTTAAGAATGAGTCTG
1 AAGACAGTTCACAAAGAT-GGTTCTGAAGACAGTTCCTAAAAGGTATTTAAGAGTGAGTCTG
* *
28143 AAGACAGTTCACAAAGATGGGTTCTGAAGACAGTTCCTTAAAAAGTATTTAAGAGTGAATCTG
1 AAGACAGTTCACAAAGAT-GGTTCTGAAGACAGTTCC-TAAAAGGTATTTAAGAGTGAGTCTG
* ** * *
28206 AAGACAGTTCACGAAGATGGTTCTGAAGACAGTTCCTGGAAGAT-TTTAAGAGTGAGGCTG
1 AAGACAGTTCACAAAGATGGTTCTGAAGACAGTTCCTAAAAGGTATTTAAGAGTGAGTCTG
28266 AAGACAG
1 AAGACAG
28273 CTTATAGAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
60 21 0.18
61 4 0.03
62 52 0.45
63 39 0.34
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (61 bp):
AAGACAGTTCACAAAGATGGTTCTGAAGACAGTTCCTAAAAGGTATTTAAGAGTGAGTCTG
Done.