Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012950.1 Corchorus olitorius cultivar O-4 contig12983, 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: 28834
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:15154 original size:22 final size:22
Alignment explanation
Indices: 15129--15254 Score: 87
Period size: 22 Copynumber: 5.8 Consensus size: 22
15119 TTGAATAATT
15129 TTATGAAATTTTGATAACTAAC
1 TTATGAAATTTTGATAACTAAC
* * *
15151 TTATTAAATTTTGAAAACTACC
1 TTATGAAATTTTGATAACTAAC
* * *
15173 ATATGAAATTTTGACAA-TTAC
1 TTATGAAATTTTGATAACTAAC
* * * *
15194 CTATAAAATTGTGATAAACT-CC
1 TTATGAAATTTTGAT-AACTAAC
* * *
15216 ATAAGAAACTTTGATAACCTAA-
1 TTATGAAATTTTGATAA-CTAAC
*
15238 TTATGAAATTTTAATAA
1 TTATGAAATTTTGATAA
15255 ACTTTCCTAT
Statistics
Matches: 77, Mismatches: 23, Indels: 8
0.71 0.21 0.07
Matches are distributed among these distances:
21 15 0.19
22 61 0.79
23 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (22 bp):
TTATGAAATTTTGATAACTAAC
Found at i:15180 original size:44 final size:44
Alignment explanation
Indices: 15130--15257 Score: 136
Period size: 44 Copynumber: 2.9 Consensus size: 44
15120 TGAATAATTT
*
15130 TATGAAATTTTGATAACTAACTTATTAAATTTTGA-AAACTACCA
1 TATGAAATTTTGATAACTAACTTATAAAATTTTGATAAACT-CCA
* * * *
15174 TATGAAATTTTGACAA-TTACCTATAAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAACTAACTTATAAAATTTTGATAAACTCCA
* * * *
15217 TAAGAAACTTTGATAACCTAA-TTATGAAATTTTAATAAACT
1 TATGAAATTTTGATAA-CTAACTTATAAAATTTTGATAAACT
15258 TTCCTATGGA
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
43 30 0.44
44 36 0.53
45 2 0.03
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACTAACTTATAAAATTTTGATAAACTCCA
Found at i:15307 original size:21 final size:21
Alignment explanation
Indices: 15260--15338 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
15250 AATAAACTTT
* * *
15260 CCTATGGATTTTG-TAACCTT
1 CCTATGAATTTTGATAATCTC
*
15280 CCTATGATTTTTGATAATCTC
1 CCTATGAATTTTGATAATCTC
*
15301 TCTATGAGATTTTG-TCAATCTC
1 CCTATGA-ATTTTGAT-AATCTC
*
15323 CCTATAAATTTTGATA
1 CCTATGAATTTTGATA
15339 TTATAGTATG
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.23
21 19 0.40
22 17 0.36
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.46
Consensus pattern (21 bp):
CCTATGAATTTTGATAATCTC
Found at i:15320 original size:22 final size:21
Alignment explanation
Indices: 15295--15335 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
15285 GATTTTTGAT
* *
15295 AATCTCTCTATGAGATTTTGTC
1 AATCTCCCTAT-AAATTTTGTC
15317 AATCTCCCTATAAATTTTG
1 AATCTCCCTATAAATTTTG
15336 ATATTATAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.44
Consensus pattern (21 bp):
AATCTCCCTATAAATTTTGTC
Found at i:20260 original size:22 final size:22
Alignment explanation
Indices: 20197--20392 Score: 96
Period size: 22 Copynumber: 9.0 Consensus size: 22
20187 TCAAATCTCA
**
20197 GATTATCAAAATTT-ATAAG-AA
1 GATTATCAAAATTTCA-AAGTGT
* * *
20218 GATTATTAAAATTTTATAGTGT
1 GATTATCAAAATTTCAAAGTGT
* *
20240 TATTATCAAAATTTCAAAGTGA
1 GATTATCAAAATTTCAAAGTGT
* *
20262 GGTTATCAAAATTACATAA-TGT
1 GATTATCAAAATTTCA-AAGTGT
* * *
20284 GATTATCAAAATTTCATAGAGG
1 GATTATCAAAATTTCAAAGTGT
* * * * * * *
20306 GGTCAGCAAAATTTTATAGAGA
1 GATTATCAAAATTTCAAAGTGT
* * *
20328 GGTTATTAAAATTTCATAAAGAG-
1 GATTATCAAAATTTC--AAAGTGT
* *
20351 G-TTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCAAAGTGT
*
20372 GATTATCAAAATTTCATAGTG
1 GATTATCAAAATTTCAAAGTG
20393 GTATTTTTGG
Statistics
Matches: 132, Mismatches: 35, Indels: 15
0.73 0.19 0.08
Matches are distributed among these distances:
20 4 0.03
21 17 0.13
22 103 0.78
23 3 0.02
24 5 0.04
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (22 bp):
GATTATCAAAATTTCAAAGTGT
Found at i:20290 original size:44 final size:44
Alignment explanation
Indices: 20197--20387 Score: 174
Period size: 44 Copynumber: 4.4 Consensus size: 44
20187 TCAAATCTCA
* * * *
20197 GATTATCAAAATTT-ATAAGA-AGATTATTAAAATTTTATAGTGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
* * *
20240 TATTATCAAAATTTCAAAGTGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * *
20284 GATTATCAAAATTTCATAGAGGGGTCAGCAAAATTTTATAGA-GA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATA-ATGT
* * * *
20328 GGTTATTAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
20372 GATTATCAAAATTTCA
1 GATTATCAAAATTTCA
20388 TAGTGGTATT
Statistics
Matches: 115, Mismatches: 28, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
43 17 0.15
44 96 0.83
45 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:20318 original size:88 final size:88
Alignment explanation
Indices: 20225--20390 Score: 235
Period size: 88 Copynumber: 1.9 Consensus size: 88
20215 GAAGATTATT
* ** * *
20225 AAAATTTTATAGTGTTATTATCAAAATTTCA-AAGTGAGGTTATCAAAATTACATAATGTGATTA
1 AAAATTTTATAGAGAGATTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATTA
20289 TCAAAATTTCATAGAGGGGTCAGC
65 TCAAAATTTCATAGAGGGGTCAGC
* * * *
20313 AAAATTTTATAGAGAGGTTATTAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTAT
1 AAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTAT
20378 CAAAATTTCATAG
66 CAAAATTTCATAG
20391 TGGTATTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
88 66 0.97
89 2 0.03
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (88 bp):
AAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTAT
CAAAATTTCATAGAGGGGTCAGC
Found at i:20518 original size:22 final size:22
Alignment explanation
Indices: 20462--20871 Score: 250
Period size: 22 Copynumber: 18.9 Consensus size: 22
20452 AAACTTTTAT
*
20462 TATGGA-GTAATCAAAATTTC-
1 TATGGAGGTTATCAAAATTTCA
*
20482 -A-GGCAGGATATCAAAATTTCA
1 TATGG-AGGTTATCAAAATTTCA
*
20503 TATGAAGGTTATCAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
** *
20525 TAGTTTA-GTTTTCAAAATTTCA
1 TA-TGGAGGTTATCAAAATTTCA
* * *
20547 TAGGGAGATTAACAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
**
20569 TAAT-GAGGTTATCAAAAAATCA
1 T-ATGGAGGTTATCAAAATTTCA
*
20591 TAGGGAGGTTATCAAAA--T--
1 TATGGAGGTTATCAAAATTTCA
* *
20609 T-TGTA-GTTATCAAGATTTCA
1 TATGGAGGTTATCAAAATTTCA
*
20629 TAAT-GAGGTTATCAAAATTTTA
1 T-ATGGAGGTTATCAAAATTTCA
*
20651 TAGGGAGGTTTATCAAAATTT--
1 TATGGAGG-TTATCAAAATTTCA
20672 TATGGGAAGGTTTATCAAAATTTCA
1 TAT-GG-AGG-TTATCAAAATTTCA
*
20697 TA-GCGAGGTTATCACAATTTCA
1 TATG-GAGGTTATCAAAATTTCA
* * *
20719 TA-GTGTGGTTATCAATATATCA
1 TATG-GAGGTTATCAAAATTTCA
*
20741 TATGGAGGTTATCAACATCTT-A
1 TATGGAGGTTATCAAAAT-TTCA
**
20763 TAGTGCTGGTTATCAAAATTTCA
1 TA-TGGAGGTTATCAAAATTTCA
*
20786 T-TAGGAAGTTATCAAAATTTCA
1 TAT-GGAGGTTATCAAAATTTCA
* *
20808 TA-GTGAGGTCT-TCAAAATTCCT
1 TATG-GAGGT-TATCAAAATTTCA
* *
20830 TAGGGAGGTTAACAAAATTTCA
1 TATGGAGGTTATCAAAATTTCA
* * **
20852 TAAGAAGGTTAAAAAAATTT
1 TATGGAGGTTATCAAAATTT
20872 TATAAAAAGG
Statistics
Matches: 306, Mismatches: 51, Indels: 64
0.73 0.12 0.15
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 4 0.01
19 2 0.01
20 14 0.05
21 9 0.03
22 208 0.68
23 55 0.18
24 1 0.00
25 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
TATGGAGGTTATCAAAATTTCA
Found at i:20547 original size:44 final size:44
Alignment explanation
Indices: 20490--20871 Score: 279
Period size: 44 Copynumber: 8.8 Consensus size: 44
20480 TCAGGCAGGA
* *
20490 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAG-TGAGGT
* * * * *
20534 TTTCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGAGGT
** *
20578 TATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GT-A-GT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGAGGT
* * * *
20616 TATCAAGATTTCATAATG-AGGTTATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCAT-AGGAAGGTTATCAAAATTTCATAGTGAGG-T
* * *
20661 TATCAAAATTTTATGGGAAGGTTTATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGGAAGG-TTATCAAAATTTCATAGTGAGGT
* * * *
20706 TATCACAATTTCATAGTG-TGGTTATCAATATATCATA-TGGAGGT
1 TATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAGT-GAGGT
* ** *
20750 TATCAACATCTT-ATAGTGCTGGTTATCAAAATTTCATTAG-GAAGT
1 TATCAAAAT-TTCATAG-GAAGGTTATCAAAATTTCA-TAGTGAGGT
* * *
20795 TATCAAAATTTCATAGTG-AGGTCT-TCAAAATTCCTTAGGGAGGT
1 TATCAAAATTTCATAG-GAAGGT-TATCAAAATTTCATAGTGAGGT
* * **
20839 TAACAAAATTTCATAAGAAGGTTAAAAAAATTT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTT
20872 TATAAAAAGG
Statistics
Matches: 270, Mismatches: 46, Indels: 44
0.75 0.13 0.12
Matches are distributed among these distances:
38 25 0.09
39 5 0.02
40 1 0.00
41 2 0.01
42 1 0.00
43 10 0.04
44 135 0.50
45 68 0.25
46 23 0.09
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (44 bp):
TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGAGGT
Found at i:20837 original size:89 final size:88
Alignment explanation
Indices: 20471--20847 Score: 262
Period size: 89 Copynumber: 4.3 Consensus size: 88
20461 TTATGGAGTA
* * * ** ***
20471 ATCAAAATT-TCAGGCAGGATATCAAAAT-TTCATATGAAGG-TTATCAAAATTTCATAGTTTAG
1 ATCAAAATTCTTAGGGAGGTTATCAAAATCTT-ATGGGAAGGTTTATCAAAATTTCATAGCGAAG
* * *
20533 TTTTCAAAATTTCATAGGGAGATT
65 TTATCAAAATTTCATAGTGAGGTT
* * ** * *
20557 AACAAAATTTCATAATGAGGTTATCAAAAAATCATA-GGG-AGG-TTATCAAAA-TT--T---GT
1 ATCAAAA-TTCTTAGGGAGGTTATC--AAAATCTTATGGGAAGGTTTATCAAAATTTCATAGCGA
* *
20613 AGTTATCAAGATTTCATAATGAGGTT
63 AGTTATCAAAATTTCATAGTGAGGTT
* * *
20639 ATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATGGGAAGGTTTATCAAAATTTCATAGCGAG
1 ATCAAAATTCT-TAGGGAGG-TTATCAAAATCTTATGGGAAGGTTTATCAAAATTTCATAGCGAA
* *
20704 GTTATCACAATTTCATAGTGTGGTT
64 GTTATCAAAATTTCATAGTGAGGTT
* * * * * **
20729 ATCAATATATCATATGGAGGTTATCAACATCTTATAGTGCTGG-TTATCAAAATTTCATTAG-GA
1 ATCAAAAT-TCTTAGGGAGGTTATCAAAATCTTAT-GGGAAGGTTTATCAAAATTTCA-TAGCGA
20792 AGTTATCAAAATTTCATAGTGAGGTCT
63 AGTTATCAAAATTTCATAGTGAGGT-T
*
20819 -TCAAAATTCCTTAGGGAGGTTAACAAAAT
1 ATCAAAATT-CTTAGGGAGGTTATCAAAAT
20848 TTCATAAGAA
Statistics
Matches: 224, Mismatches: 46, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
81 9 0.04
82 37 0.17
83 8 0.04
84 9 0.04
85 3 0.01
86 6 0.03
87 5 0.02
88 21 0.09
89 74 0.33
90 50 0.22
91 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.35
Consensus pattern (88 bp):
ATCAAAATTCTTAGGGAGGTTATCAAAATCTTATGGGAAGGTTTATCAAAATTTCATAGCGAAGT
TATCAAAATTTCATAGTGAGGTT
Found at i:20876 original size:22 final size:22
Alignment explanation
Indices: 20835--20883 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
20825 TTCCTTAGGG
* *
20835 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAAA
*
20857 AGGTTAAAAAAATTTTATAAAA
1 AGGTTAAAAAAATTTCATAAAA
20879 AGGTT
1 AGGTT
20884 CTTGAAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.31
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAAA
Found at i:23526 original size:22 final size:22
Alignment explanation
Indices: 23496--23708 Score: 139
Period size: 22 Copynumber: 9.5 Consensus size: 22
23486 TCCAACGTAG
*
23496 AAATATTGATAACCACACTACGA
1 AAAT-TTGATAACCACACTATGA
* *
23519 AAATTTGATAACCTCCCTATGA
1 AAATTTGATAACCACACTATGA
* *
23541 AAATTTGATAACCACAATGTGA
1 AAATTTGATAACCACACTATGA
* * *
23563 AATTTTGATGACCACACTGTG-
1 AAATTTGATAACCACACTATGA
* *
23584 AAATTCTAATAACCACACAATG-
1 AAATT-TGATAACCACACTATGA
** *
23606 AGTTTTGATAACCTCATTGTCTATGA
1 AAATTTGATAACCACA----CTATGA
* * *
23632 AATTTTGATAATCACATTAT-A
1 AAATTTGATAACCACACTATGA
* * *
23653 AAA-TTGGTAATCGCACTATGA
1 AAATTTGATAACCACACTATGA
*
23674 AAATTTTGATAACCACACCATG-
1 AAA-TTTGATAACCACACTATGA
23696 AAATTTCGATAAC
1 AAATTT-GATAAC
23709 TTCCCCTATA
Statistics
Matches: 148, Mismatches: 32, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
20 13 0.09
21 23 0.16
22 78 0.53
23 17 0.11
25 4 0.03
26 13 0.09
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (22 bp):
AAATTTGATAACCACACTATGA
Found at i:23796 original size:22 final size:22
Alignment explanation
Indices: 23771--23824 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
23761 TCTCCATAAT
* *
23771 ATTTTCATAACC-TCCCTATGAA
1 ATTTTGATAACCAT-CCTAGGAA
*
23793 ATTTTGTTAACCATCCTAGGAA
1 ATTTTGATAACCATCCTAGGAA
23815 ATTTTGATAA
1 ATTTTGATAA
23825 GAACAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (22 bp):
ATTTTGATAACCATCCTAGGAA
Found at i:23931 original size:22 final size:22
Alignment explanation
Indices: 23845--24084 Score: 111
Period size: 22 Copynumber: 10.8 Consensus size: 22
23835 TGATAACCTC
* *
23845 CCTTCATATGAAATTTTGTTAA
1 CCTTCCTATGAAATTTTGATAA
* *
23867 CGTT-CTAAT-TAATTTTGATAA
1 CCTTCCT-ATGAAATTTTGATAA
* * * **
23888 TC-ACACTATAAAATTTCAATAA
1 CCTTC-CTATGAAATTTTGATAA
*
23910 CCTTCGTATGAAATTTTGATAA
1 CCTTCCTATGAAATTTTGATAA
* * *
23932 TC-TCCATAAGAGATTTTGATAA
1 CCTTCC-TATGAAATTTTGATAA
** *
23954 CCTTTTTTTAATGAAATTTTGGTAA
1 CC--TTCCT-ATGAAATTTTGATAA
*
23979 CC-TCTGTATGAAATTTTGATAA
1 CCTTC-CTATGAAATTTTGATAA
* *
24001 --TTACACTACGAAGTTTTGATAA
1 CCTT-C-CTATGAAATTTTGATAA
*
24023 CC-TCCATATGAAATTTTGGTAA
1 CCTTCC-TATGAAATTTTGATAA
* *
24045 CC-ACACTATGAAATTTTAATAA
1 CCTTC-CTATGAAATTTTGATAA
*
24067 CCTTCCTATGTAATTTTG
1 CCTTCCTATGAAATTTTG
24085 GTTTGATTGT
Statistics
Matches: 158, Mismatches: 42, Indels: 36
0.67 0.18 0.15
Matches are distributed among these distances:
21 17 0.11
22 120 0.76
23 5 0.03
24 1 0.01
25 15 0.09
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
CCTTCCTATGAAATTTTGATAA
Found at i:24024 original size:44 final size:44
Alignment explanation
Indices: 23966--24084 Score: 132
Period size: 44 Copynumber: 2.7 Consensus size: 44
23956 TTTTTTTAAT
* ** **
23966 GAAATTTTGGTAACCTCTGTATGAAATTTTGATAATTACACTAC
1 GAAATTTTGATAACCTCCATATGAAATTTTGATAACCACACTAC
* * *
24010 GAAGTTTTGATAACCTCCATATGAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACCTCCATATGAAATTTTGATAACCACACTAC
* *
24054 GAAATTTTAATAACCTTCC-TATGTAATTTTG
1 GAAATTTTGATAACC-TCCATATGAAATTTTG
24085 GTTTGATTGT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 60 0.95
45 3 0.05
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (44 bp):
GAAATTTTGATAACCTCCATATGAAATTTTGATAACCACACTAC
Found at i:26976 original size:22 final size:20
Alignment explanation
Indices: 26945--27088 Score: 90
Period size: 22 Copynumber: 6.6 Consensus size: 20
26935 CTCCAATGTA
*
26945 GAAATATTGATAACCACATTTT
1 GAAAT-TTGATAACCACA-TAT
*
26967 GCAAATTTGATAACCTCATAT
1 G-AAATTTGATAACCACATAT
* *
26988 GAAATTTCGATAACCTCCCTAT
1 GAAATTT-GATAACC-ACATAT
* * *
27010 AAAATTTTGATAAACACACTGT
1 GAAA-TTTGATAACCACA-TAT
*
27032 GAAATTTGGGTAACCACACTAT
1 GAAATTT-GATAACCACA-TAT
* *
27054 GAAATTTCGATAACCTCAGTGT
1 GAAATTT-GATAACCACA-TAT
27076 GAAATTTTGATAA
1 GAAA-TTTGATAA
27089 TCTGCCTATA
Statistics
Matches: 97, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
20 6 0.06
21 14 0.14
22 67 0.69
23 10 0.10
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
GAAATTTGATAACCACATAT
Found at i:27046 original size:44 final size:44
Alignment explanation
Indices: 26972--27401 Score: 169
Period size: 44 Copynumber: 9.7 Consensus size: 44
26962 ATTTTGCAAA
*
26972 TTTGATAACCTCA-TATGAAATTTCGATAACCTCCCTATAAAAT
1 TTTGATAACCACACTATGAAATTTCGATAACCTCCCTATAAAAT
* * * * * * *
27015 TTTGATAAACACACTGTGAAATTTGGGTAACCACACTATGAAAT
1 TTTGATAACCACACTATGAAATTTCGATAACCTCCCTATAAAAT
* * * * * * * *
27059 TTCGATAACCTCAGTGTGAAATTTTGATAATCTGCCTATATAAT
1 TTTGATAACCACACTATGAAATTTCGATAACCTCCCTATAAAAT
* * * * * *
27103 TTTAATAATCACACTAAAT-AAAATT-GGTAACCGCACTATGAAAAT
1 TTTGATAACCACACT--ATGAAATTTCGATAACCTCCCTAT-AAAAT
* * *
27148 TTTGATAACCACACCATGAAATTTCGATAACCTCCATATGAGAATGAAAC
1 TTTGATAACCACACTATGAAATTTCGATAACCTCCCTAT----A--AAAT
* * * * * * *
27198 TGTGATATCCTCTCTATGTATTTTCGATAACCTCTCC-ATGAAAT
1 TTTGATAACCACACTATGAAATTTCGATAACCTC-CCTATAAAAT
* * * * * *
27242 TTTGTTAACCTCTCTAGGAAATTTTGATAA----GC-AT-AAAT
1 TTTGATAACCACACTATGAAATTTCGATAACCTCCCTATAAAAT
* * * * * ** *
27280 TTTGGTAACCTCCCTCCCTATGAAATTTTGGTAACCTCTGTATGAAAT
1 TTTGATAA----CCACACTATGAAATTTCGATAACCTCCCTATAAAAT
* * * ** *
27328 TTTGATAACTACACTATGAAGTTTTGATAACCTCTATATGAAAT
1 TTTGATAACCACACTATGAAATTTCGATAACCTCCCTATAAAAT
* * *
27372 TTTGGTAACCACACTACGAAATTTTGATAA
1 TTTGATAACCACACTATGAAATTTCGATAA
27402 TCTCTCATTG
Statistics
Matches: 287, Mismatches: 78, Indels: 43
0.70 0.19 0.11
Matches are distributed among these distances:
38 11 0.04
39 3 0.01
42 19 0.07
43 13 0.05
44 162 0.56
45 31 0.11
46 1 0.00
47 2 0.01
48 12 0.04
50 32 0.11
51 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (44 bp):
TTTGATAACCACACTATGAAATTTCGATAACCTCCCTATAAAAT
Found at i:27062 original size:66 final size:65
Alignment explanation
Indices: 26946--27088 Score: 171
Period size: 66 Copynumber: 2.2 Consensus size: 65
26936 TCCAATGTAG
* * * * * *
26946 AAATATTGATAACCACATTTTGCAAATTTGATAACCTCATATGAAATTTCGATAACCTCCCTATA
1 AAATTTTGATAAACACACTGTGCAAATTTGATAACCACATATGAAATTTCGATAACCTCACTATA
* * *
27011 AAATTTTGATAAACACACTGTG-AAATTTGGGTAACCACACTATGAAATTTCGATAACCTCAGTG
1 AAATTTTGATAAACACACTGTGCAAATTT-GATAACCACA-TATGAAATTTCGATAACCTCACTA
*
27075 TG
64 TA
27077 AAATTTTGATAA
1 AAATTTTGATAA
27089 TCTGCCTATA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
64 6 0.09
65 26 0.39
66 34 0.52
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (65 bp):
AAATTTTGATAAACACACTGTGCAAATTTGATAACCACATATGAAATTTCGATAACCTCACTATA
Found at i:27176 original size:22 final size:23
Alignment explanation
Indices: 27130--27179 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
27120 ATAAAATTGG
* * *
27130 TAACCGCACTATGAAAATTTTGA
1 TAACCACACCATGAAAATTTCGA
27153 TAACCACACCATG-AAATTTCGA
1 TAACCACACCATGAAAATTTCGA
27175 TAACC
1 TAACC
27180 TCCATATGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (23 bp):
TAACCACACCATGAAAATTTCGA
Found at i:27231 original size:22 final size:22
Alignment explanation
Indices: 27191--27407 Score: 153
Period size: 22 Copynumber: 10.0 Consensus size: 22
27181 CCATATGAGA
* * *
27191 ATGAAACTGTGATATCCTCTCT
1 ATGAAATTTTGATAACCTCTCT
* *
27213 ATG-TATTTTCGATAACCTCTCC
1 ATGAAATTTT-GATAACCTCTCT
*
27235 ATGAAATTTTGTTAACCTCTCT
1 ATGAAATTTTGATAACCTCTCT
* *
27257 AGGAAATTTTGATAA----GC-
1 ATGAAATTTTGATAACCTCTCT
*
27274 AT-AAATTTTGGTAACCTCCCTCCCT
1 ATGAAATTTTGATAACCT--CT--CT
* *
27299 ATGAAATTTTGGTAACCTCTGT
1 ATGAAATTTTGATAACCTCTCT
*
27321 ATGAAATTTTGATAA-CTACACT
1 ATGAAATTTTGATAACCT-CTCT
* *
27343 ATGAAGTTTTGATAACCTCTAT
1 ATGAAATTTTGATAACCTCTCT
* * *
27365 ATGAAATTTTGGTAACCACACT
1 ATGAAATTTTGATAACCTCTCT
* *
27387 ACGAAATTTTGATAATCTCTC
1 ATGAAATTTTGATAACCTCTC
27408 ATTGTAATTT
Statistics
Matches: 150, Mismatches: 31, Indels: 28
0.72 0.15 0.13
Matches are distributed among these distances:
16 11 0.07
17 1 0.01
18 1 0.01
21 5 0.03
22 105 0.70
23 7 0.05
24 3 0.02
25 2 0.01
26 15 0.10
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCTCT
Found at i:27417 original size:44 final size:44
Alignment explanation
Indices: 27301--27421 Score: 154
Period size: 44 Copynumber: 2.8 Consensus size: 44
27291 CCCTCCCTAT
* * * * *
27301 GAAATTTTGGTAACCTCTGTATGAAATTTTGATAACTACACTAT
1 GAAATTTTGATAACCTCTATATGAAATTTTGGTAACCACACTAC
*
27345 GAAGTTTTGATAACCTCTATATGAAATTTTGGTAACCACACTAC
1 GAAATTTTGATAACCTCTATATGAAATTTTGGTAACCACACTAC
* *
27389 GAAATTTTGATAATCTCTCAT-TGTAATTTTGGT
1 GAAATTTTGATAACCTCT-ATATGAAATTTTGGT
27422 TTGATTGTCA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
44 65 0.97
45 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (44 bp):
GAAATTTTGATAACCTCTATATGAAATTTTGGTAACCACACTAC
Found at i:28200 original size:6 final size:6
Alignment explanation
Indices: 28189--28259 Score: 124
Period size: 6 Copynumber: 11.7 Consensus size: 6
28179 AATTACGTAC
*
28189 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT CTTTGT TTTTGT TTTTGT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT
28237 TTTTGT TTTTGT ATTTTGT TTTT
1 TTTTGT TTTTGT -TTTTGT TTTT
28260 TTACAAAAGC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
6 56 0.90
7 6 0.10
ACGTcount: A:0.01, C:0.01, G:0.15, T:0.82
Consensus pattern (6 bp):
TTTTGT
Done.