Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021208.1 Corchorus olitorius cultivar O-4 contig21241, 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: 106508
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1158 original size:30 final size:30
Alignment explanation
Indices: 1087--1160 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
1077 GAACTTACAC
*
1087 AAAACGGCCAAATAAGCCCATGAACTCTAAT
1 AAAA-GGCCAAATAAGCCCATAAACTCTAAT
*** * *
1118 TGCA-GCCAAATAAGCCCCTAAACTCTTAT
1 AAAAGGCCAAATAAGCCCATAAACTCTAAT
1147 AAAAGGCCAAATAA
1 AAAAGGCCAAATAA
1161 ACCCTTTTCA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
29 23 0.70
30 9 0.27
31 1 0.03
ACGTcount: A:0.45, C:0.26, G:0.12, T:0.18
Consensus pattern (30 bp):
AAAAGGCCAAATAAGCCCATAAACTCTAAT
Found at i:2839 original size:31 final size:30
Alignment explanation
Indices: 2804--2907 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
2794 TCCCGTTTCA
*
2804 TAGAGGGACTAAATTTATCTCTTTTCAATAG
1 TAGAGGGACTAAATTGATC-CTTTTCAATAG
** *
2835 TAGAGGGACTAAATTGA-CAGATTTC-ATAA
1 TAGAGGGACTAAATTGATC-CTTTTCAATAG
* *
2864 TGGGGGGACTAAATTGATCCTCTTTCAATAG
1 TAGAGGGACTAAATTGATCCT-TTTCAATAG
*
2895 TACAGGGACTAAA
1 TAGAGGGACTAAA
2908 CAAATACTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
29 18 0.32
30 10 0.18
31 29 0.51
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (30 bp):
TAGAGGGACTAAATTGATCCTTTTCAATAG
Found at i:15391 original size:36 final size:36
Alignment explanation
Indices: 15344--15413 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
15334 TTCAATAACC
* * *
15344 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATAATTCTTA
*
15380 TTACATTTTTTGTAATTTTGATTATCATAATTCT
1 TTACATCTTTTGTAATTTTGATTATCATAATTCT
15414 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.09, T:0.59
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATAATTCTTA
Found at i:16280 original size:199 final size:198
Alignment explanation
Indices: 15937--16345 Score: 624
Period size: 199 Copynumber: 2.0 Consensus size: 198
15927 GCTTAATAAC
* *
15937 TTTATCGATGATGAATGTTATTAATTTTTTAAGTCTAAGATCACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAAATCACTAACAAAGTTGTAGTGAATAA
*
16002 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTGA
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTGA
16067 TTTATTAAATTAAATTAGATCAATATCAAACAAAATTTCAAAATT-TAAAA-ATATTAAAGATCC
131 -TTATT-AATTAAATTAGATCAATATCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCC
16130 GATTTA
193 GATTTA
* * * *
16136 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTTTAAAATTACTAACAAAGTTGTAGTTAATAA
1 TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAAATCACTAACAAAGTTGTAGTGAATAA
*
16201 GATACAACACATTACTATTATATATATAAGAACTATACCAAAAAAAAATTAGTTGAACATTAGTG
66 GATACAACACATTACTA-T-TATATATAA-AACTATACC--AAAAAAAGTAGTTGAACATTAGTG
* *
16266 GTTGATTTATTAAATTAAATTAGATCAATGTCGAACAAAATTTCAAAATTATAAAAGATATTAAG
126 GTTGA-TTATT-AATTAAATTAGATCAATATCAAACAAAATTTCAAAATTATAAAAGATATTAAG
16331 ATCCGATTTA
189 ATCCGATTTA
16341 TTTAT
1 TTTAT
16346 TATTAAGGAA
Statistics
Matches: 193, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
199 75 0.39
200 1 0.01
201 9 0.05
202 9 0.05
204 71 0.37
205 23 0.12
206 5 0.03
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (198 bp):
TTTATCAATGATGAATGTTATTAATTTTTTAAGTCTAAAATCACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAGTAGTTGAACATTAGTGGTTGA
TTATTAATTAAATTAGATCAATATCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGAT
TTA
Found at i:16451 original size:25 final size:24
Alignment explanation
Indices: 16417--16463 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
16407 ACGTTTGCAC
*
16417 AAATATCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
16442 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
16464 TGTAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:18797 original size:19 final size:17
Alignment explanation
Indices: 18761--18793 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
18751 AACAATACCC
18761 AACGACTCCTTAAAAAT
1 AACGACTCCTTAAAAAT
18778 AACGACTCCTTAAAAA
1 AACGACTCCTTAAAAA
18794 AATATGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.21
Consensus pattern (17 bp):
AACGACTCCTTAAAAAT
Found at i:30889 original size:26 final size:25
Alignment explanation
Indices: 30860--30909 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
30850 AGTAATCAGT
*
30860 TTTTATTATATATATATAAATATATA
1 TTTTATTATAAATAT-TAAATATATA
30886 TTTTATTATAAATATTAAATATAT
1 TTTTATTATAAATATTAAATATAT
30910 TTAAGATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTATTATAAATATTAAATATATA
Found at i:30895 original size:24 final size:24
Alignment explanation
Indices: 30867--30934 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
30857 AGTTTTTATT
30867 ATATATATATAAATATATATTTTA
1 ATATATATATAAATATATATTTTA
* * *
30891 TTATAAATATTAA-ATATA-TTTA
1 ATATATATATAAATATATATTTTA
* *
30913 AGATATATATATATTATATATT
1 ATATATATATA-AATATATATT
30935 AGTAATCAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
22 11 0.33
23 6 0.18
24 15 0.45
25 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (24 bp):
ATATATATATAAATATATATTTTA
Found at i:30902 original size:35 final size:35
Alignment explanation
Indices: 30863--30930 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
30853 AATCAGTTTT
* *
30863 TATTATATATATATAA-ATATATATTTTATTATAAA
1 TATTAAATATATATAAGATATATA-TATATTATAAA
*
30898 TATTAAATATATTTAAGATATATATATATTATA
1 TATTAAATATATATAAGATATATATATATTATA
30931 TATTAGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 22 0.76
36 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (35 bp):
TATTAAATATATATAAGATATATATATATTATAAA
Found at i:30921 original size:26 final size:26
Alignment explanation
Indices: 30811--30933 Score: 76
Period size: 26 Copynumber: 4.6 Consensus size: 26
30801 TATGTTTTAT
30811 TATAAATATTAAATATATTTAAGATA
1 TATAAATATTAAATATATTTAAGATA
* *
30837 TATATTATATATTAGTAATCAGT-TTTTA-TTA
1 TATA--A-ATATTA--AAT-A-TATTTAAGATA
* **
30868 TATATATA-TAAATATATATT-TTAT-
1 TATAAATATTAAATATAT-TTAAGATA
30892 TATAAATATTAAATATATTTAAGATA
1 TATAAATATTAAATATATTTAAGATA
* *
30918 TATATATATTATATAT
1 TATAAATATTAAATAT
30934 TAGTAATCAG
Statistics
Matches: 74, Mismatches: 10, Indels: 26
0.67 0.09 0.24
Matches are distributed among these distances:
23 1 0.01
24 11 0.15
25 17 0.23
26 18 0.24
27 2 0.03
28 4 0.05
29 6 0.08
31 9 0.12
32 5 0.07
33 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (26 bp):
TATAAATATTAAATATATTTAAGATA
Found at i:30974 original size:85 final size:81
Alignment explanation
Indices: 30800--30974 Score: 280
Period size: 85 Copynumber: 2.1 Consensus size: 81
30790 GAACCCGAAT
*
30800 ATATGTTTTATTATAAATATTAAATATATTTAAGATATATATTATATATTAGTAATCAGTTTTTA
1 ATATATTTTATTATAAATATTAAATATATTTAAGATATATATTATATATTAGTAATCAGTTTTTA
*
30865 TTATATATATATAAAT
66 TTATATATATATAAAG
30881 ATATATTTTATTATAAATATTAAATATATTTAAGATATATATATATTATATATTAGTAATCAGTT
1 ATATATTTTATTATAAATATTAAATATATTTAAG----ATATATATTATATATTAGTAATCAGTT
30946 TTTATTATATATATATTAAAG
62 TTTATTATATATATA-TAAAG
30967 ATA-ATTTT
1 ATATATTTT
30975 TGACCCGATT
Statistics
Matches: 87, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
81 33 0.38
85 47 0.54
86 7 0.08
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (81 bp):
ATATATTTTATTATAAATATTAAATATATTTAAGATATATATTATATATTAGTAATCAGTTTTTA
TTATATATATATAAAG
Found at i:31711 original size:7 final size:7
Alignment explanation
Indices: 31699--31723 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31689 AATTAAAAGT
31699 TATTTTG
1 TATTTTG
31706 TATTTTG
1 TATTTTG
31713 TATTTTG
1 TATTTTG
31720 TATT
1 TATT
31724 ATAAGTTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (7 bp):
TATTTTG
Found at i:32902 original size:31 final size:31
Alignment explanation
Indices: 32864--32922 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
32854 CAATGTTAGG
32864 CCAAATGTTCAATTCAGGAT-ATAACGTTTGC
1 CCAAATGTTCAATTCAGGATCA-AACGTTTGC
*
32895 CCAAATGTTCAATTTAGGATCAAACGTT
1 CCAAATGTTCAATTCAGGATCAAACGTT
32923 ACAAAACTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (31 bp):
CCAAATGTTCAATTCAGGATCAAACGTTTGC
Found at i:33117 original size:13 final size:14
Alignment explanation
Indices: 33088--33117 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33078 TAAAAACTTG
33088 AAAATAAATTTTAA
1 AAAATAAATTTTAA
*
33102 AAAATAAATTTCAA
1 AAAATAAATTTTAA
33116 AA
1 AA
33118 TTAATTATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATAAATTTTAA
Found at i:35317 original size:8 final size:8
Alignment explanation
Indices: 35294--35357 Score: 65
Period size: 8 Copynumber: 7.8 Consensus size: 8
35284 TTAAAAACAC
35294 ATTTTATTA
1 ATTTT-TTA
35303 CATTTTTTA
1 -ATTTTTTA
*
35312 ATTTTTTG
1 ATTTTTTA
*
35320 ATTTTTGA
1 ATTTTTTA
*
35328 TTTTTTTA
1 ATTTTTTA
*
35336 ATTTTTGA
1 ATTTTTTA
*
35344 TTTTTTTA
1 ATTTTTTA
35352 ATTTTT
1 ATTTTT
35358 CTTCAAATTT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
8 36 0.82
9 3 0.07
10 5 0.11
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (8 bp):
ATTTTTTA
Found at i:35325 original size:16 final size:16
Alignment explanation
Indices: 35294--35357 Score: 83
Period size: 16 Copynumber: 3.9 Consensus size: 16
35284 TTAAAAACAC
* *
35294 ATTTTATTACATTTTTT
1 ATTTTTTTA-ATTTTTG
* *
35311 AATTTTTTGATTTTTG
1 ATTTTTTTAATTTTTG
35327 ATTTTTTTAATTTTTG
1 ATTTTTTTAATTTTTG
35343 ATTTTTTTAATTTTT
1 ATTTTTTTAATTTTT
35358 CTTCAAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
16 35 0.85
17 6 0.15
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (16 bp):
ATTTTTTTAATTTTTG
Found at i:35963 original size:40 final size:40
Alignment explanation
Indices: 35919--36074 Score: 113
Period size: 40 Copynumber: 3.9 Consensus size: 40
35909 AGGGCCAAAT
* *
35919 TGCATAAACAATATATAGCATCCTAAATCAGGGACTAAAA
1 TGCATAAACAATAAATAGAATCCTAAATCAGGGACTAAAA
* * * * *
35959 TGCATTAAATAGTAAATA-AATCTTGAATCAGGGACTAAAC
1 TGCA-TAAACAATAAATAGAATCCTAAATCAGGGACTAAAA
* * * * *
35999 CGCGTAAATTAA-AAATAAAATCCTAGATCAGGGAC-AAAA
1 TGCATAAA-CAATAAATAGAATCCTAAATCAGGGACTAAAA
* *
36038 TTGCATCAAACAA-AAGACAGTATCCTAAATCAGGGAC
1 -TGCAT-AAACAATAA-ATAGAATCCTAAATCAGGGAC
36075 CATGTTGAAC
Statistics
Matches: 89, Mismatches: 21, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
39 12 0.13
40 47 0.53
41 30 0.34
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.22
Consensus pattern (40 bp):
TGCATAAACAATAAATAGAATCCTAAATCAGGGACTAAAA
Found at i:40796 original size:27 final size:27
Alignment explanation
Indices: 40717--40801 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
40707 AAACGACCAG
* **
40717 AATGCCCCTGAATGTGCAAATGACCAA
1 AATGCCCCTGAACGTGCAAATGACCCT
*
40744 AATGCCCATGAACGTGCAAATGACCCT
1 AATGCCCCTGAACGTGCAAATGACCCT
40771 AATGCCCCTGAACGTGCAAATGACCCT
1 AATGCCCCTGAACGTGCAAATGACCCT
40798 AATG
1 AATG
40802 TCAAATGAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (27 bp):
AATGCCCCTGAACGTGCAAATGACCCT
Found at i:45747 original size:74 final size:75
Alignment explanation
Indices: 45617--45776 Score: 261
Period size: 74 Copynumber: 2.1 Consensus size: 75
45607 CCACCGTAAA
* *
45617 GGGGATAAGCATCTGGTGTTTACACAAAAACCATGCCATATGCGATAGGAGAAGAGAA-GTAAAT
1 GGGGGTAA-CATCTGGTGTTTACACAAAAACCATCCCATATGCGATAGGAGAAGAGAAGGT-AAT
45681 AGTCACAAGATT
64 AGTCACAAGATT
*
45693 -GGGGTAACATCTGGTGTTTACACAAAAACCATCCCATATGCGATAGGAGAAGAGAAGGTGATAG
1 GGGGGTAACATCTGGTGTTTACACAAAAACCATCCCATATGCGATAGGAGAAGAGAAGGTAATAG
45757 TCACAAGATT
66 TCACAAGATT
45767 GGGGGTAACA
1 GGGGGTAACA
45777 ACAAAAACGG
Statistics
Matches: 79, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
74 62 0.78
75 17 0.22
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.21
Consensus pattern (75 bp):
GGGGGTAACATCTGGTGTTTACACAAAAACCATCCCATATGCGATAGGAGAAGAGAAGGTAATAG
TCACAAGATT
Found at i:49494 original size:60 final size:60
Alignment explanation
Indices: 49425--49544 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 60
49415 TTTAGGGTGG
49425 TCCAAGAGAGAACTTGTGGATGCAAGAGTCAAATCTGAATCACTTCTGGGATTGACACCA
1 TCCAAGAGAGAACTTGTGGATGCAAGAGTCAAATCTGAATCACTTCTGGGATTGACACCA
* * * *
49485 TCCAAGAGAGAGCTTGTGGATGGAAGAGTCAAATCTGAATCCCTTTTGGGATTGACACCA
1 TCCAAGAGAGAACTTGTGGATGCAAGAGTCAAATCTGAATCACTTCTGGGATTGACACCA
49545 AACCATGGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (60 bp):
TCCAAGAGAGAACTTGTGGATGCAAGAGTCAAATCTGAATCACTTCTGGGATTGACACCA
Found at i:50853 original size:7 final size:7
Alignment explanation
Indices: 50841--50867 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
50831 TCAGCCAGTC
50841 AGCCTTG
1 AGCCTTG
50848 AGCCTTG
1 AGCCTTG
50855 AGCCTTG
1 AGCCTTG
50862 AGCCTT
1 AGCCTT
50868 CATTTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.30
Consensus pattern (7 bp):
AGCCTTG
Found at i:52046 original size:45 final size:45
Alignment explanation
Indices: 51975--52104 Score: 217
Period size: 45 Copynumber: 2.9 Consensus size: 45
51965 TTTATGGCTC
* **
51975 TTATATGTATTCCTT-TTGTACATATGTGCATAATTCAGTTGCCTT
1 TTATATGTATT-CTTGGTGTATGTATGTGCATAATTCAGTTGCCTT
52020 TTATATGTATTCTTGGTGTATGTATGTGCATAATTCAGTTGCCTT
1 TTATATGTATTCTTGGTGTATGTATGTGCATAATTCAGTTGCCTT
52065 TTATATGTATTCTTGGTGTATGTATGTGCATAATTCAGTT
1 TTATATGTATTCTTGGTGTATGTATGTGCATAATTCAGTT
52105 TCGTTTACTG
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
44 3 0.04
45 78 0.96
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.49
Consensus pattern (45 bp):
TTATATGTATTCTTGGTGTATGTATGTGCATAATTCAGTTGCCTT
Found at i:54066 original size:6 final size:6
Alignment explanation
Indices: 54050--54080 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
54040 TCCCTCTTCT
54050 CTCTGGC CTCTGC CTCTGC CTCTGC CTCTGC
1 CTCT-GC CTCTGC CTCTGC CTCTGC CTCTGC
54081 TCGCCTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.00, C:0.48, G:0.19, T:0.32
Consensus pattern (6 bp):
CTCTGC
Found at i:69000 original size:21 final size:21
Alignment explanation
Indices: 68948--68998 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
68938 ATTAATGAGG
68948 ATAATCTAAATTTCCATTAGA
1 ATAATCTAAATTTCCATTAGA
68969 ATAATCTAAATTTCCATTAGA
1 ATAATCTAAATTTCCATTAGA
68990 ATAAT-TAAA
1 ATAATCTAAA
68999 ATATTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37
Consensus pattern (21 bp):
ATAATCTAAATTTCCATTAGA
Found at i:70712 original size:22 final size:22
Alignment explanation
Indices: 70686--70727 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
70676 GACAAACTCG
70686 TAACCCAAATGACCCAAGAAGT
1 TAACCCAAATGACCCAAGAAGT
**
70708 TAACCCGGATGACCCAAGAA
1 TAACCCAAATGACCCAAGAA
70728 TATTATAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.29, G:0.17, T:0.12
Consensus pattern (22 bp):
TAACCCAAATGACCCAAGAAGT
Found at i:72108 original size:150 final size:150
Alignment explanation
Indices: 71837--72132 Score: 565
Period size: 150 Copynumber: 2.0 Consensus size: 150
71827 TGAATTAGCT
* *
71837 AGAGATGGAGTAGAATTTAGGTAATACACTTTTAGAATGAAAGAGATGTCATGTGTTTTGCTTTA
1 AGAGATGGAGTAGAATTTAGATAATACACTTTTAGAATGAAAGAGATGTCATGTATTTTGCTTTA
71902 TATATGCGAATTATTTGTTTCGATGTATGAGTTTCTCCTAACTGATTAACTTACAACCAATACAA
66 TATATGCGAATTATTTGTTTCGATGTATGAGTTTCTCCTAACTGATTAACTTACAACCAATACAA
71967 TATCTTCTTACCAACCAACC
131 TATCTTCTTACCAACCAACC
71987 AGAGATGGAGTAGAATTTAGATAATACACTTTTAGAATGAAAGAGATGTCATGTATTTTGCTTTA
1 AGAGATGGAGTAGAATTTAGATAATACACTTTTAGAATGAAAGAGATGTCATGTATTTTGCTTTA
*
72052 TATATGCGAATTATTTGTTTCGATGTATGAGTTTCTCCTAACTGATTAACTTACAACCAATGCAA
66 TATATGCGAATTATTTGTTTCGATGTATGAGTTTCTCCTAACTGATTAACTTACAACCAATACAA
72117 TATCTTCTTACCAACC
131 TATCTTCTTACCAACC
72133 GACTTAAACA
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 143 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (150 bp):
AGAGATGGAGTAGAATTTAGATAATACACTTTTAGAATGAAAGAGATGTCATGTATTTTGCTTTA
TATATGCGAATTATTTGTTTCGATGTATGAGTTTCTCCTAACTGATTAACTTACAACCAATACAA
TATCTTCTTACCAACCAACC
Found at i:80602 original size:40 final size:40
Alignment explanation
Indices: 80558--80881 Score: 274
Period size: 40 Copynumber: 7.8 Consensus size: 40
80548 TACTTTACAT
*
80558 AGTTTGCCCTTCCTCACCGGAAGGTGTTGTCTAAATTACC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTACC
** *
80598 AGTTTGCCCTTCCCCACCGGAAGAAGTTGT-TCACAATTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTCT-A-AATTACC
* *
80639 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAAATTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTCT-AAATTACC
* * *
80680 AGTTTGCCCTTTCCCATCGGAAGGTGTTGTTTAAGTTTAGTTTACC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAA----A--TTACC
* * *
80726 AGTTTGTCCTTCCCCACTGGAAGGTGTTGTTTAAATT-CTC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTAC-C
* * * * * *
80766 AGTTTACCCTTTCTCATCGGAAAGTGTTGTTTAAGTTTAGTTTACC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAA----A--TTACC
* *
80812 AGTTTGCCCCTCCCCACCGGAAGGTGTTGTCTAAATTTCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTACC
* * * *
80852 AATTTGCCCTTCCTCATCGGGAGGTGTTGT
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGT
80882 TCCTATTTCT
Statistics
Matches: 233, Mismatches: 34, Indels: 34
0.77 0.11 0.11
Matches are distributed among these distances:
39 2 0.01
40 89 0.38
41 71 0.30
42 4 0.02
44 2 0.01
46 64 0.27
47 1 0.00
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (40 bp):
AGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATTACC
Found at i:80796 original size:86 final size:86
Alignment explanation
Indices: 80503--80882 Score: 416
Period size: 86 Copynumber: 4.5 Consensus size: 86
80493 TTGCCTTGTC
* * * * * * *
80503 AAATTCCCAGTTTGCCCTTCCTCATCGGGAGGTGTTGTCTAAGTCTACTTTACATAGTTTGCCCT
1 AAATTCTCAGTTTGCCCTTTCTCATCGGAAGGTGTTGTTTAAGTTTAGTTTAC-CAGTTTGCCCT
* *
80568 TCCTCACCGGAAGGTGTTGTCT
65 TCCCCACCGGAAGGTGTTGTTT
* * * ** * *
80590 AAATTAC-CAGTTTGCCCTTCCCCACCGGAAGAAGTTGTTCACA----A--TTCCCAGTTTGCCC
1 AAATT-CTCAGTTTGCCCTTTCTCATCGGAAGGTGTTGTTTA-AGTTTAGTTTACCAGTTTGCCC
80648 TTCCCCACCGGAAGGTGTTGTTT
64 TTCCCCACCGGAAGGTGTTGTTT
* * *
80671 AAAATTCCCAGTTTGCCCTTTCCCATCGGAAGGTGTTGTTTAAGTTTAGTTTACCAGTTTGTCCT
1 -AAATTCTCAGTTTGCCCTTTCTCATCGGAAGGTGTTGTTTAAGTTTAGTTTACCAGTTTGCCCT
*
80736 TCCCCACTGGAAGGTGTTGTTT
65 TCCCCACCGGAAGGTGTTGTTT
* * *
80758 AAATTCTCAGTTTACCCTTTCTCATCGGAAAGTGTTGTTTAAGTTTAGTTTACCAGTTTGCCCCT
1 AAATTCTCAGTTTGCCCTTTCTCATCGGAAGGTGTTGTTTAAGTTTAGTTTACCAGTTTGCCCTT
*
80823 CCCCACCGGAAGGTGTTGTCT
66 CCCCACCGGAAGGTGTTGTTT
* * *
80844 AAATT-TCCAATTTGCCCTTCCTCATCGGGAGGTGTTGTT
1 AAATTCT-CAGTTTGCCCTTTCTCATCGGAAGGTGTTGTT
80883 CCTATTTCTG
Statistics
Matches: 250, Mismatches: 32, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
81 32 0.13
82 37 0.15
84 1 0.00
85 2 0.01
86 110 0.44
87 66 0.26
88 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.36
Consensus pattern (86 bp):
AAATTCTCAGTTTGCCCTTTCTCATCGGAAGGTGTTGTTTAAGTTTAGTTTACCAGTTTGCCCTT
CCCCACCGGAAGGTGTTGTTT
Found at i:82117 original size:41 final size:41
Alignment explanation
Indices: 82072--82174 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 41
82062 ATTTAATATC
* * * *
82072 TTATTTATTATTTGATTCAATTTGATCCCTTATTTTGGATT
1 TTATTTATTATTTGATGCAATTTGATCCATGATTTAGGATT
* * *
82113 TTATTTACTATTTGGTGCAATTTGGTCCATGATTTAGGATT
1 TTATTTATTATTTGATGCAATTTGATCCATGATTTAGGATT
* *
82154 TTACTTATT-TTTTATGCAATT
1 TTATTTATTATTTGATGCAATT
82175 GAGTGCTTGA
Statistics
Matches: 51, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 10 0.20
41 41 0.80
ACGTcount: A:0.22, C:0.10, G:0.13, T:0.55
Consensus pattern (41 bp):
TTATTTATTATTTGATGCAATTTGATCCATGATTTAGGATT
Found at i:88466 original size:21 final size:22
Alignment explanation
Indices: 88439--88481 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
88429 AGAAAGTTAT
88439 TATATATTAAATTATTA-ATATCA
1 TATATA-TAAA-TATTATATATCA
88462 TATATATAAATATTATATAT
1 TATATATAAATATTATATAT
88482 GATGCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TATATATAAATATTATATATCA
Found at i:88855 original size:137 final size:137
Alignment explanation
Indices: 88608--88879 Score: 499
Period size: 137 Copynumber: 2.0 Consensus size: 137
88598 ATCATATGAA
* *
88608 CCCAGTCCAACCCGATTCGGATCCGGGCCAACCGCCGGTCAAATCGGTTGTTGACCGAGTCTTGA
1 CCCAGTCCAACCCGATCCGGATCCGGGCCAACCGCCGGTCAAATCGGTTGTTGACCGAGTCTTAA
*
88673 TCGGGCCCAATCTCTCCCGGTTAACCCCCCATCTCCGGACCGGATAGGCCTCAGGGTCCCGATAG
66 CCGGGCCCAATCTCTCCCGGTTAACCCCCCATCTCCGGACCGGATAGGCCTCAGGGTCCCGATAG
88738 AACCGAT
131 AACCGAT
88745 CCCAGTCCAACCCGATCCGGATCCGGGCCAACCGCCGGTCAAATCGGTTGTTGACCGAGTCTTAA
1 CCCAGTCCAACCCGATCCGGATCCGGGCCAACCGCCGGTCAAATCGGTTGTTGACCGAGTCTTAA
* *
88810 CCGGGCCCAATCTCTCCCGGTTAACCCCCCATCTCCGGACTGGATAGGCCTCAGGGTCCCGGTAG
66 CCGGGCCCAATCTCTCCCGGTTAACCCCCCATCTCCGGACCGGATAGGCCTCAGGGTCCCGATAG
88875 AACCG
131 AACCG
88880 GTCCGATCGG
Statistics
Matches: 130, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 130 1.00
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.18
Consensus pattern (137 bp):
CCCAGTCCAACCCGATCCGGATCCGGGCCAACCGCCGGTCAAATCGGTTGTTGACCGAGTCTTAA
CCGGGCCCAATCTCTCCCGGTTAACCCCCCATCTCCGGACCGGATAGGCCTCAGGGTCCCGATAG
AACCGAT
Found at i:98297 original size:17 final size:17
Alignment explanation
Indices: 98277--98327 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
98267 TCATGATTAA
98277 TATGTTTGCTCAATAAT
1 TATGTTTGCTCAATAAT
*
98294 TATGTGTG--CAAT-A-
1 TATGTTTGCTCAATAAT
*
98307 CATGTTTGCTCAATAAT
1 TATGTTTGCTCAATAAT
98324 TATG
1 TATG
98328 GTATGTCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
13 6 0.23
14 1 0.04
15 8 0.31
16 1 0.04
17 10 0.38
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (17 bp):
TATGTTTGCTCAATAAT
Done.