Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018333.1 Corchorus olitorius cultivar O-4 contig18366, 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: 62081
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:5587 original size:21 final size:20
Alignment explanation
Indices: 5549--5588 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5539 TTCCTTTTTG
**
5549 CAAAAACCTTATGTAATAAA
1 CAAAAACCTTATCCAATAAA
5569 CAAAAACTCTTATCCAATAA
1 CAAAAAC-CTTATCCAATAA
5589 TTCCTTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.53, C:0.20, G:0.03, T:0.25
Consensus pattern (20 bp):
CAAAAACCTTATCCAATAAA
Found at i:7981 original size:12 final size:12
Alignment explanation
Indices: 7964--7988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7954 GGCAAAAAAA
7964 AAACAAATAAAC
1 AAACAAATAAAC
7976 AAACAAATAAAC
1 AAACAAATAAAC
7988 A
1 A
7989 CCAAATACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (12 bp):
AAACAAATAAAC
Found at i:8387 original size:19 final size:18
Alignment explanation
Indices: 8363--8401 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
8353 CACTATAAAT
8363 ATTATATATCCTTAAGAA
1 ATTATATATCCTTAAGAA
8381 CA-T-TATATCCTTAAGAA
1 -ATTATATATCCTTAAGAA
8398 ATTA
1 ATTA
8402 ATTTGGGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.06
17 15 0.83
18 1 0.06
19 1 0.06
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
ATTATATATCCTTAAGAA
Found at i:8389 original size:17 final size:16
Alignment explanation
Indices: 8367--8401 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
8357 ATAAATATTA
8367 TATATCCTTAAGAACAT
1 TATATCCTTAAGAA-AT
8384 TATATCCTTAAGAAAT
1 TATATCCTTAAGAAAT
8400 TA
1 TA
8402 ATTTGGGTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (16 bp):
TATATCCTTAAGAAAT
Found at i:10735 original size:14 final size:13
Alignment explanation
Indices: 10714--10739 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10704 TTTTGAAGAG
10714 GTGCTTTTTAAAA
1 GTGCTTTTTAAAA
10727 GTGCTTTTTAAAA
1 GTGCTTTTTAAAA
10740 TTGGGGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTGCTTTTTAAAA
Found at i:11212 original size:8 final size:8
Alignment explanation
Indices: 11201--11245 Score: 63
Period size: 8 Copynumber: 5.4 Consensus size: 8
11191 TAAGCATATA
*
11201 TATCCTAC
1 TATCTTAC
11209 TATCTTATC
1 TATCTTA-C
11218 TTATCTTAC
1 -TATCTTAC
11227 TATCTTAC
1 TATCTTAC
11235 TATCTTAC
1 TATCTTAC
11243 TAT
1 TAT
11246 ATATACTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
8 25 0.74
9 2 0.06
10 7 0.21
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (8 bp):
TATCTTAC
Found at i:15652 original size:22 final size:22
Alignment explanation
Indices: 15624--16793 Score: 202
Period size: 22 Copynumber: 53.3 Consensus size: 22
15614 AATCTTTATA
15624 TGATAAC-CTCCTTAT-AAACTTT
1 TGATAACACTCC-TATGAAA-TTT
*
15646 TGATAACATTCCTATGAAATTT
1 TGATAACACTCCTATGAAATTT
* * **
15668 TGATAATGA-TACTATGTTATTT
1 TGATAA-CACTCCTATGAAATTT
* * * * *
15690 CGAAAACATTCCTATCAAA-TA
1 TGATAACACTCCTATGAAATTT
* *
15711 TAAGAACA-TCCCTATGAAATTT
1 TGATAACACT-CCTATGAAATTT
* *
15733 TGTTAAC-TTCCCTAT-ACAATTT
1 TGATAACACT-CCTATGA-AATTT
* *** *
15755 TGAAAACAAAACTATAAAATTT
1 TGATAACACTCCTATGAAATTT
* * *
15777 TGATAA-TCTCCATGTGAAATGT
1 TGATAACACTCC-TATGAAATTT
* * *
15799 TGGTAAGCAC-ACTATGAACTTTT
1 TGATAA-CACTCCTATGAA-ATTT
*
15822 TTATAAC-CTCCCCTATGAAATCTT
1 TGATAACACT--CCTATGAAAT-TT
* *
15846 AGTGATCACA-T--TGTGAAATTT
1 --TGATAACACTCCTATGAAATTT
* *
15867 TGATAATCAC-ACTATGAAATTG
1 TGATAA-CACTCCTATGAAATTT
* * * *
15889 TAATGAC-CTCGGTATAAAATTT
1 TGATAACACTC-CTATGAAATTT
* * *
15911 TGATAAACATTCATATAAAATTT
1 TGAT-AACACTCCTATGAAATTT
* *
15934 TTATAA-ACCTCCCTATAAAATTT
1 TGATAACA-CT-CCTATGAAATTT
*
15957 TGATAAC-CTCCTTATGAAATAT
1 TGATAACACTCC-TATGAAATTT
*
15979 TGAT-A-A-T--TA-CAAATTT
1 TGATAACACTCCTATGAAATTT
* **
15995 CGATAAC-CTCCCTATGATTTTT
1 TGATAACACT-CCTATGAAATTT
* *
16017 TGATAAC-TTCATTATGAAATTT
1 TGATAACACTC-CTATGAAATTT
*
16039 T-ATGGAC-CTCCCTATGAAATTT
1 TGAT-AACACT-CCTATGAAATTT
*
16061 TGAT-A-ACTCCTATAAAATTT
1 TGATAACACTCCTATGAAATTT
*
16081 TGA-AA-ACTAAACTATGAAATTT
1 TGATAACACT--CCTATGAAATTT
* *
16103 TGATAATC-CCCCTTTGAAATTT
1 TGATAA-CACTCCTATGAAATTT
* * *
16125 TAATAAC-CTTCATACGAAATTT
1 TGATAACAC-TCCTATGAAATTT
* * * ** *
16147 TGGTAACTGCACAAATGCAATTTT
1 TGATAAC-ACTCCTATG-AAATTT
*
16171 TGATAAC-CTCACTTTGAAA---
1 TGATAACACTC-CTATGAAATTT
**
16190 T-ACCACACT-CTA--AAATTT
1 TGATAACACTCCTATGAAATTT
* *
16208 GGATAATAACAT--TATGAAATTT
1 TGATAA-CAC-TCCTATGAAATTT
**
16230 CAATAAC-CTCCTTATGAAATTT
1 TGATAACACTCC-TATGAAATTT
* *
16252 TGCTAAC-CCCTCTATGAAATTT
1 TGATAACACTC-CTATGAAATTT
*
16274 TGATAATCA-TACTATGAAA-TT
1 TGATAA-CACTCCTATGAAATTT
16295 TGA-AAC-CTCCATATGAAATTT
1 TGATAACACTCC-TATGAAATTT
* * **
16316 TAATCACCAC-AATATGAAAATTTT
1 TGAT-AACACTCCTATG-AAA-TTT
*
16340 TCATAAC-CTCACTA-GAAAATTT
1 TGATAACACTC-CTATG-AAATTT
* *
16362 TGATAAC-CTCGCTTTTAAAAATTT
1 TGATAACACTC-C-TAT-GAAATTT
16386 TGATAAC-CTTCCTATGAAATTT
1 TGATAACAC-TCCTATGAAATTT
*
16408 CGATAACCACAT--TATG-AA-TT
1 TGATAA-CAC-TCCTATGAAATTT
* *
16428 TGATAAC-CTTCGTATGCAATTT
1 TGATAACAC-TCCTATGAAATTT
* *
16450 TGGTAATCTGA-TCTCTATGAATTTT
1 TGATAA-C--ACTC-CTATGAAATTT
*
16475 TGATAACTACT-CTATGAGATTT
1 TGATAAC-ACTCCTATGAAATTT
** *
16497 TGATTGC-TTCCTAATGAAATTT
1 TGATAACACTCCT-ATGAAATTT
* *
16519 TGAT-A-ACTAACTATAAAATTT
1 TGATAACACT-CCTATGAAATTT
* **
16540 TGATAACATTTGTATGAAATTTAGAATT
1 TGATAACACTCCTATGAAA--T----TT
* * *
16568 TTATAACATTACTATGAAATTT
1 TGATAACACTCCTATGAAATTT
* *
16590 TGGTAACCAC-ACTATGAAATCTT
1 TGATAA-CACTCCTATGAAAT-TT
* *
16613 TAATAAC-CTCCTGATAAAATTT
1 TGATAACACTCCT-ATGAAATTT
* *
16635 TGATAATTAC-ACTATGAAATTT
1 TGATAA-CACTCCTATGAAATTT
*
16657 TGATAAC-CTCGCTATGGAATTT
1 TGATAACACTC-CTATGAAATTT
*
16679 TGATAAC-CT-CTTTG--ATTT
1 TGATAACACTCCTATGAAATTT
*
16697 TGATAACCAC-ACTATGAAATTT
1 TGATAA-CACTCCTATGAAATTT
**
16719 TGATAACTTTCCTATGAAATTT
1 TGATAACACTCCTATGAAATTT
* *
16741 TAATAACCTAATCCATATGAAATTT
1 TGATAA-C-ACTCC-TATGAAATTT
16766 TGATAATCACT-CTATGAAATTT
1 TGATAA-CACTCCTATGAAATTT
*
16788 TAATAA
1 TGATAA
16794 TCTTTTGATG
Statistics
Matches: 833, Mismatches: 188, Indels: 254
0.65 0.15 0.20
Matches are distributed among these distances:
15 3 0.00
16 8 0.01
17 5 0.01
18 16 0.02
19 16 0.02
20 59 0.07
21 66 0.08
22 444 0.53
23 98 0.12
24 62 0.07
25 31 0.04
26 7 0.01
28 18 0.02
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
TGATAACACTCCTATGAAATTT
Found at i:15928 original size:23 final size:23
Alignment explanation
Indices: 15901--15984 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
15891 ATGACCTCGG
*
15901 TATAAAATTTTGATAAACATTCA
1 TATAAAATTTTGATAAACATCCA
* * *
15924 TATAAAATTTTTATAAACCTCCC
1 TATAAAATTTTGATAAACATCCA
* *
15947 TATAAAATTTTGAT-AACCTCCT
1 TATAAAATTTTGATAAACATCCA
* *
15969 TATGAAATATTGATAA
1 TATAAAATTTTGATAA
15985 TTACAAATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 19 0.37
23 33 0.63
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.39
Consensus pattern (23 bp):
TATAAAATTTTGATAAACATCCA
Found at i:16576 original size:28 final size:29
Alignment explanation
Indices: 16535--16589 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
16525 CTAACTATAA
**
16535 AATTTTGATAACATTTGTATGAAATTTAG
1 AATTTTGATAACATTACTATGAAATTTAG
16564 AATTTT-ATAACATTACTATGAAATTT
1 AATTTTGATAACATTACTATGAAATTT
16590 TGGTAACCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.45
Consensus pattern (29 bp):
AATTTTGATAACATTACTATGAAATTTAG
Found at i:16718 original size:62 final size:62
Alignment explanation
Indices: 16578--16749 Score: 186
Period size: 62 Copynumber: 2.7 Consensus size: 62
16568 TTATAACATT
* * ** *
16578 ACTATGAAATTTTGGTAAC-CACACTATGAAATCTTTAATAACCTCCTGATAAAATTTTGATAAT
1 ACTATGAAATTTTGATAACTCTC-CTATGAAAT-TTTAATAACCT-CT--T-TGATTTTGATAAC
*
16642 TAC
60 CAC
* *
16645 ACTATGAAATTTTGATAAC-CTCGCTATGGAATTTTGATAACCTCTTTGATTTTGATAACCAC
1 ACTATGAAATTTTGATAACTCTC-CTATGAAATTTTAATAACCTCTTTGATTTTGATAACCAC
*
16707 ACTATGAAATTTTGATAACTTTCCTATGAAATTTTAATAACCT
1 ACTATGAAATTTTGATAACTCTCCTATGAAATTTTAATAACCT
16750 AATCCATATG
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
62 49 0.53
63 3 0.03
65 2 0.02
66 10 0.11
67 28 0.30
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (62 bp):
ACTATGAAATTTTGATAACTCTCCTATGAAATTTTAATAACCTCTTTGATTTTGATAACCAC
Found at i:16798 original size:107 final size:106
Alignment explanation
Indices: 16586--16798 Score: 245
Period size: 107 Copynumber: 2.0 Consensus size: 106
16576 TTACTATGAA
* *
16586 ATTTTGGTAACCACACTATGAAATCTTTAATAACCTCCTGATAAAATTTTGATAATTACACTATG
1 ATTTTGATAACCACACTATGAAATCTTTAATAACCTCCTGATAAAATTTTAATAATTACACTATG
* * *
16651 AAATTTTGATAACCTCGCTATGGAATTTTGATAACCTCTTTG
66 AAATTTTGATAACCACGCTATGAAATTTTAATAA-CTCTTTG
* * * *
16693 ATTTTGATAACCACACTATGAAAT-TTTGATAACTTTCCT-ATGAAATTTTAATAACCTA-ATCC
1 ATTTTGATAACCACACTATGAAATCTTTAATAAC-CTCCTGATAAAATTTTAATAA-TTACA--C
* *
16755 ATATGAAATTTTGATAATCACTCTATGAAATTTTAATAA-TCTTT
62 -TATGAAATTTTGATAACCACGCTATGAAATTTTAATAACTCTTT
16799 TGATGCCACA
Statistics
Matches: 90, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
106 22 0.24
107 34 0.38
108 1 0.01
109 33 0.37
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (106 bp):
ATTTTGATAACCACACTATGAAATCTTTAATAACCTCCTGATAAAATTTTAATAATTACACTATG
AAATTTTGATAACCACGCTATGAAATTTTAATAACTCTTTG
Found at i:16865 original size:24 final size:24
Alignment explanation
Indices: 16830--16890 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
16820 ATAACCTTTG
* *
16830 AAATTTTAATAACCTAATCCCTAA
1 AAATTTTGATAACCTAATCCATAA
* *
16854 AAATTTTGATAACC-ACTCGATAA
1 AAATTTTGATAACCTAATCCATAA
16877 AAA-TTTGATAACCT
1 AAATTTTGATAACCT
16891 TCCTATGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 10 0.31
23 9 0.28
24 13 0.41
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (24 bp):
AAATTTTGATAACCTAATCCATAA
Found at i:16905 original size:22 final size:22
Alignment explanation
Indices: 16828--17037 Score: 92
Period size: 22 Copynumber: 9.5 Consensus size: 22
16818 TGATAACCTT
*
16828 TGAAATTTTAATAACCTAATCCCTA
1 TGAAATTTTGATAACCT--T-CCTA
* * *
16853 -AAAATTTTGATAACC-ACTCGA
1 TGAAATTTTGATAACCTTC-CTA
* *
16874 TAAAAATTTGATAACCTTCCTA
1 TGAAATTTTGATAACCTTCCTA
* * *
16896 TGAAATTTTGGTAACCGTACTA
1 TGAAATTTTGATAACCTTCCTA
* * *
16918 TGAAATTTTGGTAACC-ACAATA
1 TGAAATTTTGATAACCTTC-CTA
**
16940 TGAGTTTTTGATAACCTTCCTA
1 TGAAATTTTGATAACCTTCCTA
* * **
16962 T-AAAATTTGGTAA-CTGGACTA
1 TGAAATTTTGATAACCT-TCCTA
*
16983 CGAAATTTTGATAACC-TCCTTA
1 TGAAATTTTGATAACCTTCC-TA
* ** **
17005 CG-AATTTTGATAATGTTATTA
1 TGAAATTTTGATAACCTTCCTA
17026 TGAAATTTTGAT
1 TGAAATTTTGAT
17038 TACCATACAA
Statistics
Matches: 138, Mismatches: 36, Indels: 25
0.69 0.18 0.13
Matches are distributed among these distances:
20 3 0.02
21 28 0.20
22 91 0.66
23 3 0.02
24 13 0.09
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCCTA
Found at i:16933 original size:66 final size:65
Alignment explanation
Indices: 16854--16998 Score: 173
Period size: 66 Copynumber: 2.2 Consensus size: 65
16844 TAATCCCTAA
** * * *
16854 AAATTTTGATAACCACTCGATAAAAATTTGATAACCTTCCTATGAAATTTTGGTAACCGTACTAT
1 AAATTTTGATAACCACAAGATAAAAATTTGATAACCTTCCTAT-AAAATTTGGTAACCGGACTAC
16919 G
65 G
* * * *** *
16920 AAATTTTGGTAACCACAATATGAGTTTTTGATAACCTTCCTATAAAATTTGGTAACTGGACTACG
1 AAATTTTGATAACCACAAGATAAAAATTTGATAACCTTCCTATAAAATTTGGTAACCGGACTACG
16985 AAATTTTGATAACC
1 AAATTTTGATAACC
16999 TCCTTACGAA
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
65 31 0.47
66 35 0.53
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (65 bp):
AAATTTTGATAACCACAAGATAAAAATTTGATAACCTTCCTATAAAATTTGGTAACCGGACTACG
Found at i:17140 original size:22 final size:22
Alignment explanation
Indices: 17114--17164 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
17104 ATAATTTTCC
17114 TCATGAAAACTTGATAATCTCA
1 TCATGAAAACTTGATAATCTCA
**
17136 TCATG-AAGTTTGATAATCTCA
1 TCATGAAAACTTGATAATCTCA
*
17157 TTATGAAA
1 TCATGAAA
17165 TTTTTTGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (22 bp):
TCATGAAAACTTGATAATCTCA
Found at i:17150 original size:21 final size:21
Alignment explanation
Indices: 17124--17163 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17114 TCATGAAAAC
17124 TTGATAATCTCATCATGAAGT
1 TTGATAATCTCATCATGAAGT
*
17145 TTGATAATCTCATTATGAA
1 TTGATAATCTCATCATGAA
17164 ATTTTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (21 bp):
TTGATAATCTCATCATGAAGT
Found at i:17843 original size:22 final size:22
Alignment explanation
Indices: 17818--17874 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
17808 CGCTGTGTGG
*
17818 TTATCAAATTTTCATAGGGAGA
1 TTATCAAATTTTCATAAGGAGA
*
17840 TTATCGAAA-TTTCATAATGAGA
1 TTATC-AAATTTTCATAAGGAGA
17862 TTATC-AATTTTCA
1 TTATCAAATTTTCA
17875 CAGTGCGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 2 0.06
21 5 0.16
22 21 0.68
23 3 0.10
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (22 bp):
TTATCAAATTTTCATAAGGAGA
Found at i:18332 original size:150 final size:150
Alignment explanation
Indices: 18056--18332 Score: 317
Period size: 150 Copynumber: 1.8 Consensus size: 150
18046 CCCAACTTCC
* * *
18056 CGATTTAGCACGTTTGTGCACAAAATGTTGTTCTCGGGAAAACGCTCATTCCTAATACAGTATTT
1 CGATTTAGCACGTTTGTGCACAAAACGTTGTTCTCGAGAAAACGCTCATTCCAAATACAGTATTT
* ** *
18121 ATGAAACCAACGCTCAAACATTGTGTTTTAGAGTAAGTAACCTCATTGAAAAGTGGGCTTGCAAA
66 ATGAAACCAACGCTCAAACATCGTGTTCCAGAGTAAGTAACCTCATTGAAAAGTGGACTTGCAAA
18186 AAAAAAACTTTCTTCAATCT
131 AAAAAAACTTTCTTCAATCT
* * * * * * * *
18206 CGATTTTGCACGTTTGTGCGCACAACGTTGTTCTTGAGAAAATGTTCATTCGAAATACATTA-TT
1 CGATTTAGCACGTTTGTGCACAAAACGTTGTTCTCGAGAAAACGCTCATTCCAAATACAGTATTT
* * * * * *
18270 ATTGTAACCAACGCTCAGATATCGTGTTCCGGAGTTAGTATAGCTCATT-AGAAAGT-GACTTGC
66 A-TGAAACCAACGCTCAAACATCGTGTTCCAGAGTAAGTA-ACCTCATTGA-AAAGTGGACTTGC
18333 CAAACAAAGG
Statistics
Matches: 103, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
149 3 0.03
150 88 0.85
151 12 0.12
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (150 bp):
CGATTTAGCACGTTTGTGCACAAAACGTTGTTCTCGAGAAAACGCTCATTCCAAATACAGTATTT
ATGAAACCAACGCTCAAACATCGTGTTCCAGAGTAAGTAACCTCATTGAAAAGTGGACTTGCAAA
AAAAAAACTTTCTTCAATCT
Found at i:21189 original size:22 final size:22
Alignment explanation
Indices: 21164--21731 Score: 217
Period size: 22 Copynumber: 25.5 Consensus size: 22
21154 ACAATCAAGC
*
21164 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
21186 CAAAATTTCTTAGTGTA-GTTAC
1 CAAAATTTCATAG-GAAGGTTAT
*
21208 CAAAATTTCATATGG-AGATTAT
1 CAAAATTTCATA-GGAAGGTTAT
* *
21230 CAAAACTTCATAGTGTA-GTTAT
1 CAAAATTTCATAG-GAAGGTTAT
* *
21252 CAAAATTTCATA-CAGAGGTTAC
1 CAAAATTTCATAGGA-AGGTTAT
* **
21274 CAAAATTTTATAAAAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
21296 CAAAATTTCTTAGCG-AGGTTAAT
1 CAAAATTTCATAG-GAAGGTT-AT
* * *
21319 -AAAATTTTACACGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
21340 CGAAATTTTATAGTGTA-GTTAT
1 CAAAATTTCATAG-GAAGGTTAT
21362 CAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCATA-GGA---AGGTTAT
* *
21388 CAAAA-TT--T--G-TGCTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * * *
21404 TAAAATATCCTAGTG-AGGTTAA
1 CAAAATTTCATAG-GAAGGTTAT
*
21426 CAAAATTTCATAGGGAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
21448 AAAAAATT-AT-GGAAAGGTTAT
1 CAAAATTTCATAGG-AAGGTTAT
*
21469 CAAAATTTCATA-GAGAGGATAT
1 CAAAATTTCATAGGA-AGGTTAT
* *
21491 CACAGTTTCATTCTCATAGGGAGGTTAT
1 CA-A----AATT-TCATAGGAAGGTTAT
** * * *
21519 TGAAATTTCATAGTATGATTAT
1 CAAAATTTCATAGGAAGGTTAT
*
21541 CAAAATTTTATGAGG-AGGTTAT
1 CAAAATTTCAT-AGGAAGGTTAT
**
21563 CAAAATTTTCATAGCGCGCGCGGTTA-
1 CAAAA-TTTCATA--G-G-AAGGTTAT
* * *
21589 C-GAATTTTATAGTG-TGGTTAT
1 CAAAATTTCATAG-GAAGGTTAT
* * *
21610 CAAAATTTTATAGGGAGATTAT
1 CAAAATTTCATAGGAAGGTTAT
* * ***
21632 CAAAATTCCACACTCAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
21654 CAAAATTTCATAGTATGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* ** *
21676 CAAAATTTCACAATATGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
21698 C-AAATTGTCATAGGAAGGTTAT
1 CAAAATT-TCATAGGAAGGTTAT
*
21720 CGAAATTTCATA
1 CAAAATTTCATA
21732 ATGAGATTAT
Statistics
Matches: 407, Mismatches: 91, Indels: 96
0.69 0.15 0.16
Matches are distributed among these distances:
16 9 0.02
17 1 0.00
19 1 0.00
20 8 0.02
21 30 0.07
22 286 0.70
23 27 0.07
24 7 0.02
25 6 0.01
26 11 0.03
27 9 0.02
28 11 0.03
29 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:21747 original size:44 final size:43
Alignment explanation
Indices: 21606--21748 Score: 119
Period size: 44 Copynumber: 3.3 Consensus size: 43
21596 TATAGTGTGG
* * * * * *
21606 TTATCAAAATTTTATAGGGAGATTATCAAAATTCCACACTCA-GG
1 TTATC-AAATTTCATAGGAAGGTTATCAAAATTTCACAAT-ATGA
* * *
21650 TTATCAAAATTTCATAGTATGGTTATCAAAATTTCACAATATGG
1 TTATC-AAATTTCATAGGAAGGTTATCAAAATTTCACAATATGA
* *
21694 TTATCAAATTGTCATAGGAAGGTTATCGAAATTTCATAATGA-GA
1 TTATCAAATT-TCATAGGAAGGTTATCAAAATTTCACAAT-ATGA
*
21738 TTATTAAATTT
1 TTATCAAATTT
21749 TTTACAGTGT
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
43 7 0.08
44 75 0.90
45 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.37
Consensus pattern (43 bp):
TTATCAAATTTCATAGGAAGGTTATCAAAATTTCACAATATGA
Found at i:23526 original size:13 final size:13
Alignment explanation
Indices: 23508--23552 Score: 90
Period size: 13 Copynumber: 3.5 Consensus size: 13
23498 CTTATGCATA
23508 TACTTAAACTTAT
1 TACTTAAACTTAT
23521 TACTTAAACTTAT
1 TACTTAAACTTAT
23534 TACTTAAACTTAT
1 TACTTAAACTTAT
23547 TACTTA
1 TACTTA
23553 TGCTATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (13 bp):
TACTTAAACTTAT
Found at i:25497 original size:4 final size:4
Alignment explanation
Indices: 25488--25572 Score: 170
Period size: 4 Copynumber: 21.2 Consensus size: 4
25478 ATTAAAGCAA
25488 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
25536 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
25573 TGCGTGTATA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 81 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:48412 original size:19 final size:19
Alignment explanation
Indices: 48384--48423 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
48374 ATTTGAACTT
*
48384 TTAGCCATTTTTTTAA-GA
1 TTAGCCATTTCTTTAATGA
48402 TTAGTCCATTTCTTTAATGA
1 TTAG-CCATTTCTTTAATGA
48422 TT
1 TT
48424 TGTGTACTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 11 0.58
20 4 0.21
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (19 bp):
TTAGCCATTTCTTTAATGA
Found at i:53899 original size:30 final size:29
Alignment explanation
Indices: 53863--53935 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
53853 ATACGTGGCA
*
53863 GGTCCCTGTACTTAGAAGCAAAG-TCAATTT
1 GGTCCCTGTACTTA-AA-AAAAGATCAATTT
* *
53893 GGTCCCTTTACTCAAAAAAAGATCAATTT
1 GGTCCCTGTACTTAAAAAAAGATCAATTT
* *
53922 AGTCCATGTACTTA
1 GGTCCCTGTACTTA
53936 TAAGTTTGGA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
28 4 0.11
29 19 0.54
30 12 0.34
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (29 bp):
GGTCCCTGTACTTAAAAAAAGATCAATTT
Found at i:55121 original size:21 final size:21
Alignment explanation
Indices: 55097--55136 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55087 GGATCATTAT
*
55097 ACCAAATAAAGACAACTTTGC
1 ACCAAATAAACACAACTTTGC
*
55118 ACCAAATAGACACAACTTT
1 ACCAAATAAACACAACTTT
55137 ACAACATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.25, G:0.07, T:0.20
Consensus pattern (21 bp):
ACCAAATAAACACAACTTTGC
Found at i:55436 original size:2 final size:2
Alignment explanation
Indices: 55431--55539 Score: 51
Period size: 2 Copynumber: 59.0 Consensus size: 2
55421 TATATTTAAG
55431 AT AT AT AT AT AT -T AT AT AT AT -T AT AT AT -T AGT A- AT A- AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T
* * * * *
55470 TT TT AT -T AT AT AT AT AT AA AT AT AT AT -T TT AT -T AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
55509 AT -T AA AT AT AT TT A- AG AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55540 TAGTAATTAG
Statistics
Matches: 82, Mismatches: 12, Indels: 26
0.68 0.10 0.22
Matches are distributed among these distances:
1 11 0.13
2 69 0.84
3 2 0.02
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:55456 original size:9 final size:9
Alignment explanation
Indices: 55405--55539 Score: 63
Period size: 9 Copynumber: 15.1 Consensus size: 9
55395 TTATATATTT
*
55405 TATTATAAA
1 TATTATATA
*
55414 TATTAAATA
1 TATTATATA
55423 TATT-TA-A
1 TATTATATA
*
55430 GATATATATA
1 TAT-TATATA
55440 TATTATATA
1 TATTATATA
55449 TATTATATA
1 TATTATATA
*
55458 TTAGTA-ATA
1 -TATTATATA
55467 -AGTT-T-T-
1 TA-TTATATA
55473 TATTATATA
1 TATTATATA
*
55482 TA-TATAAA
1 TATTATATA
*
55490 TA-TATATTT
1 TATTATA-TA
*
55499 TATTATAAA
1 TATTATATA
*
55508 TATTAAATA
1 TATTATATA
55517 TATTTAAGATATA
1 TA-TT---ATATA
55530 TATTATATA
1 TATTATATA
55539 T
1 T
55540 TAGTAATTAG
Statistics
Matches: 95, Mismatches: 15, Indels: 32
0.67 0.11 0.23
Matches are distributed among these distances:
6 2 0.02
7 7 0.07
8 15 0.16
9 50 0.53
10 13 0.14
12 2 0.02
13 6 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (9 bp):
TATTATATA
Found at i:58694 original size:42 final size:43
Alignment explanation
Indices: 58643--58736 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
58633 AGTGCATTAC
*
58643 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTATCTCCATCTCTAGATAATTCATCAAAATAAAG
58684 CTAATATTCTACTTCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--TCTCCATCTCTAGATAATTCATCAAAATAAAG
58729 CTAATATT
1 CTAATATT
58737 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTATCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:60455 original size:36 final size:36
Alignment explanation
Indices: 60406--60478 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
60396 ACTCCAATAC
* *
60406 TCAAGTTAGTTAAGGGTTTAGGGGTTAAGAATTCAA
1 TCAAGTCAATTAAGGGTTTAGGGGTTAAGAATTCAA
60442 TCAAGTCAATTAAGGGTTTAGGGGTTAAGAATTCAA
1 TCAAGTCAATTAAGGGTTTAGGGGTTAAGAATTCAA
60478 T
1 T
60479 ATTTGTGTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.34, C:0.07, G:0.26, T:0.33
Consensus pattern (36 bp):
TCAAGTCAATTAAGGGTTTAGGGGTTAAGAATTCAA
Found at i:61996 original size:29 final size:28
Alignment explanation
Indices: 61952--62007 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
61942 TTCTTCAAAC
* *
61952 TTTCTAATTTCAAGAATGCTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
61980 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
62008 GTGGAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Done.