Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015737.1 Corchorus capsularis cultivar CVL-1 contig15758, 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: 60782
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:347 original size:32 final size:30
Alignment explanation
Indices: 263--423 Score: 157
Period size: 32 Copynumber: 5.3 Consensus size: 30
253 AAAAATGACA
* * *
263 CGTGGCACGTGTC-CTTTT-GTGCATGTGG
1 CGTGCCACGTGTCACTTTTGGTACACGTGG
* *
291 CATGCCATGTGTCACTTTTGGTACACGTGG
1 CGTGCCACGTGTCACTTTTGGTACACGTGG
*
321 CGTGCCACGTGTCACCTTTTTGGTACACGTGC
1 CGTGCCACGTGTCA-C-TTTTGGTACACGTGG
353 CGTGCCACGTGTCACCTTTTGGTACACGTGCG
1 CGTGCCACGTGTCA-CTTTTGGTACACGTG-G
* * * * *
385 TGTGCCACGGGTTA-TTTTTGTCCACGTGG
1 CGTGCCACGTGTCACTTTTGGTACACGTGG
*
414 CATGCCACGT
1 CGTGCCACGT
424 CGGACTCCGT
Statistics
Matches: 111, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
28 10 0.09
29 13 0.12
30 32 0.29
31 15 0.14
32 41 0.37
ACGTcount: A:0.12, C:0.27, G:0.29, T:0.32
Consensus pattern (30 bp):
CGTGCCACGTGTCACTTTTGGTACACGTGG
Found at i:2982 original size:23 final size:22
Alignment explanation
Indices: 2946--3010 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
2936 GAAGACCTCA
*
2946 ATATGAAATTTTGATAACCAAC
1 ATATGAAATATTGATAACCAAC
* * **
2968 ACTATGAGATGTTGATAACCTCC
1 A-TATGAAATATTGATAACCAAC
*
2991 ATATGATATATTGATAACCA
1 ATATGAAATATTGATAACCA
3011 CGTTATGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
ATATGAAATATTGATAACCAAC
Found at i:3004 original size:22 final size:22
Alignment explanation
Indices: 2940--3041 Score: 71
Period size: 22 Copynumber: 4.6 Consensus size: 22
2930 AATTTTGAAG
* *
2940 ACCTCAATATGAAATTTTGATA
1 ACCTCCATATGAAATATTGATA
** * *
2962 ACCAACACTATGAGATGTTGATA
1 ACCTCCA-TATGAAATATTGATA
*
2985 ACCTCCATATGATATATTGATA
1 ACCTCCATATGAAATATTGATA
* ** * *
3007 ACCACGTTATGAAA-ATTTAAAA
1 ACCTCCATATGAAATA-TTGATA
3029 ACCTCCATATGAA
1 ACCTCCATATGAA
3042 TTGTTAGTAA
Statistics
Matches: 60, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
21 1 0.02
22 41 0.68
23 18 0.30
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (22 bp):
ACCTCCATATGAAATATTGATA
Found at i:3074 original size:22 final size:22
Alignment explanation
Indices: 3049--3117 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
3039 GAATTGTTAG
* *
3049 TAATCACACTCTGTAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
3071 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* *
3093 TAATCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
3115 TAA
1 TAA
3118 ATCTTCCTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:3135 original size:22 final size:22
Alignment explanation
Indices: 3079--3185 Score: 76
Period size: 23 Copynumber: 4.7 Consensus size: 22
3069 GATAATCACA
*
3079 CTATGAAATTGTGAT-AATC-TC
1 CTATAAAATT-TGATAAATCTTC
*
3100 GCTATGAAATTTTGATAAATCTTC
1 -CTAT-AAAATTTGATAAATCTTC
* *
3124 CTATAAAATTTGGATAAACCTCC
1 CTATAAAATTT-GATAAATCTTC
*
3147 CTATAAAATTTTGATAACT-TTC
1 CTATAAAA-TTTGATAAATCTTC
* *
3169 TTATGAAATCTTGATAA
1 CTATAAAAT-TTGATAA
3186 CTACAAATTT
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.01
22 29 0.42
23 34 0.49
24 5 0.07
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (22 bp):
CTATAAAATTTGATAAATCTTC
Found at i:3218 original size:22 final size:21
Alignment explanation
Indices: 3063--3329 Score: 136
Period size: 22 Copynumber: 12.4 Consensus size: 21
3053 CACACTCTGT
*
3063 AATTTTGATAATCACACTATGA
1 AATTTTGATAATCTC-CTATGA
*
3085 AATTGTGATAATCTCGCTATGA
1 AATTTTGATAATCTC-CTATGA
*
3107 AATTTTGATAAATCTTCCTATAA
1 AATTTTGAT-AATC-TCCTATGA
* * *
3130 AATTTGGATAAACCTCCCTATAA
1 AATTTTGAT-AATCT-CCTATGA
* *
3153 AATTTTGATAACTTTCTTATGA
1 AATTTTGATAA-TCTCCTATGA
* *
3175 AATCTTGATAA----CTA-CA
1 AATTTTGATAATCTCCTATGA
*
3191 AATTTTGATAAGCTCCTTATGA
1 AATTTTGATAATCTCC-TATGA
* * *
3213 AATTTTGATCTATATACTATGA
1 AATTTTGAT-AATCTCCTATGA
* * *
3235 AATTGTGATAACCCTCTTATGA
1 AATTTTGATAA-TCTCCTATGA
* *
3257 AATTTTGA-AAACTAAACTATGA
1 AATTTTGATAATCT--CCTATGA
* ** * *
3279 ATTTTTTCTAACCTTCATATGA
1 AATTTTGATAATC-TCCTATGA
3301 AATTTTGAT-ATCCTCC-ATGA
1 AATTTTGATAAT-CTCCTATGA
3321 AATTTTGAT
1 AATTTTGAT
3330 TATTCCATAA
Statistics
Matches: 186, Mismatches: 42, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
20 16 0.09
21 8 0.04
22 103 0.55
23 43 0.23
24 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
AATTTTGATAATCTCCTATGA
Found at i:3573 original size:21 final size:21
Alignment explanation
Indices: 3547--3602 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
3537 AAACACTATA
3547 AAATTTTGATAATCTTCATAT
1 AAATTTTGATAATCTTCATAT
3568 AAATTTTGATAATCTTCATAT
1 AAATTTTGATAATCTTCATAT
3589 AAATTTTGATAATC
1 AAATTTTGATAATC
3603 CGATCTCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.46
Consensus pattern (21 bp):
AAATTTTGATAATCTTCATAT
Found at i:3635 original size:22 final size:22
Alignment explanation
Indices: 3475--3680 Score: 126
Period size: 22 Copynumber: 9.5 Consensus size: 22
3465 TGTTGACCCA
* *
3475 TCTATGAAATTCTAATAATCAC
1 TCTATGAAATTTTGATAATCAC
* *
3497 AT-TATGTAATTTTGATAATCTC
1 -TCTATGAAATTTTGATAATCAC
* * **
3519 GCTTTGAAATTTTGATAAAAAC
1 TCTATGAAATTTTGATAATCAC
* * *
3541 ACTATAAAATTTTGATAATC-T
1 TCTATGAAATTTTGATAATCAC
*
3562 TCATAT-AAATTTTGATAATC-T
1 TC-TATGAAATTTTGATAATCAC
3583 TCATAT-AAATTTTGATAATCCGATC
1 TC-TATGAAATTTTGATAAT-C-A-C
*
3608 TCTATGAAATTTCGATAATCAC
1 TCTATGAAATTTTGATAATCAC
*
3630 TCTATGAGA-TTTGATAA--AC
1 TCTATGAAATTTTGATAATCAC
* * *
3649 TTCTATCAAATTTTGGTACTC-C
1 -TCTATGAAATTTTGATAATCAC
3671 T-TATGAAATT
1 TCTATGAAATT
3681 GAGACTTTTA
Statistics
Matches: 146, Mismatches: 26, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
19 2 0.01
20 15 0.10
21 49 0.34
22 60 0.41
23 2 0.01
24 4 0.03
25 14 0.10
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (22 bp):
TCTATGAAATTTTGATAATCAC
Found at i:3663 original size:21 final size:20
Alignment explanation
Indices: 3542--3663 Score: 77
Period size: 21 Copynumber: 5.6 Consensus size: 20
3532 GATAAAAACA
*
3542 CTATAAAATTTTGATAATCTT
1 CTAT-AAATTTTGATAAACTT
*
3563 CATATAAATTTTGATAATCTT
1 C-TATAAATTTTGATAAACTT
*
3584 CATATAAATTTTGATAATCCGATCT
1 C-TATAAATTTTGATAA-AC--T-T
*
3609 CTATGAAATTTCGATAATCAC-T
1 CTAT-AAATTTTGATAA--ACTT
*
3631 CTATGAGA-TTTGATAAACTT
1 CTAT-AAATTTTGATAAACTT
3651 CTATCAAATTTTG
1 CTAT-AAATTTTG
3664 GTACTCCTTA
Statistics
Matches: 84, Mismatches: 8, Indels: 18
0.76 0.07 0.16
Matches are distributed among these distances:
19 2 0.02
20 7 0.08
21 45 0.54
22 12 0.14
24 4 0.05
25 13 0.15
26 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (20 bp):
CTATAAATTTTGATAAACTT
Found at i:3715 original size:22 final size:22
Alignment explanation
Indices: 3547--3806 Score: 107
Period size: 22 Copynumber: 11.7 Consensus size: 22
3537 AAACACTATA
*
3547 AAATTTTGATAATCTTCATAT-
1 AAATTTTGATAACCTTCATATG
*
3568 AAATTTTGATAATCTTCATAT-
1 AAATTTTGATAACCTTCATATG
3589 AAATTTTGATAATCCGATCTC-TATG
1 AAATTTTGATAA-CC--T-TCATATG
*
3614 AAATTTCGATAATCAC-TC-TATG
1 AAATTTTGATAA-C-CTTCATATG
* * *
3636 AGA-TTTGATAAACTTC-TATC
1 AAATTTTGATAACCTTCATATG
* *
3656 AAATTTTGGTACTCCTT-ATGAAATTG
1 AAATTTTGATA-ACCTTCAT---A-TG
*
3682 AGACTTTT-ATAACCTTCATATG
1 A-AATTTTGATAACCTTCATATG
* *
3704 AAATTTTGATAACC-ACACTATA
1 AAATTTTGATAACCTTCA-TATG
* **
3726 AAATTTTGATAACCTCCCCATG
1 AAATTTTGATAACCTTCATATG
* *
3748 AAATATT-AGTAACC-TCCTAATG
1 AAATTTTGA-TAACCTTCAT-ATG
* *
3770 AAATTTTGTTAACC-ACACTATG
1 AAATTTTGATAACCTTCA-TATG
3792 AAATTCTT-ATAACCT
1 AAATT-TTGATAACCT
3807 CGTTATGACA
Statistics
Matches: 185, Mismatches: 29, Indels: 48
0.71 0.11 0.18
Matches are distributed among these distances:
19 1 0.01
20 7 0.04
21 56 0.30
22 80 0.43
23 5 0.03
24 4 0.02
25 20 0.11
26 7 0.04
27 5 0.03
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACCTTCATATG
Found at i:3942 original size:22 final size:22
Alignment explanation
Indices: 3914--3962 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
3904 TAACTTGATC
3914 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
3936 CTATGAAATTTTGGTAACCCCA
1 CTATGAAATTTTGGTAACCACA
3958 CTATG
1 CTATG
3963 GAATAACCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:3990 original size:22 final size:22
Alignment explanation
Indices: 3964--4015 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
3954 CCCACTATGG
*
3964 AATAACCATCTTATGAAATTAT
1 AATAACCATCTTATAAAATTAT
*
3986 AATAACCATCTTATAAAATTTT
1 AATAACCATCTTATAAAATTAT
*
4008 GATAACCA
1 AATAACCA
4016 CATAGAGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (22 bp):
AATAACCATCTTATAAAATTAT
Found at i:4211 original size:19 final size:20
Alignment explanation
Indices: 4180--4217 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
4170 TATTAACATT
4180 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
4199 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
4218 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:4542 original size:167 final size:174
Alignment explanation
Indices: 4231--4573 Score: 468
Period size: 167 Copynumber: 2.0 Consensus size: 174
4221 AATAGTAAAG
* * * *
4231 GAAATTTGCGTGTTCATCAACTAAAATCCATTTCACAAACTTATAATTTGGTCTAAATTGAAATT
1 GAAATTTACATGTTCATCAACTAAAATCAATTTCACAAACTTATAATTCGGTCTAAATTGAAATT
4296 TTAATTAATTTTTAAATAATAAAATTATACTAAATTTTAATAATGGAAATTTAGAAATATATTTG
66 TTAATTAA--TTTAAATAATAAAATTATACTAAATTTTAATAATGGAAATTTAGAAATATATTTG
* *
4361 AAAAAGAGGGTACAATTGGAAAACATAAAGTTTCCCATTATTCGTA
129 AAAAAAAGGGTACAATCGGAAAACATAAAGTTTCCCATTATTCGTA
* *
4407 GAAATTTACATGTTCATCAA-TGAAAATCAATTTTACAAGCTTATAATTCGGTCTAAATTGAAAT
1 GAAATTTACATGTTCATCAACT-AAAATCAATTTCACAAACTTATAATTCGGTCTAAATTGAAAT
** * **
4471 TTT-A-TAA-TT-AATTTTTAAA-TA-A-TAAATTTTAATAATGTCAATTTAGAAATATATTTGA
65 TTTAATTAATTTAAATAATAAAATTATACTAAATTTTAATAATGGAAATTTAGAAATATATTTGA
* *
4529 AAAAAATGGTACAATCGGAAAACATAAAGTTTTCCATTATTCGTA
130 AAAAAAGGGTACAATCGGAAAACATAAAGTTTCCCATTATTCGTA
4574 CTTTTTTATA
Statistics
Matches: 151, Mismatches: 15, Indels: 11
0.85 0.08 0.06
Matches are distributed among these distances:
167 75 0.50
168 1 0.01
169 2 0.01
170 7 0.05
171 2 0.01
174 3 0.02
175 2 0.01
176 59 0.39
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (174 bp):
GAAATTTACATGTTCATCAACTAAAATCAATTTCACAAACTTATAATTCGGTCTAAATTGAAATT
TTAATTAATTTAAATAATAAAATTATACTAAATTTTAATAATGGAAATTTAGAAATATATTTGAA
AAAAAGGGTACAATCGGAAAACATAAAGTTTCCCATTATTCGTA
Found at i:6021 original size:30 final size:31
Alignment explanation
Indices: 5987--6050 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
5977 GGCAATTAAT
* *
5987 AAATATGTTTTAA-AAAAAGGGTACAATTGG
1 AAATATGTTTTAAGAAAAAGGGTAAAATCGG
*
6017 AAATATGTTTTAAGAATAAGGGTAAAATCGG
1 AAATATGTTTTAAGAAAAAGGGTAAAATCGG
6048 AAA
1 AAA
6051 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.48, C:0.03, G:0.20, T:0.28
Consensus pattern (31 bp):
AAATATGTTTTAAGAAAAAGGGTAAAATCGG
Found at i:8387 original size:31 final size:32
Alignment explanation
Indices: 8325--8390 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
8315 TGGCAATTTA
* *
8325 GAAATATAATTTTTTTAAAAAGAGTATAATCG
1 GAAATATAATTTTTTAAAAAAGAGTACAATCG
*
8357 GAAATAT-A-TTTTTAAAAAAGGGGTACAATCG
1 GAAATATAATTTTTTAAAAAA-GAGTACAATCG
8388 GAA
1 GAA
8391 CATAAAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 10 0.33
31 13 0.43
32 7 0.23
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.32
Consensus pattern (32 bp):
GAAATATAATTTTTTAAAAAAGAGTACAATCG
Found at i:17312 original size:254 final size:255
Alignment explanation
Indices: 16839--17355 Score: 905
Period size: 254 Copynumber: 2.0 Consensus size: 255
16829 ATATAAACAA
*
16839 TTTTAATAAGGTTTAGCCCCAATTATAAATGTTATAATTTTTTAAAGGGTAAATTTTAAATTTTG
1 TTTTAATAAGATTTAGCCCCAATTATAAATGTTATAATTTTTTAAAGGGTAAATTTTAAATTTTG
16904 ATACCCTATTAAGATTTTAGAAAATATTATAAACTATTTTTTAAAATTTTTCTTCACATAAAAAA
66 ATACCCTATTAAGATTTTAGAAAATATTATAAACTATTTTTTAAAATTTTTCTTCACATAAAAAA
** * *
16969 CTAATGATAATGATTTTTCATCTTTTATTTGGTATAAGGGTAGTTTTGACATATAAATTCTCTTT
131 CTAACCATAATGATTTTTCATCTTTTATTTGATATAAGGGTAGTTTTGACATACAAATTCTCTTT
*
17034 TTATGAACAATTATTATTTAGCAATTCTATACCCA-TTTTT-TATGCAATCATTAGACTT
196 TCATGAACAATTATTATTTAGCAATTCTATACCCACTTTTTATATGCAATCATTAGACTT
17092 TTTTAATAAGATTTAGCCCCAACTATATAAATGTTATAATTTTTTAAAGGGTAAATTTTAAATTT
1 TTTTAATAAGATTTAGCCCCAA-T-TATAAATGTTATAATTTTTTAAAGGGTAAATTTTAAATTT
* *
17157 TGATACCCTATTAAGATTTTATAAAATATTATAAACTA-TTTTTAAAATTTTTCTTGACATAAAA
64 TGATACCCTATTAAGATTTTAGAAAATATTATAAACTATTTTTTAAAATTTTTCTTCACATAAAA
17221 AACTAACCATAATGATTTTTCATCTTTTATTTGATATAAGGGTAGTTTTGACATACAAATTCTCT
129 AACTAACCATAATGATTTTTCATCTTTTATTTGATATAAGGGTAGTTTTGACATACAAATTCTCT
**
17286 TTTCATGAACAATTATTATTTAGCAATTCTATATTCACTTTTTATATGCAATCATTAGACTT
194 TTTCATGAACAATTATTATTTAGCAATTCTATACCCACTTTTTATATGCAATCATTAGACTT
17348 TTTTAATA
1 TTTTAATA
17356 CATTATTCTC
Statistics
Matches: 250, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
253 21 0.08
254 121 0.48
255 82 0.33
256 26 0.10
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (255 bp):
TTTTAATAAGATTTAGCCCCAATTATAAATGTTATAATTTTTTAAAGGGTAAATTTTAAATTTTG
ATACCCTATTAAGATTTTAGAAAATATTATAAACTATTTTTTAAAATTTTTCTTCACATAAAAAA
CTAACCATAATGATTTTTCATCTTTTATTTGATATAAGGGTAGTTTTGACATACAAATTCTCTTT
TCATGAACAATTATTATTTAGCAATTCTATACCCACTTTTTATATGCAATCATTAGACTT
Found at i:26763 original size:24 final size:24
Alignment explanation
Indices: 26736--26792 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
26726 GTAGTACCAT
**
26736 AATTCCCCTTGCCAGTAATAACAG
1 AATTCCCAATGCCAGTAATAACAG
*
26760 AATTTCCAATGCCAGTAATAACAG
1 AATTCCCAATGCCAGTAATAACAG
*
26784 AATTTCCAA
1 AATTCCCAA
26793 AAGCAGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.26
Consensus pattern (24 bp):
AATTCCCAATGCCAGTAATAACAG
Found at i:26799 original size:24 final size:24
Alignment explanation
Indices: 26746--26806 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
26736 AATTCCCCTT
*
26746 GCCAGTAATAACAGAATTTCCAAT
1 GCCAGTAATAACAGAATTTCCAAA
26770 GCCAGTAATAACAGAATTTCCAAAA
1 GCCAGTAATAACAGAATTTCC-AAA
*
26795 G-CAGTAAAAACA
1 GCCAGTAATAACA
26807 CATTCAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 31 0.91
25 3 0.09
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.20
Consensus pattern (24 bp):
GCCAGTAATAACAGAATTTCCAAA
Found at i:27888 original size:17 final size:17
Alignment explanation
Indices: 27863--27899 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
27853 AAACAAAAGC
*
27863 GGAAGCAAAAGGAAAAA
1 GGAAACAAAAGGAAAAA
*
27880 GGAAACAAAAGGAAGAA
1 GGAAACAAAAGGAAAAA
27897 GGA
1 GGA
27900 GGTATAGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.32, T:0.00
Consensus pattern (17 bp):
GGAAACAAAAGGAAAAA
Found at i:28605 original size:33 final size:33
Alignment explanation
Indices: 28568--28638 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
28558 CCGCCCTCCT
*
28568 AGGGCGGCTTACCATGGCACAGGCCGCCCCAGG
1 AGGGCGGCTTACCAGGGCACAGGCCGCCCCAGG
* *
28601 AGGGCGGCTTACCAGGGCTCATGCCGCCCCAGG
1 AGGGCGGCTTACCAGGGCACAGGCCGCCCCAGG
28634 AGGGC
1 AGGGC
28639 AGTTGAGGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.17, C:0.35, G:0.38, T:0.10
Consensus pattern (33 bp):
AGGGCGGCTTACCAGGGCACAGGCCGCCCCAGG
Found at i:30835 original size:24 final size:24
Alignment explanation
Indices: 30803--30850 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
30793 ATGGTTCGTC
30803 ACTAATTTTCCCTTAATCAAAATA
1 ACTAATTTTCCCTTAATCAAAATA
30827 ACTAATTTTCCCTTAATCAAAATA
1 ACTAATTTTCCCTTAATCAAAATA
30851 TCGAATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.38
Consensus pattern (24 bp):
ACTAATTTTCCCTTAATCAAAATA
Found at i:30857 original size:24 final size:24
Alignment explanation
Indices: 30806--30857 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
30796 GTTCGTCACT
*
30806 AATTTTCCCTTAATCAAAATAACT
1 AATTTTCCCTTAATCAAAATAACG
*
30830 AATTTTCCCTTAATCAAAATATCG
1 AATTTTCCCTTAATCAAAATAACG
30854 AATT
1 AATT
30858 CAAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.38
Consensus pattern (24 bp):
AATTTTCCCTTAATCAAAATAACG
Found at i:31190 original size:16 final size:16
Alignment explanation
Indices: 31169--31199 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31159 TAAAATTTTA
31169 TTTTTAATAATAATAT
1 TTTTTAATAATAATAT
31185 TTTTTAATAATAATA
1 TTTTTAATAATAATA
31200 AAGTATTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTTAATAATAATAT
Found at i:35216 original size:14 final size:14
Alignment explanation
Indices: 35182--35281 Score: 60
Period size: 15 Copynumber: 6.5 Consensus size: 14
35172 TTATTTATTT
35182 ATATATATAAATAA
1 ATATATATAAATAA
35196 AGT-TATA-AAAGTAA
1 A-TATATATAAA-TAA
* *
35210 ATATATATTTATTATA
1 ATATATA-TAAATA-A
35226 ATATATATAATTATAA
1 ATATATATAA--ATAA
*
35242 TTATAATTTATATAATAA
1 --AT-ATATATA-AATAA
35260 ATATATATAAAGTAA
1 ATATATATAAA-TAA
35275 ATATATA
1 ATATATA
35282 ATTACTTTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 25
0.68 0.06 0.26
Matches are distributed among these distances:
13 4 0.06
14 15 0.22
15 21 0.31
16 12 0.18
17 2 0.03
18 6 0.09
19 6 0.09
20 1 0.01
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
ATATATATAAATAA
Found at i:35217 original size:2 final size:2
Alignment explanation
Indices: 35210--35314 Score: 54
Period size: 2 Copynumber: 57.5 Consensus size: 2
35200 ATAAAAGTAA
*
35210 AT AT AT AT TT AT -T AT A- AT AT AT AT A- AT -T AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
35246 A- AT TT AT AT A- AT AA AT AT AT AT AA AGT AA AT AT AT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
*
35285 ACT TT AT AT AT AT -T AT AT AT AT A- AT AT AT A
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35315 AAGTAAACAA
Statistics
Matches: 77, Mismatches: 12, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
1 12 0.16
2 63 0.82
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35231 original size:18 final size:18
Alignment explanation
Indices: 35210--35265 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 18
35200 ATAAAAGTAA
35210 ATATATATTTATTATAAT
1 ATATATATTTATTATAAT
35228 ATATATA---ATTATAAT
1 ATATATATTTATTATAAT
35243 -TATA-ATTTA-TATAAT
1 ATATATATTTATTATAAT
*
35258 AAATATAT
1 ATATATAT
35266 ATAAAGTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 4 0.12
15 14 0.44
16 4 0.12
17 2 0.06
18 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATTTATTATAAT
Found at i:35234 original size:9 final size:9
Alignment explanation
Indices: 35209--35314 Score: 71
Period size: 9 Copynumber: 11.9 Consensus size: 9
35199 TATAAAAGTA
35209 AATATATAT
1 AATATATAT
*
35218 -TTAT-TAT
1 AATATATAT
35225 AATATATAT
1 AATATATAT
35234 AATTATAATTAT
1 AA-TAT-A-TAT
*
35246 AATTTATAT
1 AATATATAT
*
35255 AATAAATAT
1 AATATATAT
*
35264 -ATATAAAGT
1 AATATATA-T
35273 AA-ATATAT
1 AATATATAT
35281 AAT-TACT-T
1 AATATA-TAT
*
35289 TATATATAT
1 AATATATAT
*
35298 TATATATAT
1 AATATATAT
35307 AATATATA
1 AATATATA
35315 AAGTAAACAA
Statistics
Matches: 76, Mismatches: 10, Indels: 22
0.70 0.09 0.20
Matches are distributed among these distances:
7 3 0.04
8 20 0.26
9 40 0.53
10 5 0.07
11 3 0.04
12 5 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (9 bp):
AATATATAT
Found at i:35344 original size:13 final size:13
Alignment explanation
Indices: 35228--35346 Score: 64
Period size: 13 Copynumber: 9.8 Consensus size: 13
35218 TTATTATAAT
35228 ATATATAATTATA
1 ATATATAATTATA
35241 AT-TATAATT-T-
1 ATATATAATTATA
*
35251 ATATAATAAATAT-
1 ATAT-ATAATTATA
*
35264 ATATA-AAGTA-A
1 ATATATAATTATA
35275 ATATATAATTACT-
1 ATATATAATTA-TA
*
35288 TTATATATATTAT-
1 ATATATA-ATTATA
35301 ATATATAATATATA
1 ATATATAAT-TATA
* *
35315 A-A-GTAA--ACA
1 ATATATAATTATA
*
35324 ACATATAATTATA
1 ATATATAATTATA
35337 ATATATAATT
1 ATATATAATT
35347 TATATTTATT
Statistics
Matches: 82, Mismatches: 10, Indels: 28
0.68 0.08 0.23
Matches are distributed among these distances:
9 3 0.04
10 3 0.04
11 14 0.17
12 22 0.27
13 35 0.43
14 5 0.06
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.43
Consensus pattern (13 bp):
ATATATAATTATA
Found at i:36484 original size:23 final size:23
Alignment explanation
Indices: 36441--36484 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
36431 TCTCATTATC
*
36441 AAATGATAAAATATTAGAAAAGA
1 AAATGATAAAATAATAGAAAAGA
*
36464 AAATTATAATAATAATA-AAAA
1 AAATGATAA-AATAATAGAAAA
36485 TAAATAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (23 bp):
AAATGATAAAATAATAGAAAAGA
Found at i:46040 original size:25 final size:26
Alignment explanation
Indices: 46007--46056 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
45997 ATGTCTAGTT
46007 TAAAGATGACGAAAATGCCCCTGGCG
1 TAAAGATGACGAAAATGCCCCTGGCG
46033 TAAA-ATGACGAAAATGCCCCTGGC
1 TAAAGATGACGAAAATGCCCCTGGC
46057 AATTTCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (26 bp):
TAAAGATGACGAAAATGCCCCTGGCG
Found at i:60038 original size:1 final size:1
Alignment explanation
Indices: 60032--60065 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
60022 CTCACATGTC
60032 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
60066 AATAAAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.