Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013635.1 Corchorus olitorius cultivar O-4 contig13668, 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: 71111
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--44 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
43 CT
1 CT
45 AAGTCTCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3921 original size:25 final size:25
Alignment explanation
Indices: 3887--3938 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
3877 ATTTATCTTA
3887 ATATGAAATAACTATTGGAGATTCC
1 ATATGAAATAACTATTGGAGATTCC
*
3912 ATATGAAATAATTATTGGAGATTCC
1 ATATGAAATAACTATTGGAGATTCC
3937 AT
1 AT
3939 TTGATTTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (25 bp):
ATATGAAATAACTATTGGAGATTCC
Found at i:6695 original size:19 final size:19
Alignment explanation
Indices: 6671--6708 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6661 TGGCGGCTAG
* *
6671 GGTTTTGAGAAGAATAAGA
1 GGTTTTCAGAAAAATAAGA
6690 GGTTTTCAGAAAAATAAGA
1 GGTTTTCAGAAAAATAAGA
6709 AAGGAAGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.26, T:0.26
Consensus pattern (19 bp):
GGTTTTCAGAAAAATAAGA
Found at i:8283 original size:43 final size:43
Alignment explanation
Indices: 8127--8271 Score: 227
Period size: 43 Copynumber: 3.4 Consensus size: 43
8117 ATCTCTTTTT
* *
8127 CAAAAATGCCCCTTCCTGGTTGGAAAGTCCCTATTTTCATTTC
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTC
*
8170 CAAAAATGACCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTC
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTC
* * * *
8213 CAAAAATGCCTCTTCCTGGTTGGAAGGTTCTTGTTTACATTTC
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTC
8256 CAAAAATGCCCCTTCC
1 CAAAAATGCCCCTTCC
8272 CAGTCGGAAG
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 93 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (43 bp):
CAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTC
Found at i:8388 original size:47 final size:48
Alignment explanation
Indices: 8265--8594 Score: 434
Period size: 48 Copynumber: 6.8 Consensus size: 48
8255 CCAAAAATGC
* *
8265 CCCTTCCCAGTCGGAAGGTGTTGTTTTCAATGTTTTAATCCCGTTTTG
1 CCCTTCCCAGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTCGTTTTG
* * * *
8313 CCCCTCCCCACT-GGGAGGTGTTGTTTTCAATGTTTTATTCTCGTTCTG
1 -CCCTTCCCAGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTCGTTTTG
* * *
8361 CCCTTCCCACT-GGGAGGTGTTGTTTTCAATGTTTTATTCTCGTTCTG
1 CCCTTCCCAGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTCGTTTTG
**
8408 CCCTTCCTGGTCGGAAGGTGTTGTTTTCAATGTTTTATTATTCTCGTTTTG
1 CCCTTCCCAGTCGGAAGGTGTTGTTTTCAATG--TT-TTATTCTCGTTTTG
8459 CCCTTCCC-GATCGGAAGGTGTTGTTTTCAATGTTTTATTCTCGTTTTG
1 CCCTTCCCAG-TCGGAAGGTGTTGTTTTCAATGTTTTATTCTCGTTTTG
*
8507 CCCTTCCCAGTCGGAAGGTGTTGTTTTCATTGTTTTATTC-CTGTTTTG
1 CCCTTCCCAGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTC-GTTTTG
* * * *
8555 CCCTTCCCGGTCGGAATGTGTTGTTTTCAATATTTCATTC
1 CCCTTCCCAGTCGGAAGGTGTTGTTTTCAATGTTTTATTC
8595 ATGTCTTTAA
Statistics
Matches: 255, Mismatches: 19, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
47 55 0.22
48 143 0.56
49 12 0.05
50 3 0.01
51 42 0.16
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (48 bp):
CCCTTCCCAGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTCGTTTTG
Found at i:8674 original size:48 final size:48
Alignment explanation
Indices: 8603--9018 Score: 276
Period size: 48 Copynumber: 8.2 Consensus size: 48
8593 TCATGTCTTT
*
8603 AATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
1 AATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
* ** *
8651 AATGTTTTATTCTTGTTTTGCCCTTCCAAGTCGGAAGGTGTGGTTTTC
1 AATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
* *
8699 ATTGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGCTGTTGTTTTC
1 AATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
* * * *** * * ** **** *** * ***
8747 CATATTTCATTCCTGTCTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGG
1 AATGTTTTATTCCTGT-TT---TG--CCCTTCCCGGTCGGAAGGTGTTGTTTTC
* * **
8801 AAGGTGTTATT-TTCAATGTTTTATTCTCGTTTTGCCCTTCTCGGTTAGAAGGTGTTGTTTTC
1 AA--TGTT-TTATTC-CTG--------T--T-TTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
*
8863 AATGTTTTATTCCTGTTTCGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
1 AATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
* **
8911 AATATTTTATTCCTGTTTTGCCCTTCCTAGTCGGAAGGTGTTGTTTTC
1 AATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
* *
8959 AATGTTTTATTCTTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTC
1 AATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
* *
9007 AATATTTCATTC
1 AATGTTTTATTC
9019 TTGTCTTCAA
Statistics
Matches: 277, Mismatches: 70, Indels: 42
0.71 0.18 0.11
Matches are distributed among these distances:
48 223 0.81
49 3 0.01
51 1 0.00
52 2 0.01
54 11 0.04
56 6 0.02
57 3 0.01
59 4 0.01
60 7 0.03
62 12 0.04
64 2 0.01
65 1 0.00
66 1 0.00
67 1 0.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (48 bp):
AATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
Found at i:8697 original size:116 final size:116
Alignment explanation
Indices: 8487--8699 Score: 354
Period size: 116 Copynumber: 1.8 Consensus size: 116
8477 TGTTGTTTTC
* *
8487 AATGTTTTATTCTCGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCATTGTTTTATTCCTGTT
1 AATGTTTTATTCCCGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAATGTTTTATTCCTGTT
** * *
8552 TTGCCCTTCCCGGTCGGAATGTGTTGTTTTCAATATTTCATTCATGTCTTT
66 TTGCCCTTCCAAGTCGGAAGGTGTGGTTTTCAATATTTCATTCATGTCTTT
* *
8603 AATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTTGTT
1 AATGTTTTATTCCCGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAATGTTTTATTCCTGTT
8668 TTGCCCTTCCAAGTCGGAAGGTGTGGTTTTCA
66 TTGCCCTTCCAAGTCGGAAGGTGTGGTTTTCA
8700 TTGTTTTATT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
116 89 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (116 bp):
AATGTTTTATTCCCGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAATGTTTTATTCCTGTT
TTGCCCTTCCAAGTCGGAAGGTGTGGTTTTCAATATTTCATTCATGTCTTT
Found at i:8768 original size:116 final size:116
Alignment explanation
Indices: 8648--8878 Score: 329
Period size: 116 Copynumber: 2.0 Consensus size: 116
8638 AGGTGTTGTT
* * *
8648 TTCAATGTTTTATTCTTGTTTTGCCCTTCCAAGTCGGAAGGTGTGGTTTTCATTGTTTTATTC-C
1 TTCAATGTTTTATTCCTGTTTTGCCCTTCCAAGTCGGAAGGTGTGATTTTCAATGTTTTATTCTC
* *
8712 TGTTTTGCCCTTCCCGGTCGGAAGCTGTTGTTTTCCATATTTCATTCCTGTC
66 -GTTTTGCCCTTCCCGGTCAGAAGCTGTTGTTTTCAATATTTCATTCCTGTC
** *
8764 TTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTATTTTCAATGTTTTATTCTC
1 TTCAATGTTTTATTCCTGTTTTGCCCTTCCAAGTCGGAAGGTGTGATTTTCAATGTTTTATTCTC
* * * * *
8829 GTTTTGCCCTTCTCGGTTAGAAGGTGTTGTTTTCAATGTTTTATTCCTGT
66 GTTTTGCCCTTCCCGGTCAGAAGCTGTTGTTTTCAATATTTCATTCCTGT
8879 TTCGCCCTTC
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
116 100 0.99
117 1 0.01
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (116 bp):
TTCAATGTTTTATTCCTGTTTTGCCCTTCCAAGTCGGAAGGTGTGATTTTCAATGTTTTATTCTC
GTTTTGCCCTTCCCGGTCAGAAGCTGTTGTTTTCAATATTTCATTCCTGTC
Found at i:8925 original size:164 final size:163
Alignment explanation
Indices: 8433--8926 Score: 781
Period size: 164 Copynumber: 3.0 Consensus size: 163
8423 AGGTGTTGTT
* *
8433 TTCAATGTTTTATTATTCTCGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAATGTTTTATT
1 TTCAATGTTTTA-T-TCCT-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATT
8498 CTCGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTTTTCATTGTTTTATTCCTGTTTTGCCCTTCCC
63 CTCGTTTTGCCCTT-CCAGTCGGAAGGTGTTGTTTTCATTGTTTTATTCCTGTTTTGCCCTTCCC
* *
8563 GGTCGGAATGTGTTGTTTTCAATATTTCATTCATGTC
127 GGTCGGAAGGTGTTGTTTTCAATATTTCATTCCTGTC
* * *
8600 TTTAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTT
1 TTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTC
*
8665 GTTTTGCCCTTCCAAGTCGGAAGGTGTGGTTTTCATTGTTTTATTCCTGTTTTGCCCTTCCCGGT
66 GTTTTGCCCTTCC-AGTCGGAAGGTGTTGTTTTCATTGTTTTATTCCTGTTTTGCCCTTCCCGGT
* *
8730 CGGAAGCTGTTGTTTTCCATATTTCATTCCTGTC
130 CGGAAGGTGTTGTTTTCAATATTTCATTCCTGTC
*
8764 TTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTATTTTCAATGTTTTATTCTC
1 TTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTC
* ** * *
8829 GTTTTGCCCTTCTCGGTTAGAAGGTGTTGTTTTCAATGTTTTATTCCTGTTTCGCCCTTCCCGGT
66 GTTTTGCCCTTC-CAGTCGGAAGGTGTTGTTTTCATTGTTTTATTCCTGTTTTGCCCTTCCCGGT
*
8894 CGGAAGGTGTTGTTTTCAATATTTTATTCCTGT
130 CGGAAGGTGTTGTTTTCAATATTTCATTCCTGT
8927 TTTGCCCTTC
Statistics
Matches: 302, Mismatches: 23, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
163 2 0.01
164 285 0.94
165 3 0.01
166 1 0.00
167 11 0.04
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (163 bp):
TTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTC
GTTTTGCCCTTCCAGTCGGAAGGTGTTGTTTTCATTGTTTTATTCCTGTTTTGCCCTTCCCGGTC
GGAAGGTGTTGTTTTCAATATTTCATTCCTGTC
Found at i:9022 original size:48 final size:48
Alignment explanation
Indices: 8764--9018 Score: 386
Period size: 48 Copynumber: 5.3 Consensus size: 48
8754 CATTCCTGTC
*
8764 TTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTATT
1 TTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
* **
8812 TTCAATGTTTTATT-CTCGTTTTGCCCTTCTCGGTTAGAAGGTGTTGTT
1 TTCAATGTTTTATTCCT-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
*
8860 TTCAATGTTTTATTCCTGTTTCGCCCTTCCCGGTCGGAAGGTGTTGTT
1 TTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
* **
8908 TTCAATATTTTATTCCTGTTTTGCCCTTCCTAGTCGGAAGGTGTTGTT
1 TTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
* *
8956 TTCAATGTTTTATTCTTGTTTTGCCCTTCCCAGTCGGAAGGTGTTGTT
1 TTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
* *
9004 TTCAATATTTCATTC
1 TTCAATGTTTTATTC
9019 TTGTCTTCAA
Statistics
Matches: 188, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
47 2 0.01
48 184 0.98
49 2 0.01
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (48 bp):
TTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
Found at i:11151 original size:22 final size:24
Alignment explanation
Indices: 11108--11151 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
11098 AGCATTATTA
*
11108 TGAAAACTAATATTATTGAATCGT
1 TGAAAACTAATATTATTCAATCGT
11132 TGAAAAC-AAT-TTATTCAATC
1 TGAAAACTAATATTATTCAATC
11152 ATACACCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 3 0.16
24 7 0.37
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (24 bp):
TGAAAACTAATATTATTCAATCGT
Found at i:21701 original size:29 final size:31
Alignment explanation
Indices: 21654--21728 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
21644 TCTTATAGCA
*
21654 AAGGGATTTTTTTGGCCC-AAA-AAAAAGAT
1 AAGGGATTTATTTGGCCCAAAATAAAAAGAT
* * *
21683 GAGGGATTTATTTGTCCCAAAATAAAAAGGT
1 AAGGGATTTATTTGGCCCAAAATAAAAAGAT
21714 AAGGGATTTATTTGG
1 AAGGGATTTATTTGG
21729 TATTTAAGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 15 0.39
30 3 0.08
31 20 0.53
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (31 bp):
AAGGGATTTATTTGGCCCAAAATAAAAAGAT
Found at i:23963 original size:2 final size:2
Alignment explanation
Indices: 23952--23985 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
23942 CCTCAATTTA
23952 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23986 ATTTCCATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27838 original size:42 final size:42
Alignment explanation
Indices: 27748--27842 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
27738 CACGAGTTAA
* * * *
27748 ACTTACGGGACAAACTCAGTTTACAAGTATTTGAAAAGCCAG
1 ACTTATGGGACAAACCCAGTTGACAAGTATTTGAAAAACCAG
* *
27790 ACTTATGGGACAAACCCAGTTGACAATTATTTGAAAAACTAG
1 ACTTATGGGACAAACCCAGTTGACAAGTATTTGAAAAACCAG
**
27832 GTTTATGGGAC
1 ACTTATGGGAC
27843 TGACAACTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (42 bp):
ACTTATGGGACAAACCCAGTTGACAAGTATTTGAAAAACCAG
Found at i:28028 original size:13 final size:13
Alignment explanation
Indices: 28010--28034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28000 TTGGAATTCC
28010 AAATAATATTTAT
1 AAATAATATTTAT
28023 AAATAATATTTA
1 AAATAATATTTA
28035 GAATATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:28436 original size:19 final size:19
Alignment explanation
Indices: 28408--28473 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
28398 TGGGCTATGA
*
28408 AGTTTTTGAATAGAGGTCT
1 AGTTTATGAATAGAGGTCT
**
28427 AGTTTATGAATAG-GCCCT
1 AGTTTATGAATAGAGGTCT
* *
28445 TGTGTAT---TAGAGGTCT
1 AGTTTATGAATAGAGGTCT
28461 AGTTTATGAATAG
1 AGTTTATGAATAG
28474 GCCCAAAAGA
Statistics
Matches: 34, Mismatches: 9, Indels: 8
0.67 0.18 0.16
Matches are distributed among these distances:
15 3 0.09
16 8 0.24
18 8 0.24
19 15 0.44
ACGTcount: A:0.27, C:0.08, G:0.26, T:0.39
Consensus pattern (19 bp):
AGTTTATGAATAGAGGTCT
Found at i:34709 original size:14 final size:14
Alignment explanation
Indices: 34692--34718 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34682 GGTAAAACCT
34692 CAAAAAAAAAAAAC
1 CAAAAAAAAAAAAC
34706 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
34719 GAAGAAGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAAAAC
Found at i:46810 original size:17 final size:17
Alignment explanation
Indices: 46788--46823 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
46778 GTCGATTGTA
46788 CCCAAATTCTTATTAAG
1 CCCAAATTCTTATTAAG
46805 CCCAAATTCTTATTAAG
1 CCCAAATTCTTATTAAG
46822 CC
1 CC
46824 TTGGTTCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (17 bp):
CCCAAATTCTTATTAAG
Found at i:50722 original size:37 final size:35
Alignment explanation
Indices: 50640--50768 Score: 145
Period size: 35 Copynumber: 3.6 Consensus size: 35
50630 TTTTTTTTTT
*
50640 TTTTTAAATTGGGAAAGTTCCCACCAGTTTTTAAG
1 TTTTTAAATTGGGAAAGTTCCCACCAGTTTTAAAG
* *
50675 TTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAG
1 TTTTTAAATTGGGAAAGTTCCCA-CCAGTTTT-AAAG
* *
50712 TTTTTAAATTGGAAAACTTCCCACCAAGTTTT--AG
1 TTTTTAAATTGGGAAAGTTCCCACC-AGTTTTAAAG
* *
50746 TTTTCAATTTAGGGAAAGTTCCC
1 TTTTTAAATT-GGGAAAGTTCCC
50769 GTCATTTTCG
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
34 10 0.13
35 32 0.41
36 8 0.10
37 29 0.37
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (35 bp):
TTTTTAAATTGGGAAAGTTCCCACCAGTTTTAAAG
Found at i:53685 original size:21 final size:21
Alignment explanation
Indices: 53648--53691 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
53638 GCGCCCACAC
* *
53648 GGTTTGTCTGAAGACCCATGT
1 GGTTTGTCTGAACACCCAAGT
*
53669 GGTTTGTCTGATCACCCAAGT
1 GGTTTGTCTGAACACCCAAGT
53690 GG
1 GG
53692 GCAATGTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (21 bp):
GGTTTGTCTGAACACCCAAGT
Found at i:56025 original size:29 final size:30
Alignment explanation
Indices: 55988--56047 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
55978 AATTCTTTCC
* *
55988 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
56017 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
56048 CATGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
31 9 0.33
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.38
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Found at i:57891 original size:21 final size:21
Alignment explanation
Indices: 57865--57924 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
57855 AATGGCGATG
57865 GCACGGGCATGGCCGGTGGTA
1 GCACGGGCATGGCCGGTGGTA
* ** *
57886 GCACGGGCTTAACCGGTGGTG
1 GCACGGGCATGGCCGGTGGTA
*
57907 GCACGGTGTATGGCCGGT
1 GCACGG-GCATGGCCGGT
57925 TGTGGCTTGG
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.18
Consensus pattern (21 bp):
GCACGGGCATGGCCGGTGGTA
Found at i:61484 original size:15 final size:16
Alignment explanation
Indices: 61464--61498 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
61454 TTTAAAAATC
61464 ACAATTAAA-AAGAAA
1 ACAATTAAACAAGAAA
*
61479 ACAATTAAACTAGAAA
1 ACAATTAAACAAGAAA
61495 ACAA
1 ACAA
61499 AGCAAAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (16 bp):
ACAATTAAACAAGAAA
Found at i:62277 original size:11 final size:11
Alignment explanation
Indices: 62261--62286 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
62251 CCTTACCTAA
62261 AAAACTAGAAG
1 AAAACTAGAAG
62272 AAAACTAGAAG
1 AAAACTAGAAG
62283 AAAA
1 AAAA
62287 GATCTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:62904 original size:29 final size:30
Alignment explanation
Indices: 62872--62932 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
62862 AATTCTTTCC
* *
62872 TCTTGAAATAATTCTTCAAT-GTCTTCAAA
1 TCTTCAAATAAGTCTTCAATAGTCTTCAAA
62901 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAGTCTTCAAT-AGTCTTCAAA
62932 T
1 T
62933 ACGAACTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 18 0.64
31 10 0.36
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (30 bp):
TCTTCAAATAAGTCTTCAATAGTCTTCAAA
Found at i:62918 original size:12 final size:12
Alignment explanation
Indices: 62901--62933 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
62891 TGTCTTCAAA
62901 TCTTCAAATAAG
1 TCTTCAAATAAG
*
62913 TCTTC-AATGAG
1 TCTTCAAATAAG
62924 TCTTCAAATA
1 TCTTCAAATA
62934 CGAACTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (12 bp):
TCTTCAAATAAG
Done.