Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016044.1 Corchorus olitorius cultivar O-4 contig16077, 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: 67161
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3456 original size:16 final size:15
Alignment explanation
Indices: 3435--3474 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3425 TTACTTTGCT
3435 TTGTTTTCTAGTATAA
1 TTGTTTTCT-GTATAA
* *
3451 TTGTTTTCTTTTTAA
1 TTGTTTTCTGTATAA
3466 TTGTTTTCT
1 TTGTTTTCT
3475 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (15 bp):
TTGTTTTCTGTATAA
Found at i:3468 original size:15 final size:15
Alignment explanation
Indices: 3448--3476 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3438 TTTTCTAGTA
3448 TAATTGTTTTCTTTT
1 TAATTGTTTTCTTTT
3463 TAATTGTTTTCTTT
1 TAATTGTTTTCTTT
3477 CAACCTCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TAATTGTTTTCTTTT
Found at i:3795 original size:26 final size:24
Alignment explanation
Indices: 3739--3806 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 24
3729 AAGTTTTGTG
3739 TTTTGCGTCA-AGAAAAAAAAAGTT
1 TTTTGCGTCATA-AAAAAAAAAGTT
*
3763 TTTTGCGTTATAATAAAAAAAA-TT
1 TTTTGCGTCATAA-AAAAAAAAGTT
3787 GTTTCTGCGTCATAAAAAAA
1 -TTT-TGCGTCATAAAAAAA
3807 TATTTTCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 12 0.32
25 17 0.45
26 9 0.24
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (24 bp):
TTTTGCGTCATAAAAAAAAAAGTT
Found at i:10101 original size:15 final size:16
Alignment explanation
Indices: 10068--10107 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
10058 TTACTTTGCT
10068 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
10084 TTGTTTTCTA-TTTAA
1 TTGTTTTCTAGTATAA
10099 TTGTTTTCT
1 TTGTTTTCT
10108 TTCAACCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.65
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:11118 original size:3 final size:3
Alignment explanation
Indices: 11110--11147 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
11100 GTTACTAACC
11110 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11148 TTTCAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:15622 original size:21 final size:21
Alignment explanation
Indices: 15589--15637 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
15579 AGGAATTGTA
**
15589 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
15609 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
15630 GCATTCCT
1 GC-TTCCT
15638 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:25229 original size:72 final size:72
Alignment explanation
Indices: 25112--25309 Score: 281
Period size: 72 Copynumber: 2.8 Consensus size: 72
25102 CTTCTTCATC
25112 GCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATCATCAC
1 GCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATCATCAC
25177 CTTAATT
66 CTTAATT
* * * **
25184 GCGATTGTAGCCGAAGCAGTTCCCACATTTGGCAGTCCTTCGCACAATTCTTATATGATCATCTT
1 GCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATCATCAC
* *
25249 TTTCATT
66 CTTAATT
* * ** *
25256 GTGATTGTAGTCGAGGCAGTTCCCACA-TTGATAGTCCTTCGCATAATCCTTACA
1 GCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
25310 ACTACCTTCC
Statistics
Matches: 111, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
71 22 0.20
72 89 0.80
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.32
Consensus pattern (72 bp):
GCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATCATCAC
CTTAATT
Found at i:25975 original size:16 final size:16
Alignment explanation
Indices: 25954--25991 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
25944 CCTGCCACAA
*
25954 CAGAATGTTACCGCAG
1 CAGAATGTCACCGCAG
25970 CAGAATGTCACCGCAG
1 CAGAATGTCACCGCAG
*
25986 CGGAAT
1 CAGAAT
25992 ATACAAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (16 bp):
CAGAATGTCACCGCAG
Found at i:28580 original size:44 final size:43
Alignment explanation
Indices: 28532--28823 Score: 308
Period size: 44 Copynumber: 6.8 Consensus size: 43
28522 CCCCCTCCCC
28532 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTCTCT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCT-TCT
* * * * * *
28576 AAAGTCCTCAAACACATTTATAACATAGAGGC-A-TCTATACA
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTTCT
28617 AAAGTCCCCCAAACACATTTATAACACAGGGGCAATTCTCTTTCT
1 AAAGT-CCCCAAACACATTTATAACACAGGGGCAATTCTC-TTCT
* * * * *
28662 AAAGTCCTCAAACACATTTATAACACAGAGGC-A-TCTATACG
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTTCT
*
28703 AAAGTCCCCAAACACATTTATAGCACAGGGGCAATTCTCTTTCT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTC-TTCT
* ** * *
28747 AAAGTCCTCAAACACATTTATAACACAGATGC-A-TCTATACT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTTCT
* ** * *
28788 AAAGTTCGTAAACACAATTATAACACAAGGGCAATT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATT
28824 TCTATATGGC
Statistics
Matches: 203, Mismatches: 36, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
41 65 0.32
42 36 0.18
43 8 0.04
44 87 0.43
45 7 0.03
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (43 bp):
AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTTCT
Found at i:28759 original size:85 final size:85
Alignment explanation
Indices: 28532--28823 Score: 476
Period size: 85 Copynumber: 3.4 Consensus size: 85
28522 CCCCCTCCCC
*
28532 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTCTCTAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTTTCTAAAGTCCTCAAACACATTTAT
*
28597 AACATAGAGGCATCTATACA
66 AACACAGAGGCATCTATACA
28617 AAAGTCCCCCAAACACATTTATAACACAGGGGCAATTCTCTTTCTAAAGTCCTCAAACACATTTA
1 AAAGT-CCCCAAACACATTTATAACACAGGGGCAATTCTCTTTCTAAAGTCCTCAAACACATTTA
*
28682 TAACACAGAGGCATCTATACG
65 TAACACAGAGGCATCTATACA
*
28703 AAAGTCCCCAAACACATTTATAGCACAGGGGCAATTCTCTTTCTAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTTTCTAAAGTCCTCAAACACATTTAT
* *
28768 AACACAGATGCATCTATACT
66 AACACAGAGGCATCTATACA
* ** * *
28788 AAAGTTCGTAAACACAATTATAACACAAGGGCAATT
1 AAAGTCCCCAAACACATTTATAACACAGGGGCAATT
28824 TCTATATGGC
Statistics
Matches: 194, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
85 112 0.58
86 82 0.42
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (85 bp):
AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTTTCTAAAGTCCTCAAACACATTTAT
AACACAGAGGCATCTATACA
Found at i:32301 original size:18 final size:18
Alignment explanation
Indices: 32278--32334 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 18
32268 TGATTTACTT
32278 ATTTGATACTAAATCTTC
1 ATTTGATACTAAATCTTC
*
32296 ATTTGATTTATAATAAATCTTC
1 ATTTG----ATACTAAATCTTC
*
32318 ATTTGATACTAACTCTT
1 ATTTGATACTAAATCTT
32335 GTGGAGATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 15 0.47
22 17 0.53
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.47
Consensus pattern (18 bp):
ATTTGATACTAAATCTTC
Found at i:32312 original size:22 final size:23
Alignment explanation
Indices: 32278--32324 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
32268 TGATTTACTT
*
32278 ATTTGATACTAAATCTTCATTTG
1 ATTTGATAATAAATCTTCATTTG
32301 ATTT-ATAATAAATCTTCATTTG
1 ATTTGATAATAAATCTTCATTTG
32323 AT
1 AT
32325 ACTAACTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (23 bp):
ATTTGATAATAAATCTTCATTTG
Found at i:34286 original size:37 final size:37
Alignment explanation
Indices: 34236--34310 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
34226 GCATCTTTGG
34236 CATCTCCTTGGTGCTTGAAACATGTTGTGTGATATCT
1 CATCTCCTTGGTGCTTGAAACATGTTGTGTGATATCT
34273 CATCTCCTTGGTGCTTGAAACATGTTGTGTGATATCT
1 CATCTCCTTGGTGCTTGAAACATGTTGTGTGATATCT
34310 C
1 C
34311 CTTGATCTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.40
Consensus pattern (37 bp):
CATCTCCTTGGTGCTTGAAACATGTTGTGTGATATCT
Found at i:40176 original size:18 final size:18
Alignment explanation
Indices: 40153--40221 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
40143 TACAAAATAT
40153 TGTTCCACTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
* * *
40171 TGTTCCACTTCTGCAGAA
1 TGTTCCACTGCCGCAGGA
* * *
40189 TATTGCATTGCCGCAGGA
1 TGTTCCACTGCCGCAGGA
*
40207 TGTTCTACTGCCGCA
1 TGTTCCACTGCCGCA
40222 AGAACCTTTA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.29
Consensus pattern (18 bp):
TGTTCCACTGCCGCAGGA
Found at i:42946 original size:22 final size:22
Alignment explanation
Indices: 42921--43312 Score: 148
Period size: 22 Copynumber: 17.7 Consensus size: 22
42911 ATGATCTCTT
42921 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCA
* **
42943 TATGAAATTTTAATAACGAT-A
1 TATGAAATTTTGATAACCTTCA
* * * **
42964 CTATGCAATTTGGAGAACCTTTT
1 -TATGAAATTTTGATAACCTTCA
* * *
42987 TGTCAATATTTT-TTAACCTTC-
1 TATGAA-ATTTTGATAACCTTCA
* * * *
43008 TCATAAAATTTTGTTAACCTCCC
1 T-ATGAAATTTTGATAACCTTCA
* *
43031 TAAGGAATTTTGA-AGACC-TCA
1 TATGAAATTTTGATA-ACCTTCA
43052 CTATGAAATTTTGATAA-CTTCCCA
1 -TATGAAATTTTGATAACCTT--CA
**
43076 -ATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTTCA
* * *
43097 CTATGAGATGTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTTCA
* * * *
43120 TATGATATATTGATAACC-ACGT
1 TATGAAATTTTGATAACCTTC-A
* * * *
43142 TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTTCA
43164 TATG-AATTGTTAGTAATAACAC-TC-
1 TATGAAATT-TT-G--ATAAC-CTTCA
* *
43188 --TGAAATTTTGATAATC-ACA
1 TATGAAATTTTGATAACCTTCA
* * *
43207 CTATGAAATTGTGATAACC-ACGC
1 -TATGAAATTTTGATAACCTTC-A
*
43230 TATGAAATTTTGATAAACCTTCT
1 TATGAAATTTTGAT-AACCTTCA
* * *
43253 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCA
* *
43276 TATAAAATTTTGATAACCGTCA
1 TATGAAATTTTGATAACCTTCA
43298 TATGAAATTTTGATA
1 TATGAAATTTTGATA
43313 TCCTCCCTGA
Statistics
Matches: 276, Mismatches: 64, Indels: 60
0.69 0.16 0.15
Matches are distributed among these distances:
18 2 0.01
19 4 0.01
21 17 0.06
22 177 0.64
23 67 0.24
24 3 0.01
25 5 0.02
26 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:43061 original size:44 final size:45
Alignment explanation
Indices: 43013--43312 Score: 167
Period size: 44 Copynumber: 6.7 Consensus size: 45
43003 CCTTCTCATA
* * *
43013 AAATTTTGTTAACCTCCCTAA-GGAATTTTGA-AGACC-TCACTATG
1 AAATTTTGATAACCTCCC-AATGAAATTTTGATA-ACCAACACTATG
*
43057 AAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACACTATG
1 AAATTTTGATAACCTCCCAATGAAATTTTGATAACCAACACTATG
* * * * **
43102 AGATGTTGATAACCT-CCATATGATATATTGATAACC-ACGTTATG
1 AAATTTTGATAACCTCCCA-ATGAAATTTTGATAACCAACACTATG
* * * * *
43146 AAAATTTAAAAACCT-CCATATG-AATTGTT-AGTAA-TAACACTCTG
1 AAATTTTGATAACCTCCCA-ATGAAATT-TTGA-TAACCAACACTATG
* * * * * *
43190 AAATTTTGATAATCACACTATGAAATTGTGATAACC-ACGCTATG
1 AAATTTTGATAACCTCCCAATGAAATTTTGATAACCAACACTATG
* ** * * * *
43234 AAATTTTGATAAACCTTCTTATAAAATTTTGATAAACC-TCCCTATA
1 AAATTTTGAT-AACCTCCCAATGAAATTTTGAT-AACCAACACTATG
43280 AAATTTTGATAACCGT--CATATGAAATTTTGATA
1 AAATTTTGATAACC-TCCCA-ATGAAATTTTGATA
43313 TCCTCCCTGA
Statistics
Matches: 195, Mismatches: 46, Indels: 30
0.72 0.17 0.11
Matches are distributed among these distances:
43 5 0.03
44 98 0.50
45 72 0.37
46 20 0.10
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (45 bp):
AAATTTTGATAACCTCCCAATGAAATTTTGATAACCAACACTATG
Found at i:43260 original size:23 final size:23
Alignment explanation
Indices: 43234--43312 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 23
43224 CCACGCTATG
*
43234 AAATTTTGATAAACCTTCTTATA
1 AAATTTTGATAAACCTTCATATA
* *
43257 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTTCATATA
* *
43280 AAATTTTGAT-AACCGTCATATG
1 AAATTTTGATAAACCTTCATATA
43302 AAATTTTGATA
1 AAATTTTGATA
43313 TCCTCCCTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
22 18 0.37
23 31 0.63
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAACCTTCATATA
Found at i:43571 original size:22 final size:22
Alignment explanation
Indices: 43410--43842 Score: 160
Period size: 22 Copynumber: 19.9 Consensus size: 22
43400 CCAGAAATAC
* **
43410 CACTATGAAATTTTGGTAATAA
1 CACTATGAAATTTTGATAACCA
* * * *
43432 CATTTTGAAAATTTGATAA-CT
1 CACTATGAAATTTTGATAACCA
** * *
43453 CTTTATGAAATTTTGAAAACCT
1 CACTATGAAATTTTGATAACCA
* * * * *
43475 CTCTATAAAATTTTGTTGACCC
1 CACTATGAAATTTTGATAACCA
* *
43497 CTCTATGAAATTTTGATAATCA
1 CACTATGAAATTTTGATAACCA
* ** * *
43519 CATTGCGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * *
43541 CGCTTTGAAATTTTGATAACAA
1 CACTATGAAATTTTGATAACCA
* **
43563 CACTATGAAATTTTAATAATCTT
1 CACTATGAAATTTTGATAA-CCA
* *
43586 C-CTAT-AAATTTTCAT----T
1 CACTATGAAATTTTGATAACCA
* * * *
43602 CTCTAAGAAATTTCGATAATCA
1 CACTATGAAATTTTGATAACCA
* *
43624 CTCTATGAGA-TTTGATAACCA
1 CACTATGAAATTTTGATAACCA
* * *
43645 -TCTATCAAATTTTTG-TACTCCTTA
1 CACTATGAAA-TTTTGATA-ACC--A
* * *
43669 TGA-AATTGAAACTTTT-ATAACCTT
1 -CACTA-TGAAA-TTTTGATAACC-A
43693 CA-TATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCA
**
43714 CACTAAAAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCA
*
43736 CACTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCA
* * * *
43758 CCCCATGAAATATT-AGTAACCT
1 CACTATGAAATTTTGA-TAACCA
*
43780 C-CTTATGAAATTTTGTTAACCA
1 CAC-TATGAAATTTTGATAACCA
*
43802 CACTATGAAATTCTT-ATAACCT
1 CACTATGAAATT-TTGATAACCA
* *
43824 CGCTATGACATTTTGATAA
1 CACTATGAAATTTTGATAA
43843 TCTCTTTGAT
Statistics
Matches: 309, Mismatches: 77, Indels: 50
0.71 0.18 0.11
Matches are distributed among these distances:
16 2 0.01
17 3 0.01
18 8 0.03
20 7 0.02
21 45 0.15
22 222 0.72
23 7 0.02
24 2 0.01
25 3 0.01
26 10 0.03
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCA
Found at i:43656 original size:20 final size:22
Alignment explanation
Indices: 43609--43656 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
43599 ATTCTCTAAG
* *
43609 AAATTTCGATAATCACTCTATG
1 AAATTTCGATAACCACTCTATC
*
43631 AGATTT-GATAACCA-TCTATC
1 AAATTTCGATAACCACTCTATC
43651 AAATTT
1 AAATTT
43657 TTGTACTCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 10 0.45
21 7 0.32
22 5 0.23
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (22 bp):
AAATTTCGATAACCACTCTATC
Found at i:43743 original size:44 final size:42
Alignment explanation
Indices: 43675--44080 Score: 199
Period size: 44 Copynumber: 9.4 Consensus size: 42
43665 CTTATGAAAT
*
43675 TGAAACTTTTATAACCTTCATATGAAATTTTGATAACCACACTA
1 TGAAA-TTTTATAACC-TCCTATGAAATTTTGATAACCACACTA
** * * * *
43719 AAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCA
1 TGAAATTTT-ATAACCTC-CTATGAAATTTTGATAACCACACTA
* *
43763 TGAAATATTAGTAACCTCCTTATGAAATTTTGTTAACCACACTA
1 TGAAATTTTA-TAACCTCC-TATGAAATTTTGATAACCACACTA
* *
43807 TGAAATTCTTATAACCTCGCTATGACATTTTGAT----A-A-TC
1 TGAAATT-TTATAACCTC-CTATGAAATTTTGATAACCACACTA
* * * * *
43845 T---CTTTGATAACCTTTCTATAAAATTGTGATAACCACACTA
1 TGAAATTTTATAACC-TCCTATGAAATTTTGATAACCACACTA
* * * *
43885 TGAAATTTCAATAACTTTCCTAAGAAATTTTAATAACCTGATC-CTA
1 TGAAATTT-TATAAC-CTCCTATGAAATTTTGATAACC--A-CACTA
* **
43931 TGAAATTTTTTGGTAA-CTACACTATGAAATTTTGATAACC-TTCTCA
1 TGAAA--TTTT-ATAACCT-C-CTATGAAATTTTGATAACCACACT-A
* * *
43977 TGGAATTTTGATAACCTTCTCATGAAATTTTGATAACCACATTA
1 TGAAATTTT-ATAACCTCCT-ATGAAATTTTGATAACCACACTA
* * * * * *
44021 GGGAATTTTGATAACCTCCTCATGATATTATAATAACCATC-TTA
1 TGAAATTTT-ATAACCTCCT-ATGAAATTTTGATAACCA-CACTA
44065 TGAAATTTTGATAACC
1 TGAAATTTT-ATAACC
44081 ACATAGAGAC
Statistics
Matches: 277, Mismatches: 53, Indels: 64
0.70 0.13 0.16
Matches are distributed among these distances:
34 19 0.07
35 3 0.01
38 3 0.01
39 2 0.01
40 3 0.01
43 12 0.04
44 185 0.67
45 10 0.04
46 15 0.05
47 2 0.01
48 23 0.08
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (42 bp):
TGAAATTTTATAACCTCCTATGAAATTTTGATAACCACACTA
Found at i:43766 original size:66 final size:66
Alignment explanation
Indices: 43696--44083 Score: 185
Period size: 66 Copynumber: 5.6 Consensus size: 66
43686 TAACCTTCAT
43696 ATGAAATTTTGATAACCACAC-TAAAAAATTTTGATAACCACACTATGAAATT-TTGATAACCTC
1 ATGAAATTTTGATAACCAC-CTTAAAAAATTTTGATAACCACACTATGAAATTCTT-ATAACCTC
43759 CCC
64 CCC
* * ** * *
43762 ATGAAATATT-AGTAACCTCCTTATGAAATTTTGTTAACCACACTATGAAATTCTTATAACCTCG
1 ATGAAATTTTGA-TAACCACCTTAAAAAATTTTGATAACCACACTATGAAATTCTTATAACCTCC
*
43826 CT
65 CC
* * *
43828 ATGACATTTTGATAATCTCTTTGATAACCTTTCTATAAAATTGTGATAACCACACTATGAAATT-
1 ATGAAATTTTGATAA-C-C-------ACC--T-TAAAAAATTTTGATAACCACACTATGAAATTC
* * * *
43892 TCAATAACTTTCCT
54 T-TATAACCTCCCC
* * * ** * *
43906 AAGAAATTTTAATAACCTGATCCTATGAAATTTTTTGGTAACTACACTATGAAATT-TTGATAAC
1 ATGAAATTTTGATAACC--A-CCT-TAAAAAATTTTGATAACCACACTATGAAATTCTT-ATAAC
* *
43970 CTTCTC
61 CTCCCC
* ** * ** * * *
43976 ATGGAATTTTGATAACCTTCTCATGAAATTTTGATAACCACATTAGGGAATT-TTGATAACCTCC
1 ATGAAATTTTGATAACCACCTTAAAAAATTTTGATAACCACACTATGAAATTCTT-ATAACCTCC
*
44040 TC
65 CC
* * * * **
44042 ATGATATTATAATAACCATCTTATGAAATTTTGATAACCACA
1 ATGAAATTTTGATAACCACCTTAAAAAATTTTGATAACCACA
44084 TAGAGACAAG
Statistics
Matches: 247, Mismatches: 56, Indels: 38
0.72 0.16 0.11
Matches are distributed among these distances:
65 2 0.01
66 132 0.53
67 6 0.02
68 1 0.00
70 48 0.19
71 2 0.01
72 2 0.01
75 2 0.01
76 1 0.00
77 3 0.01
78 48 0.19
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (66 bp):
ATGAAATTTTGATAACCACCTTAAAAAATTTTGATAACCACACTATGAAATTCTTATAACCTCCC
C
Found at i:43969 original size:22 final size:22
Alignment explanation
Indices: 43860--44035 Score: 90
Period size: 22 Copynumber: 7.8 Consensus size: 22
43850 GATAACCTTT
* * *
43860 CTATAAAATTGTGATAACCACA
1 CTATGAAATTTTGATAACTACA
** *
43882 CTATGAAATTTCAATAACTTTC-
1 CTATGAAATTTTGATAAC-TACA
* *
43904 CTAAGAAATTTTAATAACCTGATC-
1 CTATGAAATTTTGATAA-CT-A-CA
*
43928 CTATGAAATTTTTTGGTAACTACA
1 CTATGAAA--TTTTGATAACTACA
* *
43952 CTATGAAATTTTGATAACCTTCT
1 CTATGAAATTTTGATAA-CTACA
* * *
43975 C-ATGGAATTTTGATAACCTTCT
1 CTATGAAATTTTGATAA-CTACA
*
43997 C-ATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACTACA
* * *
44018 TTAGGGAATTTTGATAAC
1 CTATGAAATTTTGATAAC
44036 CTCCTCATGA
Statistics
Matches: 122, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.02
22 87 0.71
23 7 0.06
24 17 0.14
25 2 0.02
26 7 0.06
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (22 bp):
CTATGAAATTTTGATAACTACA
Found at i:44084 original size:66 final size:66
Alignment explanation
Indices: 43958--44084 Score: 193
Period size: 66 Copynumber: 1.9 Consensus size: 66
43948 TACACTATGA
* * * *
43958 AATTTTGATAACCTTCTCATGGAATTTTGATAACCTTCTCATGAAATTTTGATAACCACATTAGG
1 AATTTTGATAACCTCCTCATGGAATTATAATAACCATCTCATGAAATTTTGATAACCACATTAGG
44023 G
66 G
*
44024 AATTTTGATAACCTCCTCAT-GATATTATAATAACCATCTTATGAAATTTTGATAACCACAT
1 AATTTTGATAACCTCCTCATGGA-ATTATAATAACCATCTCATGAAATTTTGATAACCACAT
44085 AGAGACAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 2 0.04
66 53 0.96
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (66 bp):
AATTTTGATAACCTCCTCATGGAATTATAATAACCATCTCATGAAATTTTGATAACCACATTAGG
G
Found at i:48345 original size:29 final size:30
Alignment explanation
Indices: 48268--48334 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
48258 CATTCCAAGG
* *
48268 CTCAAAAACCATCTCTCAGAGATTCCACAT
1 CTCAAAAACCATCTCTTAGAGATTACACAT
48298 CTCAAAAACCATCTCTTAGAGATTACACAT
1 CTCAAAAACCATCTCTTAGAGATTACACAT
48328 CTCAAAA
1 CTCAAAA
48335 CATTTTCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.40, C:0.30, G:0.06, T:0.24
Consensus pattern (30 bp):
CTCAAAAACCATCTCTTAGAGATTACACAT
Found at i:63031 original size:6 final size:6
Alignment explanation
Indices: 63020--63044 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
63010 GGGCTTTAAA
63020 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
63045 TGAGAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:67138 original size:19 final size:20
Alignment explanation
Indices: 67114--67151 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
67104 ATTTATCATT
67114 TAATGGGTAG-TTTTATTTA
1 TAATGGGTAGTTTTTATTTA
67133 TAATGGGTAGTTTTTATTT
1 TAATGGGTAGTTTTTATTT
67152 TGTTTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (20 bp):
TAATGGGTAGTTTTTATTTA
Done.