Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014794.1 Corchorus olitorius cultivar O-4 contig14827, 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: 41165
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:203 original size:22 final size:24
Alignment explanation
Indices: 168--226 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
158 ATAAATGTTG
* *
168 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
190 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
213 CTTGATAATATCTT
1 C-TGATAAT-TCTT
227 GCCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 7 0.23
25 2 0.07
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:274 original size:2 final size:2
Alignment explanation
Indices: 267--294 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
257 CCATAACACT
267 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
295 CACATATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1828 original size:22 final size:22
Alignment explanation
Indices: 1801--1848 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1791 ATTACACTAT
*
1801 TTTTGATGACC-TCCTTATGAAA
1 TTTTGATAACCTTCC-TATGAAA
1823 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCTTCCTATGAAA
1845 TTTT
1 TTTT
1849 AACAACGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTTGATAACCTTCCTATGAAA
Found at i:2023 original size:45 final size:44
Alignment explanation
Indices: 1952--2036 Score: 100
Period size: 45 Copynumber: 1.9 Consensus size: 44
1942 CTATAAAATT
* * *
1952 TTGATAACTTCCCAATGAAATTTTGATGATCAACATTATGAGATG
1 TTGATAACCTCCCAATGAAATATTGAT-AACAACATTATGAGATG
* *
1997 TTGATAACCT-CCATATGATATATTGATAACCACATTATGA
1 TTGATAACCTCCCA-ATGAAATATTGATAACAACATTATGA
2037 AAATTTCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
44 14 0.41
45 20 0.59
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (44 bp):
TTGATAACCTCCCAATGAAATATTGATAACAACATTATGAGATG
Found at i:2035 original size:22 final size:23
Alignment explanation
Indices: 1984--2036 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
1974 TTGATGATCA
*
1984 ACATTATGAGATGTTGATAACCT
1 ACATTATGAGATATTGATAACCT
* *
2007 CCA-TATGATATATTGATAACC-
1 ACATTATGAGATATTGATAACCT
2028 ACATTATGA
1 ACATTATGA
2037 AAATTTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 2 0.08
22 21 0.84
23 2 0.08
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (23 bp):
ACATTATGAGATATTGATAACCT
Found at i:2092 original size:22 final size:22
Alignment explanation
Indices: 2058--2113 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2048 CCTCCATTTG
* * *
2058 AATTGTTAGTAATTACACTCTGA
1 AATTGTGA-TAATCACACTATGA
* *
2081 AATTTTGATAATCATACTATGA
1 AATTGTGATAATCACACTATGA
2103 AATTGTGATAA
1 AATTGTGATAA
2114 CCTCGCTATA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (22 bp):
AATTGTGATAATCACACTATGA
Found at i:2122 original size:22 final size:21
Alignment explanation
Indices: 2080--2349 Score: 115
Period size: 22 Copynumber: 12.5 Consensus size: 21
2070 TTACACTCTG
* * *
2080 AAATTTTGATAATCATACTATG
1 AAATTTTGATAA-CCTCCTATA
*
2102 AAATTGTGATAACCTCGCTATA
1 AAATTTTGATAACCTC-CTATA
2124 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AACCT-CCTATA
*
2147 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCC-TATA
* * *
2169 AAATCTTGAT-A---GCTA-C
1 AAATTTTGATAACCTCCTATA
2185 AAATTTTGATAACCTCCCTAT-
1 AAATTTTGATAACCT-CCTATA
* ** *
2206 GAATGTTTGATAACCTAATTATG
1 AAAT-TTTGATAACCT-CCTATA
* * *
2229 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCT-CCTATA
* * * * *
2251 TAATTTTGATCTACATACTATG
1 AAATTTTGAT-AACCTCCTATA
* *
2273 AAATTTTGATAACCCTCTTATG
1 AAATTTTGATAA-CCTCCTATA
* * *
2295 AAATTTTGA-AAACTAAACTATT
1 AAATTTTGATAACCT--CCTATA
*
2317 AAATTTTGATAACCTTC-ATAA
1 AAATTTTGATAACCTCCTAT-A
2338 GAAATTTTGATA
1 -AAATTTTGATA
2350 TCCTTCCTGA
Statistics
Matches: 190, Mismatches: 39, Indels: 38
0.71 0.15 0.14
Matches are distributed among these distances:
16 9 0.05
17 3 0.02
18 1 0.01
20 4 0.02
21 15 0.08
22 128 0.67
23 29 0.15
24 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (21 bp):
AAATTTTGATAACCTCCTATA
Found at i:2129 original size:44 final size:43
Alignment explanation
Indices: 2078--2349 Score: 211
Period size: 44 Copynumber: 6.3 Consensus size: 43
2068 AATTACACTC
* *
2078 TGAAATTTTGATAATCATACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAAACATACTATGAAATTTTGATAACCTC-CTA
* * * *
2122 TAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAAACAT-ACTATGAAATTTTGATAACCTCC-TA
* *
2167 TGAAATCTTGAT-AGC-TAC----AAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAAACATACTATGAAATTTTGATAACCT-CCTA
* * * *
2205 TG-AATGTTTGAT-AACCTAATTATGAAATTTTGTTAATCTCCCTA
1 TGAAAT-TTTGATAAACAT-ACTATGAAATTTTGATAACCT-CCTA
* ** *
2249 TGTAATTTTGATCTACATACTATGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAAACATACTATGAAATTTTGATAA-CCTCCTA
* * *
2293 TGAAATTTTGA-AAACTAAACTATTAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAAAC-ATACTATGAAATTTTGATAACC-TCCTA
*
2337 AGAAATTTTGATA
1 TGAAATTTTGATA
2350 TCCTTCCTGA
Statistics
Matches: 184, Mismatches: 28, Indels: 31
0.76 0.12 0.13
Matches are distributed among these distances:
37 3 0.02
38 26 0.14
39 3 0.02
40 1 0.01
42 1 0.01
43 5 0.03
44 105 0.57
45 40 0.22
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (43 bp):
TGAAATTTTGATAAACATACTATGAAATTTTGATAACCTCCTA
Found at i:2363 original size:20 final size:21
Alignment explanation
Indices: 2272--2365 Score: 66
Period size: 22 Copynumber: 4.4 Consensus size: 21
2262 TACATACTAT
* *
2272 GAAATTTTGATAACCCTCTTA
1 GAAATTTTGATAACCTTCATA
* **
2293 TGAAATTTTGA-AAACTAAACTA
1 -GAAATTTTGATAACCTTCA-TA
*
2315 TTAAATTTTGATAACCTTCATAA
1 -GAAATTTTGATAACCTTCAT-A
* *
2338 GAAATTTTGATATCCTTCCT-
1 GAAATTTTGATAACCTTCATA
2358 GAAATTTT
1 GAAATTTT
2366 AATTACTCCA
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
20 8 0.14
21 3 0.05
22 40 0.70
23 6 0.11
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (21 bp):
GAAATTTTGATAACCTTCATA
Found at i:2544 original size:66 final size:65
Alignment explanation
Indices: 2474--2640 Score: 174
Period size: 66 Copynumber: 2.5 Consensus size: 65
2464 AATTACATTT
* ** * * ** *
2474 TGAAAATTTGATAATTTCTTTATGAAATTTTGATAACCTCTCTATAAAATTTTGTTGACCCCTCT
1 TGAAATTTTGATAATTTC-TTATGAAATTTTGATAACCTCGATATAAAATTTTGATAACAACACT
2539 A
65 A
** * * *
2540 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGATTTGAAATTTTGATAACAACACT
1 TGAAATTTTGATAATTTC-TTATGAAATTTTGATAACCTCGATATAAAATTTTGATAACAACACT
2605 A
65 A
*
2606 TGAAATTTTGATAATCTTCCTAT-AAATTTTGATAA
1 TGAAATTTTGATAAT-TTCTTATGAAATTTTGATAA
2641 TCCAATTTCT
Statistics
Matches: 82, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
65 11 0.13
66 70 0.85
67 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.43
Consensus pattern (65 bp):
TGAAATTTTGATAATTTCTTATGAAATTTTGATAACCTCGATATAAAATTTTGATAACAACACTA
Found at i:2628 original size:22 final size:23
Alignment explanation
Indices: 2447--2890 Score: 141
Period size: 22 Copynumber: 20.0 Consensus size: 23
2437 CCAGAAGTTC
* *
2447 CACTATGAAATTTTGGTAAT-TA
1 CACTATGAAATTTTGATAATCTT
* * *
2469 CATTTTGAAAATTTGATAAT-TT
1 CACTATGAAATTTTGATAATCTT
** *
2491 CTTTATGAAATTTTGATAA-CCT
1 CACTATGAAATTTTGATAATCTT
* * * * **
2513 CTCTATAAAATTTTGTTGA-CCC
1 CACTATGAAATTTTGATAATCTT
* *
2535 CTCTATGAAATTTTGATAATC-A
1 CACTATGAAATTTTGATAATCTT
* * *
2557 CATTATGTAATTTTGATAA-CCT
1 CACTATGAAATTTTGATAATCTT
* **
2579 CGA-TTTGAAATTTTGATAA-CAA
1 C-ACTATGAAATTTTGATAATCTT
2601 CACTATGAAATTTTGATAATCTT
1 CACTATGAAATTTTGATAATCTT
2624 C-CTAT-AAATTTTGATAATCCAATT
1 CACTATGAAATTTTGATAAT-C--TT
* * *
2648 -TCTATGAAATTTCGATAATC-A
1 CACTATGAAATTTTGATAATCTT
*
2669 CACTATGAGA-TTTGATAAT-TT
1 CACTATGAAATTTTGATAATCTT
* * * *
2690 -TCTATCAAATTTTGGTACTCCTT
1 CACTATGAAATTTTGATAAT-CTT
* *
2713 -A-TGAAATTGAGACTTTT-ATAACCTT
1 CACT---A-TGA-AATTTTGATAATCTT
*
2738 CA-TATGAAATTTTGATAATC-A
1 CACTATGAAATTTTGATAATCTT
** **
2759 CACTAAAAAATTTTGATAA-CCA
1 CACTATGAAATTTTGATAATCTT
*
2781 CACTATGAAATTTTGATAA-CCT
1 CACTATGAAATTTTGATAATCTT
* * * *
2803 CCCCATGAAATATT-AGTAACCTT
1 CACTATGAAATTTTGA-TAATCTT
* * * *
2826 CA-TATGAGATTTTGTTAAGC-A
1 CACTATGAAATTTTGATAATCTT
*
2847 CACTATGAAATTCTT-ATAA-CCT
1 CACTATGAAATT-TTGATAATCTT
* **
2869 CGCTATGGCATTTTGATAATCT
1 CACTATGAAATTTTGATAATCT
2891 CTTTGATAAC
Statistics
Matches: 317, Mismatches: 72, Indels: 65
0.70 0.16 0.14
Matches are distributed among these distances:
20 6 0.02
21 44 0.14
22 220 0.69
23 13 0.04
24 7 0.02
25 16 0.05
26 6 0.02
27 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (23 bp):
CACTATGAAATTTTGATAATCTT
Found at i:2838 original size:66 final size:66
Alignment explanation
Indices: 2766--3124 Score: 229
Period size: 66 Copynumber: 5.2 Consensus size: 66
2756 TCACACTAAA
*
2766 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATATTAGTAACCTTCATAT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATATTAATAACCTTCATAT
2831 G
66 G
* * * * * *
2832 AGATTTTGTTAAGCACACTATGAAATTCTT-ATAACCTCGCTATGGCATTTTGATAATCTCTTTG
1 AAATTTTGATAACCACACTATGAAATT-TTGATAACCTC-C----CCA---TGA-AA--T-ATTA
** *
2896 ATAACCTTTCTATA
53 ATAACCTTCATATG
* * ** * * * *
2910 AAATTGTGATAACCACACCATGAAATTTCAATAACCTTCCTAAGAAAT-TTAAATAACCTGATCC
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATATT-AATAACCT--TCA
2974 TATG
63 TATG
* * * * * * *
2978 AAATTTTGGTAACTACACTATGAAATTTTGATAACTTTCCCATTAAATTTTTATAA-CTTCCATA
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATATTAATAACCTT-CATA
3042 TG
65 TG
* * * * * * * *
3044 AAATTTTGGTAACCATACTATGGAATTTTGATAATCTCCTCATGAAATAATAATAACCATCTTAT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATATTAATAACCTTCATAT
*
3109 A
66 G
*
3110 AAATTTTGATTACCA
1 AAATTTTGATAACCA
3125 TACAGAGTCA
Statistics
Matches: 222, Mismatches: 51, Indels: 40
0.71 0.16 0.13
Matches are distributed among these distances:
65 3 0.01
66 106 0.48
67 8 0.04
68 47 0.21
69 4 0.02
70 2 0.01
71 2 0.01
73 1 0.00
74 3 0.01
75 2 0.01
77 3 0.01
78 41 0.18
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (66 bp):
AAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCCATGAAATATTAATAACCTTCATAT
G
Found at i:2980 original size:24 final size:22
Alignment explanation
Indices: 2929--3049 Score: 75
Period size: 22 Copynumber: 5.4 Consensus size: 22
2919 TAACCACACC
*
2929 ATGAAATTTCAATAACCTTCCT
1 ATGAAATTTAAATAACCTTCCT
*
2951 AAGAAATTTAAATAACCTGATCCT
1 ATGAAATTTAAATAACCT--TCCT
*** *
2975 ATGAAATTTTGGTAA-CTACACT
1 ATGAAATTTAAATAACCTTC-CT
** * *
2997 ATGAAATTTTGATAACTTTCCC
1 ATGAAATTTAAATAACCTTCCT
* **
3019 ATTAAATTTTTATAA-CTTCCAT
1 ATGAAATTTAAATAACCTTCC-T
3041 ATGAAATTT
1 ATGAAATTT
3050 TGGTAACCAT
Statistics
Matches: 78, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
21 5 0.06
22 54 0.69
23 4 0.05
24 15 0.19
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (22 bp):
ATGAAATTTAAATAACCTTCCT
Found at i:3001 original size:22 final size:21
Alignment explanation
Indices: 2972--3091 Score: 91
Period size: 22 Copynumber: 5.5 Consensus size: 21
2962 ATAACCTGAT
*
2972 CCTATGAAATTTTGGTAACTA
1 CCTATGAAATTTTGATAACTA
*
2993 CACTATGAAATTTTGATAACTTT
1 C-CTATGAAATTTTGATAAC-TA
* * * *
3016 CCCATTAAATTTTTATAACTT
1 CCTATGAAATTTTGATAACTA
*
3037 CCATATGAAATTTTGGTAACCATA
1 CC-TATGAAATTTTGATAA-C-TA
*
3061 -CTATGGAATTTTGATAATCT-
1 CCTATGAAATTTTGATAA-CTA
3081 CCTCATGAAAT
1 CCT-ATGAAAT
3092 AATAATAACC
Statistics
Matches: 78, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
21 8 0.10
22 65 0.83
23 4 0.05
24 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (21 bp):
CCTATGAAATTTTGATAACTA
Found at i:3012 original size:68 final size:65
Alignment explanation
Indices: 2896--3077 Score: 175
Period size: 68 Copynumber: 2.7 Consensus size: 65
2886 AATCTCTTTG
* * * * * ** *
2896 ATAACCTTTCTATAAAATTGTGATAACCACACCATGAAATTTCAATAACCTTCCTAAGAAATTTA
1 ATAA-CTTCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCAAGAAATTTA
2961 A
65 A
* * **
2962 ATAACCTGATCCTATGAAATTTTGGTAACTACACTATGAAATTTTGATAACTTTCCCATTAAATT
1 ATAA-CT--TCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCAAGAAATT
**
3027 TTT
63 TAA
* *
3030 ATAACTTCCATATGAAATTTTGGTAACCATACTATGGAATTTTGATAA
1 ATAACTTCC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAA
3078 TCTCCTCATG
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
65 3 0.03
66 42 0.44
67 2 0.02
68 49 0.51
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (65 bp):
ATAACTTCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCAAGAAATTTAA
Found at i:6247 original size:35 final size:35
Alignment explanation
Indices: 6201--6327 Score: 101
Period size: 35 Copynumber: 3.4 Consensus size: 35
6191 AAGTTGAGGC
6201 AATTTGTATTTTTGTAGGTAGAATAAAATAAAAAG
1 AATTTGTATTTTTGTAGGTAGAATAAAATAAAAAG
* ** ** *
6236 AATTTGTATTTTTAGTAGTACTAGTGCTACAATCATTTTAAGG
1 AATTTGTATTTTT-GTAG--GTAG-AATA-AA--A-TAAAAAG
* *
6279 CAATTTGTATTTTTGTAGGTAAAATAAAATAAAAAT
1 -AATTTGTATTTTTGTAGGTAGAATAAAATAAAAAG
6315 AATTTGTATTTTT
1 AATTTGTATTTTT
6328 ATTTTTTGAA
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
35 26 0.38
36 7 0.10
37 1 0.01
38 3 0.04
39 4 0.06
40 4 0.06
41 2 0.03
42 1 0.01
43 8 0.12
44 13 0.19
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (35 bp):
AATTTGTATTTTTGTAGGTAGAATAAAATAAAAAG
Found at i:20435 original size:30 final size:28
Alignment explanation
Indices: 20390--20448 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 28
20380 TTTCAATCTT
*
20390 TGATGATTTTATGACTGGTTAGTAGTAC
1 TGATGATTTTATGACTGATTAGTAGTAC
20418 TGATGATGTTATATGACTGATTAGTAGTAC
1 TGATGAT-TT-TATGACTGATTAGTAGTAC
20448 T
1 T
20449 ATTCAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 7 0.25
29 2 0.07
30 19 0.68
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.42
Consensus pattern (28 bp):
TGATGATTTTATGACTGATTAGTAGTAC
Found at i:28715 original size:38 final size:39
Alignment explanation
Indices: 28663--28740 Score: 149
Period size: 38 Copynumber: 2.0 Consensus size: 39
28653 ATGTTCTACA
28663 CAATCCCCTTGGGATCCCATTCCTGAATAATTTGAATGG
1 CAATCCCCTTGGGATCCCATTCCTGAATAATTTGAATGG
28702 CAAT-CCCTTGGGATCCCATTCCTGAATAATTTGAATGG
1 CAATCCCCTTGGGATCCCATTCCTGAATAATTTGAATGG
28740 C
1 C
28741 GCACCTAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
38 35 0.90
39 4 0.10
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (39 bp):
CAATCCCCTTGGGATCCCATTCCTGAATAATTTGAATGG
Found at i:33291 original size:8 final size:8
Alignment explanation
Indices: 33261--33290 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
33251 TGCTTTGGAT
33261 TTGGAAGA
1 TTGGAAGA
33269 TTGGAAGA
1 TTGGAAGA
*
33277 TTGGAATA
1 TTGGAAGA
33285 TTGGAA
1 TTGGAA
33291 TCTGGTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (8 bp):
TTGGAAGA
Found at i:34127 original size:6 final size:6
Alignment explanation
Indices: 34116--34141 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
34106 CACTTTTGTG
34116 AGGCAA AGGCAA AGGCAA AGGCAA AG
1 AGGCAA AGGCAA AGGCAA AGGCAA AG
34142 TCAGCCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.35, T:0.00
Consensus pattern (6 bp):
AGGCAA
Found at i:35387 original size:17 final size:18
Alignment explanation
Indices: 35365--35401 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
35355 ACATCAAAAT
35365 TAAAAATAAAA-TA-ATAG
1 TAAAAA-AAAACTATATAG
35382 TAAAAAAAAACTATATAG
1 TAAAAAAAAACTATATAG
35400 TA
1 TA
35402 GTACAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 8 0.44
18 6 0.33
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (18 bp):
TAAAAAAAAACTATATAG
Found at i:37379 original size:21 final size:21
Alignment explanation
Indices: 37344--37385 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
37334 TATGGGTGTG
*
37344 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
37366 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
37386 GACCGAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:37963 original size:7 final size:7
Alignment explanation
Indices: 37924--37962 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
37914 CTTGAAGATT
37924 GATTGAA
1 GATTGAA
37931 GATTGAA
1 GATTGAA
37938 GATTGAA
1 GATTGAA
*
37945 GATTTAA
1 GATTGAA
*
37952 GATTTAA
1 GATTGAA
37959 GATT
1 GATT
37963 TGATGGAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (7 bp):
GATTGAA
Found at i:38273 original size:21 final size:21
Alignment explanation
Indices: 38238--38279 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38228 TATGGGTGTG
*
38238 TGTGATTGTTTGGTTTGGTAGA
1 TGTGATTGATTGGTTT-GTAGA
38260 TGTGA-TGATTGGTTTGTAGA
1 TGTGATTGATTGGTTTGTAGA
38280 GACCGAGCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
TGTGATTGATTGGTTTGTAGA
Found at i:39071 original size:22 final size:22
Alignment explanation
Indices: 38949--39365 Score: 192
Period size: 22 Copynumber: 19.1 Consensus size: 22
38939 GAATTTCAAG
38949 AACCTCCATATGAAATTTTG-T
1 AACCTCCATATGAAATTTTGAT
* * * *
38970 CAACTTCCCTATAAAATTTTGTT
1 -AACCTCCATATGAAATTTTGAT
* *
38993 ACACTCTCTATA-AAAATTTTGAT
1 A-AC-CTCCATATGAAATTTTGAT
*
39016 AA--TCAACTAATGAAATTTTGAT
1 AACCTCCA-T-ATGAAATTTTGAT
*
39038 AACCACCCA-ATGAAATTTTGAT
1 AACC-TCCATATGAAATTTTGAT
* * *
39060 AACCTCCAAATGAAATGTTGGT
1 AACCTCCATATGAAATTTTGAT
* *
39082 AAGCGCACATTATGAAATTTTGAT
1 AACCTC-CA-TATGAAATTTTGAT
* * * *
39106 AACC-CTCAGATAAAATATTGGT
1 AACCTC-CATATGAAATTTTGAT
* *
39128 AA--TCGTATTAAGAAATTTTGAT
1 AACCTC-CA-TATGAAATTTTGAT
*
39150 AACCATACC--ATGAAATTGTGAT
1 AACC-T-CCATATGAAATTTTGAT
*
39172 -ACCT-CACTATGAAATTTTTAT
1 AACCTCCA-TATGAAATTTTGAT
* *
39193 AAACCTCCCTA--AAATTTTAAT
1 -AACCTCCATATGAAATTTTGAT
* *
39214 AACCTCCATTTGGAATTTTGAT
1 AACCTCCATATGAAATTTTGAT
* *
39236 AACCT-C--GTGAAATTTTGAA
1 AACCTCCATATGAAATTTTGAT
*
39255 AACCACC-TCATGAAATTTTGAT
1 AACCTCCAT-ATGAAATTTTGAT
*
39277 AACCAT-CTTATGAAATTTTGAT
1 AACC-TCCATATGAAATTTTGAT
* * *
39299 AACATCCCTAT-AAATTTTTTAT
1 AACCTCCATATGAAA-TTTTGAT
* * *
39321 AACCTCCTTATAAAATTTTGTT
1 AACCTCCATATGAAATTTTGAT
* *
39343 AACCTCCA-ACGACATTTTGAT
1 AACCTCCATATGAAATTTTGAT
39364 AA
1 AA
39366 GAACACTATT
Statistics
Matches: 299, Mismatches: 62, Indels: 69
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.00
19 17 0.06
20 11 0.04
21 45 0.15
22 173 0.58
23 29 0.10
24 19 0.06
25 3 0.01
26 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
AACCTCCATATGAAATTTTGAT
Found at i:39105 original size:46 final size:44
Alignment explanation
Indices: 39047--39153 Score: 126
Period size: 46 Copynumber: 2.4 Consensus size: 44
39037 TAACCACCCA
* *
39047 ATGAAATTTTGATAA-CCTCCAAATGAAATGTTGGTAAGCGCACATT
1 ATGAAATTTTGATAACCCT-CAAATAAAATATTGGTAAGCG--CATT
* * *
39093 ATGAAATTTTGATAACCCTCAGATAAAATATTGGTAATCGTATT
1 ATGAAATTTTGATAACCCTCAAATAAAATATTGGTAAGCGCATT
*
39137 AAGAAATTTTGATAACC
1 ATGAAATTTTGATAACC
39154 ATACCATGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
44 19 0.35
46 32 0.59
47 3 0.06
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (44 bp):
ATGAAATTTTGATAACCCTCAAATAAAATATTGGTAAGCGCATT
Found at i:39517 original size:22 final size:21
Alignment explanation
Indices: 39446--39517 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
39436 TCTCCCAATA
* * *
39446 AAATTTTGAGAACCACACTAT
1 AAATTTTGATAAACTCACTAT
* *
39467 CAAATTTTGTTAATCTCACTAT
1 -AAATTTTGATAAACTCACTAT
*
39489 AAATTTTGATAAACTCATTAT
1 AAATTTTGATAAACTCACTAT
39510 GAAATTTT
1 -AAATTTT
39518 AATTACCACA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 18 0.43
22 24 0.57
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (21 bp):
AAATTTTGATAAACTCACTAT
Found at i:39633 original size:22 final size:22
Alignment explanation
Indices: 39570--39653 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 22
39560 TACCACATTG
* *
39570 TAAAATTTTGATAACCACGCTA
1 TAAAATTTTGATAACCTCCCTA
* ** *
39592 TGAAATTTTGATAATTTCCCTT
1 TAAAATTTTGATAACCTCCCTA
* *
39614 TAAAATTTCGATAACCTCCCCA
1 TAAAATTTTGATAACCTCCCTA
*
39636 TGAAAA-TTTGTTAACCTC
1 T-AAAATTTTGATAACCTC
39654 TATGAAATTG
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
22 43 0.91
23 4 0.09
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (22 bp):
TAAAATTTTGATAACCTCCCTA
Found at i:39766 original size:22 final size:21
Alignment explanation
Indices: 39750--40109 Score: 195
Period size: 22 Copynumber: 15.9 Consensus size: 21
39740 TATAAGCACA
*
39750 CTATGAAATTTTGATAATCTTC
1 CTATGAAATTTTGATAA-CCTC
39772 CTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAACCTC
* * *
39793 CATATAAAATTTCGATAATCTCC
1 C-TATGAAATTTTGATAACCT-C
39816 CTATGAAATTTTGATAACCTC
1 CTATGAAATTTTGATAACCTC
* * *
39837 CATATAAAATTTCGATAATCTCC
1 C-TATGAAATTTTGATAACCT-C
**
39860 CTATGAAATTTTGATAACCAGA
1 CTATGAAATTTTGATAACC-TC
* * *
39882 GTATGAAATTTT-AGTATCATC
1 CTATGAAATTTTGA-TAACCTC
*
39903 ACTGTGAAATTTTGAATTTCAATAACCTC
1 -CTATGAAATTTTG-------ATAACCTC
39932 CTTATGAAATTTTGATAACCTTC
1 C-TATGAAATTTTGATAACC-TC
* *
39955 ATATGAAATTTTGATAACGTC
1 CTATGAAATTTTGATAACCTC
*
39976 CTTATGAAATTTTATTTTAATAACCTC
1 C-TATG-AA----ATTTTGATAACCTC
* *
40003 CTTATGAAAATTTGATAACATGC
1 C-TATGAAATTTTGATAACCT-C
*
40026 C-ATGAAATTGTGATAA-CTAC
1 CTATGAAATTTTGATAACCT-C
* * *
40046 ACTATAAAATTTTAATATCCTAC
1 -CTATGAAATTTTGATAACCT-C
* * *
40069 CTATAAAATTTTGGTAACCAC
1 CTATGAAATTTTGATAACCTC
* *
40090 ACTATAAAATTTTGAGAACC
1 -CTATGAAATTTTGATAACC
40110 ACACTAATTT
Statistics
Matches: 263, Mismatches: 47, Indels: 56
0.72 0.13 0.15
Matches are distributed among these distances:
20 2 0.01
21 24 0.09
22 185 0.70
23 14 0.05
26 2 0.01
27 18 0.07
28 1 0.00
29 16 0.06
30 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCTC
Found at i:39804 original size:44 final size:44
Alignment explanation
Indices: 39751--39988 Score: 230
Period size: 44 Copynumber: 5.2 Consensus size: 44
39741 ATAAGCACAC
39751 TATGAAATTTTGATAATCTTCCTATGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAATCTTCCTATGAAATTTTGATAACCTCCA
* * *
39795 TATAAAATTTCGATAATCTCCCTATGAAATTTTGATAACCTCCA
1 TATGAAATTTTGATAATCTTCCTATGAAATTTTGATAACCTCCA
* * * **
39839 TATAAAATTTCGATAATCTCCCTATGAAATTTTGATAACC-AGA
1 TATGAAATTTTGATAATCTTCCTATGAAATTTTGATAACCTCCA
* * *
39882 GTATGAAATTTT-AGT-ATCATCACTGTGAAATTTTGAATTTCAATAACCTCCT
1 -TATGAAATTTTGA-TAATCTTC-CTATGAAATTTTG-------ATAACCTCCA
* * * *
39934 TATGAAATTTTGATAACCTTCATATGAAATTTTGATAACGTCCT
1 TATGAAATTTTGATAATCTTCCTATGAAATTTTGATAACCTCCA
39978 TATGAAATTTT
1 TATGAAATTTT
39989 ATTTTAATAA
Statistics
Matches: 163, Mismatches: 18, Indels: 26
0.79 0.09 0.13
Matches are distributed among these distances:
43 6 0.04
44 123 0.75
51 29 0.18
52 5 0.03
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (44 bp):
TATGAAATTTTGATAATCTTCCTATGAAATTTTGATAACCTCCA
Found at i:39963 original size:73 final size:72
Alignment explanation
Indices: 39844--40021 Score: 202
Period size: 73 Copynumber: 2.5 Consensus size: 72
39834 CTCCATATAA
* * * * * *
39844 AATTTCGATAATCTCCCTATGAAATTTTGATAACCAGAGTATGAAATTTT-AGTATCATCAC-TG
1 AATTTCAATAACCTCCTTATGAAATTTTGATAACCACAGTATGAAATTTTGA-TAACATC-CTTA
39907 TGAAATTTT
64 TGAAATTTT
* *
39916 GAATTTCAATAACCTCCTTATGAAATTTTGATAACCTTCA-TATGAAATTTTGATAACGTCCTTA
1 -AATTTCAATAACCTCCTTATGAAATTTTGATAACC-ACAGTATGAAATTTTGATAACATCCTTA
39980 TGAAATTTT
64 TGAAATTTT
* *
39989 -ATTTTAATAACCTCCTTATGAAAATTTGATAAC
1 AATTTCAATAACCTCCTTATGAAATTTTGATAAC
40022 ATGCCATGAA
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
71 31 0.34
72 1 0.01
73 58 0.63
74 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (72 bp):
AATTTCAATAACCTCCTTATGAAATTTTGATAACCACAGTATGAAATTTTGATAACATCCTTATG
AAATTTT
Found at i:40120 original size:18 final size:18
Alignment explanation
Indices: 40097--40131 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40087 CACACTATAA
40097 AATTTTGAG-AACCACACT
1 AATTTT-AGTAACCACACT
40115 AATTTTAGTAACCACAC
1 AATTTTAGTAACCACAC
40132 AATGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.29
Consensus pattern (18 bp):
AATTTTAGTAACCACACT
Done.