Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010796.1 Corchorus capsularis cultivar CVL-1 contig10817, 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: 7198
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:2224 original size:38 final size:38
Alignment explanation
Indices: 2169--2336 Score: 232
Period size: 38 Copynumber: 4.4 Consensus size: 38
2159 CCTTGCTGAT
* *
2169 TTAAGAGTC-AAGATAATAGTAACCAGT-TAATTAAGTAA
1 TTAAGAGTCAAAG-TAATAGTAACCAGTAAAATTGA-TAA
* *
2207 TTAAGAGTTAAAGTAATAGTAATCAGTAAAATTGATAA
1 TTAAGAGTCAAAGTAATAGTAACCAGTAAAATTGATAA
2245 TTAAGAGTCAAAGTAATAGTAACCAGTAAAATTGATAA
1 TTAAGAGTCAAAGTAATAGTAACCAGTAAAATTGATAA
* * *
2283 TCATGAGTCAAAGTAATAGTAATCAGTAAAATTGATAA
1 TTAAGAGTCAAAGTAATAGTAACCAGTAAAATTGATAA
*
2321 TTAAGAGTCAAGGTAA
1 TTAAGAGTCAAAGTAA
2337 AAATAGTAAT
Statistics
Matches: 116, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
38 108 0.93
39 8 0.07
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.29
Consensus pattern (38 bp):
TTAAGAGTCAAAGTAATAGTAACCAGTAAAATTGATAA
Found at i:2296 original size:76 final size:76
Alignment explanation
Indices: 2169--2399 Score: 253
Period size: 76 Copynumber: 3.1 Consensus size: 76
2159 CCTTGCTGAT
* * *
2169 TTAAGAGTC-AAGATAATAGTAACCAGTTAATTAAGTAATTAAGAGTTAAAGTAATAGTAATCAG
1 TTAAGAGTCAAAG-TAATAGTAACCAGTAAATTAAGTAATCAAGAGTCAAAGTAATAGTAATCAG
2233 TAAAATTGATAA
65 TAAAATTGATAA
* *
2245 TTAAGAGTCAAAGTAATAGTAACCAGTAAAATTGA-TAATCATGAGTCAAAGTAATAGTAATCAG
1 TTAAGAGTCAAAGTAATAGTAACCAGT-AAATTAAGTAATCAAGAGTCAAAGTAATAGTAATCAG
2309 TAAAATTGATAA
65 TAAAATTGATAA
* * * * *
2321 TTAAGAGTCAAGGTAAAAATAGTAATCAATAAA-TCAGTAATTAAGAGTC-AAG-AGAT--TAAT
1 TTAAGAGTCAAAGT---AATAGTAACCAGTAAATTAAGTAATCAAGAGTCAAAGTA-ATAGTAAT
*
2381 CAGT-AAATTGATAC
62 CAGTAAAATTGATAA
2395 TTAAG
1 TTAAG
2400 GGAGAAAGTG
Statistics
Matches: 136, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
74 14 0.10
75 8 0.06
76 75 0.55
77 15 0.11
78 13 0.10
79 11 0.08
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (76 bp):
TTAAGAGTCAAAGTAATAGTAACCAGTAAATTAAGTAATCAAGAGTCAAAGTAATAGTAATCAGT
AAAATTGATAA
Found at i:2476 original size:21 final size:20
Alignment explanation
Indices: 2446--2562 Score: 92
Period size: 21 Copynumber: 5.5 Consensus size: 20
2436 AGAAGTAAAG
*
2446 GTAACCAGTAAGAGTAAAATA
1 GTAATCAGTAAGAGTAAAA-A
* * *
2467 GTAATAAGTAAAAAGTAAAAG
1 GTAATCAGT-AAGAGTAAAAA
* *
2488 GTAGTCAGTAAGAGTAAGAGA
1 GTAATCAGTAAGAGTAA-AAA
*
2509 GTAATTAGTAAAGAAG-AAAAA
1 GTAATCAGT-AAG-AGTAAAAA
*
2530 GGTAATCAGTATGAGTAAAACA
1 -GTAATCAGTAAGAGTAAAA-A
2552 GTAATCAGTAA
1 GTAATCAGTAA
2563 AAAAAGTAAT
Statistics
Matches: 74, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
20 9 0.12
21 40 0.54
22 23 0.31
23 2 0.03
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.21
Consensus pattern (20 bp):
GTAATCAGTAAGAGTAAAAA
Found at i:2546 original size:43 final size:42
Alignment explanation
Indices: 2434--2563 Score: 154
Period size: 43 Copynumber: 3.1 Consensus size: 42
2424 TAATTAAGGA
* * *
2434 AAAGAAGTAAAGGTAACCAGTAAGAGTAAAATAGTAATAAGT
1 AAAGAAGAAAAGGTAATCAGTAAGAGTAAAACAGTAATAAGT
* * * *
2476 AAA-AAGTAAAAGGTAGTCAGTAAGAGTAAGAGAGTAATTAGT
1 AAAGAAG-AAAAGGTAATCAGTAAGAGTAAAACAGTAATAAGT
* *
2518 AAAGAAGAAAAAGGTAATCAGTATGAGTAAAACAGTAATCAGT
1 AAAGAAG-AAAAGGTAATCAGTAAGAGTAAAACAGTAATAAGT
2561 AAA
1 AAA
2564 AAAAGTAATA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
41 3 0.04
42 35 0.47
43 36 0.49
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.19
Consensus pattern (42 bp):
AAAGAAGAAAAGGTAATCAGTAAGAGTAAAACAGTAATAAGT
Found at i:2579 original size:43 final size:42
Alignment explanation
Indices: 2423--2586 Score: 152
Period size: 43 Copynumber: 3.8 Consensus size: 42
2413 TTAGTGATCG
* * * *
2423 GTAATTAAGGAAAAGAAGTAAAGGTAACCAGTAAGAGTAAAATA
1 GTAA-TAAGTAAAA-AAGTAAAAGTAATCAGTAAGAGTAAAACA
* * *
2467 GTAATAAGT-AAAAAGTAAAAGGTAGTCAGTAAGAGTAAGAGA
1 GTAATAAGTAAAAAAGTAAAA-GTAATCAGTAAGAGTAAAACA
* * * *
2509 GTAATTAGTAAAGAAGAAAAAGGTAATCAGTATGAGTAAAACA
1 GTAATAAGTAAAAAAGTAAAA-GTAATCAGTAAGAGTAAAACA
*
2552 GTAATCAGTAAAAAAAGTAATAA-TAATCAGTAAGA
1 GTAATAAGT-AAAAAAGTAA-AAGTAATCAGTAAGA
2587 AGCAATGGTA
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
41 7 0.07
42 28 0.28
43 50 0.51
44 12 0.12
45 2 0.02
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.20
Consensus pattern (42 bp):
GTAATAAGTAAAAAAGTAAAAGTAATCAGTAAGAGTAAAACA
Found at i:2598 original size:85 final size:84
Alignment explanation
Indices: 2434--2622 Score: 190
Period size: 85 Copynumber: 2.2 Consensus size: 84
2424 TAATTAAGGA
* * * *
2434 AAAGAAG-TAAAGGTAACCAGTAAGAGTAAAATAGTAATAAGTAAAAAGTAAAAGGTAGTCAGTA
1 AAAGAAGAAAAAGGTAATCAGTAAGAGTAAAACAGTAATAAGTAAAAAGTAAAA-GTAATCAGTA
* *
2498 AGAGTAAGAGAGTAATTAGT
65 AGAGCAAGAGAGTAATCAGT
* *
2518 AAAGAAGAAAAAGGTAATCAGTATGAGTAAAACAGTAATCAGTAAAAAAAGTAATAA-TAATCAG
1 AAAGAAGAAAAAGGTAATCAGTAAGAGTAAAACAGTAATAAGT--AAAAAGTAA-AAGTAATCAG
* *
2582 TAAGAAGCAA-TG-GTAATCATT
63 TAAG-AGCAAGAGAGTAATCAGT
*
2603 AAA-AAGTAAAAAGCTAATCA
1 AAAGAAG-AAAAAGGTAATCA
2623 ATAAAAAGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
84 10 0.11
85 52 0.59
86 11 0.12
87 13 0.15
88 2 0.02
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (84 bp):
AAAGAAGAAAAAGGTAATCAGTAAGAGTAAAACAGTAATAAGTAAAAAGTAAAAGTAATCAGTAA
GAGCAAGAGAGTAATCAGT
Found at i:2686 original size:27 final size:29
Alignment explanation
Indices: 2627--2688 Score: 74
Period size: 32 Copynumber: 2.1 Consensus size: 29
2617 TAATCAATAA
*
2627 AAAGTAAAAGTAAAAGAAGTAATCAGCAGAGT
1 AAAGTAAAAGTAAAAGAAGCAAT-A-CA-AGT
2659 AAAGTAAAAGTAAAAGAAGCAAT-C-AGT
1 AAAGTAAAAGTAAAAGAAGCAATACAAGT
2686 AAA
1 AAA
2689 AGGAAGAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.21
29 1 0.03
32 22 0.76
ACGTcount: A:0.60, C:0.06, G:0.19, T:0.15
Consensus pattern (29 bp):
AAAGTAAAAGTAAAAGAAGCAATACAAGT
Found at i:2726 original size:20 final size:20
Alignment explanation
Indices: 2654--2728 Score: 55
Period size: 20 Copynumber: 3.7 Consensus size: 20
2644 AGTAATCAGC
2654 AGAGT-AAAGTAAAAGTAAA
1 AGAGTAAAAGTAAAAGTAAA
* * * *
2673 AGAAGCAATCAGTAAAAGGAAG
1 AG-AGTAA-AAGTAAAAGTAAA
**
2695 A-AGTCATCAGTAAAAGTAAA
1 AGAGT-AAAAGTAAAAGTAAA
2715 AGAGTAAAAGTAAA
1 AGAGTAAAAGTAAA
2729 GGAAGTAATC
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
19 2 0.05
20 23 0.56
21 5 0.12
22 11 0.27
ACGTcount: A:0.59, C:0.05, G:0.21, T:0.15
Consensus pattern (20 bp):
AGAGTAAAAGTAAAAGTAAA
Found at i:2779 original size:36 final size:36
Alignment explanation
Indices: 2692--2805 Score: 128
Period size: 36 Copynumber: 3.3 Consensus size: 36
2682 CAGTAAAAGG
* *
2692 AAGAAGTCATCAGTAAAAGTAAAAGAGTAAAAGTAA
1 AAGAAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
* *
2728 AGGAAGTAATCAGTAGAAGTGAAAGAGTAAAAGTAA
1 AAGAAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
** * *
2764 AATTAGTAATCAGTAG-A--AAAA-AGCAAAAGTAC
1 AAGAAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
2796 AAGAAGTAAT
1 AAGAAGTAAT
2806 TAAGAGTAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 17 0.26
33 3 0.05
35 1 0.02
36 45 0.68
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (36 bp):
AAGAAGTAATCAGTAGAAGTAAAAGAGTAAAAGTAA
Found at i:3799 original size:14 final size:14
Alignment explanation
Indices: 3780--3838 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
3770 TTCTCACTCC
3780 TTACTATTTTTTCT
1 TTACTATTTTTTCT
**
3794 TTACTAATTACTT-T
1 TTACT-ATTTTTTCT
* **
3808 TTACTCTTTACTCT
1 TTACTATTTTTTCT
3822 TTACTATTTTTTCT
1 TTACTATTTTTTCT
3836 TTA
1 TTA
3839 TTGATTACTC
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
13 3 0.09
14 26 0.76
15 5 0.15
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (14 bp):
TTACTATTTTTTCT
Found at i:3860 original size:14 final size:14
Alignment explanation
Indices: 3791--3860 Score: 54
Period size: 14 Copynumber: 5.0 Consensus size: 14
3781 TACTATTTTT
**
3791 TCTTTACTAATTAC
1 TCTTTACTTTTTAC
* *
3805 TTTTTACTCTTTAC
1 TCTTTACTTTTTAC
*
3819 TCTTTACTATTTT-T
1 TCTTTACT-TTTTAC
*
3833 TCTTTA-TTGATTAC
1 TCTTTACTT-TTTAC
3847 TCTTTACTTTTTAC
1 TCTTTACTTTTTAC
3861 AAATTACCAT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
12 1 0.02
13 3 0.07
14 34 0.79
15 5 0.12
ACGTcount: A:0.19, C:0.19, G:0.01, T:0.61
Consensus pattern (14 bp):
TCTTTACTTTTTAC
Found at i:3873 original size:42 final size:42
Alignment explanation
Indices: 3780--4047 Score: 160
Period size: 42 Copynumber: 6.5 Consensus size: 42
3770 TTCTCACTCC
* * * **
3780 TTACTATTTTTTCTTTACTAATTACTTTTTACTCTTTACTCT
1 TTACCATTTTTTCTTTACTAATTACTCTTTACTTTTTACTAA
* * * *
3822 TTACTATTTTTTCTTTATTGATTACTCTTTACTTTTTACAAA
1 TTACCATTTTTTCTTTACTAATTACTCTTTACTTTTTACTAA
* *
3864 TTACCATTTTACTT-TTCACTAATTAC-CTTTACTTTTTTTCTAA
1 TTACCATTTT--TTCTTTACTAATTACTCTTTAC-TTTTTACTAA
* *
3907 TTACCATTTTACTT-TTCACTAATTAC-CTTTACTTTTTACTGA
1 TTACCATTTT--TTCTTTACTAATTACTCTTTACTTTTTACTAA
* ** ** * *
3949 TTACTATTTTACCCTTT-CCGA-TACCTTTTTACTTTTTACTGA
1 TTACCATTTT-TTCTTTACTAATTA-CTCTTTACTTTTTACTAA
** * * * *
3991 TTACCATTACTTC-TTACTGATTACT-ATTACTCTTTACTGA
1 TTACCATTTTTTCTTTACTAATTACTCTTTACTTTTTACTAA
*
4031 TTA-C-TTTTTACTTTACT
1 TTACCATTTTTTCTTTACT
4048 CTTTACCATT
Statistics
Matches: 183, Mismatches: 34, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
38 4 0.02
39 6 0.03
40 20 0.11
41 9 0.05
42 93 0.51
43 49 0.27
44 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.02, T:0.56
Consensus pattern (42 bp):
TTACCATTTTTTCTTTACTAATTACTCTTTACTTTTTACTAA
Found at i:3877 original size:22 final size:22
Alignment explanation
Indices: 3849--4068 Score: 153
Period size: 20 Copynumber: 10.6 Consensus size: 22
3839 TTGATTACTC
*
3849 TTTACTTTTTACAAATTACCAT
1 TTTACTTTTTACTAATTACCAT
*
3871 TTTACTTTTCACTAATTACC--
1 TTTACTTTTTACTAATTACCAT
*
3891 TTTACTTTTTTTCTAATTACCAT
1 TTTAC-TTTTTACTAATTACCAT
*
3914 TTTACTTTTCACTAATTACC--
1 TTTACTTTTTACTAATTACCAT
* *
3934 TTTACTTTTTACTGATTACTAT
1 TTTACTTTTTACTAATTACCAT
** ** *
3956 TTTACCCTTT-CCGA-TACCTT
1 TTTACTTTTTACTAATTACCAT
*
3976 TTTACTTTTTACTGATTACCA-
1 TTTACTTTTTACTAATTACCAT
* *
3997 -TTACTTCTTACTGATTA-C-T
1 TTTACTTTTTACTAATTACCAT
* * * *
4016 ATTACTCTTTACTGATTA-CTT
1 TTTACTTTTTACTAATTACCAT
**
4037 TTTAC--TTTACTCTTTACCAT
1 TTTACTTTTTACTAATTACCAT
4057 TTT-CTTTTTACT
1 TTTACTTTTTACT
4069 GATCTCTCTT
Statistics
Matches: 160, Mismatches: 25, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
19 11 0.07
20 71 0.44
21 30 0.19
22 43 0.27
23 5 0.03
ACGTcount: A:0.22, C:0.21, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTACTTTTTACTAATTACCAT
Found at i:3909 original size:43 final size:42
Alignment explanation
Indices: 3842--4044 Score: 188
Period size: 43 Copynumber: 4.9 Consensus size: 42
3832 TTCTTTATTG
*
3842 ATTACTCTTTACTTTTTACAAATTACCATTTTACTTTTCACTA
1 ATTAC-CTTTACTTTTTACTAATTACCATTTTACTTTTCACTA
*
3885 ATTACCTTTACTTTTTTTCTAATTACCATTTTACTTTTCACTA
1 ATTACCTTTAC-TTTTTACTAATTACCATTTTACTTTTCACTA
* * * *
3928 ATTACCTTTACTTTTTACTGATTACTATTTTACCCTTTC-C-G
1 ATTACCTTTACTTTTTACTAATTACCATTTTA-CTTTTCACTA
* *
3969 A-TACCTTTTTACTTTTTACTGATTACCA--TTACTTCTT-ACTG
1 ATTACC--TTTACTTTTTACTAATTACCATTTTACTT-TTCACTA
* * *
4010 ATTA-CTATTACTCTTTACTGATTA-CTTTTTACTTT
1 ATTACCT-TTACTTTTTACTAATTACCATTTTACTTT
4045 ACTCTTTACC
Statistics
Matches: 138, Mismatches: 11, Indels: 25
0.79 0.06 0.14
Matches are distributed among these distances:
39 4 0.03
40 27 0.20
41 10 0.07
42 47 0.34
43 50 0.36
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.53
Consensus pattern (42 bp):
ATTACCTTTACTTTTTACTAATTACCATTTTACTTTTCACTA
Found at i:4020 original size:13 final size:14
Alignment explanation
Indices: 3984--4035 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
3974 TTTTTACTTT
3984 TTACTGATTAC-CA
1 TTACTGATTACTCA
** *
3997 TTACTTCTTACTGA
1 TTACTGATTACTCA
*
4011 TTACT-ATTACTCT
1 TTACTGATTACTCA
4024 TTACTGATTACT
1 TTACTGATTACT
4036 TTTTACTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 19 0.61
14 12 0.39
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48
Consensus pattern (14 bp):
TTACTGATTACTCA
Found at i:4063 original size:26 final size:27
Alignment explanation
Indices: 3977--4082 Score: 87
Period size: 26 Copynumber: 3.9 Consensus size: 27
3967 CGATACCTTT
*
3977 TTACTTTTTACTGATTAC-CATTACTTC-
1 TTACTTTTTACT-ATTACTCTTTAC-TCA
** *
4004 TTACTGATTACTATTACTCTTTACTGA
1 TTACTTTTTACTATTACTCTTTACTCA
4031 TTACTTTTTACT-TTACTCTTTAC-CA
1 TTACTTTTTACTATTACTCTTTACTCA
*
4056 TTTTCTTTTTACTGATCT-CTCTTTACT
1 -TTACTTTTTACT-AT-TACTCTTTACT
4083 TTACTCTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
25 1 0.02
26 28 0.44
27 25 0.39
28 9 0.14
29 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.55
Consensus pattern (27 bp):
TTACTTTTTACTATTACTCTTTACTCA
Found at i:4067 original size:40 final size:40
Alignment explanation
Indices: 3970--4099 Score: 131
Period size: 40 Copynumber: 3.2 Consensus size: 40
3960 CCCTTTCCGA
* * **
3970 TACCTTTTTACTTTTTACTGATTAC-CATTACTTCTTACTGAT
1 TACCATTTT-CTTTTTACTGATTACTCTTTAC-T-TTACTCTT
* * * *
4012 TACTA-TTACTCTTTACTGATTACTTTTTACTTTACTCTT
1 TACCATTTTCTTTTTACTGATTACTCTTTACTTTACTCTT
4051 TACCATTTTCTTTTTACTGATCT-CTCTTTACTTTACTCTT
1 TACCATTTTCTTTTTACTGAT-TACTCTTTACTTTACTCTT
4091 TACCATTTT
1 TACCATTTT
4100 ACTAATTACT
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
39 10 0.14
40 53 0.73
41 7 0.10
42 3 0.04
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.55
Consensus pattern (40 bp):
TACCATTTTCTTTTTACTGATTACTCTTTACTTTACTCTT
Found at i:4137 original size:29 final size:27
Alignment explanation
Indices: 4074--4151 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 27
4064 TTACTGATCT
4074 CTCTTTACTTTACTCTTTACCATTTTA
1 CTCTTTACTTTACTCTTTACCATTTTA
** * *
4101 CTAATTACTCTTCATTCTTTACCATTTTT
1 CTCTTTACT-TT-ACTCTTTACCATTTTA
*
4130 TTCTTTACTGATTACTCTTTAC
1 CTCTTTACT--TTACTCTTTAC
4152 TCTTTACCAT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
27 7 0.18
28 2 0.05
29 28 0.72
30 2 0.05
ACGTcount: A:0.19, C:0.24, G:0.01, T:0.55
Consensus pattern (27 bp):
CTCTTTACTTTACTCTTTACCATTTTA
Found at i:4137 original size:36 final size:34
Alignment explanation
Indices: 4097--4182 Score: 118
Period size: 36 Copynumber: 2.5 Consensus size: 34
4087 TCTTTACCAT
* *
4097 TTTACTAATTACTCTTCATTCTTTACCATTTTTTTC
1 TTTACTGATTACTCTTCACTCTTTACCA--TTTTTC
*
4133 TTTACTGATTACTCTTTACTCTTTACCATTTTTC
1 TTTACTGATTACTCTTCACTCTTTACCATTTTTC
*
4167 TTCACTGATTACTCTT
1 TTTACTGATTACTCTT
4183 TACTGATCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 21 0.46
36 25 0.54
ACGTcount: A:0.19, C:0.23, G:0.02, T:0.56
Consensus pattern (34 bp):
TTTACTGATTACTCTTCACTCTTTACCATTTTTC
Found at i:4187 original size:14 final size:14
Alignment explanation
Indices: 4165--4219 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
4155 TTACCATTTT
*
4165 TCTTCACTGATTAC
1 TCTTTACTGATTAC
*
4179 TCTTTACTGATCAC
1 TCTTTACTGATTAC
**
4193 TGATTACT-ATTAC
1 TCTTTACTGATTAC
*
4206 TC-TTACTAATTAC
1 TCTTTACTGATTAC
4219 T
1 T
4220 ATTACTCTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
12 5 0.15
13 11 0.32
14 18 0.53
ACGTcount: A:0.25, C:0.24, G:0.05, T:0.45
Consensus pattern (14 bp):
TCTTTACTGATTAC
Found at i:4233 original size:20 final size:20
Alignment explanation
Indices: 4195--4284 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
4185 CTGATCACTG
4195 ATTACTATTACTC-TTACTA
1 ATTACTATTACTCTTTACTA
4214 ATTACTATTACTCTTTACTA
1 ATTACTATTACTCTTTACTA
* ** *
4234 ATTACCATTTTTCCTTTTACTG
1 ATTACTATTACT-C-TTTACTA
* *
4256 ATCA-TCATTACTTTTTACTA
1 ATTACT-ATTACTCTTTACTA
4276 ATTACTATT
1 ATTACTATT
4285 TTACCCTTTC
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
19 13 0.24
20 27 0.49
21 2 0.04
22 13 0.24
ACGTcount: A:0.28, C:0.20, G:0.01, T:0.51
Consensus pattern (20 bp):
ATTACTATTACTCTTTACTA
Found at i:4318 original size:15 final size:14
Alignment explanation
Indices: 4301--4355 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
4291 TTTCCGATAC
4301 CTTTTTACTGATTA
1 CTTTTTACTGATTA
**
4315 CCTTTTTACTTTTTA
1 -CTTTTTACTGATTA
*
4330 CTGTTTACT-ATTA
1 CTTTTTACTGATTA
*
4343 CTTCTTACTGATT
1 CTTTTTACTGATT
4356 TCTATTACTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
13 10 0.30
14 11 0.33
15 12 0.36
ACGTcount: A:0.18, C:0.18, G:0.05, T:0.58
Consensus pattern (14 bp):
CTTTTTACTGATTA
Found at i:4329 original size:22 final size:20
Alignment explanation
Indices: 4301--4373 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
4291 TTTCCGATAC
*
4301 CTTTTTACTGATTACCTTTTTA
1 CTTTTTACTGATTA-C-TATTA
*
4323 CTTTTTACTGTTTACTATTA
1 CTTTTTACTGATTACTATTA
* *
4343 CTTCTTACTGATTTCTATTA
1 CTTTTTACTGATTACTATTA
*
4363 CTCTTTACTGA
1 CTTTTTACTGA
4374 AAACAAAGGC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 30 0.68
21 1 0.02
22 13 0.30
ACGTcount: A:0.19, C:0.19, G:0.05, T:0.56
Consensus pattern (20 bp):
CTTTTTACTGATTACTATTA
Done.