Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1380
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: 15224
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Found at i:2542 original size:33 final size:32
Alignment explanation
Indices: 2492--2710 Score: 189
Period size: 33 Copynumber: 6.8 Consensus size: 32
2482 CTTCTTTTCA
* *
2492 AAGCCCACAACTACATGGCACTCTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCAC-CTTTTCCTTTT
* * * **
2525 AAGTCCACAATTCCATGGCACCTTTTTTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
* *
2557 AAAGCCCACAACTCTGTGGCACTTTTTTCCTTTT
1 -AAGCCCACAACTCCGTGGCAC-CTTTTCCTTTT
*
2591 AAGTCCACAACTCCGTGGCA-C----CCTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
* *
2618 AAAGCCCACAACTCCGTGGCACTCTTTCCCCTCTTA
1 -AAGCCCACAACTCCGTGGCAC-CTTT-TCCT-TTT
2654 AAGCCCACAACTCCGTGGCACCTTATT-CTTTT
1 AAGCCCACAACTCCGTGGCACCTT-TTCCTTTT
* * *
2686 AAGTCCACAACTTCGTGGCATCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
2711 CACCCCTTCA
Statistics
Matches: 152, Mismatches: 22, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
27 6 0.04
28 19 0.12
30 1 0.01
31 1 0.01
32 32 0.21
33 55 0.36
34 11 0.07
35 25 0.16
36 2 0.01
ACGTcount: A:0.22, C:0.33, G:0.12, T:0.33
Consensus pattern (32 bp):
AAGCCCACAACTCCGTGGCACCTTTTCCTTTT
Found at i:2577 original size:66 final size:65
Alignment explanation
Indices: 2458--2710 Score: 247
Period size: 66 Copynumber: 3.9 Consensus size: 65
2448 AAATACCTTC
* ** * *
2458 TTTAAGTCCACGACTCTATGGCA--TCTTCTTTTCAAAGCCCACAACTAC-ATGGCACTCTTTTC
1 TTTAAGTCCACAACTCCGTGGCACCTTTTCTTTT-AAAGCCCACAACT-CTGTGGCACTCTTTTC
2520 CT
64 CT
* * * *
2522 TTTAAGTCCACAATTCCATGGCACCTTTTTTTTTTAAAGCCCACAACTCTGTGGCACTTTTTTCC
1 TTTAAGTCCACAACTCCGTGGCACC-TTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTCC
2587 T
65 T
* *
2588 TTTAAGTCCACAACTCCGTGGCACC----CTTTTAAAGCCCACAACTCCGTGGCACTCTTTCCCC
1 TTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTT-TCC
2649 T
65 T
* * *
2650 CTTAAAGCCCACAACTCCGTGGCACCTTATTCTTTT-AAGTCCACAACT-TCGTGGCA-TCTTT
1 -TTTAAGTCCACAACTCCGTGGCACCTT-TTCTTTTAAAGCCCACAACTCT-GTGGCACTCTTT
2711 CACCCCTTCA
Statistics
Matches: 160, Mismatches: 17, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
61 29 0.18
62 3 0.02
63 23 0.14
64 20 0.12
65 1 0.01
66 55 0.34
67 24 0.15
68 5 0.03
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (65 bp):
TTTAAGTCCACAACTCCGTGGCACCTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTCCT
Found at i:2630 original size:28 final size:28
Alignment explanation
Indices: 2553--2644 Score: 96
Period size: 28 Copynumber: 3.1 Consensus size: 28
2543 CACCTTTTTT
*
2553 TTTTAAAGCCCACAACTCTGTGGCACTTTTTTCC
1 TTTTAAAGCCCACAACTCCGTGGCAC------CC
*
2587 TTTT-AAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAACTCCGTGGCACCC
*
2614 TTTTAAAGCCCACAACTCCGTGGCACTC
1 TTTTAAAGCCCACAACTCCGTGGCACCC
2642 TTT
1 TTT
2645 CCCCTCTTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.11
28 24 0.45
33 19 0.36
34 4 0.08
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.33
Consensus pattern (28 bp):
TTTTAAAGCCCACAACTCCGTGGCACCC
Found at i:2662 original size:35 final size:35
Alignment explanation
Indices: 2611--2729 Score: 124
Period size: 35 Copynumber: 3.5 Consensus size: 35
2601 CTCCGTGGCA
*
2611 CCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTC
1 CCCTCTTAAAGCCCACAACTCCGTGGCACTCTTTC
2646 CCCTCTTAAAGCCCACAACTCCGTGGCAC-CTTAT-
1 CCCTCTTAAAGCCCACAACTCCGTGGCACTCTT-TC
* * * *
2680 -TCT-TTTAAGTCCACAACTTCGTGGCA-TCTTTC
1 CCCTCTTAAAGCCCACAACTCCGTGGCACTCTTTC
2712 ACCC-CTTCAAAGCCCACA
1 -CCCTCTT-AAAGCCCACA
2730 CAAGTCGGTG
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
31 1 0.01
32 23 0.33
33 2 0.03
34 6 0.09
35 37 0.54
ACGTcount: A:0.23, C:0.39, G:0.11, T:0.28
Consensus pattern (35 bp):
CCCTCTTAAAGCCCACAACTCCGTGGCACTCTTTC
Found at i:2724 original size:67 final size:63
Alignment explanation
Indices: 2553--2760 Score: 201
Period size: 61 Copynumber: 3.2 Consensus size: 63
2543 CACCTTTTTT
* ** * *
2553 TTTTAAAGCCCACAACTCTGTGGCACT-TTTTTCCT-TTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTCCCCTCTTAAAGCCCACAACTCCGTGGCACCC
2614 TTTTAAAGCCCACAACTCCGTGGCACTCTTTCCCCTCTTAAAGCCCACAACTCCGTGGCACCTTA
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTCCCCTCTTAAAGCCCACAACTCCGTGGCACC---
2679 TTC
63 --C
* * * * *
2682 TTTT-AAGTCCACAACTTCGTGGCA-TCTTTCACCC-CTTCAAAGCCCACACAAGTCGGTGGCAA
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTC-CCCTCTT-AAAG-CC-CACAACTCCGTGGCAC
2744 CC
62 CC
2746 TTTTCAAAGCCCACA
1 TTTT-AAAGCCCACA
2761 CAAGTCGGTG
Statistics
Matches: 123, Mismatches: 11, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
61 26 0.21
62 6 0.05
63 23 0.19
64 5 0.04
66 17 0.14
67 25 0.20
68 7 0.06
69 14 0.11
ACGTcount: A:0.24, C:0.35, G:0.13, T:0.28
Consensus pattern (63 bp):
TTTTAAAGCCCACAACTCCGTGGCACTCTTTCCCCTCTTAAAGCCCACAACTCCGTGGCACCC
Found at i:2752 original size:31 final size:31
Alignment explanation
Indices: 2717--2869 Score: 227
Period size: 33 Copynumber: 4.8 Consensus size: 31
2707 CTTTCACCCC
2717 TTCAAAGCCCACACAAGTCGGTGGCAACCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCTT
*
2748 TTCAAAGCCCACACAAGTCGGTGACAACCTTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACC-TT
* *
2780 TTCTAAAGCCCACATAAGTCGGTGGCAACCCT
1 TTC-AAAGCCCACACAAGTCGGTGGCAACCTT
2812 TT-AAAGCCCACACAAGTCGGTGGCAACCTT
1 TTCAAAGCCCACACAAGTCGGTGGCAACCTT
*
2842 CTTCAAAAGCCCACACAAGTTGGTGGCA
1 -TTC-AAAGCCCACACAAGTCGGTGGCA
2870 TATTCCTTTA
Statistics
Matches: 110, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.24
31 30 0.27
32 8 0.07
33 46 0.42
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (31 bp):
TTCAAAGCCCACACAAGTCGGTGGCAACCTT
Found at i:2839 original size:63 final size:64
Alignment explanation
Indices: 2716--2869 Score: 240
Period size: 63 Copynumber: 2.4 Consensus size: 64
2706 TCTTTCACCC
*
2716 CTTC-AAAGCCCACACAAGTCGGTGGCAACCTTTTCAAAGCCCACACAAGTCGGTGACAACCTT
1 CTTCAAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACACAAGTCGGTGACAACCTT
* * * *
2779 TTTCTAAAGCCCACATAAGTCGGTGGCAACCCTTT-AAAGCCCACACAAGTCGGTGGCAACCTT
1 CTTCAAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACACAAGTCGGTGACAACCTT
*
2842 CTTCAAAAGCCCACACAAGTTGGTGGCA
1 CTTCAAAAGCCCACACAAGTCGGTGGCA
2870 TATTCCTTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
63 54 0.66
64 28 0.34
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (64 bp):
CTTCAAAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACACAAGTCGGTGACAACCTT
Found at i:2930 original size:43 final size:43
Alignment explanation
Indices: 2874--3240 Score: 394
Period size: 43 Copynumber: 8.1 Consensus size: 43
2864 GTGGCATATT
*
2874 CCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
* * *
2917 CCTTTAAGTCCAATATCGCTGGCCTGGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
*
2960 CCTTTGTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
1 -C-----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
** * *
3009 CCTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
3052 CCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
** * * *
3101 CCTCCAAG-CCTAATATCGTTGGCCTTGAATCAGCATATTGGCA
1 CCTTTAAGTCC-AATATAGCTGGCCTTGAATCAGCACATTGGCA
* *
3144 TCTTCATCTTTAAGTCCAATGTAGATGGCCTTGAATCAGCACATTGGCA
1 ----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
* *
3193 CCTTTAAGTCCAATATAACTGGCCTTGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
3236 CCTTT
1 CCTTT
3241 TCCATCTTTA
Statistics
Matches: 272, Mismatches: 32, Indels: 40
0.79 0.09 0.12
Matches are distributed among these distances:
42 2 0.01
43 153 0.56
44 1 0.00
45 2 0.01
47 2 0.01
48 1 0.00
49 109 0.40
50 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (43 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA
Found at i:3032 original size:92 final size:92
Alignment explanation
Indices: 2875--3284 Score: 651
Period size: 92 Copynumber: 4.4 Consensus size: 92
2865 TGGCATATTC
**
2875 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC
* **
2940 CTGGAATCAGCATATTGGCACCTTTGT
66 CTTGAATCAGCATATTGGCACCTTCAT
2967 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC
3032 CTTGAATCAGCATATTGGCACCTTCAT
66 CTTGAATCAGCATATTGGCACCTTCAT
* *
3059 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAG-CCTAATATCGTTGG
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCC-AATATCGCTGG
*
3123 CCTTGAATCAGCATATTGGCATCTTCAT
65 CCTTGAATCAGCATATTGGCACCTTCAT
* ** **
3151 CTTTAAGTCCAATGTAGATGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAACTGGC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC
3216 CTTGAATCAGCATATTGGCACCTTTTCCAT
66 CTTGAATCAGCATATTGGCACC--TT-CAT
*
3246 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
3285 ACATCCTTTT
Statistics
Matches: 295, Mismatches: 18, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
91 2 0.01
92 249 0.84
93 2 0.01
94 2 0.01
95 40 0.14
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (92 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCCAAGTCCAATATCGCTGGC
CTTGAATCAGCATATTGGCACCTTCAT
Found at i:3272 original size:52 final size:55
Alignment explanation
Indices: 3194--3316 Score: 162
Period size: 52 Copynumber: 2.3 Consensus size: 55
3184 ACATTGGCAC
* *
3194 CTTTAAGTCCAATATAACTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAACTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * *
3246 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTTCTCAT
1 CTTTAAGTCCAATATAACTGGCCTTGAATCAGCACATTGACATCC-TTTTTCTCAT
*
3302 CTTTAAGCCCAATAT
1 CTTTAAGTCCAATAT
3317 TGTTAGTCGT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
52 37 0.63
53 2 0.03
55 5 0.08
56 15 0.25
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (55 bp):
CTTTAAGTCCAATATAACTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:3438 original size:49 final size:49
Alignment explanation
Indices: 3363--3853 Score: 498
Period size: 49 Copynumber: 10.2 Consensus size: 49
3353 TTTTTCTCAT
* * *
3363 CTTCATCGTTAAGTCCAATATCGCTGGCCTTGAATCAGCGTATTAGCAC
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
** * *
3412 CTTCATCTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCATATTGTCAC
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
* * * * * *
3461 CTTCTTCTTTAAGTCCAATGTAGCTGGTCTTGAATAAGCACATTGGCA-
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
3509 ---C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
* * * * * * *
3553 CATCATCTTTAAGTCTAATGTAGCCGACCTTGAATCAGCACATTGGCA-
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
*
3601 ATTC--C---AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
* * * *
3645 CCTCATCTTTTAAG-CACAATGTCGCTGGCCTTGAATCAACACATTGGCA-
1 CTTCATC-TTTAAGTC-CAATATCGCTGGCCTTGAATCAGCATATTGGCAC
*
3694 ---C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGC
1 CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
* *
3738 CTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCGTC
1 C--T-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC
* * *
3791 TTTGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 -CT-TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
3842 CTTCATCTTTAA
1 CTTCATCTTTAA
3854 CATTCCTAAG
Statistics
Matches: 367, Mismatches: 49, Indels: 52
0.78 0.10 0.11
Matches are distributed among these distances:
43 104 0.28
44 4 0.01
45 1 0.00
46 3 0.01
47 1 0.00
48 2 0.01
49 131 0.36
50 35 0.10
51 1 0.00
52 84 0.23
53 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
CTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:3530 original size:43 final size:43
Alignment explanation
Indices: 3467--3844 Score: 256
Period size: 43 Copynumber: 8.1 Consensus size: 43
3457 TCACCTTCTT
* * * *
3467 CTTTAAGTCCAATGTAGCTGGTCTTGAATAAGCACATTGGCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
*
3510 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGG---CA-C
* * * * *
3557 ATCTTTAAGTCTAATGTAGCCGACCTTGAATCAGCACATTGGCA-
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
3601 ATTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTC
1 CTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA----C
* *
3649 ATCTTTTAAG-CACAATGTCGCTGGCCTTGAATCAACACATTGGCAC
1 --C-TTTAAGTC-CAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* *
3695 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT---G-----G-CAC
* * *
3747 CTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCGTCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT---G-----G-CAC
*
3799 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
3842 CTT
1 CTT
3845 CATCTTTAAC
Statistics
Matches: 275, Mismatches: 34, Indels: 52
0.76 0.09 0.14
Matches are distributed among these distances:
42 2 0.01
43 104 0.38
44 3 0.01
46 6 0.02
47 1 0.00
49 36 0.13
50 33 0.12
51 3 0.01
52 87 0.32
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:3543 original size:92 final size:92
Alignment explanation
Indices: 3418--3853 Score: 491
Period size: 92 Copynumber: 4.6 Consensus size: 92
3408 GCACCTTCAT
** * * *
3418 CTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCATATTGTCACCTTCTTCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
*
3483 GCTGGTCTTGAATAAGCACATTGGCAC
66 GCTGGCCTTGAATAAGCACATTGGCAC
* *
3510 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGTCTAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
* * *
3575 GCCGACCTTGAATCAGCACATTGGCA-
66 GCTGGCCTTGAATAAGCACATTGGCAC
* * *
3601 ATTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTCATCTTTTAAG-CACAAT
1 CTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTC-CAAT
*
3665 GTCGCTGGCCTTGAATCAA-CACATTGGCAC
63 GTAGCTGGCCTTGAAT-AAGCACATTGGCAC
*
3695 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAAT
* * * * * *
3760 ATCGCTGGCCTTAAATCAGCATATTGGCGTCTTTGTCAT
63 GTAGCTGGCCTTGAATAAGCACATT---G-----G-CAC
* *
3799 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAA
3854 CATTCCTAAG
Statistics
Matches: 294, Mismatches: 31, Indels: 29
0.83 0.09 0.08
Matches are distributed among these distances:
91 2 0.01
92 126 0.43
93 71 0.24
94 4 0.01
95 29 0.10
96 6 0.02
98 1 0.00
101 10 0.03
102 1 0.00
103 1 0.00
104 43 0.15
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
GCTGGCCTTGAATAAGCACATTGGCAC
Found at i:3777 original size:52 final size:52
Alignment explanation
Indices: 3695--3844 Score: 255
Period size: 52 Copynumber: 2.9 Consensus size: 52
3685 ACATTGGCAC
3695 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
* *
3747 CTTTAAGTCCAATATCGCTGGCCTTAAATCAGCATATTGGCGTCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
* * *
3799 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTT
3845 CATCTTTAAC
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 91 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
Found at i:4724 original size:13 final size:13
Alignment explanation
Indices: 4706--4795 Score: 63
Period size: 13 Copynumber: 5.9 Consensus size: 13
4696 CATAAAGTGT
4706 TGTATCGATACAA
1 TGTATCGATACAA
4719 TGTATCGATACATAAA
1 TGTATCGATAC---AA
4735 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
4752 TGTATCGATACATAAGTA
1 TGTATCGATAC---A--A
4770 TTGTATCGATACAA
1 -TGTATCGATACAA
4784 TGTATCGATACA
1 TGTATCGATACA
4796 TAAGTTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 26
0.71 0.00 0.29
Matches are distributed among these distances:
13 34 0.53
14 1 0.02
16 4 0.06
17 2 0.03
18 1 0.02
19 11 0.17
20 11 0.17
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4744 original size:20 final size:20
Alignment explanation
Indices: 4685--4750 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
4675 TTTCAATGAT
*
4685 TTGTATTGATACATAAAGTG
1 TTGTATCGATACATAAAGTG
4705 TTGTATCGATAC---AA---
1 TTGTATCGATACATAAAGTG
4719 -TGTATCGATACATAAAGTG
1 TTGTATCGATACATAAAGTG
4738 TTGTATCGATACA
1 TTGTATCGATACA
4751 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 11 0.29
16 2 0.05
17 2 0.05
20 23 0.61
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (20 bp):
TTGTATCGATACATAAAGTG
Found at i:4776 original size:19 final size:19
Alignment explanation
Indices: 4719--4814 Score: 81
Period size: 19 Copynumber: 5.6 Consensus size: 19
4709 ATCGATACAA
*
4719 TGTATCGATACATAAAGTGT
1 TGTATCGATACAT-AAGTAT
4739 TGTATCGATAC---A--A-
1 TGTATCGATACATAAGTAT
4752 TGTATCGATACATAAGTAT
1 TGTATCGATACATAAGTAT
4771 TGTATCGATAC---A--A-
1 TGTATCGATACATAAGTAT
*
4784 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTAT
4803 TGTATCGATACA
1 TGTATCGATACA
4815 ATTTAAGCTA
Statistics
Matches: 62, Mismatches: 2, Indels: 25
0.70 0.02 0.28
Matches are distributed among these distances:
13 22 0.35
14 1 0.02
16 4 0.06
18 1 0.02
19 23 0.37
20 11 0.18
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTAT
Found at i:4779 original size:32 final size:33
Alignment explanation
Indices: 4686--4816 Score: 221
Period size: 32 Copynumber: 4.0 Consensus size: 33
4676 TTCAATGATT
*
4686 TGTATTGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
4719 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
4752 TGTATCGATACAT-AAGTATTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
4784 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
4816 T
1 T
4817 TTAAGCTACT
Statistics
Matches: 95, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 50 0.53
33 45 0.47
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:4783 original size:65 final size:65
Alignment explanation
Indices: 4686--4816 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
4676 TTCAATGATT
* *
4686 TGTATTGATACATAAAGTGTTGTATCGATACAATGTATCGATACATAAAGTGTTGTATCGATACA
1 TGTATCGATACATAAAGTATTGTATCGATACAATGTATCGATACAT-AAGTGTTGTATCGATACA
4751 A
65 A
*
4752 TGTATCGATACAT-AAGTATTGTATCGATACAATGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTATTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAA
4816 T
1 T
4817 TTAAGCTACT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 19 0.31
65 31 0.50
66 12 0.19
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (65 bp):
TGTATCGATACATAAAGTATTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:4842 original size:65 final size:65
Alignment explanation
Indices: 4708--4847 Score: 160
Period size: 65 Copynumber: 2.2 Consensus size: 65
4698 TAAAGTGTTG
* ** * *
4708 TATCGATACAATGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACATAAGTATTG
1 TATCGATACAATGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATACATAAAAAATA
* * *
4773 TATCGATACAATGTATCGATACAT-AAGTTTTGTATCGATACAATTTA-AGCTAC-TGCCAAAAA
1 TATCGATACAATGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATACAT---AAAAA
4835 ATA
63 ATA
4838 TATCGATACA
1 TATCGATACA
4848 TTACTCAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 1 0.02
63 4 0.06
64 21 0.33
65 38 0.59
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (65 bp):
TATCGATACAATGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATACATAAAAAATA
Found at i:4875 original size:13 final size:13
Alignment explanation
Indices: 4857--4881 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4847 ATTACTCAAA
4857 TATATCGATACAT
1 TATATCGATACAT
4870 TATATCGATACA
1 TATATCGATACA
4882 CTGATCTTTG
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:4895 original size:151 final size:152
Alignment explanation
Indices: 4738--5053 Score: 607
Period size: 151 Copynumber: 2.1 Consensus size: 152
4728 ACATAAAGTG
4738 TTGTATCGATACAATGTATCGATACATAAGTATTGTATCGATACAATGTATCGATACATAAGTTT
1 TTGTATCGATACAATGTATCGATACATAAGTATTGTATCGATACAATGTATCGATACATAAGTTT
4803 TGTATCGATACAATTTAAGCTACTGCC-AAAAAATATATCGATACATTACTCAAATATATCGATA
66 TGTATCGATACAATTTAAGCTACTGCCAAAAAAATATATCGATACATTACTCAAATATATCGATA
4867 CATTATATCGATACACTGATCT
131 CATTATATCGATACACTGATCT
4889 TTGTATCGATACAATGTATCGATACATAAGTATTGTATCGATACAATGTATCGATACATAAGTTT
1 TTGTATCGATACAATGTATCGATACATAAGTATTGTATCGATACAATGTATCGATACATAAGTTT
*
4954 TGTATCGATACAATTTAAGCTACTGCCAAAAAAATTTATCGATACATTACTCAAATATATCGATA
66 TGTATCGATACAATTTAAGCTACTGCCAAAAAAATATATCGATACATTACTCAAATATATCGATA
5019 CATTATATCGATACACTGATCT
131 CATTATATCGATACACTGATCT
*
5041 TTGTATTGATACA
1 TTGTATCGATACA
5054 TGCAAGCAAA
Statistics
Matches: 162, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
151 92 0.57
152 70 0.43
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (152 bp):
TTGTATCGATACAATGTATCGATACATAAGTATTGTATCGATACAATGTATCGATACATAAGTTT
TGTATCGATACAATTTAAGCTACTGCCAAAAAAATATATCGATACATTACTCAAATATATCGATA
CATTATATCGATACACTGATCT
Found at i:4908 original size:13 final size:13
Alignment explanation
Indices: 4890--4946 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
4880 CACTGATCTT
4890 TGTATCGATACAA
1 TGTATCGATACAA
4903 TGTATCGATACATAAGTA
1 TGTATCGATAC---A--A
4921 TTGTATCGATACAA
1 -TGTATCGATACAA
4935 TGTATCGATACA
1 TGTATCGATACA
4947 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4927 original size:19 final size:19
Alignment explanation
Indices: 4903--4965 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
4893 ATCGATACAA
4903 TGTATCGATACATAAGTAT
1 TGTATCGATACATAAGTAT
4922 TGTATCGATAC---A--A-
1 TGTATCGATACATAAGTAT
*
4935 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTAT
4954 TGTATCGATACA
1 TGTATCGATACA
4966 ATTTAAGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
16 2 0.05
19 23 0.62
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATAAGTAT
Found at i:4930 original size:32 final size:32
Alignment explanation
Indices: 4889--4967 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
4879 ACACTGATCT
4889 TTGTATCGATACAATGTATCGATACATAAGTA
1 TTGTATCGATACAATGTATCGATACATAAGTA
*
4921 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTA
4953 TTGTATCGATACAAT
1 TTGTATCGATACAAT
4968 TTAAGCTACT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTA
Found at i:5027 original size:13 final size:13
Alignment explanation
Indices: 5009--5033 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4999 ATTACTCAAA
5009 TATATCGATACAT
1 TATATCGATACAT
5022 TATATCGATACA
1 TATATCGATACA
5034 CTGATCTTTG
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TATATCGATACAT
Found at i:5082 original size:52 final size:50
Alignment explanation
Indices: 5024--5170 Score: 195
Period size: 52 Copynumber: 2.8 Consensus size: 50
5014 CGATACATTA
* *
5024 TATCGATACACTGATCTTTGTATTGATACATGCAAGCAAATTTGCCCAGATG
1 TATCGATACACT-AT-TATGTATCGATACATGCAAGCAAATTTGCCCAGATG
* *
5076 TATCGATACACTATAAAATGTATCGATACATGCAAGCAAATTTGCCCATATG
1 TATCGATACACTAT--TATGTATCGATACATGCAAGCAAATTTGCCCAGATG
*
5128 TATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTT
1 TATCGATACACTATT--ATGTATCGATACATGCAAGCAAATTT
5171 TCATATTTCG
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (50 bp):
TATCGATACACTATTATGTATCGATACATGCAAGCAAATTTGCCCAGATG
Found at i:7297 original size:24 final size:26
Alignment explanation
Indices: 7270--7323 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
7260 TCAAAAAATT
7270 ATTCAT-C-GGGGACACTCCAACCCC
1 ATTCATCCAGGGGACACTCCAACCCC
*
7294 ATTCTTCCGAGGGGACACTCCAACCCC
1 ATTCATCC-AGGGGACACTCCAACCCC
7321 ATT
1 ATT
7324 TTCAACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 1 0.04
27 20 0.77
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (26 bp):
ATTCATCCAGGGGACACTCCAACCCC
Found at i:8501 original size:18 final size:19
Alignment explanation
Indices: 8478--8517 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
8468 TAGTTATGCT
*
8478 TAAAATATT-TTATATTTA
1 TAAAATATTGTTATATTAA
*
8496 TAAAATTTTGTTATATTAA
1 TAAAATATTGTTATATTAA
8515 TAA
1 TAA
8518 TTTGTGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TAAAATATTGTTATATTAA
Found at i:8511 original size:19 final size:19
Alignment explanation
Indices: 8478--8529 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
8468 TAGTTATGCT
*
8478 TAAAATATT-TTATATTTA
1 TAAAATTTTGTTATATTTA
8496 TAAAATTTTGTTATA-TTA
1 TAAAATTTTGTTATATTTA
*
8514 -ATAATTTGTGTTATAT
1 TAAAATTT-TGTTATAT
8530 AAATTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 6 0.21
18 18 0.62
19 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
TAAAATTTTGTTATATTTA
Found at i:8903 original size:16 final size:18
Alignment explanation
Indices: 8872--8907 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
8862 AATAATTAAA
8872 ATAAATATGATGAAAAAT
1 ATAAATATGATGAAAAAT
8890 ATAAATAT-AT-AAAAAT
1 ATAAATATGATGAAAAAT
8906 AT
1 AT
8908 CAAAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
ATAAATATGATGAAAAAT
Found at i:12825 original size:6 final size:6
Alignment explanation
Indices: 12814--12866 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
12804 GAGAGCACTC
* *
12814 TATATA TATATA TATATA TATATA TATATA TATACA TATATA CATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
*
12862 CATAT
1 TATAT
12867 TTGAAACTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:12827 original size:8 final size:8
Alignment explanation
Indices: 12814--12866 Score: 79
Period size: 8 Copynumber: 6.6 Consensus size: 8
12804 GAGAGCACTC
12814 TATATATA
1 TATATATA
12822 TATATATA
1 TATATATA
12830 TATATATA
1 TATATATA
12838 TATATATA
1 TATATATA
*
12846 TACATATA
1 TATATATA
*
12854 TACATATA
1 TATATATA
*
12862 CATAT
1 TATAT
12867 TTGAAACTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (8 bp):
TATATATA
Found at i:12833 original size:14 final size:14
Alignment explanation
Indices: 12814--12866 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
12804 GAGAGCACTC
*
12814 TATATATATATATA
1 TATATACATATATA
*
12828 TATATATATATATA
1 TATATACATATATA
12842 TATATACATATATA
1 TATATACATATATA
*
12856 CATATACATAT
1 TATATACATAT
12867 TTGAAACTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATACATATATA
Done.