Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015246.1 Corchorus olitorius cultivar O-4 contig15279, 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: 14605
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Found at i:2242 original size:20 final size:20
Alignment explanation
Indices: 2176--2241 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
2166 CGGAAGGTGT
*
2176 TGTTTTCAATGTTTTATTCT
1 TGTTTTCAATGTTTTATTCC
*
2196 TCTTTTCAATGTTTTATTCC
1 TGTTTTCAATGTTTTATTCC
* *
2216 TGTTTTGAATATTTTATTCC
1 TGTTTTCAATGTTTTATTCC
2236 TGTTTT
1 TGTTTT
2242 GCCCTTCCCG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.15, C:0.12, G:0.09, T:0.64
Consensus pattern (20 bp):
TGTTTTCAATGTTTTATTCC
Found at i:2279 original size:48 final size:48
Alignment explanation
Indices: 2216--2337 Score: 181
Period size: 48 Copynumber: 2.5 Consensus size: 48
2206 GTTTTATTCC
* * * *
2216 TGTTTTGAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGATGT
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGATGA
* * *
2264 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCTAGTCGGAAGGTGA
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGATGA
2312 TGTTTTCAATGTTTTATTCCTGTTTT
1 TGTTTTCAATGTTTTATTCCTGTTTT
2338 CAATATTTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.14, C:0.18, G:0.19, T:0.49
Consensus pattern (48 bp):
TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCAGTCGGAAGATGA
Found at i:2336 original size:68 final size:68
Alignment explanation
Indices: 2264--3334 Score: 858
Period size: 68 Copynumber: 15.8 Consensus size: 68
2254 CGGAAGATGT
** *
2264 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCTAGTCGGAAGGTGATGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
2329 TCC
66 TCC
* * * *
2332 TGTTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTTGGAAGGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
*
2397 TCT
66 TCC
* *
2400 TGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCACGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
2465 TCC
66 TCC
* * * *
2468 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCATTGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
**
2533 TGT
66 TCC
* * ** ***** * * ** *** **
2536 TCTTTTCAATGTTTTATTCCTGTTTT-CAATATTTTATTC---ATGTTTTGCCCTTCCCGGTCGG
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCT-TCCCGGTCGGAAGGTGTTG-TTTTCAATGT-TT
* ****
2597 AAGAGGT
63 TA-TTCC
* *
2604 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTTGGAAGGTGATGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
2669 TCC
66 TCC
* * *
2672 TGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAAGGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
*
2737 TCT
66 TCC
** * *
2740 TGTTTTCAATGTTTTATTCCCAATCTGCCCTTTCCCGGTCGGAAGGTGTTGTTTTTAATGTTTTA
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCC-TTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
*
2805 TTCT
65 TTCC
* *
2809 TGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
*
2874 TCT
66 TCC
* * ** ***** * * ** *** **
2877 TCTTTTCAATGTTTTATTCCTGTTTT-CAATATTTTATTC---ATGTTTTGCCCTTCCCGGTCGA
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCT-TCCCGGTCGGAAGGTGTTG-TTTTCAATGT-TT
* ****
2938 AAGAGGT
63 TA-TTCC
* *
2945 TGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGGTCGAAAGGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
3010 TCC
66 TCC
* * * * *
3013 TGTTTGCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAGGGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
3078 TCC
66 TCC
** * * ** ***** ** * * * ** **
3081 TACTTTCAATGTTTTGTTCCTGTTTT-CAATATTTTATTC---CTGTTTTGCCCTTCCGGTCGGA
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCT-TCCCGGTCGGAAGGTGTTG--TTTTCAAT-GTT
** *
3142 AGAGGT--
62 TTA-TTCC
* *
3148 TGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGGTCGGAATGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
3213 TCC
66 TCC
* * * *
3216 TGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAGGGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
3281 TCC
66 TCC
** ** *
3284 TACTTTCAATG-TTTATTCCCGTTTTGCCCTTCCCCATCGGAAGGGGTTGTT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
3335 CATATTCTCT
Statistics
Matches: 772, Mismatches: 203, Indels: 57
0.75 0.20 0.06
Matches are distributed among these distances:
65 17 0.02
66 11 0.01
67 74 0.10
68 575 0.74
69 68 0.09
70 16 0.02
71 11 0.01
ACGTcount: A:0.14, C:0.19, G:0.18, T:0.49
Consensus pattern (68 bp):
TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
TCC
Found at i:2337 original size:20 final size:20
Alignment explanation
Indices: 2312--2357 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2302 CGGAAGGTGA
* *
2312 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATATTTCATTCC
2332 TGTTTTCAATATTTCATTCC
1 TGTTTTCAATATTTCATTCC
2352 TGTTTT
1 TGTTTT
2358 GCCCTTCCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.61
Consensus pattern (20 bp):
TGTTTTCAATATTTCATTCC
Found at i:2404 original size:20 final size:20
Alignment explanation
Indices: 2379--2425 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2369 TTGGAAGGTG
2379 TTGTTTTCAATGTTTTATTC
1 TTGTTTTCAATGTTTTATTC
2399 TTGTTTTCAATGTTTTATTC
1 TTGTTTTCAATGTTTTATTC
*
2419 TCGTTTT
1 TTGTTTT
2426 GCCCTTCACG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.13, C:0.11, G:0.11, T:0.66
Consensus pattern (20 bp):
TTGTTTTCAATGTTTTATTC
Found at i:2473 original size:20 final size:20
Alignment explanation
Indices: 2448--2493 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2438 CGGAAGGTGT
*
2448 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATATTTTATTCC
2468 TGTTTTCAATATTTTATTCC
1 TGTTTTCAATATTTTATTCC
2488 TGTTTT
1 TGTTTT
2494 GCCCTTCCCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.13, G:0.09, T:0.63
Consensus pattern (20 bp):
TGTTTTCAATATTTTATTCC
Found at i:2541 original size:20 final size:20
Alignment explanation
Indices: 2513--2573 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2503 GATCGGAAGG
* *
2513 TGTTGTTTTCATTGTTTTAT
1 TGTTCTTTTCAATGTTTTAT
2533 TGTTCTTTTCAATGTTTTAT
1 TGTTCTTTTCAATGTTTTAT
** * *
2553 TCCTGTTTTCAATATTTTAT
1 TGTTCTTTTCAATGTTTTAT
2573 T
1 T
2574 CATGTTTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.66
Consensus pattern (20 bp):
TGTTCTTTTCAATGTTTTAT
Found at i:2542 original size:88 final size:88
Alignment explanation
Indices: 2445--2621 Score: 302
Period size: 88 Copynumber: 2.0 Consensus size: 88
2435 GGTCGGAAGG
* *
2445 TGTTGTTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGATCGGA
1 TGTTCTTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGATCGGA
*
2510 AG-GTGTTGTTTTCATTGTTTTAT
66 AGAG-GTTGTTTTCAATGTTTTAT
*
2533 TGTTCTTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTCGGA
1 TGTTCTTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGATCGGA
2598 AGAGGTTGTTTTCAATGTTTTAT
66 AGAGGTTGTTTTCAATGTTTTAT
2621 T
1 T
2622 CCCGTTTTGC
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
88 83 0.99
89 1 0.01
ACGTcount: A:0.15, C:0.16, G:0.16, T:0.54
Consensus pattern (88 bp):
TGTTCTTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGATCGGA
AGAGGTTGTTTTCAATGTTTTAT
Found at i:2574 original size:20 final size:20
Alignment explanation
Indices: 2538--2581 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2528 TTTATTGTTC
* *
2538 TTTTCAATGTTTTATTCCTG
1 TTTTCAATATTTTATTCATG
2558 TTTTCAATATTTTATTCATG
1 TTTTCAATATTTTATTCATG
2578 TTTT
1 TTTT
2582 GCCCTTCCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.11, G:0.07, T:0.64
Consensus pattern (20 bp):
TTTTCAATATTTTATTCATG
Found at i:2609 original size:48 final size:48
Alignment explanation
Indices: 2556--2677 Score: 183
Period size: 48 Copynumber: 2.5 Consensus size: 48
2546 GTTTTATTCC
* * *
2556 TGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTCGGAAGAG-GT
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAG-GTGA
* *
2604 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTTGGAAGGTGA
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGA
2652 TGTTTTCAATGTTTTATTCCTGTTTT
1 TGTTTTCAATGTTTTATTCCTGTTTT
2678 CAATATTTCA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
47 1 0.01
48 66 0.99
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (48 bp):
TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGA
Found at i:2677 original size:20 final size:20
Alignment explanation
Indices: 2652--2697 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2642 TGGAAGGTGA
* *
2652 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATATTTCATTCC
2672 TGTTTTCAATATTTCATTCC
1 TGTTTTCAATATTTCATTCC
*
2692 CGTTTT
1 TGTTTT
2698 GCCCTTCCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.17, G:0.09, T:0.59
Consensus pattern (20 bp):
TGTTTTCAATATTTCATTCC
Found at i:2744 original size:20 final size:20
Alignment explanation
Indices: 2719--2758 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2709 TCGGAAGGTG
2719 TTGTTTTCAATGTTTTATTC
1 TTGTTTTCAATGTTTTATTC
2739 TTGTTTTCAATGTTTTATTC
1 TTGTTTTCAATGTTTTATTC
2759 CCAATCTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (20 bp):
TTGTTTTCAATGTTTTATTC
Found at i:2813 original size:20 final size:20
Alignment explanation
Indices: 2788--2834 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2778 TCGGAAGGTG
* *
2788 TTGTTTTTAATGTTTTATTC
1 TTGTTTTCAATATTTTATTC
2808 TTGTTTTCAATATTTTATTC
1 TTGTTTTCAATATTTTATTC
*
2828 CTGTTTT
1 TTGTTTT
2835 GCCCTTCCCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.09, G:0.09, T:0.68
Consensus pattern (20 bp):
TTGTTTTCAATATTTTATTC
Found at i:2907 original size:88 final size:88
Alignment explanation
Indices: 2791--2964 Score: 296
Period size: 88 Copynumber: 2.0 Consensus size: 88
2781 GAAGGTGTTG
* * * *
2791 TTTTTAATGTTTTATTCTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAG-GT
1 TTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTCGAAAGAG-
2855 GTTGTTTTCAATGTTTTATTCTTC
65 GTTGTTTTCAATGTTTTATTCTTC
2879 TTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTCGAAAGAGG
1 TTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTCGAAAGAGG
2944 TTGTTTTCAATGTTTTATTCT
66 TTGTTTTCAATGTTTTATTCT
2965 CGTTTTGCCC
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 80 0.99
89 1 0.01
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.54
Consensus pattern (88 bp):
TTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTCGAAAGAGG
TTGTTTTCAATGTTTTATTCTTC
Found at i:2920 original size:20 final size:20
Alignment explanation
Indices: 2857--2922 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
2847 CGGAAGGTGT
*
2857 TGTTTTCAATGTTTTATTCT
1 TGTTTTCAATGTTTTATTCA
* *
2877 TCTTTTCAATGTTTTATTCC
1 TGTTTTCAATGTTTTATTCA
*
2897 TGTTTTCAATATTTTATTCA
1 TGTTTTCAATGTTTTATTCA
2917 TGTTTT
1 TGTTTT
2923 GCCCTTCCCG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.17, C:0.12, G:0.08, T:0.64
Consensus pattern (20 bp):
TGTTTTCAATGTTTTATTCA
Found at i:2951 original size:48 final size:47
Alignment explanation
Indices: 2897--3017 Score: 190
Period size: 48 Copynumber: 2.5 Consensus size: 47
2887 GTTTTATTCC
*
2897 TGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGTCGAAAGAG-GT
1 TGTTTTCAATGTTTTATTC-TGTTTTGCCCTTCCCGGTCGAAAG-GTGT
2945 TGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGGTCGAAAGGTGT
1 TGTTTTCAATGTTTTATTCT-GTTTTGCCCTTCCCGGTCGAAAGGTGT
2993 TGTTTTCAATGTTTTATTCCTGTTT
1 TGTTTTCAATGTTTTATT-CTGTTT
3018 GCAATATTTC
Statistics
Matches: 69, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
47 2 0.03
48 65 0.94
49 2 0.03
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.49
Consensus pattern (47 bp):
TGTTTTCAATGTTTTATTCTGTTTTGCCCTTCCCGGTCGAAAGGTGT
Found at i:3022 original size:20 final size:20
Alignment explanation
Indices: 2993--3037 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2983 CGAAAGGTGT
* * *
2993 TGTTTTCAATGTTTTATTCC
1 TGTTTGCAATATTTCATTCC
3013 TGTTTGCAATATTTCATTCC
1 TGTTTGCAATATTTCATTCC
*
3033 CGTTT
1 TGTTT
3038 TGCCCTTCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.56
Consensus pattern (20 bp):
TGTTTGCAATATTTCATTCC
Found at i:3113 original size:88 final size:87
Alignment explanation
Indices: 2996--3166 Score: 263
Period size: 88 Copynumber: 2.0 Consensus size: 87
2986 AAGGTGTTGT
*
2996 TTTCAATGTTTTATTCCTGTTTGCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGG-AGGGTG
1 TTTCAATGTTTTATTCCTGTTTGCAATATTTCATTCCCGTTTTGCCCTT-CCGATCGGAAGAG-G
3060 TTGTTTTCAATGTTTTATTCCTAC
64 TTGTTTTCAATGTTTTATTCCTAC
* * * * *
3084 TTTCAATGTTTTGTTCCTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCGGTCGGAAGAGGTT
1 TTTCAATGTTTTATTCCTGTTTGCAATATTTCATTCCCGTTTTGCCCTTCCGATCGGAAGAGGTT
3149 GTTTTCAATGTTTTATTC
66 GTTTTCAATGTTTTATTC
3167 TCGTTTTGCC
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
87 28 0.37
88 48 0.63
ACGTcount: A:0.15, C:0.19, G:0.16, T:0.50
Consensus pattern (87 bp):
TTTCAATGTTTTATTCCTGTTTGCAATATTTCATTCCCGTTTTGCCCTTCCGATCGGAAGAGGTT
GTTTTCAATGTTTTATTCCTAC
Found at i:3122 original size:20 final size:20
Alignment explanation
Indices: 3061--3126 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
3051 CGGAGGGTGT
3061 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATGTTTTATTCC
** *
3081 TACTTTCAATGTTTTGTTCC
1 TGTTTTCAATGTTTTATTCC
*
3101 TGTTTTCAATATTTTATTCC
1 TGTTTTCAATGTTTTATTCC
3121 TGTTTT
1 TGTTTT
3127 GCCCTTCCGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.61
Consensus pattern (20 bp):
TGTTTTCAATGTTTTATTCC
Found at i:3154 original size:47 final size:48
Alignment explanation
Indices: 3101--3221 Score: 185
Period size: 48 Copynumber: 2.5 Consensus size: 48
3091 GTTTTGTTCC
*
3101 TGTTTTCAATATTTTATTCCTGTTTTGCCCTT-CCGGTCGGAA-GAGGT
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAATG-GGT
*
3148 TGTTTTCAATGTTTTATT-CTCGTTTTGCCCTTCCCGGTCGGAATGTGT
1 TGTTTTCAATGTTTTATTCCT-GTTTTGCCCTTCCCGGTCGGAATGGGT
3196 TGTTTTCAATGTTTTATTCCTGTTTT
1 TGTTTTCAATGTTTTATTCCTGTTTT
3222 CAATATTTCA
Statistics
Matches: 68, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
46 2 0.03
47 28 0.41
48 35 0.51
49 3 0.04
ACGTcount: A:0.12, C:0.18, G:0.19, T:0.50
Consensus pattern (48 bp):
TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAATGGGT
Found at i:3221 original size:20 final size:20
Alignment explanation
Indices: 3196--3241 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
3186 CGGAATGTGT
* *
3196 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATATTTCATTCC
3216 TGTTTTCAATATTTCATTCC
1 TGTTTTCAATATTTCATTCC
*
3236 CGTTTT
1 TGTTTT
3242 GCCCTTCCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.17, G:0.09, T:0.59
Consensus pattern (20 bp):
TGTTTTCAATATTTCATTCC
Found at i:3230 original size:203 final size:204
Alignment explanation
Indices: 2739--3308 Score: 939
Period size: 203 Copynumber: 2.8 Consensus size: 204
2729 TGTTTTATTC
* ** * *
2739 TTGTTTTCAATGTTTTATTCCCAATCTGCCCTTTCCCGGTCGGAAGGTGTTGTTTTTAATGTTTT
1 TTGTTTTCAATGTTTTATTCTCGTTTTGCCC-TTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
* * * * *
2804 ATTCTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGT
65 ATTCCTGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAGGGTGTTGTTTTCAATGT
*
2869 TTTATT-CTTCTTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCG
130 TTTATTCCTAC-TTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCG
2933 GTCGAAAGAGG
194 GTCGAAAGAGG
*
2944 TTGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGGTCGAAAGGTGTTGTTTTCAATGTTTTA
1 TTGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
*
3009 TTCCTGTTTGCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAGGGTGTTGTTTTCAATGTT
66 TTCCTGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAGGGTGTTGTTTTCAATGTT
* *
3074 TTATTCCTACTTTCAATGTTTTGTTCCTGTTTTCAATATTTTATTCCTGTTTTGCCCTT-CCGGT
131 TTATTCCTACTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGT
*
3138 CGGAAGAGG
196 CGAAAGAGG
*
3147 TTGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGGTCGGAATGTGTTGTTTTCAATGTTTTA
1 TTGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
3212 TTCCTGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAGGGTGTTGTTTTCAATGTT
66 TTCCTGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAGGGTGTTGTTTTCAATGTT
*
3277 TTATTCCTACTTTCAATG-TTTATTCCCGTTTT
131 TTATTCCTACTTTCAATGTTTTATTCCTGTTTT
3309 GCCCTTCCCC
Statistics
Matches: 343, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
202 12 0.03
203 158 0.46
204 143 0.42
205 30 0.09
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.49
Consensus pattern (204 bp):
TTGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
TTCCTGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGATCGGAGGGTGTTGTTTTCAATGTT
TTATTCCTACTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCATGTTTTGCCCTTCCCGGT
CGAAAGAGG
Found at i:7482 original size:19 final size:18
Alignment explanation
Indices: 7449--7484 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7439 TTGAAATTAT
7449 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
7467 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
7485 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:9069 original size:16 final size:16
Alignment explanation
Indices: 9014--9069 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
9004 TAGATAGTTT
*
9014 ATTAATGAAACTTGAAA
1 ATTAAAGAAA-TTGAAA
* *
9031 ATTAAAGACATAT-AAG
1 ATTAAAGAAAT-TGAAA
*
9047 ATAAAAGAAATTGAAA
1 ATTAAAGAAATTGAAA
9063 ATTAAAG
1 ATTAAAG
9070 CATAAATTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
15 1 0.03
16 20 0.67
17 9 0.30
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.25
Consensus pattern (16 bp):
ATTAAAGAAATTGAAA
Found at i:13457 original size:11 final size:11
Alignment explanation
Indices: 13441--13466 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13431 AGATAAATTC
13441 TTTTCTTCTAG
1 TTTTCTTCTAG
13452 TTTTCTTCTAG
1 TTTTCTTCTAG
13463 TTTT
1 TTTT
13467 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Done.