Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014343.1 Corchorus olitorius cultivar O-4 contig14376, 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: 4827
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Found at i:2276 original size:35 final size:35
Alignment explanation
Indices: 2221--2756 Score: 199
Period size: 36 Copynumber: 16.3 Consensus size: 35
2211 GTTGCTAAAG
* * * *
2221 ATTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCA
1 ATTTATTTCAATCGATCCAGGGCGATCTTTCTTCA
* *
2256 ATTCATTTCAATCGATCCAGGGTGATCTTTCTTCA
1 ATTTATTTCAATCGATCCAGGGCGATCTTTCTTCA
* * * *
2291 ATTTACTTCAGTTGATCCAAGGCGATCTTCTCTTCA
1 ATTTATTTCAATCGATCCAGGGCGATCTT-TCTTCA
* *
2327 GTTTATTTCAATCAATCCA----G-T-TTAT-TTCA
1 ATTTATTTCAATCGATCCAGGGCGATCTT-TCTTCA
* * * **
2356 GTTGA-TCCAGGGCGAT-C-------T-TTTCTTCA
1 ATTTATTTCA-ATCGATCCAGGGCGATCTTTCTTCA
* * *
2382 GTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCA
1 ATTTATTTCAATCGATCCAGGGCGATC-TTTCTTCA
* *
2418 GTTTATTTCAATTGATCCAGGGCGATC-TT-TTC-
1 ATTTATTTCAATCGATCCAGGGCGATCTTTCTTCA
* * *
2450 ------TTCAGTTGATCTAGGGCGATCTTCTCTTCA
1 ATTTATTTCAATCGATCCAGGGCGATCTT-TCTTCA
* * * * *
2480 GTTTATTTCAATTGATCCGGGGTGGTCTTTCTTCA
1 ATTTATTTCAATCGATCCAGGGCGATCTTTCTTCA
* * *
2515 GTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCA
1 ATTTATTTCAATCGATCCAGGGCGATC-TTTCTTCA
* * * *
2551 GTTTATTTCAATTGATCCGGGGCAATCTTTTCTTCA
1 ATTTATTTCAATCGATCCAGGGCGATC-TTTCTTCA
* * * *
2587 GTTTATTTCAGTTGATCGAGGGCGATC-TT-TTC-
1 ATTTATTTCAATCGATCCAGGGCGATCTTTCTTCA
*
2619 -----TTT-AATTGATCCAGGGCGATCTTTCCTT-A
1 ATTTATTTCAATCGATCCAGGGCGATCTTT-CTTCA
* * * * *
2648 GTTTATTTCAGTTGATCGAGGACGATC-TT-TTC-
1 ATTTATTTCAATCGATCCAGGGCGATCTTTCTTCA
* *
2680 -----TTT-AATTGATCCAGGGCGATCTTTCCTCA
1 ATTTATTTCAATCGATCCAGGGCGATCTTTCTTCA
* * *
2709 ATTTACTTCAATAGATCCAGGGCGATCTTCTCTGCA
1 ATTTATTTCAATCGATCCAGGGCGATCTT-TCTTCA
*
2745 GTTTATTTCAAT
1 ATTTATTTCAAT
2757 TGACTGCAAA
Statistics
Matches: 394, Mismatches: 61, Indels: 91
0.72 0.11 0.17
Matches are distributed among these distances:
25 1 0.00
26 65 0.16
27 15 0.04
28 7 0.02
29 16 0.04
30 3 0.01
31 1 0.00
32 3 0.01
33 6 0.02
34 12 0.03
35 115 0.29
36 150 0.38
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.42
Consensus pattern (35 bp):
ATTTATTTCAATCGATCCAGGGCGATCTTTCTTCA
Found at i:2391 original size:36 final size:36
Alignment explanation
Indices: 2344--2759 Score: 403
Period size: 36 Copynumber: 12.5 Consensus size: 36
2334 TCAATCAATC
2344 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
2380 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
*
2416 CAGTTTATTTCAATTGATCCAGGGCGATC--TT-TT
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
* *
2449 C-------TTCAGTTGATCTAGGGCGATCTTCTCTT
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
* * * *
2478 CAGTTTATTTCAATTGATCCGGGGTGGTC-TTTCTT
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
2513 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
* * *
2549 CAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTT
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
*
2585 CAGTTTATTTCAGTTGATCGAGGGCGATC--TT-TT
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
*
2618 C--TTTA----A-TTGATCCAGGGCGATCTTTCCTT
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
* *
2647 -AGTTTATTTCAGTTGATCGAGGACGATC--TT-TT
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
*
2679 C--TTTA----A-TTGATCCAGGGCGATC-TTTCCT
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
* * * * * *
2707 CAATTTACTTCAATAGATCCAGGGCGATCTTCTCTG
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
*
2743 CAGTTTATTTCAATTGA
1 CAGTTTATTTCAGTTGA
2760 CTGCAAAATG
Statistics
Matches: 312, Mismatches: 36, Indels: 64
0.76 0.09 0.16
Matches are distributed among these distances:
26 48 0.15
27 4 0.01
28 4 0.01
29 5 0.02
30 8 0.03
31 8 0.03
32 2 0.01
33 7 0.02
34 6 0.02
35 59 0.19
36 161 0.52
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (36 bp):
CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTT
Found at i:2455 original size:62 final size:62
Alignment explanation
Indices: 2388--2589 Score: 269
Period size: 62 Copynumber: 3.1 Consensus size: 62
2378 TTCAGTTTAT
*
2388 TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTTTTC
1 TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCGATCTTTTC
* * * *
2450 TTCAGTTGATCTAGGGCGATCTTCTCTTCAGTTTATTTCAATTGATCCGGGGTGGTCTTTCTTC
1 TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCGATC-TT-TTC
*
2514 AGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCAATCT
1 -------TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCGATCT
2579 TTTC
59 TTTC
2583 TTCAGTT
1 TTCAGTT
2590 TATTTCAGTT
Statistics
Matches: 121, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
62 59 0.49
63 2 0.02
64 3 0.02
69 3 0.02
70 2 0.02
71 52 0.43
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.44
Consensus pattern (62 bp):
TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCGATCTTTTC
Found at i:2480 original size:26 final size:26
Alignment explanation
Indices: 2424--2482 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
2414 TTCAGTTTAT
* *
2424 TTCAATTGATCCAGGGCGATCTTTTC
1 TTCAGTTGATCCAGGGCGATCTTCTC
*
2450 TTCAGTTGATCTAGGGCGATCTTCTC
1 TTCAGTTGATCCAGGGCGATCTTCTC
2476 TTCAGTT
1 TTCAGTT
2483 TATTTCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (26 bp):
TTCAGTTGATCCAGGGCGATCTTCTC
Found at i:2544 original size:169 final size:166
Alignment explanation
Indices: 2344--2759 Score: 555
Period size: 169 Copynumber: 2.5 Consensus size: 166
2334 TCAATCAATC
*
2344 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATC
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATC
* *
2409 TTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCAGTTGATCTAGGGCGATC-TT
66 TTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCAATTGATCCAGGGCGATCTTT
** *
2473 CTCTTCAGTTTATTTCAATTGATCCG-GGGTGGTCTTTCTT
131 C-CTT-AGTTTATTTCAATTGAT-CGAGGACGATC-TT-TT
* *
2513 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCAATC
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATC
* * *
2578 TTTTCTTCAGTTTATTTCAGTTGATCGAGGGCGATCTTTTCTTTAATTGATCCAGGGCGATCTTT
66 TTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCAATTGATCCAGGGCGATCTTT
*
2643 CCTTAGTTTATTTCAGTTGATCGAGGACGATCTTTT
131 CCTTAGTTTATTTCAATTGATCGAGGACGATCTTTT
* * * *
2679 C--TTTA----A-TTGATCCAGGGCGATC-TTTCCTCAATTTACTTCAATAGATCCAGGGCGATC
1 CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATC
* *
2736 TTCTCTGCAGTTTATTTCAATTGA
66 TTTTCTTCAGTTTATTTCAATTGA
2760 CTGCAAAATG
Statistics
Matches: 224, Mismatches: 21, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
158 50 0.22
159 16 0.07
160 1 0.00
164 4 0.02
166 3 0.01
167 4 0.02
168 21 0.09
169 122 0.54
170 3 0.01
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (166 bp):
CAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATC
TTTTCTTCAGTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCAATTGATCCAGGGCGATCTTT
CCTTAGTTTATTTCAATTGATCGAGGACGATCTTTT
Found at i:2566 original size:71 final size:72
Alignment explanation
Indices: 2450--2681 Score: 281
Period size: 71 Copynumber: 3.4 Consensus size: 72
2440 CGATCTTTTC
* * ***
2450 TTCAGTTGATCTAGGGCGATCTTCTCTTCAGTTTATTTCAATTGATCCGGGGTGGTC-TTTCTTC
1 TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTTC
2514 AGTTTAT
66 AGTTTAT
2521 TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTTC
1 TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTTC
2586 AGTTTAT
66 AGTTTAT
* * * *
2593 TTCAGTTGATCGAGGGCGATC--TT-TTC------TTT-AATTGATCCAGGGCGATCTTTCCTT-
1 TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTTC
2647 AGTTTAT
66 AGTTTAT
* *
2654 TTCAGTTGATCGAGGACGATCTTTTCTT
1 TTCAGTTGATCCAGGGCGATCTTTTCTT
2682 TAATTGATCC
Statistics
Matches: 147, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
61 27 0.18
62 22 0.15
63 5 0.03
64 2 0.01
69 3 0.02
70 2 0.01
71 52 0.35
72 34 0.23
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (72 bp):
TTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTTC
AGTTTAT
Found at i:2626 original size:133 final size:133
Alignment explanation
Indices: 2222--2681 Score: 451
Period size: 133 Copynumber: 3.5 Consensus size: 133
2212 TTGCTAAAGA
* * * * * * * *
2222 TTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAATTCATTTCAATCGATCCAGGGTGATC-TTT
1 TTTATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * * * * * *
2286 CTTCAATTTACTTCAGTTGATCCAAGGCGATCTTCTCTTCAGTTTAT-T---TCAATCA----AT
66 CTTCAGTTTATTTCAATTGATCCAGGGCAATCTTTTCTTCAGTTGATCTAGGGCGATCAGCGCAT
2343 CCAG
131 -CAG
*
2347 TTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTT
1 TTTATTTCAATTGATCCAGGGCGATC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTT
* ** * *
2412 TCTTCAGTTTATTTCAATTGATCCAGGGCGATCTTTTCTTCAGTTGATCTAGGGCGATCTTCTCT
65 TCTTCAGTTTATTTCAATTGATCCAGGGCAATCTTTTCTTCAGTTGATCTAGGGCGATCAGCGCA
2477 TCAG
130 TCAG
* * *
2481 TTTATTTCAATTGATCCGGGGTGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
1 TTTATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * ** *
2546 CTTCAGTTTATTTCAATTGATCCGGGGCAATCTTTTCTTCAGTTTATTTCA-GTTGATCGAGGGC
66 CTTCAGTTTATTTCAATTGATCCAGGGCAATCTTTTCTTCAGTTGATCT-AGGGCGATC-AGCGC
*
2610 GATC-T
129 -ATCAG
* * *
2615 TTTCTTT-AATTGATCCAGGGCGATCTTTCCTT-AGTTTATTTCAGTTGATCGAGGACGATCTTT
1 TTTATTTCAATTGATCCAGGGCGATCTTT-CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTT
2678 TCTT
65 TCTT
2682 TAATTGATCC
Statistics
Matches: 282, Mismatches: 39, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
125 24 0.09
126 30 0.11
127 44 0.16
128 1 0.00
131 4 0.01
133 140 0.50
134 36 0.13
135 3 0.01
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (133 bp):
TTTATTTCAATTGATCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
CTTCAGTTTATTTCAATTGATCCAGGGCAATCTTTTCTTCAGTTGATCTAGGGCGATCAGCGCAT
CAG
Found at i:2661 original size:61 final size:61
Alignment explanation
Indices: 2560--2737 Score: 257
Period size: 61 Copynumber: 2.9 Consensus size: 61
2550 AGTTTATTTC
* * *
2560 AATTGATCCGGGGCAATCTTTTCTTCAGTTTATTTCAGTTGATCGAGGGCGATCTTTTCTTT
1 AATTGATCCAGGGCGATCTTTCCTT-AGTTTATTTCAGTTGATCGAGGGCGATCTTTTCTTT
*
2622 AATTGATCCAGGGCGATCTTTCCTTAGTTTATTTCAGTTGATCGAGGACGATCTTTTCTTT
1 AATTGATCCAGGGCGATCTTTCCTTAGTTTATTTCAGTTGATCGAGGGCGATCTTTTCTTT
* * * * * *
2683 AATTGATCCAGGGCGATCTTTCCTCAATTTACTTCAATAGATCCAGGGCGATCTT
1 AATTGATCCAGGGCGATCTTTCCTTAGTTTATTTCAGTTGATCGAGGGCGATCTT
2738 CTCTGCAGTT
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
61 83 0.79
62 22 0.21
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (61 bp):
AATTGATCCAGGGCGATCTTTCCTTAGTTTATTTCAGTTGATCGAGGGCGATCTTTTCTTT
Found at i:2711 original size:25 final size:26
Alignment explanation
Indices: 2659--2711 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
2649 TTTATTTCAG
* * *
2659 TTGATCGAGGACGATCTTTTCTTTAA
1 TTGATCCAGGACGATCTTTTCCTCAA
*
2685 TTGATCCAGGGCGATC-TTTCCTCAA
1 TTGATCCAGGACGATCTTTTCCTCAA
2710 TT
1 TT
2712 TACTTCAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (26 bp):
TTGATCCAGGACGATCTTTTCCTCAA
Found at i:3058 original size:30 final size:30
Alignment explanation
Indices: 3022--3891 Score: 1178
Period size: 30 Copynumber: 29.1 Consensus size: 30
3012 GCTTTATCAT
*
3022 CTTTATTTTAATCCTGGTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* * * *
3052 CTTTATTTTAATCATGTTTGAAGATCGTCG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* *
3082 CTTTATTTTAATCCTGGTTGAGGATCATTA
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* * * *
3112 CCTTATTTTAATCCTGGTTGAGGATCGTTA
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* * *
3142 CTTTATTTTAATCTTGGTTGAGGATCGTTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* *
3172 CTTTATTCTAATCCTGTTTGAAGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* * * *
3202 CTCTATGTTAATCTTGGTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* * * *
3232 CTTCATTTTAATCCTGGTTGAGGATCGTTA
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* *
3262 CTTTATTTTAATCTTGGTTGAGGATC----
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* *
3288 CTTTATTTTAATCCTGGTTGAGGATCGTTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
3318 CTTTATTTTAATCCTGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* * * *
3348 CTTTATTATAATCTTGTTTGAGGATCGTCG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* * *
3378 CTTTGTTTTAATCCTGGTTGAGGATCATTA
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* * * * *
3408 CCTCATTTTAATCCTGGTTGAGGATCGTCG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
3438 CTTTATTTTAATCCTCG-TTGAGGATCATTG
1 CTTTATTTTAATCCT-GTTTGAGGATCATTG
3468 CTTTATTTTAATCCTGGTTT-AGGATCATTG
1 CTTTATTTTAATCCT-GTTTGAGGATCATTG
*
3498 CTTTATTTTAATCATGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
*
3528 CTTTATTTTAGTCCTGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* *
3558 CTTTCTTTTTATTCCTGTTTGAGGATCATTG
1 CTTT-ATTTTAATCCTGTTTGAGGATCATTG
*
3589 CTTTATTTTAGTCCTGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
3619 CTTTATTTTAATCCTGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
*
3649 CTTTATTTTAGTCCTGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
3679 CTTTATTTTAATCCTGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
3709 CTTTATTTTAATCCTGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* *
3739 CTTTATTTTAGTCATGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
3769 CTTTATTTTAATCCTGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
*
3799 CTTCATTTTAATCCTGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* *
3829 TTTTATTTTAGTCCTGTTTGAGGATCATTG
1 CTTTATTTTAATCCTGTTTGAGGATCATTG
* *
3859 TTTTATTTTTATCCTGGTTT-AGGATCATTG
1 CTTTATTTTAATCCT-GTTTGAGGATCATTG
3889 CTT
1 CTT
3892 CATCAGTTAA
Statistics
Matches: 750, Mismatches: 81, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
26 25 0.03
29 4 0.01
30 686 0.91
31 35 0.05
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (30 bp):
CTTTATTTTAATCCTGTTTGAGGATCATTG
Found at i:4059 original size:39 final size:39
Alignment explanation
Indices: 3973--4059 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 39
3963 TTTGAATCTT
*
3973 GATCATTGCTTTATCAGTTATATTTCAGTCATGATTTAA
1 GATCATTGCTTTATCAATTATATTTCAGTCATGATTTAA
* * * * * *
4012 CATTATTGCTTTGTCAATTTTATTTC-GATCCTGATTTAG
1 GATCATTGCTTTATCAATTATATTTCAG-TCATGATTTAA
4051 GATCATTGC
1 GATCATTGC
4060 CTATTAGTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (39 bp):
GATCATTGCTTTATCAATTATATTTCAGTCATGATTTAA
Found at i:4430 original size:27 final size:28
Alignment explanation
Indices: 4400--4453 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 28
4390 GGGTCACATA
*
4400 GGGGCATTTTGGTCA-TTTGCACATTCG
1 GGGGCATTATGGTCATTTTGCACATTCG
4427 GGGGCATTATGGTCATTTTTGCACATT
1 GGGGCATTATGGTCA-TTTTGCACATT
4454 TTGGAGCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 14 0.58
29 10 0.42
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (28 bp):
GGGGCATTATGGTCATTTTGCACATTCG
Found at i:4462 original size:29 final size:28
Alignment explanation
Indices: 4407--4476 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
4397 ATAGGGGCAT
*
4407 TTTGGTCA--TTTGCACATTCGGGGGCA
1 TTTGGTCATTTTTGCACATTCGGGAGCA
**
4433 TTATGGTCATTTTTGCACATTTTGGAGCA
1 TT-TGGTCATTTTTGCACATTCGGGAGCA
*
4462 TCTTGGTCTTTTTTG
1 T-TTGGTCATTTTTG
4477 TGTATTTTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.06
27 6 0.17
29 27 0.75
30 1 0.03
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.46
Consensus pattern (28 bp):
TTTGGTCATTTTTGCACATTCGGGAGCA
Done.