Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022855.1 Corchorus olitorius cultivar O-4 contig22888, 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: 23074
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2103 original size:54 final size:54
Alignment explanation
Indices: 2030--2593 Score: 771
Period size: 54 Copynumber: 10.5 Consensus size: 54
2020 CGATCTTTTA
* * * * * * *
2030 AAGTTTTCAAAGATCTAAGTTGA-CGATCAAATGACCCTGTGAGGTCTTTAATAG
1 AAGTTTTCAGAGATTTAAGTTGATC-TTCAGATGGCCCTGTGCGGTCTTTCATAG
*
2084 AAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGGCCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTCTTTCATAG
* *
2138 AAGTTTTCAGATATTTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTCTTTCATAG
* * *
2192 AAGTTTTCAAAGATTTAAGTTGATCTTCAGATGGCCCTGTGTGGTCTCTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTCTTTCATAG
2246 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTCTTTCATAG
2300 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTCTTTCATAG
*
2354 AAGTTTTCAGAGATTTAAGTTGATCGTCAGATGGCCCTGTGCGGTC-TTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTCTTTCATAG
* **
2407 AAGTTTTCAGATATTTAAGTTGATCTTCAGATAACCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTCTTTCATAG
** * * * * *
2461 AAAATTTCAAAGATTTAAGTTGA-CTTTAAGATGACCCAGTGCGGTCTTCCATAG
1 AAGTTTTCAGAGATTTAAGTTGATC-TTCAGATGGCCCTGTGCGGTCTTTCATAG
* * * * *
2515 AAGCTTTT-ATAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGTCATTCCA-AG
1 AAG-TTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTC-TTTCATAG
*
2569 AAGTTTTTAGAGA-TTAGAGTTGATC
1 AAGTTTTCAGAGATTTA-AGTTGATC
2594 CCTAGATGAT
Statistics
Matches: 463, Mismatches: 39, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
53 56 0.12
54 397 0.86
55 10 0.02
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (54 bp):
AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTCTTTCATAG
Found at i:2601 original size:108 final size:108
Alignment explanation
Indices: 2080--3504 Score: 781
Period size: 108 Copynumber: 13.3 Consensus size: 108
2070 GAGGTCTTTA
* * * * *
2080 ATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGGCCCTGTGCGGTC-TTTCATAGAAGTTT
1 ATAGAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGTCATTCCA-AGAAGTTT
* * * * * *
2144 TCAGATATTTA-AGTTGAT-CTTCAGATGACCCTGTGCGGTCTTTC
65 TCAGAGA-TCAGAGTTGATCCCT-AGATGATCCAGTGCGGTCTTCC
* * * * *
2188 ATAGAAGTTTTCAAAGATTTAAGTTGATCTTCAGATGGCCCTGTGTGGTC--TCTCATAGAAGTT
1 ATAGAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGTCATTC-CA-AGAAGTT
* * ** * *
2251 TTCAGAGATTTA-AGTTGAT-CTTCAGATGGCCCTGTGCGGTCTTTC
64 TTCAGAGA-TCAGAGTTGATCCCT-AGATGATCCAGTGCGGTCTTCC
* * * *
2296 ATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGGCCCTGTGCGGTC-TTTCATAGAAGTTT
1 ATAGAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGTCATTCCA-AGAAGTTT
* * ** *
2360 TCAGAGATTTA-AGTTGAT-CGTCAGATGGCCCTGTGCGGTCTT-C
65 TCAGAGA-TCAGAGTTGATCCCT-AGATGATCCAGTGCGGTCTTCC
* * * * * **
2403 ATAGAAGTTTTCAGATATTTAAGTTGATCTTCAGATAACCCTGTGCGGTC-TTTCATAGAAAATT
1 ATAGAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGTCATTCCA-AGAAGTTT
* * ** *
2467 TCAAAGATTTA-AGTTGA-CTTTAAGATGACCCAGTGCGGTCTTCC
65 TCAGAGA-TCAGAGTTGATCCCT-AGATGATCCAGTGCGGTCTTCC
*
2511 ATAGAAGCTTTT-ATAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGTCATTCCAAGAAGTTT
1 ATAGAAG-TTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGTCATTCCAAGAAGTTT
* * *
2575 TTAGAGATTAGAGTTGATCCCTAGATGATCCAGTGCGATCATTCC
65 TCAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTC-TTCC
* * *** *
2620 A-AGTAGTTCTCTTTGATC-AGAGTTGATC-CCAGATGACCCAGTGCGGTCATTCCAAGAAGTTT
1 ATAGAAGTTTTCAGAGATCTA-AGTTGATCTTCAGATGACCCAGTGCGGTCATTCCAAGAAGTTT
**
2682 TTTGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCCTTCC
65 TCAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGGT-CTTCC
* * * ** *
2727 A-AGAAGTTTTC-GAAGATC-AGAGTTGATCTCCATATGATCTGGTGC--TCATTCCAAAAAGTT
1 ATAGAAGTTTTCAG-AGATCTA-AGTTGATCTTCAGATGACCCAGTGCGGTCATTCCAAGAAGTT
* * * *
2787 TTCA-ATGATCAGAATTGATCTCC-AAATGATCCAGTGTGGTTCATCC
64 TTCAGA-GATCAGAGTTGATC-CCTAGATGATCCAGTGCGG-TCTTCC
* * * ** *
2833 -TAGAAGTTTTC-GAAGAT-TAGATTTGATCTTCAGATGATCCGGTGTAGTCATTTCAAGAAGTT
1 ATAGAAGTTTTCAG-AGATCTA-AGTTGATCTTCAGATGACCCAGTGCGGTCATTCCAAGAAGTT
* ** * ** * *
2895 TTC-GATGATCAGAGTTGAT--CT-CAT--TTTA-AGAAGTTTTCG
64 TTCAGA-GATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCTTCC
* * ** * * *** * ** *** * *
2934 ATGATCAGAGTTGATCTCA-TTTTAAAAAG-TTTTC-GATGATCAGAGTTGATCTCATTTCAAAA
1 AT-A-GA-AGTT-TTCAGAGATCTAAGTTGATCTTCAGATGA-CCCAG-TGCGGTCATTCCAAGA
* * * *
2996 AGTTTTCAGTGTTCAGAGTTGATCCCCAGATGATCCAGCGCGGTCATTCC
60 AGTTTTCAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTC-TTCC
* * * * * *
3046 A-AGAAGTTTTTAGAGACCATAA-TTGATCCTCAGATGATCCTGTGTGGTCATTCCAAGAAGTTT
1 ATAGAAGTTTTCAGAGATC-TAAGTTGATCTTCAGATGACCCAGTGCGGTCATTCCAAGAAGTTT
* *
3109 TCA-ATGATCAGAGTCGATCCC-AGATGATCCAGTGCGGTCTTTC
65 TCAGA-GATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCTTCC
* * * * **
3152 ACAGAAGTTTTTAGAGATC-AGAGTTGATC-CCTAGATGATCTGGTGCGGTCATTCCAAG-A-TT
1 ATAGAAGTTTTCAGAGATCTA-AGTTGATCTTC-AGATGACCCAGTGCGGTCATTCCAAGAAGTT
* * **
3213 TGTTAGAGATCAGAGTTGAT-CCTAGACGATCCAGTGCGGTCATTTG
64 T-TCAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTC-TTCC
* *
3259 A-AGAAGTTTT-AGAGATC-AGAGTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAGAAGTTT
1 ATAGAAGTTTTCAGAGATCTA-AGTTGATCTTCAGATGACCCAGTGCGGTCATTCCAAGAAGTTT
* * * * * *
3320 T-AAATGATCAGAGTTTATCCCTAGATGATCTAGTGTGGTTATTCT
65 TCAGA-GATCAGAGTTGATCCCTAGATGATCCAGTGCGG-TCTTCC
* * * * * * *
3365 A-AGATGTTTTAAGAGATCAAAGTTGATCCTCAGATGATCCAGTGCGGTAATTCTAAGAAGTTTT
1 ATAGAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGTCATTCCAAGAAGTTTT
* * * *
3429 CTA-TGATCAGAGTTGATCTCC-A-ATTGATACAATGCAGTCATTCC
66 C-AGAGATCAGAGTTGATC-CCTAGA-TGATCCAGTGCGGTC-TTCC
3473 A-AGAAGTTTTC-GATGATC-AGAGTTGATCTTCA
1 ATAGAAGTTTTCAGA-GATCTA-AGTTGATCTTCA
3505 ATTTGATCCC
Statistics
Matches: 1086, Mismatches: 163, Indels: 136
0.78 0.12 0.10
Matches are distributed among these distances:
101 3 0.00
102 3 0.00
103 8 0.01
104 32 0.03
105 81 0.07
106 168 0.15
107 293 0.27
108 456 0.42
109 26 0.02
110 9 0.01
111 3 0.00
112 4 0.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (108 bp):
ATAGAAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCAGTGCGGTCATTCCAAGAAGTTTT
CAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCTTCC
Found at i:2926 original size:35 final size:35
Alignment explanation
Indices: 2880--3019 Score: 219
Period size: 35 Copynumber: 4.0 Consensus size: 35
2870 TCCGGTGTAG
*
2880 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAAAAGTTTTCGATGATCAGAGTTGATC
* *
2915 TCATTTTAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAAAAGTTTTCGATGATCAGAGTTGATC
*
2950 TCATTTTAAAAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAAAAGTTTTCGATGATCAGAGTTGATC
*
2985 TCATTTCAAAAAGTTTTC-AGTGTTCAGAGTTGATC
1 TCATTTCAAAAAGTTTTCGA-TGATCAGAGTTGATC
3020 CCCAGATGAT
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
34 1 0.01
35 99 0.99
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (35 bp):
TCATTTCAAAAAGTTTTCGATGATCAGAGTTGATC
Found at i:3320 original size:319 final size:317
Alignment explanation
Indices: 2489--3527 Score: 886
Period size: 319 Copynumber: 3.2 Consensus size: 317
2479 GTTGACTTTA
* * *
2489 AGATGACCCAGTGCGGTC-TTCCATAGAAGCTTTTATAGATCTA-AGTTGATCTTCAGATGACCC
1 AGATGATCCAGTGCGGTCTTTCCA-AGAAG-TTTTAGAGATC-AGAGTTGATCTTCAGATGATCC
* * *
2552 AGTGCGGTCATTCCAAGAAGTTTTTAGAGATTAGAGTTGATCCCTAGATGATCCAGTGCGATCAT
63 GGTGCGGTCATTCCAAGAA-TTTTTAGAGATCAGAGTTGAT-CCTAGAAGATCCAGTGCGATCAT
** ** *
2617 TCCAAGTAGTTCTCTTTGATCAGAGTTGATCCCAGATGACCCAGTGCGGTCATTCCAAGAAGTTT
126 TTGAAGTAGTT-T-TAAGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTT
** * * *
2682 TTTGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCCTTCCAAGAAG-TTTTCGAAGATCA
189 TAAGTGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAG-AGATCA
* * * * *
2746 GAGTTGAT-CTCCATATGAT-CTG-GTGCTCATTCCAAAAAGTTTTCAATGATCAGAATTGATCT
253 -AATTGATCCT-CAGATGATCCTGTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCT
2808 CC
316 CC
* * * * * * *
2810 AAATGATCCAGTGTGGT-TCATCCTAGAAGTTTTCGAAGATTAGATTTGATCTTCAGATGATCCG
1 AGATGATCCAGTGCGGTCT-TTCCAAGAAGTTTTAG-AGATCAGAGTTGATCTTCAGATGATCCG
** * * * * *
2874 GTGTAGTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTTAAGAAGTTTTC-GAT--
64 GTGCGGTCATTCCAAGAATTTTTAGA-GATCAGAGTTGATC-C----T-AGAAG-ATCCAG-TGC
* ** * * *** *
2936 GATCAGAGTTGATCTCA-TTTTAA-A--A-AGTT--T-TC-GATGATCAGAGTTGATCTCATTTC
120 GATC--ATTTGAAGT-AGTTTTAAGATCAGAGTTGATCCCAGATGATC-CAG-TGCGGTCATTCC
* * * * *
2992 AAAAAGTTTTCAGTGTTCAGAGTTGATCCCCAGATGATCCAGCGCGGTCATTCCAAGAAGTTTTT
180 AAGAAGTTTTAAGTGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTT
*
3057 AGAGACCATAATTGATCCTCAGATGATCCTGTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAG
245 AGAGATCA-AATTGATCCTCAGATGATCCTGTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAG
*
3122 TCGATC-CC
309 TTGATCTCC
* *
3130 AGATGATCCAGTGCGGTCTTT-CACAGAAGTTTTTAGAGATCAGAGTTGATC-CCTAGATGATCT
1 AGATGATCCAGTGCGGTCTTTCCA-AGAAG-TTTTAGAGATCAGAGTTGATCTTC-AGATGATCC
* *
3193 GGTGCGGTCATTCCAAG-ATTTGTTAGAGATCAGAGTTGATCCTAGACGATCCAGTGCGGTCATT
63 GGTGCGGTCATTCCAAGAATTT-TTAGAGATCAGAGTTGATCCTAGAAGATCCAGTGCGATCATT
*
3257 TGAAGAAGTTTTAGAGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTA
127 TGAAGTAGTTTTA-AGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTA
* * * * * * * *
3322 AATGATCAGAGTTTATCCCTAGATGATCTAGTGTGGTTATTCTAAGATGTTTTAAGAGATCAAAG
191 AGTGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAAA-
* * * * *
3387 TTGATCCTCAGATGATCCAGTGCGGTAATTCTAAGAAGTTTTCTATGATCAGAGTTGATCTCC
255 TTGATCCTCAGATGATCCTGTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCC
* * * * *
3450 A-ATTGATACAATGCAGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATCTTCA-ATTTGATC
1 AGA-TGATCCAGTGCGGTCTTTCCAAGAAGTTTTAGA-GATCAGAGTTGATCTTCAGA--TGATC
* *
3513 CCGTGTGGTCATTCC
62 CGGTGCGGTCATTCC
3528 GAAAAGTTTC
Statistics
Matches: 562, Mismatches: 108, Indels: 96
0.73 0.14 0.13
Matches are distributed among these distances:
311 1 0.00
312 13 0.02
313 6 0.01
314 5 0.01
316 1 0.00
317 10 0.02
318 6 0.01
319 228 0.41
320 124 0.22
321 141 0.25
322 4 0.01
324 1 0.00
325 6 0.01
326 6 0.01
327 9 0.02
328 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (317 bp):
AGATGATCCAGTGCGGTCTTTCCAAGAAGTTTTAGAGATCAGAGTTGATCTTCAGATGATCCGGT
GCGGTCATTCCAAGAATTTTTAGAGATCAGAGTTGATCCTAGAAGATCCAGTGCGATCATTTGAA
GTAGTTTTAAGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTAAGTGA
TCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAAATTGATC
CTCAGATGATCCTGTGTGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCC
Found at i:3507 original size:54 final size:53
Alignment explanation
Indices: 2489--3500 Score: 721
Period size: 54 Copynumber: 19.0 Consensus size: 53
2479 GTTGACTTTA
* * *
2489 AGATGACCCAGTGCGGTC-TTCCATAGAAGCTTTTATA-GATCTA-AGTTGATCTTC
1 AGATGATCCAGTGCGGTCATTCCA-AGAAG-TTTTAGATGATC-AGAGTTGATC-CC
* *
2543 AGATGACCCAGTGCGGTCATTCCAAGAAGTTTTTAGA-GATTAGAGTTGATCCC
1 AGATGATCCAGTGCGGTCATTCCAAGAAG-TTTTAGATGATCAGAGTTGATCCC
* * * ***
2596 TAGATGATCCAGTGCGATCATTCCAAGTAGTTCTCTTTGATCAGAGTTGATCCC
1 -AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTAGATGATCAGAGTTGATCCC
* *
2650 AGATGACCCAGTGCGGTCATTCCAAGAAGTTTTTTGA-GATCAGAGTTGATCCC
1 AGATGATCCAGTGCGGTCATTCCAAGAAG-TTTTAGATGATCAGAGTTGATCCC
* * *
2703 TAGATGATCCAGTGCGGTCCTTCCAAGAAGTTTTCGAAGATCAGAGTTGATCTCC
1 -AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTAGATGATCAGAGTTGATC-CC
* ** * *
2758 ATATGATCTGGTGC--TCATTCCAAAAAGTTTTCA-ATGATCAGAATTGATCTCC
1 AGATGATCCAGTGCGGTCATTCCAAGAAGTTTT-AGATGATCAGAGTTGATC-CC
* * * * * * * *
2810 AAATGATCCAGTGTGGTTCA-TCCTAGAAGTTTTCGAAGATTAGATTTGATCTTC
1 AGATGATCCAGTGCGG-TCATTCCAAGAAGTTTTAGATGATCAGAGTTGATC-CC
* ** * * *
2864 AGATGATCCGGTGTAGTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTAGATGATCAGAGTTGATCCC
** * *** * * * * ** * * *
2917 ATTTTAAGAAGTTTTCGATGA-T-C-AG-AGTTGATCT-CATTTTAAAAAGTT--T-TC
1 AGATGATCCAG--TGCGGTCATTCCAAGAAGTT--T-TAGATGAT-CAGAGTTGATCCC
* *** * * *
2968 -GATGATCAGAGTTGATCTCATTTCAAAAAGTTTTCAG-TGTTCAGAGTTGATCCCC
1 AGATGATC-CAG-TGCGGTCATTCCAAGAAGTTTT-AGATGATCAGAGTTGAT-CCC
* * * *
3023 AGATGATCCAGCGCGGTCATTCCAAGAAGTTTTTAGA-GACCATAATTGATCCTC
1 AGATGATCCAGTGCGGTCATTCCAAGAAG-TTTTAGATGATCAGAGTTGATCC-C
* * *
3077 AGATGATCCTGTGTGGTCATTCCAAGAAGTTTTCA-ATGATCAGAGTCGATCCC
1 AGATGATCCAGTGCGGTCATTCCAAGAAGTTTT-AGATGATCAGAGTTGATCCC
*
3130 AGATGATCCAGTGCGGTC-TTTCACAGAAGTTTTTAGA-GATCAGAGTTGATCCC
1 AGATGATCCAGTGCGGTCATTCCA-AGAAG-TTTTAGATGATCAGAGTTGATCCC
** * *
3183 TAGATGATCTGGTGCGGTCATTCCAAG-ATTTGTTAGA-GATCAGAGTTGATCCT
1 -AGATGATCCAGTGCGGTCATTCCAAGAAGTT-TTAGATGATCAGAGTTGATCCC
* **
3236 AGACGATCCAGTGCGGTCATTTGAAGAAGTTTTAGA-GATCAGAGTTGATCCC
1 AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTAGATGATCAGAGTTGATCCC
* *
3288 AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTAAATGATCAGAGTTTATCCC
1 AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTAGATGATCAGAGTTGATCCC
* * * * * *
3341 TAGATGATCTAGTGTGGTTATTCTAAGATGTTTTAAGA-GATCAAAGTTGATCCTC
1 -AGATGATCCAGTGCGGTCATTCCAAGAAGTTTT-AGATGATCAGAGTTGATCC-C
* * **
3396 AGATGATCCAGTGCGGTAATTCTAAGAAGTTTTCTATGATCAGAGTTGATCTCC
1 AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTAGATGATCAGAGTTGATC-CC
* * * *
3450 A-ATTGATACAATGCAGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 AGA-TGATCCAGTGCGGTCATTCCAAGAAGTTTTAGATGATCAGAGTTGATC
3501 TTCAATTTGA
Statistics
Matches: 764, Mismatches: 143, Indels: 102
0.76 0.14 0.10
Matches are distributed among these distances:
50 6 0.01
51 15 0.02
52 129 0.17
53 155 0.20
54 424 0.55
55 28 0.04
56 7 0.01
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (53 bp):
AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTAGATGATCAGAGTTGATCCC
Found at i:4009 original size:24 final size:24
Alignment explanation
Indices: 3981--4027 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3971 CCTCCAGGAG
*
3981 AAAAAGAAGCTTTGGCAAAAAAAA
1 AAAAAAAAGCTTTGGCAAAAAAAA
4005 AAAAAAAAGCTTTGGCAAAAAAA
1 AAAAAAAAGCTTTGGCAAAAAAA
4028 TTAAGGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.15, T:0.13
Consensus pattern (24 bp):
AAAAAAAAGCTTTGGCAAAAAAAA
Found at i:5142 original size:20 final size:19
Alignment explanation
Indices: 5037--5148 Score: 67
Period size: 20 Copynumber: 5.8 Consensus size: 19
5027 TTTATTTATT
5037 TATTATTATTATCTATCT-
1 TATTATTATTATCTATCTA
**
5055 CCTT-TT-TTATCTAT-T-
1 TATTATTATTATCTATCTA
5070 TATTATTTACTT-TCCTATCTA
1 TATTA-TTA-TTAT-CTATCTA
5091 TTTATTATTATTATCTATCTA
1 --TATTATTATTATCTATCTA
* *
5112 T-TTACCCTATTATCTATGTAA
1 TATTA--TTATTATCTATCT-A
5133 TATTATTATTATCTAT
1 TATTATTATTATCTAT
5149 TTATTTACTT
Statistics
Matches: 73, Mismatches: 7, Indels: 26
0.69 0.07 0.25
Matches are distributed among these distances:
15 3 0.04
16 8 0.11
17 4 0.05
18 6 0.08
19 7 0.10
20 22 0.30
21 11 0.15
22 7 0.10
23 5 0.07
ACGTcount: A:0.26, C:0.14, G:0.01, T:0.59
Consensus pattern (19 bp):
TATTATTATTATCTATCTA
Found at i:5651 original size:54 final size:54
Alignment explanation
Indices: 5587--6101 Score: 539
Period size: 54 Copynumber: 9.6 Consensus size: 54
5577 AGAGTTGATC
* * *
5587 TCATTTCAAGAAGTTTTCAGTGATCAGAGTTGATCCCCAGATGATCCAGCGCGG
1 TCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
* * * *
5641 TCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCCTCAGATGATCCTGTGCGA
1 TCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
*
5695 TCATTCCAAGAAGTTTTCA-ATGATCAGAGTCGAT-CCCAGATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAGA-GATCAGAGTTGATCCCCAGATGATCCAGTGCGG
* * * *
5748 TCTTTCACAA-AAGTTTTTAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGA
1 TCATTC-CAAGAAGTTTTCAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
* * * * * *
5802 TCATTCCAAG-ATTTTTTAGAGATCAGAGTTGATCCCTAAACGAGCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
* **
5855 TTATTTGAAGAAGTTTT-AGAGATCAGAGTTGAT-CCCAGATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
* * * * *
5907 CCATTCCAAGAAGTTTT-AAATGATCAGTGTTGATCCCTAGATGATCTAGTGCGG
1 TCATTCCAAGAAGTTTTCAGA-GATCAGAGTTGATCCCCAGATGATCCAGTGCGG
* * * * **
5961 TTATTCTAAGATGTTTTAAGAGATCAGAGTTGATCCTTAGATGATCCAGTGCGG
1 TCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
* * * * * *
6015 TAATTCCAAGAAGTTTTCTA-TGATCAGAGTTGATCTCCA-ATTGATACAATGCAG
1 TCATTCCAAGAAGTTTTC-AGAGATCAGAGTTGATCCCCAGA-TGATCCAGTGCGG
*
6069 TCAATT-CAAGATGTTTTC-GATGATCAGAGTTGA
1 TC-ATTCCAAGAAGTTTTCAGA-GATCAGAGTTGA
6102 CCTTCAATTT
Statistics
Matches: 386, Mismatches: 61, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
52 30 0.08
53 119 0.31
54 231 0.60
55 6 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (54 bp):
TCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
Found at i:7684 original size:40 final size:35
Alignment explanation
Indices: 7602--7704 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 35
7592 TTTATCTATT
*
7602 TATTTATTATTATTATCTATCTACTTT--TGTTATC
1 TATTTATTATTATTATCTATCTA-TTTACTATTATC
7636 TATTTATTATTATTATCTATCTATTTACCCTATTATC
1 TATTTATTATTATTATCTATCTATTTA--CTATTATC
*
7673 TATGTAATATTATTATTATCTATTTATTTACT
1 TAT-T--TATTATTATTATCTATCTATTTACT
7705 TTTCACTTAC
Statistics
Matches: 60, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
33 3 0.05
34 23 0.38
37 9 0.15
38 3 0.05
40 22 0.37
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.59
Consensus pattern (35 bp):
TATTTATTATTATTATCTATCTATTTACTATTATC
Found at i:7689 original size:20 final size:19
Alignment explanation
Indices: 7606--7695 Score: 82
Period size: 20 Copynumber: 4.8 Consensus size: 19
7596 TCTATTTATT
7606 TATTATTATTATCTATCTA
1 TATTATTATTATCTATCTA
* *
7625 -CTT-TTGTTATCTAT-T-
1 TATTATTATTATCTATCTA
7640 TATTATTATTATCTATCTA
1 TATTATTATTATCTATCTA
* *
7659 T-TTACCCTATTATCTATGTAA
1 TATTA--TTATTATCTATCT-A
7680 TATTATTATTATCTAT
1 TATTATTATTATCTAT
7696 TTATTTACTT
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
16 3 0.05
17 20 0.36
18 6 0.11
19 1 0.02
20 21 0.38
21 2 0.04
22 3 0.05
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.58
Consensus pattern (19 bp):
TATTATTATTATCTATCTA
Found at i:7700 original size:17 final size:17
Alignment explanation
Indices: 7602--7700 Score: 92
Period size: 17 Copynumber: 5.5 Consensus size: 17
7592 TTTATCTATT
7602 TATTTATTATTATTATC
1 TATTTATTATTATTATC
* *
7619 TATCTACTT-TTGTTATC
1 TATTTA-TTATTATTATC
7636 TATTTATTATTATTATC
1 TATTTATTATTATTATC
* *
7653 TATCTATTTACCCTATTATC
1 TATTTA-TTA--TTATTATC
7673 TATGTAATATTATTATTATC
1 TAT-T--TATTATTATTATC
7693 TATTTATT
1 TATTTATT
7701 TACTTTTCAC
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
16 2 0.03
17 33 0.50
18 5 0.08
19 1 0.02
20 20 0.30
22 3 0.05
23 2 0.03
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTTATTATTATTATC
Found at i:8197 original size:54 final size:53
Alignment explanation
Indices: 8133--8649 Score: 489
Period size: 54 Copynumber: 9.7 Consensus size: 53
8123 AGAGTTGATC
* * *
8133 TCATTTCAAGAAGTTTTCAGTGATCAGAGTTGATCACCAGATGATCCAGCGCGG
1 TCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATC-CCAGATGATCCAGTGCGG
* * * *
8187 TCATTCCAAGAAGTTTTTAGAGATCAAAGTTGATCCTCAGATGATCCTGTGCGA
1 TCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCC-CAGATGATCCAGTGCGG
* * *
8241 TCATTCCAAGAAGTTTTCA-ATGATCACAGTCGAT-CCAGATGATCCAGTGCAG
1 TCATTCCAAGAAGTTTTCAGA-GATCAGAGTTGATCCCAGATGATCCAGTGCGG
* * *
8293 TC-TTTCACAGAAGTTTTTAGAGATCAGAGCTGATCCCCAGATGATCCAGTGCGG
1 TCATTCCA-AGAAGTTTTCAGAGATCAGAGTTGAT-CCCAGATGATCCAGTGCGG
* * * * * *
8347 TCATTCCAAG-ATTTTTTAGAGATCATAGTTGATCCCTAGACGAGCCAGTGCGA
1 TCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCCC-AGATGATCCAGTGCGG
* ** *
8400 TTATTTGAAGAAGTTTT-AGAGATCAGAGTTGATCCCCAGATGATCCATTGCGG
1 TCATTCCAAGAAGTTTTCAGAGATCAGAGTTGAT-CCCAGATGATCCAGTGCGG
* * *
8453 CCATTCCAAGAAGTTTT-AAATGATCAGAGTTGATCCCTAGATGATCTAGTGCGG
1 TCATTCCAAGAAGTTTTCAGA-GATCAGAGTTGATCCC-AGATGATCCAGTGCGG
* * * *
8507 TTATTCTAA-AATGTTTTAAGAGATCAGAGTTGATCCTCAGATGATCCAGTGCAG
1 TCATTCCAAGAA-GTTTTCAGAGATCAGAGTTGATCC-CAGATGATCCAGTGCGG
* * * * *
8561 TAATTCCAAGAAGTTTTCTA-TGATCAGAGTTGATCTCCA-ATTGATACAATGCAG
1 TCATTCCAAGAAGTTTTC-AGAGATCAGAGTTGATC-CCAGA-TGATCCAGTGCGG
*
8615 TCAATT-CAAGATGTTTTC-GATGATCAGAGTTGATC
1 TC-ATTCCAAGAAGTTTTCAGA-GATCAGAGTTGATC
8650 TTCAATTTGA
Statistics
Matches: 384, Mismatches: 57, Indels: 44
0.79 0.12 0.09
Matches are distributed among these distances:
51 4 0.01
52 39 0.10
53 92 0.24
54 235 0.61
55 14 0.04
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (53 bp):
TCATTCCAAGAAGTTTTCAGAGATCAGAGTTGATCCCAGATGATCCAGTGCGG
Found at i:8441 original size:160 final size:159
Alignment explanation
Indices: 8136--8595 Score: 520
Period size: 160 Copynumber: 2.9 Consensus size: 159
8126 GTTGATCTCA
* * * * *
8136 TTTCA-AGAAGTTTTCAGTGATCAGAGTTGATCACCAGATGATCCAGCGCGGTCATTCCAAGAAG
1 TTTCACAGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAG-AT
* *
8200 TTTTTAGAGATCAAAGTTGATCCTCAGATGATCCTGTGCGATCATTCCAAGAAGTTTTCAATGAT
65 TTTTTAGAGATCAAAGTTGATCCTCAGATGATCCAGTGCGATAATTCCAAGAAGTTTT-AATGAT
* * *
8265 CACAGTCGAT-CCAGATGATCCAGTGCAGTC
129 CAGAGTTGATCCCAGATGATCCAGTGCAGCC
*
8295 TTTCACAGAAGTTTTTAGAGATCAGAGCTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGATT
1 TTTCACAGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGATT
* * * * **
8360 TTTTAGAGATCATAGTTGATCC-CTAGACGAGCCAGTGCGATTATTTGAAGAAGTTTTAGA-GAT
66 TTTTAGAGATCAAAGTTGATCCTC-AGATGATCCAGTGCGATAATTCCAAGAAGTTTTA-ATGAT
* *
8423 CAGAGTTGATCCCCAGATGATCCATTGCGGCC
129 CAGAGTTGAT-CCCAGATGATCCAGTGCAGCC
* * * * * * *
8455 ATTC-CAAGAAG-TTTTAAATGATCAGAGTTGATCCCTAGATGATCTAGTGCGGTTATTCTAAAA
1 TTTCAC-AGAAGTTTTTAGA-GATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGA
* * *
8518 TGTTTTAAGAGATCAGAGTTGATCCTCAGATGATCCAGTGC-AGTAATTCCAAGAAGTTTTCTAT
64 T-TTTTTAGAGATCAAAGTTGATCCTCAGATGATCCAGTGCGA-TAATTCCAAGAAGTTTT-AAT
8582 GATCAGAGTTGATC
126 GATCAGAGTTGATC
8596 TCCAATTGAT
Statistics
Matches: 255, Mismatches: 34, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
158 13 0.05
159 63 0.25
160 116 0.45
161 49 0.19
162 14 0.05
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (159 bp):
TTTCACAGAAGTTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGGTCATTCCAAGATT
TTTTAGAGATCAAAGTTGATCCTCAGATGATCCAGTGCGATAATTCCAAGAAGTTTTAATGATCA
GAGTTGATCCCAGATGATCCAGTGCAGCC
Found at i:8629 original size:108 final size:105
Alignment explanation
Indices: 8133--8649 Score: 542
Period size: 108 Copynumber: 4.8 Consensus size: 105
8123 AGAGTTGATC
* * * *
8133 TCATTTCAAGAAGTTTTCAGTGATCAGAGTTGATCACCAGATGATCCAGCGCGGTCATTCCAAGA
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC-CCAGATGATCCAGTGCAGTCATT-CAAGA
* * * *
8198 AGTTTTTAGAGATCAAAGTTGATCCTCAGATGATCCTGTGCGA
64 AG-TTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
* * *
8241 TCATTCCAAGAAGTTTTCAATGATCACAGTCGAT-CCAGATGATCCAGTGCAGTCTTTCACAGAA
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCAGATGATCCAGTGCAGTCATTCA-AGAA
*
8305 GTTTTTAGAGATCAGAGCTGATCCCCAGATGATCCAGTGCGG
65 G-TTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
* * * * * * *
8347 TCATTCCAAG-ATTTTTTAGA-GATCATAGTTGATCCCTAGACGAGCCAGTGC-GATTATTTGAA
1 TCATTCCAAGAAGTTTTCA-ATGATCAGAGTTGATCCC-AGATGATCCAGTGCAG-TCA-TTCAA
*
8409 GAAGTTTTAGAGATCAGAGTTGATCCCCAGATGATCCATTGCGG
62 GAAGTTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
* * * * *
8453 CCATTCCAAGAAGTTTTAAATGATCAGAGTTGATCCCTAGATGATCTAGTGCGGTTATTCTAA-A
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCC-AGATGATCCAGTGCAGTCATTC-AAGA
* *
8517 ATGTTTTAAGAGATCAGAGTTGATCCTCAGATGATCCAGTGCAG
64 A-GTTTT-AGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
* * * *
8561 TAATTCCAAGAAGTTTTCTATGATCAGAGTTGATCTCCA-ATTGATACAATGCAGTCAATTCAAG
1 TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC-CCAGA-TGATCCAGTGCAGTC-ATTCAAG
* *
8625 ATGTTTTCGATGATCAGAGTTGATC
63 AAGTTTTAGA-GATCAGAGTTGATC
8650 TTCAATTTGA
Statistics
Matches: 347, Mismatches: 45, Indels: 34
0.81 0.11 0.08
Matches are distributed among these distances:
105 19 0.05
106 127 0.37
107 64 0.18
108 130 0.37
109 7 0.02
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (105 bp):
TCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCCCAGATGATCCAGTGCAGTCATTCAAGAAG
TTTTAGAGATCAGAGTTGATCCCCAGATGATCCAGTGCGG
Found at i:10445 original size:23 final size:21
Alignment explanation
Indices: 10415--10508 Score: 86
Period size: 20 Copynumber: 4.5 Consensus size: 21
10405 TACTTTTTTT
10415 TATCTATTTATTATTTACTT-TCC
1 TATCTATTTATTA-TTA-TTAT-C
10438 TATCTATTTATTATTATTATC
1 TATCTATTTATTATTATTATC
***
10459 TATCTATTTA-CCCTATTATC
1 TATCTATTTATTATTATTATC
* *
10479 TATGTA-ATATTATTATTATC
1 TATCTATTTATTATTATTATC
*
10499 TATTTATTTA
1 TATCTATTTA
10509 CTTTTCACTT
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
19 2 0.03
20 24 0.41
21 15 0.26
22 4 0.07
23 13 0.22
ACGTcount: A:0.28, C:0.13, G:0.01, T:0.59
Consensus pattern (21 bp):
TATCTATTTATTATTATTATC
Found at i:10467 original size:37 final size:36
Alignment explanation
Indices: 10400--10512 Score: 102
Period size: 37 Copynumber: 3.0 Consensus size: 36
10390 GGAGTATTAT
* * *
10400 CTATCTACTTT-TTTTTATCTATTTATTATTTACTTTC
1 CTATCTA-TTTATTATTAT-TATCTATTATTTACTTTA
**
10437 CTATCTATTTATTATTATTATCTATCTATTTACCCTA
1 CTATCTATTTATTATTATTATCTAT-TATTTACTTTA
*
10474 TTATCTATGTAATATTATTATTATCTATTTATTTACTTT
1 CTATCTAT-T--TATTATTATTATCTA-TTATTTACTTT
10513 TCACTTACCT
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
36 9 0.15
37 28 0.45
38 1 0.02
40 23 0.37
41 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.01, T:0.60
Consensus pattern (36 bp):
CTATCTATTTATTATTATTATCTATTATTTACTTTA
Found at i:10495 original size:20 final size:19
Alignment explanation
Indices: 10394--10501 Score: 66
Period size: 20 Copynumber: 5.5 Consensus size: 19
10384 ACAGATGGAG
10394 TATTATCTATCTACT-TT-T
1 TATTATCTATCTA-TATTAT
*
10412 TTTTATCTAT-T-TATTATT
1 TATTATCTATCTATATTA-T
10430 TACTT-TCCTATCTATTTATTAT
1 TA-TTAT-CTATCTA--TATTAT
*
10452 TATTATCTATCTAT-TTACCC
1 TATTATCTATCTATATTA--T
*
10472 TATTATCTATGTAATATTAT
1 TATTATCTATCT-ATATTAT
10492 TATTATCTAT
1 TATTATCTAT
10502 TTATTTACTT
Statistics
Matches: 71, Mismatches: 5, Indels: 26
0.70 0.05 0.25
Matches are distributed among these distances:
15 1 0.01
16 2 0.03
17 1 0.01
18 15 0.21
19 7 0.10
20 22 0.31
21 11 0.15
22 7 0.10
23 5 0.07
ACGTcount: A:0.26, C:0.14, G:0.01, T:0.59
Consensus pattern (19 bp):
TATTATCTATCTATATTAT
Found at i:13613 original size:11 final size:10
Alignment explanation
Indices: 13597--13655 Score: 59
Period size: 11 Copynumber: 5.7 Consensus size: 10
13587 AAGTTCGTGT
13597 TTGAAGACTTA
1 TTGAAGA-TTA
*
13608 TTGAAGATAA
1 TTGAAGATTA
13618 TTTGAAGA-T-
1 -TTGAAGATTA
13627 TTGAAGATTA
1 TTGAAGATTA
13637 TTGAAGAATTA
1 TTGAAG-ATTA
13648 TTTGAAGA
1 -TTGAAGA
13656 GGCAAGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
8 7 0.17
9 1 0.02
10 8 0.20
11 19 0.46
12 6 0.15
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:13632 original size:19 final size:18
Alignment explanation
Indices: 13608--13643 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13598 TGAAGACTTA
13608 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
13627 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
13644 ATTATTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:13632 original size:30 final size:30
Alignment explanation
Indices: 13596--13655 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
13586 GAAGTTCGTG
13596 TTTGAAGACTTATTGAAG-ATAATTTGAAGA
1 TTTGAAGA-TTATTGAAGAATAATTTGAAGA
*
13626 TTTGAAGATTATTGAAGAATTATTTGAAGA
1 TTTGAAGATTATTGAAGAATAATTTGAAGA
13656 GGCAAGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (30 bp):
TTTGAAGATTATTGAAGAATAATTTGAAGA
Found at i:17226 original size:14 final size:15
Alignment explanation
Indices: 17198--17226 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17188 CTCCATTTAC
17198 TTTTTCTTTGCATTG
1 TTTTTCTTTGCATTG
17213 TTTTTCTTTG-ATTG
1 TTTTTCTTTGCATTG
17227 ATTGCCTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.07, C:0.10, G:0.14, T:0.69
Consensus pattern (15 bp):
TTTTTCTTTGCATTG
Found at i:17916 original size:17 final size:18
Alignment explanation
Indices: 17896--17931 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17886 GTAGTTTTTT
17896 TAAAAA-AAATGTTTTCA
1 TAAAAAGAAATGTTTTCA
*
17913 TAAAAAGAAGTGTTTTCA
1 TAAAAAGAAATGTTTTCA
17931 T
1 T
17932 GCAAGAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (18 bp):
TAAAAAGAAATGTTTTCA
Found at i:19052 original size:19 final size:18
Alignment explanation
Indices: 19028--19063 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19018 TGAAAACTTA
19028 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
19047 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
19064 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:20623 original size:27 final size:26
Alignment explanation
Indices: 20593--20892 Score: 139
Period size: 27 Copynumber: 12.7 Consensus size: 26
20583 TTTGGTAAGA
20593 AAAAATGGAATTTGGTAATTAAAGAGT
1 AAAAATGGAATTTGGTAATT-AAGAGT
* * *
20620 AAAAGTGAAATTTGGTAACTAAG-GT
1 AAAAATGGAATTTGGTAATTAAGAGT
* *
20645 -TAAATGGTATTTGG----TAAGA--
1 AAAAATGGAATTTGGTAATTAAGAGT
20664 AAAAATGGAATTTGG----TAAGA--
1 AAAAATGGAATTTGGTAATTAAGAGT
20684 AAAAATGGAATTTGGTAATTAAAGAGT
1 AAAAATGGAATTTGGTAATT-AAGAGT
* *
20711 AAAAGTGAAATTTGGTAATTAAG-GT
1 AAAAATGGAATTTGGTAATTAAGAGT
* *
20736 -TAAATGGTATTTGG----TAA-A--
1 AAAAATGGAATTTGGTAATTAAGAGT
20754 AAAAATGGAATTTGGTAATTAAAGAGT
1 AAAAATGGAATTTGGTAATT-AAGAGT
* * *
20781 AAAAGTGAAATTTGGTAACTAAG-GT
1 AAAAATGGAATTTGGTAATTAAGAGT
*
20806 -TAAATGGAA--T--TAA--AA-AGT
1 AAAAATGGAATTTGGTAATTAAGAGT
**
20824 AAAAATGGAATTTAATAATTAAAGAG-
1 AAAAATGGAATTTGGTAATT-AAGAGT
* *
20850 AAAAAGTGAAATTTGGTAACTAAG-GT
1 AAAAA-TGGAATTTGGTAATTAAGAGT
* *
20876 -TAAATGGTATTTGGTAA
1 AAAAATGGAATTTGGTAA
20893 AAAAAACGAA
Statistics
Matches: 211, Mismatches: 31, Indels: 65
0.69 0.10 0.21
Matches are distributed among these distances:
18 4 0.02
19 20 0.09
20 42 0.20
21 1 0.00
22 1 0.00
23 4 0.02
24 40 0.19
25 15 0.07
26 19 0.09
27 65 0.31
ACGTcount: A:0.46, C:0.01, G:0.22, T:0.30
Consensus pattern (26 bp):
AAAAATGGAATTTGGTAATTAAGAGT
Found at i:20662 original size:71 final size:71
Alignment explanation
Indices: 20546--20681 Score: 263
Period size: 71 Copynumber: 1.9 Consensus size: 71
20536 AAAAGGGTAA
20546 AGTAAAAATGAAATTTGGTAACTAAGGTTAAATGGTATTTGGTAAGAAAAAATGGAATTTGGTAA
1 AGTAAAAATGAAATTTGGTAACTAAGGTTAAATGGTATTTGGTAAGAAAAAATGGAATTTGGTAA
20611 TTAAAG
66 TTAAAG
*
20617 AGTAAAAGTGAAATTTGGTAACTAAGGTTAAATGGTATTTGGTAAGAAAAAATGGAATTTGGTAA
1 AGTAAAAATGAAATTTGGTAACTAAGGTTAAATGGTATTTGGTAAGAAAAAATGGAATTTGGTAA
20682 GAAAAAATGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.44, C:0.01, G:0.24, T:0.31
Consensus pattern (71 bp):
AGTAAAAATGAAATTTGGTAACTAAGGTTAAATGGTATTTGGTAAGAAAAAATGGAATTTGGTAA
TTAAAG
Found at i:20669 original size:20 final size:20
Alignment explanation
Indices: 20646--20701 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
20636 AACTAAGGTT
*
20646 AAATGGTATTTGGTAAGAAA
1 AAATGGAATTTGGTAAGAAA
20666 AAATGGAATTTGGTAAGAAA
1 AAATGGAATTTGGTAAGAAA
20686 AAATGGAATTTGGTAA
1 AAATGGAATTTGGTAA
20702 TTAAAGAGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (20 bp):
AAATGGAATTTGGTAAGAAA
Found at i:20687 original size:91 final size:90
Alignment explanation
Indices: 20575--20771 Score: 367
Period size: 91 Copynumber: 2.2 Consensus size: 90
20565 AACTAAGGTT
*
20575 AAATGGTATTTGGTAAGAAAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAACT
1 AAATGGAATTTGGTAAGAAAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAACT
20640 AAGGTTAAATGGTATTTGGTAAGAAA
66 AAGGTTAAATGGTATTTGGTAA-AAA
*
20666 AAATGGAATTTGGTAAGAAAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAATT
1 AAATGGAATTTGGTAAGAAAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAACT
20731 AAGGTTAAATGGTATTTGGTAAAAA
66 AAGGTTAAATGGTATTTGGTAAAAA
20756 AAATGGAATTTGGTAA
1 AAATGGAATTTGGTAA
20772 TTAAAGAGTA
Statistics
Matches: 104, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
90 19 0.18
91 85 0.82
ACGTcount: A:0.45, C:0.01, G:0.24, T:0.31
Consensus pattern (90 bp):
AAATGGAATTTGGTAAGAAAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAACT
AAGGTTAAATGGTATTTGGTAAAAA
Found at i:20772 original size:70 final size:70
Alignment explanation
Indices: 20666--20965 Score: 361
Period size: 70 Copynumber: 4.1 Consensus size: 70
20656 TGGTAAGAAA
* *
20666 AAATGGAATTTGGTAAGAAAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAATT
1 AAATGGTATTTGGTAA-AAAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAACT
20731 AAGGTT
65 AAGGTT
20737 AAATGGTATTTGGTAAAAAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAACTA
1 AAATGGTATTTGGTAAAAAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAACTA
20802 AGGTT
66 AGGTT
* ** ** *
20807 AAATGG-AATT-AAAAAGTAAAAATGGAATTTAATAATTAAAGAGAAAAAGTGAAATTTGGTAAC
1 AAATGGTATTTGGTAAA--AAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAAC
20870 TAAGGTT
64 TAAGGTT
20877 AAATGGTATTTGGTAAAAAAAACGAAATGAATGAAATTTGGTAATTAAAGGTAAAGTAAAAGTGA
1 AAATGGTATTTGGT---AAAAA--AAATG---G-AATTTGGTAATTAAA-G---AGTAAAAGTGA
*
20942 AATTTCGTAACTAAGGTT
53 AATTTGGTAACTAAGGTT
20960 AAATGG
1 AAATGG
20966 AATTAAAGAG
Statistics
Matches: 197, Mismatches: 15, Indels: 22
0.84 0.06 0.09
Matches are distributed among these distances:
68 3 0.02
69 3 0.02
70 115 0.58
71 18 0.09
73 2 0.01
75 8 0.04
78 1 0.01
79 13 0.07
80 1 0.01
83 33 0.17
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (70 bp):
AAATGGTATTTGGTAAAAAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAACTA
AGGTT
Found at i:20843 original size:140 final size:146
Alignment explanation
Indices: 20680--20989 Score: 443
Period size: 140 Copynumber: 2.1 Consensus size: 146
20670 GGAATTTGGT
** * *
20680 AAGAAAAAATGGAATTTGGTAATTAAAGAGTAAAAGTGAAATTTGGTAATTAAGGTTAAATGGTA
1 AAGAAAAAATGGAATTTAATAATTAAAGAGAAAAAGTGAAATTTGGTAACTAAGGTTAAATGGTA
*
20745 TTTGGT-AAAAA-AAATG-G-AATTTGGTAATTAAA-G-AGTAAAAGTGAAATTTGGTAACTAAG
66 TTTGGTAAAAAACAAATGAGAAATTTGGTAATTAAAGGAAGTAAAAGTGAAATTTCGTAACTAAG
20804 GTTAAATGGAATTAAA
131 GTTAAATGGAATTAAA
*
20820 AAGTAAAAATGGAATTTAATAATTAAAGAGAAAAAGTGAAATTTGGTAACTAAGGTTAAATGGTA
1 AAGAAAAAATGGAATTTAATAATTAAAGAGAAAAAGTGAAATTTGGTAACTAAGGTTAAATGGTA
20885 TTTGGTAAAAAAAACGAAATGAATGAAATTTGGTAATTAAAGGTAAAGTAAAAGTGAAATTTCGT
66 TTTGGT--AAAAAAC-AAATG-A-GAAATTTGGTAATTAAAGG--AAGTAAAAGTGAAATTTCGT
20950 AACTAAGGTTAAATGGAATTAAA
124 AACTAAGGTTAAATGGAATTAAA
* *
20973 GAGAAAAAATGAAATTT
1 AAGAAAAAATGGAATTT
20990 GGTAACTAAG
Statistics
Matches: 148, Mismatches: 9, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
140 66 0.45
143 5 0.03
145 5 0.03
148 1 0.01
149 15 0.10
150 1 0.01
153 55 0.37
ACGTcount: A:0.49, C:0.02, G:0.21, T:0.29
Consensus pattern (146 bp):
AAGAAAAAATGGAATTTAATAATTAAAGAGAAAAAGTGAAATTTGGTAACTAAGGTTAAATGGTA
TTTGGTAAAAAACAAATGAGAAATTTGGTAATTAAAGGAAGTAAAAGTGAAATTTCGTAACTAAG
GTTAAATGGAATTAAA
Found at i:21023 original size:43 final size:42
Alignment explanation
Indices: 20934--21036 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 42
20924 AAGGTAAAGT
* *
20934 AAAAGTGAAATTTCGTAACTAAGGTTAAATGGAATTAAAGAGA
1 AAAAATGAAATTTGGTAACTAAGGTTAAATGGAATTAAAG-GA
* **
20977 AAAAATGAAATTTGGTAACTAAGGTTAAATGGTATT-TTGGTA
1 AAAAATGAAATTTGGTAACTAAGGTTAAATGGAATTAAAGG-A
*
21019 AAAAATGAAACTTGGTAA
1 AAAAATGAAATTTGGTAA
21037 TTAAAGTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.02
42 19 0.36
43 33 0.62
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (42 bp):
AAAAATGAAATTTGGTAACTAAGGTTAAATGGAATTAAAGGA
Found at i:21207 original size:35 final size:34
Alignment explanation
Indices: 21168--21278 Score: 118
Period size: 34 Copynumber: 3.2 Consensus size: 34
21158 AAAGTATTTA
21168 AAAAAGGAATAGAATGGTATTTTGATAATTAAAG-T
1 AAAAAGGAATA-AATGGTA-TTTGATAATTAAAGCT
* * *
21203 AAAAAAGGAGTAAAATGGTATTTGGTAATTAAAGCA
1 -AAAAAGGAAT-AAATGGTATTTGATAATTAAAGCT
* *
21239 AAAAAGGTAA-AATTGGTATTTGATAATTAAAGTT
1 AAAAAGG-AATAAATGGTATTTGATAATTAAAGCT
21273 AAAAAG
1 AAAAAG
21279 AGTAAAAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
34 26 0.41
35 20 0.31
36 17 0.27
37 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.20, T:0.29
Consensus pattern (34 bp):
AAAAAGGAATAAATGGTATTTGATAATTAAAGCT
Found at i:21284 original size:35 final size:35
Alignment explanation
Indices: 21182--21293 Score: 156
Period size: 34 Copynumber: 3.2 Consensus size: 35
21172 AGGAATAGAA
21182 TGGTATTTTGATAATTAAAGTAAAAAAGGAGTAAAA-
1 TGGTA-TTTGATAATTAAAGTAAAAAA-GAGTAAAAT
* *
21218 TGGTATTTGGTAATTAAAGCAAAAAAG-GTAAAAT
1 TGGTATTTGATAATTAAAGTAAAAAAGAGTAAAAT
*
21252 TGGTATTTGATAATTAAAGTTAAAAAGAGTAAAAAT
1 TGGTATTTGATAATTAAAGTAAAAAAGAGT-AAAAT
21288 TGGTAT
1 TGGTAT
21294 AAAGGAAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
33 6 0.09
34 25 0.37
35 21 0.31
36 16 0.24
ACGTcount: A:0.47, C:0.01, G:0.20, T:0.32
Consensus pattern (35 bp):
TGGTATTTGATAATTAAAGTAAAAAAGAGTAAAAT
Found at i:21309 original size:61 final size:66
Alignment explanation
Indices: 21182--21319 Score: 178
Period size: 61 Copynumber: 2.1 Consensus size: 66
21172 AGGAATAGAA
21182 TGGTATTTTGATAATTAAAGTAAAAAAGGAGTAAAATGGTATTTGGTAATTAAAGCAAAAAAGGT
1 TGGTA-TTTGATAATTAAAGTAAAAAAGGAGTAAAA--G-ATTTGGTAATTAAAGCAAAAAAGGT
21247 AAAAT
62 AAAAT
* * *
21252 TGGTATTTGATAATTAAAGTTAAAAA-GAGTAAAA-A-TTGGT-A-TAAAGGAAAAAGGGTAAAA
1 TGGTATTTGATAATTAAAGTAAAAAAGGAGTAAAAGATTTGGTAATTAAAGCAAAAAAGGTAAAA
21312 T
66 T
21313 TGGTATT
1 TGGTATT
21320 CAGTAATCAG
Statistics
Matches: 65, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
61 25 0.38
62 1 0.02
63 5 0.08
64 1 0.02
68 8 0.12
69 20 0.31
70 5 0.08
ACGTcount: A:0.48, C:0.01, G:0.21, T:0.30
Consensus pattern (66 bp):
TGGTATTTGATAATTAAAGTAAAAAAGGAGTAAAAGATTTGGTAATTAAAGCAAAAAAGGTAAAA
T
Found at i:22837 original size:16 final size:16
Alignment explanation
Indices: 22795--22838 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
22785 ACCCGCCCGA
*
22795 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
* *
22811 ACCTGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
22827 ACCCGAACCCGA
1 ACCCGAACCCGA
22839 GGCAGCCCGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.39, G:0.16, T:0.09
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:23042 original size:2 final size:2
Alignment explanation
Indices: 23035--23074 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
23025 AACTACTAAA
*
23035 AT AT AT AT A- AT -T AG AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Done.