Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015196.1 Corchorus capsularis cultivar CVL-1 contig15217, 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: 16634
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Found at i:48 original size:11 final size:11
Alignment explanation
Indices: 45--74 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
35 TTTTTTTTAA
45 TTTTTAAATTT
1 TTTTTAAATTT
*
56 TTTTTGAATTT
1 TTTTTAAATTT
67 TTTTTAAA
1 TTTTTAAA
75 AGATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (11 bp):
TTTTTAAATTT
Found at i:565 original size:12 final size:12
Alignment explanation
Indices: 548--578 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
538 CCTGGCAATC
548 CGTGTTTCGTGT
1 CGTGTTTCGTGT
560 CGTGTTTCGTGT
1 CGTGTTTCGTGT
572 CGTGTTT
1 CGTGTTT
579 ACATAGGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52
Consensus pattern (12 bp):
CGTGTTTCGTGT
Found at i:807 original size:14 final size:14
Alignment explanation
Indices: 788--815 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
778 TTAACTAAAC
788 TATATATATAATTA
1 TATATATATAATTA
802 TATATATATAATTA
1 TATATATATAATTA
816 AAGATAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATATATAATTA
Found at i:988 original size:20 final size:21
Alignment explanation
Indices: 951--993 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
941 AACCCGTTAA
*
951 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
972 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
992 TT
1 TT
994 GACATGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:1059 original size:42 final size:43
Alignment explanation
Indices: 981--1063 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
971 CTTAAACGTG
* *
981 TTAATCGTGTCTTGACATGATTACGACACGAAACACGATAATC
1 TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC
*
1024 TTAATCGTGTC-CGACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATTAC-GACACGAAACACGATAA
1064 GTCAAACACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.03
42 24 0.67
43 11 0.31
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATC
Found at i:1954 original size:24 final size:24
Alignment explanation
Indices: 1878--1955 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
1868 ACCATGTTTA
* * * *
1878 ATGGTTGGCGCACTGCCACTTCGG
1 ATGGTGGGTGCACTCCCACTTCCG
* * *
1902 ATGGGGGGTGTACTCCCGCTTCCG
1 ATGGTGGGTGCACTCCCACTTCCG
*
1926 ATGGTGGGTGCACTCCCACTTCTG
1 ATGGTGGGTGCACTCCCACTTCCG
1950 ATGGTG
1 ATGGTG
1956 AGCATTCTAC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.12, C:0.27, G:0.35, T:0.27
Consensus pattern (24 bp):
ATGGTGGGTGCACTCCCACTTCCG
Found at i:1975 original size:24 final size:22
Alignment explanation
Indices: 1938--1994 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 22
1928 GGTGGGTGCA
*
1938 CTCCCACTTCTGATGGTGAGCATT
1 CTCCCA-TT-TGATGATGAGCATT
1962 CTACCTCATTTGATGATGAGCATT
1 CT-CC-CATTTGATGATGAGCATT
1986 CTCCCATTT
1 CTCCCATTT
1995 TTTATGGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.17
23 2 0.07
24 17 0.57
25 4 0.13
26 2 0.07
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.37
Consensus pattern (22 bp):
CTCCCATTTGATGATGAGCATT
Found at i:2259 original size:28 final size:28
Alignment explanation
Indices: 2218--2365 Score: 174
Period size: 28 Copynumber: 5.3 Consensus size: 28
2208 CTTCGAGAGT
* * *
2218 GTACTACCTCTTCGTGATCTATGGGAGC
1 GTACTACCGCTTCGCGGTCTATGGGAGC
* *
2246 ATACTACCGCTTCGCGGTC-ATTGAGAGC
1 GTACTACCGCTTCGCGGTCTA-TGGGAGC
*
2274 GTACTACCGCTTCGCAGTC-ATTGGGAGC
1 GTACTACCGCTTCGCGGTCTA-TGGGAGC
* *
2302 GTACTAGCGCTTCGCGGTCTTTGGGAGC
1 GTACTACCGCTTCGCGGTCTATGGGAGC
* *
2330 GTACTACCGTTTCGCGGTCTTTGGGAGC
1 GTACTACCGCTTCGCGGTCTATGGGAGC
2358 GTACTACC
1 GTACTACC
2366 AATCTATAGG
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
27 1 0.01
28 104 0.99
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.28
Consensus pattern (28 bp):
GTACTACCGCTTCGCGGTCTATGGGAGC
Found at i:2767 original size:16 final size:16
Alignment explanation
Indices: 2746--2778 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2736 GATCTTGATT
2746 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
2762 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
2778 C
1 C
2779 CTTTGTAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.27, G:0.18, T:0.42
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:5281 original size:55 final size:54
Alignment explanation
Indices: 5212--5468 Score: 286
Period size: 55 Copynumber: 4.7 Consensus size: 54
5202 AAGACCCAAG
* * * * *
5212 TGACCAGGACTCAAGCAATCAAAATTTATTGTTCGCTCGTCCTGGCGTTCGTCT
1 TGACTAGGACTCAAGCGATCAAAATTTATTATTCGCTCGTCCTGGTGTTCATCT
* * * *
5266 CTGACTAGGGCTCAAGCGATCAAACTTTATTATTCGCTGGCCCTGGTGTTCATCT
1 -TGACTAGGACTCAAGCGATCAAAATTTATTATTCGCTCGTCCTGGTGTTCATCT
* *
5321 TCGACTAGGACTCAAGCGATCAAAATTTATTATTCGCTCGTCCTAGTGCTCATCT
1 T-GACTAGGACTCAAGCGATCAAAATTTATTATTCGCTCGTCCTGGTGTTCATCT
* * * * *
5376 GCTGACCAGGGCTC-AGACGATC-AACTTTATT-TCCGCTCGTCTTGGTGTTCATCT
1 --TGACTAGGACTCAAG-CGATCAAAATTTATTATTCGCTCGTCCTGGTGTTCATCT
*
5430 TCGACTATGACTCAAGCGATCAAAATTTATTATTCGCTC
1 T-GACTAGGACTCAAGCGATCAAAATTTATTATTCGCTC
5469 ACCCTAGTAC
Statistics
Matches: 167, Mismatches: 27, Indels: 16
0.80 0.13 0.08
Matches are distributed among these distances:
52 1 0.01
53 13 0.08
54 30 0.18
55 108 0.65
56 14 0.08
57 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (54 bp):
TGACTAGGACTCAAGCGATCAAAATTTATTATTCGCTCGTCCTGGTGTTCATCT
Found at i:5452 original size:109 final size:110
Alignment explanation
Indices: 5217--5483 Score: 360
Period size: 109 Copynumber: 2.4 Consensus size: 110
5207 CCAAGTGACC
* * * * * * *
5217 AGGACTCAAGCAATCAAAATTTATTGTTCGCTCGTCCTGGCGTTCGTCTCTGACTAGGGCTCAAG
1 AGGACTCAAGCGATCAAAATTTATTATTCGCTCGTCCTAGTGCTCATCTCTGACCAGGGCTCAAG
* *
5282 CGATCAAACTTTATTATTCGCTGGCCCTGGTGTTCATCTTCGACT
66 CGATCAAACTTTATTATCCGCTCGCCCTGGTGTTCATCTTCGACT
5327 AGGACTCAAGCGATCAAAATTTATTATTCGCTCGTCCTAGTGCTCATCTGCTGACCAGGGCTC-A
1 AGGACTCAAGCGATCAAAATTTATTATTCGCTCGTCCTAGTGCTCATCT-CTGACCAGGGCTCAA
* *
5391 GACGATC-AACTTTATT-TCCGCTCGTCTTGGTGTTCATCTTCGACT
65 G-CGATCAAACTTTATTATCCGCTCGCCCTGGTGTTCATCTTCGACT
* ** *
5436 ATGACTCAAGCGATCAAAATTTATTATTCGCTCACCCTAGTACTCATC
1 AGGACTCAAGCGATCAAAATTTATTATTCGCTCGTCCTAGTGCTCATC
5484 ATGGTTTGCT
Statistics
Matches: 140, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
109 69 0.49
110 54 0.39
111 17 0.12
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (110 bp):
AGGACTCAAGCGATCAAAATTTATTATTCGCTCGTCCTAGTGCTCATCTCTGACCAGGGCTCAAG
CGATCAAACTTTATTATCCGCTCGCCCTGGTGTTCATCTTCGACT
Found at i:6412 original size:61 final size:61
Alignment explanation
Indices: 6316--6564 Score: 344
Period size: 61 Copynumber: 4.0 Consensus size: 61
6306 TGGTGTTTTT
* * * *
6316 TTTTTTTTTTGCTCTAGCTTTTGCCTAAGCTGTCCTTTGCAGGATTTTCAACTTAGCGAGC
1 TTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAGGATTTTCAACTTAGCGAGC
* *
6377 TTTTTTTTGTGCTCTAACTTTTGTCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
1 TTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAGGATTTTCAACTTAGCGAGC
*
6438 ---TTTTTGTGCTCTAACTTTTGCCTAAACCGTCATTTGCAGGATTTTCAACTTAGCGAGC
1 TTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAGGATTTTCAACTTAGCGAGC
*
6496 GTTTTTTTTTTTTGTGCTCTTAA-TTTTGCCTAAGCCGTCATTTGCAAGATTTTCAACTTAGCGA
1 -----TTTTTTTTGTGCTC-TAACTTTTGCCTAAGCCGTCATTTGCAGGATTTTCAACTTAGCGA
6560 GC
60 GC
6562 TTT
1 TTT
6565 GCAAGTAGTT
Statistics
Matches: 170, Mismatches: 9, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
58 55 0.32
61 60 0.35
66 52 0.31
67 3 0.02
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (61 bp):
TTTTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAGGATTTTCAACTTAGCGAGC
Found at i:6474 original size:58 final size:59
Alignment explanation
Indices: 6318--6564 Score: 318
Period size: 58 Copynumber: 4.1 Consensus size: 59
6308 GTGTTTTTTT
* * * *
6318 TTTTTTTTGCTCTAGCTTTTGCCTAAGCTGTCCTTTGCAGGATTTTCAACTTAGCGAGC
1 TTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAGGATTTTCAACTTAGCGAGC
* *
6377 TTTTTTTTGTGCTCTAACTTTTGTCTAAGCCGTCCTTTGCAGGATTTTCAACTTAGCGAGC
1 --TTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAGGATTTTCAACTTAGCGAGC
*
6438 -TTTTTGTGCTCTAACTTTTGCCTAAACCGTCATTTGCAGGATTTTCAACTTAGCGAGC
1 TTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAGGATTTTCAACTTAGCGAGC
*
6496 GTTTTTTTTTTTTGTGCTCTTAA-TTTTGCCTAAGCCGTCATTTGCAAGATTTTCAACTTAGCGA
1 -------TTTTTTGTGCTC-TAACTTTTGCCTAAGCCGTCATTTGCAGGATTTTCAACTTAGCGA
6560 GC
58 GC
6562 TTT
1 TTT
6565 GCAAGTAGTT
Statistics
Matches: 168, Mismatches: 9, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
58 55 0.33
59 3 0.02
61 55 0.33
66 52 0.31
67 3 0.02
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (59 bp):
TTTTTTGTGCTCTAACTTTTGCCTAAGCCGTCATTTGCAGGATTTTCAACTTAGCGAGC
Found at i:6547 original size:66 final size:66
Alignment explanation
Indices: 6438--6561 Score: 214
Period size: 66 Copynumber: 1.9 Consensus size: 66
6428 CTTAGCGAGC
*
6438 TTTTTGTGCTCTAACTTTTGCCTAAACCGTCATTTGCAGGATTTTCAACTTAGCGAGCGTTTTTT
1 TTTTTGTGCTCTAACTTTTGCCTAAACCGTCATTTGCAAGATTTTCAACTTAGCGAGCGTTTTTT
6503 T
66 T
*
6504 TTTTTGTGCTCTTAA-TTTTGCCTAAGCCGTCATTTGCAAGATTTTCAACTTAGCGAGC
1 TTTTTGTGCTC-TAACTTTTGCCTAAACCGTCATTTGCAAGATTTTCAACTTAGCGAGC
6562 TTTGCAAGTA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
66 52 0.95
67 3 0.05
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (66 bp):
TTTTTGTGCTCTAACTTTTGCCTAAACCGTCATTTGCAAGATTTTCAACTTAGCGAGCGTTTTTT
T
Found at i:11083 original size:28 final size:28
Alignment explanation
Indices: 11043--11141 Score: 137
Period size: 28 Copynumber: 3.5 Consensus size: 28
11033 TTGTCTACAA
*
11043 TGGGAGCATACTACCGCTTCGCGGTCAT
1 TGGGAGCGTACTACCGCTTCGCGGTCAT
* *
11071 TGGGAGCGTACTACCACTTCGTGGTCAT
1 TGGGAGCGTACTACCGCTTCGCGGTCAT
*
11099 TGGGAGCGTACTACCGCTTCGCGGGC-T
1 TGGGAGCGTACTACCGCTTCGCGGTCAT
*
11126 TGGAGGGCGTACTACC
1 TGG-GAGCGTACTACC
11142 ACGTCGCGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
27 4 0.06
28 59 0.94
ACGTcount: A:0.16, C:0.27, G:0.32, T:0.24
Consensus pattern (28 bp):
TGGGAGCGTACTACCGCTTCGCGGTCAT
Found at i:11167 original size:29 final size:29
Alignment explanation
Indices: 11106--11439 Score: 357
Period size: 29 Copynumber: 11.2 Consensus size: 29
11096 CATTGGGAGC
* ** *
11106 GTACTACCGCTTCGCGGGC-TTGGAGGGC
1 GTACTACCACTTCGCGAACTTTGGAGGGA
*
11134 GTACTACCACGTCGCGAACTTTGGAGGGA
1 GTACTACCACTTCGCGAACTTTGGAGGGA
* *
11163 GTACTACCATTTCGTGAACTTTGGAGGGA
1 GTACTACCACTTCGCGAACTTTGGAGGGA
* * *
11192 GTACCACCACTTCGTGAGCTTTGGAGGGA
1 GTACTACCACTTCGCGAACTTTGGAGGGA
* * *
11221 TTACTATCACTTCGCGAACTTTGGAGGGC
1 GTACTACCACTTCGCGAACTTTGGAGGGA
11250 GTACTACCACTTCGCGAACTTTGGAGGGA
1 GTACTACCACTTCGCGAACTTTGGAGGGA
*
11279 GTACTACCACTTCGTGAACTTCGTGAGCTTTGGAGGGA
1 GTACTACCACTTC--G-----C--GAACTTTGGAGGGA
* * *
11317 GTACTACCACTTCGTGAGCTTTGGAGGGC
1 GTACTACCACTTCGCGAACTTTGGAGGGA
** *
11346 GTACTGTCACTTCGTGAACTTTGGAGGGA
1 GTACTACCACTTCGCGAACTTTGGAGGGA
*
11375 GTACTACCATTTCGCGAACTTTGGAGGGA
1 GTACTACCACTTCGCGAACTTTGGAGGGA
* *
11404 GTACTACCACTTCGC-AATCTTTGGGGGGC
1 GTACTACCACTTCGCGAA-CTTTGGAGGGA
11433 GTACTAC
1 GTACTAC
11440 TGCTTCTTTC
Statistics
Matches: 261, Mismatches: 34, Indels: 21
0.83 0.11 0.07
Matches are distributed among these distances:
28 17 0.07
29 215 0.82
31 1 0.00
36 2 0.01
38 26 0.10
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (29 bp):
GTACTACCACTTCGCGAACTTTGGAGGGA
Found at i:11310 original size:38 final size:38
Alignment explanation
Indices: 11258--11333 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
11248 GCGTACTACC
11258 ACTTCGCGAACTTTGGAGGGAGTACTACCACTTCGTGA
1 ACTTCGCGAACTTTGGAGGGAGTACTACCACTTCGTGA
* *
11296 ACTTCGTGAGCTTTGGAGGGAGTACTACCACTTCGTGA
1 ACTTCGCGAACTTTGGAGGGAGTACTACCACTTCGTGA
11334 GCTTTGGAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (38 bp):
ACTTCGCGAACTTTGGAGGGAGTACTACCACTTCGTGA
Found at i:11365 original size:96 final size:96
Alignment explanation
Indices: 11200--11439 Score: 311
Period size: 96 Copynumber: 2.6 Consensus size: 96
11190 GAGTACCACC
* *
11200 ACTTCGTGAGCTTTGGAGGGATTACTATCACTTCGCGAACTTTGGAGGGCGTACTACCACTTCGC
1 ACTTCGTGAGCTTTGGAGGGAGTACTACCACTTCGCGAACTTTGGAGGGCGTACTACCACTTCGC
*
11265 GAACTTTGGAGGGAGTACTACCACTTCGTGA
66 GAACTTTGGAGGGAGTACTACCACTTCGCGA
* * ** *
11296 ACTTCGTGAGCTTTGGAGGGAGTACTACCACTTCGTGAGCTTTGGAGGGCGTACTGTCACTTCGT
1 ACTTCGTGAGCTTTGGAGGGAGTACTACCACTTCGCGAACTTTGGAGGGCGTACTACCACTTCGC
*
11361 GAACTTTGGAGGGAGTACTACCATTTCGCG-
66 GAACTTTGGAGGGAGTACTACCACTTCGCGA
*
11391 A-------A-CTTTGGAGGGAGTACTACCACTTCGC-AATCTTTGGGGGGCGTACTAC
1 ACTTCGTGAGCTTTGGAGGGAGTACTACCACTTCGCGAA-CTTTGGAGGGCGTACTAC
11440 TGCTTCTTTC
Statistics
Matches: 129, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
86 1 0.01
87 40 0.31
88 1 0.01
95 1 0.01
96 86 0.67
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (96 bp):
ACTTCGTGAGCTTTGGAGGGAGTACTACCACTTCGCGAACTTTGGAGGGCGTACTACCACTTCGC
GAACTTTGGAGGGAGTACTACCACTTCGCGA
Found at i:11395 original size:125 final size:125
Alignment explanation
Indices: 11173--11417 Score: 418
Period size: 125 Copynumber: 2.0 Consensus size: 125
11163 GTACTACCAT
*
11173 TTCGTGAACTTTGGAGGGAGTACCACCACTTCGTGAGCTTTGGAGGGATTACTATCACTTCGCGA
1 TTCGTGAACTTTGGAGGGAGTACCACCACTTCGTGAGCTTTGGAGGGAGTACTATCACTTCGCGA
*
11238 ACTTTGGAGGGCGTACTACCACTTCGCGAACTTTGGAGGGAGTACTACCACTTCGTGAAC
66 ACTTTGGAGGGAGTACTACCACTTCGCGAACTTTGGAGGGAGTACTACCACTTCGTGAAC
* * * * *
11298 TTCGTGAGCTTTGGAGGGAGTACTACCACTTCGTGAGCTTTGGAGGGCGTACTGTCACTTCGTGA
1 TTCGTGAACTTTGGAGGGAGTACCACCACTTCGTGAGCTTTGGAGGGAGTACTATCACTTCGCGA
*
11363 ACTTTGGAGGGAGTACTACCATTTCGCGAACTTTGGAGGGAGTACTACCACTTCG
66 ACTTTGGAGGGAGTACTACCACTTCGCGAACTTTGGAGGGAGTACTACCACTTCG
11418 CAATCTTTGG
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
125 112 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (125 bp):
TTCGTGAACTTTGGAGGGAGTACCACCACTTCGTGAGCTTTGGAGGGAGTACTATCACTTCGCGA
ACTTTGGAGGGAGTACTACCACTTCGCGAACTTTGGAGGGAGTACTACCACTTCGTGAAC
Found at i:11396 original size:154 final size:154
Alignment explanation
Indices: 11152--11439 Score: 443
Period size: 154 Copynumber: 1.9 Consensus size: 154
11142 ACGTCGCGAA
* *
11152 CTTTGGAGGGAGTACTACCATTTCGTGAACTTTGGAGGGAGTACCACCACTTCGTGAGCTTTGGA
1 CTTTGGAGGGAGTACTACCACTTCGTGAACTTTGGAGGGAGTACCACCACTTCGTGAACTTTGGA
* * *
11217 GGGATTACTATCACTTCGCGAACTTTGGAGGGCGTACTACCACTTCGCGAA-CTTTGGAGGGAGT
66 GGGAGTACTACCACTTCGCGAACTTTGGAGGGAGTACTACCACTTCGC-AATCTTTGGAGGGAGT
11281 ACTACCACTTCGTGAACTTCGTGAG
130 ACTACCACTTCGTGAACTTCGTGAG
* * ***
11306 CTTTGGAGGGAGTACTACCACTTCGTGAGCTTTGGAGGGCGTACTGTCACTTCGTGAACTTTGGA
1 CTTTGGAGGGAGTACTACCACTTCGTGAACTTTGGAGGGAGTACCACCACTTCGTGAACTTTGGA
* * *
11371 GGGAGTACTACCATTTCGCGAACTTTGGAGGGAGTACTACCACTTCGCAATCTTTGGGGGGCGTA
66 GGGAGTACTACCACTTCGCGAACTTTGGAGGGAGTACTACCACTTCGCAATCTTTGGAGGGAGTA
11436 CTAC
131 CTAC
11440 TGCTTCTTTC
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
153 2 0.02
154 118 0.98
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (154 bp):
CTTTGGAGGGAGTACTACCACTTCGTGAACTTTGGAGGGAGTACCACCACTTCGTGAACTTTGGA
GGGAGTACTACCACTTCGCGAACTTTGGAGGGAGTACTACCACTTCGCAATCTTTGGAGGGAGTA
CTACCACTTCGTGAACTTCGTGAG
Found at i:12199 original size:28 final size:28
Alignment explanation
Indices: 12099--12236 Score: 161
Period size: 28 Copynumber: 4.8 Consensus size: 28
12089 ATTTGGACTC
*
12099 TATCTAGGCTGTATGCCTTTGGAAATTTT
1 TATCTAGGCTGTATGCCTTTGGGAA-TTT
* * *
12128 TGTATAGACTGTATGCCTTTGGGAAATTT
1 TATCTAGGCTGTATGCCTTTGGG-AATTT
* * *
12157 T-TGTATGGGTTGTATGCCTTTGGGGATTT
1 TATCTA--GGCTGTATGCCTTTGGGAATTT
*
12186 TATCTAGGCTGTATGCCTTTGGAAATTT
1 TATCTAGGCTGTATGCCTTTGGGAATTT
12214 TATCTAGGCTGTATGCCTTTGGG
1 TATCTAGGCTGTATGCCTTTGGG
12237 GGGTGCCCAT
Statistics
Matches: 92, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
28 44 0.48
29 28 0.30
30 20 0.22
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.43
Consensus pattern (28 bp):
TATCTAGGCTGTATGCCTTTGGGAATTT
Found at i:12453 original size:59 final size:59
Alignment explanation
Indices: 12255--12459 Score: 198
Period size: 59 Copynumber: 3.5 Consensus size: 59
12245 ATTTTAGGTT
** ** * * * *
12255 GTGCGACCGAGGGATGCTC-ATTTTTCTTATCACAT-GAGTGGGGGATACCCATTGGGTC
1 GTGCGACCGAGGGATGCTCGATCGTTCTTATTGC-TCGTGTGGGGGATACCCACTAGGCC
* ** * * ** * * * * *
12313 ATATGACCAAGGGATGCTCGGTTTTTCTTATTGTTTGTGTGGGGGATACCCATTTGGTC
1 GTGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATACCCACTAGGCC
12372 GTGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATACCCACTAGGCC
1 GTGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATACCCACTAGGCC
*
12431 GTGCGACTGAGGGATGCTCGATCGTTCTT
1 GTGCGACCGAGGGATGCTCGATCGTTCTT
12460 GCTTTCCATA
Statistics
Matches: 122, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
58 16 0.13
59 106 0.87
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.31
Consensus pattern (59 bp):
GTGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATACCCACTAGGCC
Found at i:16378 original size:15 final size:16
Alignment explanation
Indices: 16352--16390 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
16342 CTTCTTATAT
16352 TATATATATCTAATGA
1 TATATATATCTAATGA
16368 TATAT-TATCTAATG-
1 TATATATATCTAATGA
*
16382 TATGTATAT
1 TATATATAT
16391 GTGTATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 12 0.57
16 5 0.24
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (16 bp):
TATATATATCTAATGA
Done.