Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011036.1 Corchorus capsularis cultivar CVL-1 contig11057, 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: 43716
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:685 original size:3 final size:3
Alignment explanation
Indices: 677--702 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
667 GATTAGGACC
677 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
703 GCTAAAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5944 original size:2 final size:2
Alignment explanation
Indices: 5937--5969 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5927 TTATAGATAA
5937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5970 GACTTCAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13880 original size:2 final size:2
Alignment explanation
Indices: 13873--13908 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13863 CGAAGGCACC
13873 AT AT AT AT AT 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
13909 TTGTAGTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20018 original size:2 final size:2
Alignment explanation
Indices: 20013--20041 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20003 TAAAAAAAAA
20013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20042 ATTAAACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27059 original size:2 final size:2
Alignment explanation
Indices: 27047--27078 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27037 TAACAAGTTC
27047 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27079 TGGCCAGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:39031 original size:32 final size:31
Alignment explanation
Indices: 38978--39057 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 31
38968 GCAATGGGCT
* *
38978 TTGGTGTGGGCATTGCTGATGGAACTTCTTC
1 TTGGTGTCGGCATTGCTGATGGAACTTCTCC
*
39009 TTGGTGTCGGCATTTGCTGATGGAACTTGTCC
1 TTGGTGTCGGCA-TTGCTGATGGAACTTCTCC
39041 TTGGTGTCGGCACTTGC
1 TTGGTGTCGGCA-TTGC
39058 ATATGGCCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 11 0.25
32 33 0.75
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.38
Consensus pattern (31 bp):
TTGGTGTCGGCATTGCTGATGGAACTTCTCC
Found at i:39540 original size:21 final size:20
Alignment explanation
Indices: 39510--39549 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
39500 CCTCGCACCC
39510 TGGGGCGCCTTGGGGCCACT
1 TGGGGCGCCTTGGGGCCACT
39530 TGGGGTCGCCTTGGGGCCAC
1 TGGGG-CGCCTTGGGGCCAC
39550 CTCGGGGGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.05, C:0.30, G:0.45, T:0.20
Consensus pattern (20 bp):
TGGGGCGCCTTGGGGCCACT
Found at i:39803 original size:32 final size:32
Alignment explanation
Indices: 39753--40039 Score: 280
Period size: 32 Copynumber: 9.2 Consensus size: 32
39743 TCGACACTCT
* ** * *
39753 CCGATGGGCCTTATCCTTGGTGTCAGCATTTG
1 CCGATGGCCCTTGGCCTTGGCGTCGGCATTTG
* *
39785 CCGATGGCCCTAGGCCTTGGAGTCGGCATTTG
1 CCGATGGCCCTTGGCCTTGGCGTCGGCATTTG
* *
39817 CCGATGG-CCTTGGCTTTGGCGTTGGCATTTG
1 CCGATGGCCCTTGGCCTTGGCGTCGGCATTTG
* *
39848 CCGATGGCCC-TGGCCTTGACGTTGGCATTTG
1 CCGATGGCCCTTGGCCTTGGCGTCGGCATTTG
* * *
39879 CTGATGGCCCTTGGTCTTGGCGTCGGAATTTG
1 CCGATGGCCCTTGGCCTTGGCGTCGGCATTTG
** * * *
39911 -C-AT--CGATTGGCCTTGGCGCCAGCATTTC
1 CCGATGGCCCTTGGCCTTGGCGTCGGCATTTG
39939 CCGATGGCCCTTGGCCTTGGCGTCGGCATTTG
1 CCGATGGCCCTTGGCCTTGGCGTCGGCATTTG
* * * **
39971 CCGACGTCCCTTGGCATTGGTATCGGCATTTG
1 CCGATGGCCCTTGGCCTTGGCGTCGGCATTTG
* * *
40003 CCGACGTCCCTTGGCATTGGCGTCGGCATTTG
1 CCGATGGCCCTTGGCCTTGGCGTCGGCATTTG
*
40035 TCGAT
1 CCGAT
40040 TGCGTCGGAA
Statistics
Matches: 210, Mismatches: 39, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
28 18 0.09
29 1 0.00
30 4 0.02
31 55 0.26
32 132 0.63
ACGTcount: A:0.10, C:0.28, G:0.31, T:0.31
Consensus pattern (32 bp):
CCGATGGCCCTTGGCCTTGGCGTCGGCATTTG
Found at i:40635 original size:50 final size:50
Alignment explanation
Indices: 40574--40701 Score: 197
Period size: 50 Copynumber: 2.6 Consensus size: 50
40564 CCCTAAGCTC
* *
40574 GAACAAGTGCTCCCCGCACTGATCACAAATCTAAGCTTT-CCTCAAGCTTA
1 GAACAAGTGCTCCCCGCACTGATTACAAAACTAAGCTTTGCC-CAAGCTTA
40624 GAACAAGTGCTCCCCGC-CTTGATTACAAAACTAAGCTTTGCCCAAGCTTA
1 GAACAAGTGCTCCCCGCAC-TGATTACAAAACTAAGCTTTGCCCAAGCTTA
*
40674 GAACAAGTGCTCCTCGCACTGATTACAA
1 GAACAAGTGCTCCCCGCACTGATTACAA
40702 TCAAAGAGAT
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
49 1 0.01
50 68 0.94
51 3 0.04
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (50 bp):
GAACAAGTGCTCCCCGCACTGATTACAAAACTAAGCTTTGCCCAAGCTTA
Found at i:41312 original size:22 final size:22
Alignment explanation
Indices: 41262--41333 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
41252 CATGCACCTC
* *
41262 GCACCTTGGGGGC-GCCTTGGGG
1 GCACCTT-GGGGCAACCTCGGGG
*
41284 CCA-CTTGGGGCAACCTCGGGG
1 GCACCTTGGGGCAACCTCGGGG
* **
41305 GCGCCTTGGGGCCTCCTCGGGG
1 GCACCTTGGGGCAACCTCGGGG
41327 GCACCTT
1 GCACCTT
41334 TGGTCCCTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.12
21 11 0.28
22 24 0.60
ACGTcount: A:0.07, C:0.33, G:0.42, T:0.18
Consensus pattern (22 bp):
GCACCTTGGGGCAACCTCGGGG
Found at i:42313 original size:91 final size:93
Alignment explanation
Indices: 42150--42362 Score: 252
Period size: 91 Copynumber: 2.3 Consensus size: 93
42140 CCGTGACACA
*
42150 TGGCCTTGGCGTCGGCATTTGCCGATGGCCTTGTCGGAATTTGATGATGTCCCTTATTACGTTGG
1 TGGCCTTGGCGTCGGCATTTGCCGATGGCC-TGTCGGAATTTGATGATGTCCCTTATCACGTTGG
** *
42215 CGTTGGCATCGGCATTTGACGATGGCATG
65 CACTGGCATCAGCATTTGACGATGGCATG
* * * *
42244 TGGCCTTGGTGTCGGCATTTGCTGATTG-C-GTCGGAATTTGATGATGTCCCTTGTCCAC-TTGG
1 TGGCCTTGGCGTCGGCATTTGCCGATGGCCTGTCGGAATTTGATGATGTCCCTTAT-CACGTTGG
* ***
42306 CACTGGCATCAGCATTTGCCGATGGCCCA
65 CACTGGCATCAGCATTTGACGATGGCATG
** *
42335 TGGCCTTGGAATCAGCATTTGCCGATGG
1 TGGCCTTGGCGTCGGCATTTGCCGATGG
42363 TCCATGGCCT
Statistics
Matches: 101, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
91 73 0.72
92 2 0.02
93 1 0.01
94 25 0.25
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.32
Consensus pattern (93 bp):
TGGCCTTGGCGTCGGCATTTGCCGATGGCCTGTCGGAATTTGATGATGTCCCTTATCACGTTGGC
ACTGGCATCAGCATTTGACGATGGCATG
Found at i:42354 original size:32 final size:32
Alignment explanation
Indices: 42309--42424 Score: 153
Period size: 32 Copynumber: 3.6 Consensus size: 32
42299 CACTTGGCAC
42309 TGGCATCAGCATTTGCCGATGGCCCATGGCCT
1 TGGCATCAGCATTTGCCGATGGCCCATGGCCT
* *
42341 TGGAATCAGCATTTGCCGATGGTCCATGGCCT
1 TGGCATCAGCATTTGCCGATGGCCCATGGCCT
* * * * *
42373 TGGCGTCGGCATTTGCTGATGGCCCGTTGCCT
1 TGGCATCAGCATTTGCCGATGGCCCATGGCCT
42405 TGGCATC-GCCATTTGCCGAT
1 TGGCATCAG-CATTTGCCGAT
42425 TGCGTCCGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
31 1 0.01
32 71 0.99
ACGTcount: A:0.14, C:0.28, G:0.29, T:0.28
Consensus pattern (32 bp):
TGGCATCAGCATTTGCCGATGGCCCATGGCCT
Found at i:42509 original size:155 final size:154
Alignment explanation
Indices: 42212--42535 Score: 402
Period size: 155 Copynumber: 2.1 Consensus size: 154
42202 CTTATTACGT
* * * ** * * *
42212 TGGCGTTGGCATCGGCATTTGACGATGGCATGTGGCCTTGGTGTCGGCATTTGCTGATTGCGTCG
1 TGGCCTTGGCGTCGGCATTTGACGATGGCACGTGGCCTTGGCATCGCCATTTGCCGATTGCGTCC
*
42277 GAATTTGATGATGTCCCTTGTCCACTTGGCACTGGCATCAGCATTTGCCGATGGCCCATGGCCTT
66 GAATTTGATGATGTCCCTTGTCCACTTGGAACTGGCATCAGCATTTGCCGATGGCCCATGGCCTT
* *
42342 GGAATCAGCATTTGCCGATGGTCCA
131 GGAATCAGCATTTGCCCAT-GCCCA
* *
42367 TGGCCTTGGCGTCGGCATTTG-CTGATGGCCCGTTGCCTTGGCATCGCCATTTGCCGATTGCGTC
1 TGGCCTTGGCGTCGGCATTTGAC-GATGGCACGTGGCCTTGGCATCGCCATTTGCCGATTGCGTC
* * * * *
42431 CGAATTTTATGATGTCCCTTGTCCCCTTGGAATTGGCATCGGCATTTGCCGATGGACC-TAGGCC
65 CGAATTTGATGATGTCCCTTGTCCACTTGGAACTGGCATCAGCATTTGCCGATGGCCCAT-GGCC
** *
42495 TTGGCGTC-GACATTTGCCCATGCCCT
129 TTGGAATCAG-CATTTGCCCATGCCCA
42521 TGGCCTTGGCGTCGG
1 TGGCCTTGGCGTCGG
42536 TAGTTGCCGA
Statistics
Matches: 145, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
154 21 0.14
155 124 0.86
ACGTcount: A:0.13, C:0.27, G:0.30, T:0.31
Consensus pattern (154 bp):
TGGCCTTGGCGTCGGCATTTGACGATGGCACGTGGCCTTGGCATCGCCATTTGCCGATTGCGTCC
GAATTTGATGATGTCCCTTGTCCACTTGGAACTGGCATCAGCATTTGCCGATGGCCCATGGCCTT
GGAATCAGCATTTGCCCATGCCCA
Found at i:42529 original size:31 final size:32
Alignment explanation
Indices: 42454--42534 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 32
42444 GTCCCTTGTC
** * * *
42454 CCCTTGGAATTGGCATCGGCATTTGCCGATGG
1 CCCTTGGCCTTGGCGTCGACATTTGCCCATGG
* *
42486 ACCTAGGCCTTGGCGTCGACATTTGCCCAT-G
1 CCCTTGGCCTTGGCGTCGACATTTGCCCATGG
42517 CCCTTGGCCTTGGCGTCG
1 CCCTTGGCCTTGGCGTCG
42535 GTAGTTGCCG
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 17 0.43
32 23 0.57
ACGTcount: A:0.12, C:0.31, G:0.30, T:0.27
Consensus pattern (32 bp):
CCCTTGGCCTTGGCGTCGACATTTGCCCATGG
Found at i:42543 original size:31 final size:32
Alignment explanation
Indices: 42491--42555 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
42481 GATGGACCTA
*
42491 GGCCTTGGCGTCGACATTTGCCCATG-CCCTT
1 GGCCTTGGCGTCGACAGTTGCCCATGTCCCTT
** *
42522 GGCCTTGGCGTCGGTAGTTGCCGATGTCCCTT
1 GGCCTTGGCGTCGACAGTTGCCCATGTCCCTT
42554 GG
1 GG
42556 TGCCGACGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.08, C:0.31, G:0.32, T:0.29
Consensus pattern (32 bp):
GGCCTTGGCGTCGACAGTTGCCCATGTCCCTT
Found at i:43035 original size:22 final size:22
Alignment explanation
Indices: 42958--43035 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 22
42948 CATGCACCTC
* * *
42958 GCACCTTGGGGGCGCCTTGGGG
1 GCACCTTGGGGCCTCCTCGGGG
* **
42980 CCA-CTTGGGGCAACCTCGGGG
1 GCACCTTGGGGCCTCCTCGGGG
*
43001 GCGCCTTGGGGCCTCCTCGGGG
1 GCACCTTGGGGCCTCCTCGGGG
*
43023 GCACCTTTGGGCC
1 GCACCTTGGGGCC
43036 CTAACGCGGG
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 15 0.34
22 29 0.66
ACGTcount: A:0.06, C:0.33, G:0.42, T:0.18
Consensus pattern (22 bp):
GCACCTTGGGGCCTCCTCGGGG
Found at i:43371 original size:91 final size:93
Alignment explanation
Indices: 43174--43403 Score: 277
Period size: 91 Copynumber: 2.5 Consensus size: 93
43164 TGTGGCGTCG
* * *
43174 GCATTTGCCGATGGCCCATGGCCTTGGCGTAGGCATTTGCCGATGGCCTTGTCGGAATTTGATGA
1 GCATTTGCCGATGGCCCATGGCCTTGGAGTCGGCATTTGCCGATGGCC-TGTCGAAATTTGATGA
* ** * *
43239 TGTCCCTTGTTACGTTGGCGTTGGCATCG
65 TGTCCCTTGTCACGTTGGCACTAGCATCA
* * * * * * *
43268 GCATTTGACGATGGCACGTTGCCTTGGTGTCGGCATTTGCTGATTG-C-GTCGAAATTTGATGAT
1 GCATTTGCCGATGGCCCATGGCCTTGGAGTCGGCATTTGCCGATGGCCTGTCGAAATTTGATGAT
43331 GTCCCTTGTCCAC-TTGGCACTAGCATCA
66 GTCCCTTGT-CACGTTGGCACTAGCATCA
*
43359 GCATTTGCCGATGGCCCATGGCCTTGGAATCGGCATTTGCCGATG
1 GCATTTGCCGATGGCCCATGGCCTTGGAGTCGGCATTTGCCGATG
43404 CCCATTGCCT
Statistics
Matches: 113, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
91 72 0.64
92 2 0.02
93 1 0.01
94 38 0.34
ACGTcount: A:0.15, C:0.24, G:0.30, T:0.31
Consensus pattern (93 bp):
GCATTTGCCGATGGCCCATGGCCTTGGAGTCGGCATTTGCCGATGGCCTGTCGAAATTTGATGAT
GTCCCTTGTCACGTTGGCACTAGCATCA
Found at i:43414 original size:31 final size:32
Alignment explanation
Indices: 43353--43485 Score: 160
Period size: 32 Copynumber: 4.2 Consensus size: 32
43343 CTTGGCACTA
*
43353 GCATCAGCATTTGCCGATGGCCCATGGCCTTG
1 GCATCGGCATTTGCCGATGGCCCATGGCCTTG
* *
43385 GAATCGGCATTTGCCGAT-GCCCATTGCCTTG
1 GCATCGGCATTTGCCGATGGCCCATGGCCTTG
* * *
43416 GCGTCGGTATTTGCCGATGGTCCATGGCCTTG
1 GCATCGGCATTTGCCGATGGCCCATGGCCTTG
* * * * *
43448 GCGTCGGCATTTTCTGATGGCCCGTTGCCTTG
1 GCATCGGCATTTGCCGATGGCCCATGGCCTTG
43480 GCATCG
1 GCATCG
43486 CTATATGCCG
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
31 27 0.32
32 58 0.68
ACGTcount: A:0.12, C:0.29, G:0.30, T:0.29
Consensus pattern (32 bp):
GCATCGGCATTTGCCGATGGCCCATGGCCTTG
Found at i:43524 original size:186 final size:178
Alignment explanation
Indices: 43254--43668 Score: 435
Period size: 186 Copynumber: 2.3 Consensus size: 178
43244 CTTGTTACGT
* * * ** * *
43254 TGGCGTTGGCATCGGCATTTGACGATGGCACGTTGCCTTGGTGTCGGCATTTGCTGATTGCGTCG
1 TGGCCTTGGCGTCGGCATTT-ACGATGGCCCGTTGCCTTGGCATCGGCATATGCCGATTGCGTCG
43319 AAATTTGATGATGTCCCTTGTCCACTTGGCACTAGCATCAGCATTTGCCGATGGCCC-ATGGCCT
65 AAATTTGATGATGTCCCTTGTCCACTT-G-----GCATCAGCATTTGCCGATGGCCCTA-GGCCT
* * * *
43383 TGGAATCGGCATTTGCCGATGCCCATT-GCCTTGGCGTCGGTATTTGCCGATGGTCCA
123 TGGAATCGGCATTTGCCCATGCCC-TTGGCCCTGGCGTCGGTAGTTGCCGAT-GCCCA
*
43440 TGGCCTTGGCGTCGGCATTTTCTGATGGCCCGTTGCCTTGGCATC-GCTATATGCCGATTGCGTC
1 TGGCCTTGGCGTCGGCATTTAC-GATGGCCCGTTGCCTTGGCATCGGC-ATATGCCGATTGCGT-
** * * ** * *
43504 CG-AATTTTTTGATGTCCCTTGTCCCCTTGGCATCGGCATTTGTTGATGGCCCTAGGTCTTGGCA
63 CGAAATTTGATGATGTCCCTTGTCCACTTGGCATCAGCATTTGCCGATGGCCCTAGGCCTTGGAA
*
43568 TCGGCATTTGCCCATGCCCTTGGCCCTGGCGTTGGTAGTTGCCGATGCCCA
128 TCGGCATTTGCCCATGCCCTTGGCCCTGGCGTCGGTAGTTGCCGATGCCCA
* * * *
43619 TGGCCTTGACGTCGGCATTTGCCGATGGCCC-TTGGTCTTGGCGTCGGCAT
1 TGGCCTTGGCGTCGGCATTT-ACGATGGCCCGTT-GCCTTGGCATCGGCAT
43669 TTGACGATGC
Statistics
Matches: 196, Mismatches: 25, Indels: 23
0.80 0.10 0.09
Matches are distributed among these distances:
178 2 0.01
179 44 0.22
180 70 0.36
181 1 0.01
185 4 0.02
186 73 0.37
187 2 0.01
ACGTcount: A:0.12, C:0.27, G:0.29, T:0.32
Consensus pattern (178 bp):
TGGCCTTGGCGTCGGCATTTACGATGGCCCGTTGCCTTGGCATCGGCATATGCCGATTGCGTCGA
AATTTGATGATGTCCCTTGTCCACTTGGCATCAGCATTTGCCGATGGCCCTAGGCCTTGGAATCG
GCATTTGCCCATGCCCTTGGCCCTGGCGTCGGTAGTTGCCGATGCCCA
Found at i:43641 original size:31 final size:31
Alignment explanation
Indices: 43528--43707 Score: 173
Period size: 31 Copynumber: 5.7 Consensus size: 31
43518 TCCCTTGTCC
* **
43528 CCTTGGCATCGGCATTTGTTGATGGCCC-TAGG
1 CCTTGGCGTCGGCATTTGCCGAT-GCCCAT-GG
* * * *
43560 TCTTGGCATCGGCATTTGCCCATGCCCTTGG
1 CCTTGGCGTCGGCATTTGCCGATGCCCATGG
* * * *
43591 CCCTGGCGTTGGTAGTTGCCGATGCCCATGG
1 CCTTGGCGTCGGCATTTGCCGATGCCCATGG
* *
43622 CCTTGACGTCGGCATTTGCCGATGGCCCTTGG
1 CCTTGGCGTCGGCATTTGCCGAT-GCCCATGG
* *
43654 TCTTGGCGTCGGCATTTGACGATGCCCATGG
1 CCTTGGCGTCGGCATTTGCCGATGCCCATGG
* *
43685 CCTTGGTGTGGGCATTTGCCGAT
1 CCTTGGCGTCGGCATTTGCCGAT
43708 TGCGTCCGA
Statistics
Matches: 120, Mismatches: 26, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
31 73 0.61
32 47 0.39
ACGTcount: A:0.11, C:0.28, G:0.32, T:0.30
Consensus pattern (31 bp):
CCTTGGCGTCGGCATTTGCCGATGCCCATGG
Found at i:43677 original size:63 final size:62
Alignment explanation
Indices: 43568--43707 Score: 181
Period size: 63 Copynumber: 2.2 Consensus size: 62
43558 GGTCTTGGCA
* * * *
43568 TCGGCATTTGCCCATGCCCTTGGCCCTGGCGTTGGTAGTTGCCGATGCCCATGGCCTTGACG
1 TCGGCATTTGCCGATGCCCTTGGCCCTGGCGTCGGCAGTTGACGATGCCCATGGCCTTGACG
* * * **
43630 TCGGCATTTGCCGATGGCCCTTGGTCTTGGCGTCGGCATTTGACGATGCCCATGGCCTTGGTG
1 TCGGCATTTGCCGAT-GCCCTTGGCCCTGGCGTCGGCAGTTGACGATGCCCATGGCCTTGACG
*
43693 TGGGCATTTGCCGAT
1 TCGGCATTTGCCGAT
43708 TGCGTCCGA
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
62 14 0.21
63 53 0.79
ACGTcount: A:0.10, C:0.29, G:0.32, T:0.29
Consensus pattern (62 bp):
TCGGCATTTGCCGATGCCCTTGGCCCTGGCGTCGGCAGTTGACGATGCCCATGGCCTTGACG
Found at i:43704 original size:94 final size:94
Alignment explanation
Indices: 43536--43707 Score: 236
Period size: 94 Copynumber: 1.8 Consensus size: 94
43526 CCCCTTGGCA
** * * *
43536 TCGGCATTTGTTGATGGCCCTAGGTCTTGGCATCGGCATTTGCCCATGCCCTTGGCCCTGGCGTT
1 TCGGCATTTGCCGATGGCCCTAGGTCTTGGCATCGGCATTTGACCATGCCCATGGCCCTGGCGTG
*
43601 GGTAGTTGCCGATGCCCATGGCCTTGACG
66 GGCAGTTGCCGATGCCCATGGCCTTGACG
* * * * *
43630 TCGGCATTTGCCGATGGCCCTTGGTCTTGGCGTCGGCATTTGACGATGCCCATGGCCTTGGTGTG
1 TCGGCATTTGCCGATGGCCCTAGGTCTTGGCATCGGCATTTGACCATGCCCATGGCCCTGGCGTG
*
43695 GGCATTTGCCGAT
66 GGCAGTTGCCGAT
43708 TGCGTCCGA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
94 66 1.00
ACGTcount: A:0.10, C:0.27, G:0.32, T:0.30
Consensus pattern (94 bp):
TCGGCATTTGCCGATGGCCCTAGGTCTTGGCATCGGCATTTGACCATGCCCATGGCCCTGGCGTG
GGCAGTTGCCGATGCCCATGGCCTTGACG
Done.