Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019630.1 Corchorus olitorius cultivar O-4 contig19663, 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: 90921
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:3102 original size:13 final size:13
Alignment explanation
Indices: 3082--3114 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3072 GTATACAAAT
3082 TATATATTTTT-G
1 TATATATTTTTCG
3094 TAGTATATTTTTCG
1 TA-TATATTTTTCG
3108 TATATAT
1 TATATAT
3115 AGAGAGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 14 0.74
14 3 0.16
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (13 bp):
TATATATTTTTCG
Found at i:4910 original size:12 final size:12
Alignment explanation
Indices: 4879--4910 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4869 ACCTGGCAAT
*
4879 TCGTGTTCCGTG
1 TCGTGTTTCGTG
4891 TCGTGTTTCGTG
1 TCGTGTTTCGTG
4903 TCGTGTTT
1 TCGTGTTT
4911 ACATAGGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.19, G:0.31, T:0.50
Consensus pattern (12 bp):
TCGTGTTTCGTG
Found at i:6512 original size:21 final size:19
Alignment explanation
Indices: 6486--6541 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
6476 GCTACTTTGA
*
6486 TAATCTCATTTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
6507 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
6526 TAATCTCATCTGTACA
1 TAATCTCATCTGTACA
6542 ATTGTTGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:7799 original size:42 final size:43
Alignment explanation
Indices: 7752--7834 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 43
7742 TGTGTTTGAC
*
7752 TTATCGTGTCTCGTGTCTGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTGTCTCGTGTCTGAATCGTGTCAAGACACGATTAAGA
* *
7794 TTATCGTGTTTCGTGTCTTAATCGTGTCAAGACACGATTAA
1 TTATCGTGTCTCGTGTCTGAATCGTGTCAAGACACGATTAA
7835 CACGTTTAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 26 0.70
43 11 0.30
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (43 bp):
TTATCGTGTCTCGTGTCTGAATCGTGTCAAGACACGATTAAGA
Found at i:7845 original size:20 final size:21
Alignment explanation
Indices: 7822--7864 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
7812 TAATCGTGTC
*
7822 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
7842 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
7863 AA
1 AA
7865 TTAACGGGTT
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:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:8344 original size:12 final size:12
Alignment explanation
Indices: 8324--8354 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
8314 ACCCTATGTA
8324 AACACGACACGG
1 AACACGACACGG
*
8336 AATACGACACGG
1 AACACGACACGG
8348 AACACGA
1 AACACGA
8355 ATTGCCAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.29, G:0.23, T:0.03
Consensus pattern (12 bp):
AACACGACACGG
Found at i:9225 original size:2 final size:2
Alignment explanation
Indices: 9218--9251 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9208 GTTAGGGGTG
9218 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
9252 CTCGAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13210 original size:14 final size:13
Alignment explanation
Indices: 13188--13217 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
13178 TAGGTAGCTG
13188 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
13201 TTTTTCTCTTTTTC
1 TTTTT-TCTTTTTC
13215 TTT
1 TTT
13218 CGATGGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:13945 original size:14 final size:14
Alignment explanation
Indices: 13926--13952 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13916 ATTATTATCT
13926 ATACAATATATACA
1 ATACAATATATACA
13940 ATACAATATATAC
1 ATACAATATATAC
13953 TAATTATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (14 bp):
ATACAATATATACA
Found at i:25795 original size:50 final size:50
Alignment explanation
Indices: 25727--25823 Score: 167
Period size: 50 Copynumber: 1.9 Consensus size: 50
25717 AAATCTTTTG
* *
25727 AAACTAAGCACTTCACATCTCAATTATTTGAAGTTCATATCTTTAATTTA
1 AAACTAAGCACTTAACATCTCAATGATTTGAAGTTCATATCTTTAATTTA
*
25777 AAACTAAGCACTTAACATCTCAATGATTTGGAGTTCATATCTTTAAT
1 AAACTAAGCACTTAACATCTCAATGATTTGAAGTTCATATCTTTAAT
25824 CTACGTCATG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (50 bp):
AAACTAAGCACTTAACATCTCAATGATTTGAAGTTCATATCTTTAATTTA
Found at i:30177 original size:28 final size:27
Alignment explanation
Indices: 30135--30189 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
30125 TTTTTATTTG
*
30135 AGTTTGTTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTTGAGTCAGTTTCGAGTC
30161 AGTTTGTTTTTTCGAGTCAGTTTCGAGTC
1 AGTTTG-TTTTT-GAGTCAGTTTCGAGTC
30190 TAGTCTCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 5 0.20
28 9 0.36
29 5 0.20
ACGTcount: A:0.13, C:0.11, G:0.27, T:0.49
Consensus pattern (27 bp):
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Found at i:35068 original size:111 final size:111
Alignment explanation
Indices: 34874--35095 Score: 354
Period size: 111 Copynumber: 2.0 Consensus size: 111
34864 ATGTTAAATG
* *
34874 AATATGCCTTTTCTGTTTTACATATGGCTATATGGGTGTAAGTACCATTACTTGCATTTAACTTT
1 AATATGCCTTCTCTGTTTTACATATGGCTATATGGGTGTAAGTACCATAACTTGCATTTAACTTT
** * *
34939 GTTGATGGCCTTCACATTATTTTGATTAATGGCCATTTACTTAATT
66 GTTGATAACCATCACATTATTTTGAATAATGGCCATTTACTTAATT
* * *
34985 AATATGCCTTCTCTGTTTTACATATGGCTATATGGGTGTATGTACCATAACTTGCATTTGATTTT
1 AATATGCCTTCTCTGTTTTACATATGGCTATATGGGTGTAAGTACCATAACTTGCATTTAACTTT
*
35050 GTTGATAACCATCACATTATTTTGAATAATGGCCTTTTACTTAATT
66 GTTGATAACCATCACATTATTTTGAATAATGGCCATTTACTTAATT
35096 GATTTGTTGT
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (111 bp):
AATATGCCTTCTCTGTTTTACATATGGCTATATGGGTGTAAGTACCATAACTTGCATTTAACTTT
GTTGATAACCATCACATTATTTTGAATAATGGCCATTTACTTAATT
Found at i:39492 original size:29 final size:29
Alignment explanation
Indices: 39460--39516 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
39450 ATTATGATTA
*
39460 TTTTACATCAATTTGAGACTGAATTTTTT
1 TTTTACATCAATTTGAGACTGAAATTTTT
***
39489 TTTTGGTTCAATTTGAGACTGAAATTTT
1 TTTTACATCAATTTGAGACTGAAATTTT
39517 AATACTTTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTTACATCAATTTGAGACTGAAATTTTT
Found at i:55409 original size:21 final size:22
Alignment explanation
Indices: 55375--55415 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
55365 ATGGATCAAC
*
55375 ATATAATGCATGGAGAAATTAG
1 ATATAATGCATGGAAAAATTAG
55397 ATATAAT-CATGGAAAAATT
1 ATATAATGCATGGAAAAATT
55416 TGGAAACTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (22 bp):
ATATAATGCATGGAAAAATTAG
Found at i:61164 original size:13 final size:13
Alignment explanation
Indices: 61146--61175 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
61136 TCTCATAGTC
61146 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
61159 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
61172 AAAA
1 AAAA
61176 TTACCTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:61596 original size:26 final size:26
Alignment explanation
Indices: 61567--61618 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
61557 AAGAAATCGA
61567 ATTTAGAT-GTGATTTTAAGAAAATTT
1 ATTT-GATAGTGATTTTAAGAAAATTT
61593 ATTTGATAAGTGATTTTAAGAAAATT
1 ATTTGAT-AGTGATTTTAAGAAAATT
61619 CAGTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 3 0.12
26 4 0.17
27 17 0.71
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.44
Consensus pattern (26 bp):
ATTTGATAGTGATTTTAAGAAAATTT
Found at i:66276 original size:318 final size:302
Alignment explanation
Indices: 65698--66299 Score: 744
Period size: 305 Copynumber: 1.9 Consensus size: 302
65688 CTTTGTTTAT
65698 ACTTTCTTGTCATGTCTGTTGCACACGTTTGCATATATTGCTTCTTTTCTGCAATGGGTTGTTTC
1 ACTTTCTTGTCATGTCTGTTGCACACGTTTGCATATATTGCTTCTTTTCTGCAATGGGTTGTTTC
*
65763 CATTTTGCAAGTTCTGAGTTTCTGGGTTATATTTTGATCATATTTGCTATGAGTTGGTTTTTCAT
66 C----T-CAAGTTCTGAGTTTCTGGGTTATATTTTGATCATATTTGATATGAGTTGGTTTTTCAT
65828 GCTGCAATTTGATCACTATGATACTTTTTTTTAACATGGTTCAGAAAGTTTAGACATTGTAACCT
126 GCTGCAATTTGATCACTATGATACTTTTTTTTAACATGGTTCAGAAA---TAG--ATTGTAA-C-
*
65893 GATCAGCTTTGAGTGGCTTATGAATTTTGGGCAGTTTTATTAATTCCCCTCTTTTTGATTGGTTT
184 GATCAGCTTTGAGTGGCTTATGAATTTTGGACAGTTTTATTAATTCCCCTCTTTTTGATTGGTTT
65958 TTATGTGTGTTTTTAATGAAAGTTTAATGGATTTGAAACCAAATTTATAGGTTG
249 TTATGTGTGTTTTTAATGAAAGTTTAATGGATTTGAAACCAAATTTATAGGTTG
*
66012 ACTTTCTTGTCATGTCTGTTGCACATGTTTGCATATATTATTGCTTCTTTTCTGCAATGGGTTGT
1 ACTTTCTTGTCATGTCTGTTGCACACGTTTGC--ATA-TATTGCTTCTTTTCTGCAATGGGTTGT
66077 TTCC-C-AGTTCTGAGTTTCTGGGTTATATTTTGAATTTTTGATCATATTTGATATGAGTTGGTT
63 TTCCTCAAGTTCTGAGTTTCTGGG-T-TA---T--A-TTTTGATCATATTTGATATGAGTTGGTT
* *
66140 TTTGCATGCTGCAATTTGATCACTATGATACTGTTTTTTTAACATGG-TCCGGAA-AG-TT-T-A
120 TTT-CATGCTGCAATTTGATCACTATGATACT-TTTTTTTAACATGGTTCAGAAATAGATTGTAA
* * *
66200 -GA-CAGCTTTGAGTGGCTTATGAATTTTGGACTGTTCTT-TT-TTTCCCCTCTTTTTGTTATGG
183 CGATCAGCTTTGAGTGGCTTATGAATTTTGGACAGTT-TTATTAATTCCCCTCTTTTTGAT-TGG
* * ** *
66261 CTTTT-TGTGTGGTTTTCTTGAACA-TTTAATGGGTTTGAA
246 TTTTTATGTGTGTTTTTAATGAA-AGTTTAATGGATTTGAA
66300 CAAATTGATG
Statistics
Matches: 259, Mismatches: 13, Indels: 41
0.83 0.04 0.13
Matches are distributed among these distances:
305 43 0.17
306 41 0.16
307 4 0.02
310 18 0.07
311 3 0.01
312 4 0.02
314 31 0.12
315 3 0.01
316 3 0.01
317 32 0.12
318 30 0.12
319 33 0.13
320 14 0.05
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (302 bp):
ACTTTCTTGTCATGTCTGTTGCACACGTTTGCATATATTGCTTCTTTTCTGCAATGGGTTGTTTC
CTCAAGTTCTGAGTTTCTGGGTTATATTTTGATCATATTTGATATGAGTTGGTTTTTCATGCTGC
AATTTGATCACTATGATACTTTTTTTTAACATGGTTCAGAAATAGATTGTAACGATCAGCTTTGA
GTGGCTTATGAATTTTGGACAGTTTTATTAATTCCCCTCTTTTTGATTGGTTTTTATGTGTGTTT
TTAATGAAAGTTTAATGGATTTGAAACCAAATTTATAGGTTG
Found at i:69353 original size:64 final size:64
Alignment explanation
Indices: 69252--69381 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
69242 CCACAGCGCC
69252 TTGAGGTTGGGATGTTCTATGAGGCTTGAAGAAGTGGTTGTAACAGACAGGCATCAAATAGAAG
1 TTGAGGTTGGGATGTTCTATGAGGCTTGAAGAAGTGGTTGTAACAGACAGGCATCAAATAGAAG
69316 TTGAGGTTGGGATGTTCTATGAGGCTTGAAGAAGTGGTTGTAACAGACAGGCATCAAATAGAAG
1 TTGAGGTTGGGATGTTCTATGAGGCTTGAAGAAGTGGTTGTAACAGACAGGCATCAAATAGAAG
69380 TT
1 TT
69382 TATATACGCG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.31, C:0.09, G:0.32, T:0.28
Consensus pattern (64 bp):
TTGAGGTTGGGATGTTCTATGAGGCTTGAAGAAGTGGTTGTAACAGACAGGCATCAAATAGAAG
Found at i:75290 original size:3 final size:3
Alignment explanation
Indices: 75282--75326 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
75272 TATCATTATG
* * *
75282 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATT ATT ATG ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
75327 TTGAAAGGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:81856 original size:31 final size:31
Alignment explanation
Indices: 81818--81878 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
81808 TAAGTCTCAA
81818 ATATTGCAAAATCAGCTCAAATCAGTCCCTG
1 ATATTGCAAAATCAGCTCAAATCAGTCCCTG
* *
81849 ATATTGCAAAATCGGCTCAAATGAGTCCCT
1 ATATTGCAAAATCAGCTCAAATCAGTCCCT
81879 AAAGTCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (31 bp):
ATATTGCAAAATCAGCTCAAATCAGTCCCTG
Found at i:82968 original size:15 final size:16
Alignment explanation
Indices: 82943--82975 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
82933 CAAAACAAAC
82943 AGCAACAACCACAACA
1 AGCAACAACCACAACA
82959 AGCAAC-ACCACAACA
1 AGCAACAACCACAACA
82974 AG
1 AG
82976 ACCAGAGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.55, C:0.36, G:0.09, T:0.00
Consensus pattern (16 bp):
AGCAACAACCACAACA
Found at i:83261 original size:2 final size:2
Alignment explanation
Indices: 83254--83278 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
83244 AGGGTTTTAG
83254 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 A
83279 ACTAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:86198 original size:2 final size:2
Alignment explanation
Indices: 86191--86221 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
86181 CCAAGAATAC
*
86191 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
86222 CATACTAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:86356 original size:23 final size:23
Alignment explanation
Indices: 86329--86383 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
86319 TAATTACACT
*
86329 ATTTTTAATGATC-TCCTTATGAA
1 ATTTTTAATAATCTTCC-TATGAA
*
86352 A-TTTTGATAATCTTCCTATGAA
1 ATTTTTAATAATCTTCCTATGAA
86374 A-TTTTAATAA
1 ATTTTTAATAA
86384 CGATACTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (23 bp):
ATTTTTAATAATCTTCCTATGAA
Found at i:86364 original size:22 final size:21
Alignment explanation
Indices: 86341--86926 Score: 227
Period size: 22 Copynumber: 27.2 Consensus size: 21
86331 TTTTAATGAT
86341 CTCCTTATGAAATTTTGATAATC
1 CTCC-TATGAAATTTTGATAA-C
* *
86364 TTCCTATGAAATTTTAATAAC
1 CTCCTATGAAATTTTGATAAC
* * * * * *
86385 GATACTATGGAATTTCGAGAATT
1 -CTCCTATGAAATTTTGATAA-C
* ** * *
86408 TTTTTATAAAATTTT-TTAAC
1 CTCCTATGAAATTTTGATAAC
* *
86428 CTTCTTATGAAATTTTGTTAAC
1 C-TCCTATGAAATTTTGATAAC
* *
86450 CTCCCTAAGGAATTTTGA-AGAC
1 CT-CCTATGAAATTTTGATA-AC
86472 CTCACTATGAAATTTTGATAAC
1 CTC-CTATGAAATTTTGATAAC
* *
86494 TTCCCAATGAAATTTTGATAAC
1 CT-CCTATGAAATTTTGATAAC
* * *
86516 CAACACTATGAGATGTTGATAAC
1 C-TC-CTATGAAATTTTGATAAC
* *
86539 CTCCATATGATATATTGATAAC
1 CTCC-TATGAAATTTTGATAAC
* * * * *
86561 CACGTTATGAAAATTTAAAAAC
1 CTC-CTATGAAATTTTGATAAC
* *
86583 ATTCATATG-AATTGTT-AGTAATC
1 -CTCCTATGAAATT-TTGA-TAA-C
* * * *
86606 ATACTCTGAAATTTTGATAAT
1 CTCCTATGAAATTTTGATAAC
* *
86627 CACACTATGAAATTGTGATAAC
1 CTC-CTATGAAATTTTGATAAC
86649 CTCGCTATGAAATTTTGATAAATC
1 CTC-CTATGAAATTTTGAT-AA-C
* *
86673 TTCCTATAAAATTTTGATAAC
1 CTCCTATGAAATTTTGATAAC
*
86694 CTCCTTATGAAATCTTGATAA-
1 CTCC-TATGAAATTTTGATAAC
*
86715 ---CTA-CAAATTTTGATAAC
1 CTCCTATGAAATTTTGATAAC
**
86732 CTCCCTATGATTTTTTGATAAC
1 CT-CCTATGAAATTTTGATAAC
* ** *
86754 CTCATTATGAAATTTTTTTAAT
1 CTC-CTATGAAATTTTGATAAC
*
86776 CTCCCTATGAAATTTTGA-AAA
1 CT-CCTATGAAATTTTGATAAC
*
86797 CTAAACTATGAAATTTTGATAAC
1 CT--CCTATGAAATTTTGATAAC
* * *
86820 CTTCATATGAAATTTTGACATC
1 C-TCCTATGAAATTTTGATAAC
*
86842 CTGCC--TGAAATTTTGATTA-
1 CT-CCTATGAAATTTTGATAAC
* * *
86861 CTCCATAATAAAAGTTTAATAAC
1 CTCC-T-ATGAAATTTTGATAAC
*
86884 CAT-CT-T--AA-TTTGGTAAC
1 C-TCCTATGAAATTTTGATAAC
*
86901 CATACTATGAAATTTTGATAAC
1 C-TCCTATGAAATTTTGATAAC
86923 CTCC
1 CTCC
86927 CCAGAAATAC
Statistics
Matches: 415, Mismatches: 102, Indels: 94
0.68 0.17 0.15
Matches are distributed among these distances:
16 11 0.03
17 12 0.03
18 7 0.02
19 3 0.01
20 12 0.03
21 40 0.10
22 275 0.66
23 50 0.12
24 5 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (21 bp):
CTCCTATGAAATTTTGATAAC
Found at i:86440 original size:21 final size:22
Alignment explanation
Indices: 86411--86451 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
86401 GAGAATTTTT
86411 TTATAAAATTTT-TTAACCTTC
1 TTATAAAATTTTGTTAACCTTC
*
86432 TTATGAAATTTTGTTAACCT
1 TTATAAAATTTTGTTAACCT
86452 CCCTAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (22 bp):
TTATAAAATTTTGTTAACCTTC
Found at i:86485 original size:44 final size:45
Alignment explanation
Indices: 86433--86562 Score: 133
Period size: 45 Copynumber: 2.9 Consensus size: 45
86423 TTAACCTTCT
* * *
86433 TATGAAATTTTGTTAACCTCCCTAA-GGAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATAACCTCCC-AATGAAATTTTGATA-ACCAACAC
*
86477 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTCCCAATGAAATTTTGATAACCAACAC
* * * *
86522 TATGAGATGTTGATAACCT-CCATATGATATATTGATAACCA
1 TATGAAATTTTGATAACCTCCCA-ATGAAATTTTGATAACCA
86563 CGTTATGAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
43 2 0.03
44 35 0.48
45 36 0.49
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (45 bp):
TATGAAATTTTGATAACCTCCCAATGAAATTTTGATAACCAACAC
Found at i:86660 original size:44 final size:43
Alignment explanation
Indices: 86612--87176 Score: 229
Period size: 44 Copynumber: 13.3 Consensus size: 43
86602 AATCATACTC
*
86612 TGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTC-CTA
* *
86656 TGAAATTTTGATAAATCTTC-CTATAAAATTTTGATAACCTCCTTA
1 TGAAATTTTGAT-AATC-ACACTATGAAATTTTGATAACCTCC-TA
* *
86701 TGAAATCTTG---AT-A-ACTA-CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCT-CCTA
** * * * ** *
86739 TGATTTTTTGATAACCTCATTATGAAATTTTTTTAATCTCCCTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCT-CCTA
* * *
86783 TGAAATTTTGA-AAACTAAACTATGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAATC-ACACTATGAAATTTTGATAACC-TCCTA
* * * *
86827 TGAAATTTTGA-CATC-CTGC-CTGAAATTTTGATTA-CTCCATAA
1 TGAAATTTTGATAATCAC-ACTATGAAATTTTGATAACCTCC-T-A
* * * * *
86869 TAAAAGTTTAATAA-C-CATCT-T--AA-TTTGGTAACCATACTA
1 TGAAATTTTGATAATCACA-CTATGAAATTTTGATAACC-TCCTA
* * * * *
86908 TGAAATTTTGATAACCTCCCCA-G-AA-----AT-ACC-ACTA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCCTA
* * * *
86942 TGAAATTTTAGA-AATCACATTTTGAAAATTTGATAACCTCTTTA
1 TGAAATTTT-GATAATCACACTATGAAATTTTGATAACCTC-CTA
* * * * * *
86986 TGAAATTTTGATAA-CTTCTCTATAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAATC-ACACTATGAAATTTTGATAACCTC-CTA
* * * *
87030 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTTGCTT
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACC-TCCTA
* * ** *
87074 TGAAATTTTGATAATAACACTATAAAATTTTGATAATATTCTCA
1 TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCCT-A
* * *
87118 T-AAATTTTGATAATCTGATCTCTATGAAATTTCGATAACCACTCTA
1 TGAAATTTTGATAATC--A-CACTATGAAATTTTGATAACCTC-CTA
*
87164 TGAGA-TTTGATAA
1 TGAAATTTTGATAA
87177 CCTTCTCAAA
Statistics
Matches: 383, Mismatches: 92, Indels: 90
0.68 0.16 0.16
Matches are distributed among these distances:
34 17 0.04
35 3 0.01
36 5 0.01
37 1 0.00
38 24 0.06
39 23 0.06
40 8 0.02
41 12 0.03
42 29 0.08
43 27 0.07
44 166 0.43
45 37 0.10
46 27 0.07
47 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (43 bp):
TGAAATTTTGATAATCACACTATGAAATTTTGATAACCTCCTA
Found at i:86989 original size:22 final size:22
Alignment explanation
Indices: 86964--87179 Score: 145
Period size: 22 Copynumber: 9.8 Consensus size: 22
86954 AATCACATTT
* *
86964 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
*
86986 TGAAATTTTGATAACTTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
87008 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
87030 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* *
87052 TGTAATTTTGATAACCT-TGCTT
1 TGAAATTTTGATAACCTCT-CTA
*** *
87074 TGAAATTTTGATAATAACACTA
1 TGAAATTTTGATAACCTCTCTA
* **
87096 TAAAATTTTGATAATAT-TCTCA
1 TGAAATTTTGATAACCTCTCT-A
*
87118 T-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CTCTCTA
* *
87142 TGAAATTTCGATAACCACTCTA
1 TGAAATTTTGATAACCTCTCTA
*
87164 TGAGA-TTTGATAACCT
1 TGAAATTTTGATAACCT
87180 TCTCAAATCT
Statistics
Matches: 151, Mismatches: 33, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.01
21 23 0.15
22 107 0.71
23 1 0.01
24 5 0.03
25 14 0.09
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Done.