Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021930.1 Corchorus olitorius cultivar O-4 contig21963, 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: 71950
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:684 original size:43 final size:42
Alignment explanation
Indices: 615--696 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 42
605 AAAAAAAATG
*
615 CCGCCTATTTTTTGTTTAACAAAATTTTCCCACTCAAATAAAC
1 CCGCCTATTTTTTATTTAACAAAATTTTCCCACT-AAATAAAC
** *
658 CCGCCTA-TTTTTATTTCCCAATAATTTTCCCTCTAAATA
1 CCGCCTATTTTTTATTTAACAA-AATTTTCCCACTAAATA
697 CTTGTTACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 16 0.47
43 18 0.53
ACGTcount: A:0.29, C:0.27, G:0.04, T:0.40
Consensus pattern (42 bp):
CCGCCTATTTTTTATTTAACAAAATTTTCCCACTAAATAAAC
Found at i:1107 original size:16 final size:14
Alignment explanation
Indices: 1075--1101 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1065 AATGACCAAG
1075 TTTTGTAACAGAAT
1 TTTTGTAACAGAAT
1089 TTTTGTAACAGAA
1 TTTTGTAACAGAA
1102 AATTTTCCCG
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:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
TTTTGTAACAGAAT
Found at i:7034 original size:92 final size:89
Alignment explanation
Indices: 6847--7024 Score: 214
Period size: 92 Copynumber: 2.0 Consensus size: 89
6837 CTTAGAGTTA
*** * * ** *
6847 TTTTTCAAGTTGACCGTGCATTGGTCCTTTTCATCATTAATTCAGAAGTTTTCAGTTTCAACCTC
1 TTTTTCAAGTTGACCGCAAATTGGTCCTTTTCATCATCAATTCAGAAGTTTTCAATGACAACATC
*
6912 AGACTCAGAGTTATTTTTCAAGTTG
66 AGACTCAGAGTTATTTTCCAAG-TG
*
6937 TTTTTCAAAGTTGACCGCAAATTGGTCCCTTTTCATCATCAA-TCAAGGAGTTTTCAATGACAAC
1 TTTTTC-AAGTTGACCGCAAATTGGT-CCTTTTCATCATCAATTC-AGAAGTTTTCAATGACAAC
*
7001 ATCAGATTCAGAGTTATTTTCCAA
63 ATCAGACTCAGAGTTATTTTCCAA
7025 AGGTATTTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
90 6 0.08
91 18 0.24
92 50 0.68
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (89 bp):
TTTTTCAAGTTGACCGCAAATTGGTCCTTTTCATCATCAATTCAGAAGTTTTCAATGACAACATC
AGACTCAGAGTTATTTTCCAAGTG
Found at i:7180 original size:50 final size:50
Alignment explanation
Indices: 7099--7943 Score: 1285
Period size: 50 Copynumber: 16.9 Consensus size: 50
7089 TCCATCCGAA
*
7099 AACATAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
* *
7149 AATATGGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
* * *
7199 AACACAGGCTTTTCCACAAGCGAAACTCGTTTCCATACGAGACAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
** * *
7249 AACACCGGCTTTTCCACAAGTCAAACTCGTTTCCATACGAATCAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
** * *
7299 AACACCGGCTTTTCCACAAGCCAAACTCGTTTCTATACGAGTCAACTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
* * *
7349 AACATAGGCTTTTCCACAAGCCGAAGTCGTTTCCATATGAGTCAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
** *
7399 AACACGGGCTTTTCCACAAGCCAAACTCGTTTTCATACGAGTCAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
* * *
7449 AATATAGGCTTTTCCACAAGTCGAACTCGTTTCCATACGAGTCAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
* * *
7499 AATATAGGCTTTTCCACAAGCCAAACTCGTTTCTATACGAGTCAACTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
* *
7549 AACATAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATT
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
* *
7599 AACATGGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
*
7649 AACACAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
* * *
7699 AACAGAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCTC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
* *
7749 AACATAGGCTCTTCCACAAGCCAATCTCGTTTCCATACGAGTCAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
* *
7799 AACATAGGTTTTTCCACAAGCCAATCTCGTTTCCATACGAGTCAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
*
7849 AACATAGGTTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
* * * * * *
7899 AATATAGACTTTTCCATAAGTCAAACACGTTTCCATATGAGTCAA
1 AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAA
7944 GCTTTACTTC
Statistics
Matches: 727, Mismatches: 68, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 727 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (50 bp):
AACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATC
Found at i:8306 original size:27 final size:27
Alignment explanation
Indices: 8247--8351 Score: 113
Period size: 28 Copynumber: 3.8 Consensus size: 27
8237 ATCTAAAGGA
* *
8247 ATTTTGAGTCATTTTCAAAATCCAGGGGC
1 ATTTTG-GTCATTTGC-ACATCCAGGGGC
* *
8276 ATTTTGGTCATTTGCACATTCAGGGGT
1 ATTTTGGTCATTTGCACATCCAGGGGC
* *
8303 ATTTTAGTCATTTTGCACGTCCAGGGGC
1 ATTTTGGTCA-TTTGCACATCCAGGGGC
*
8331 ATTTTGGTCATTTCCAC-TCCA
1 ATTTTGGTCATTTGCACATCCA
8352 TTGCTCAAGT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.06
27 24 0.37
28 31 0.48
29 6 0.09
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (27 bp):
ATTTTGGTCATTTGCACATCCAGGGGC
Found at i:15840 original size:27 final size:28
Alignment explanation
Indices: 15782--15840 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
15772 TAAGAAAAAC
15782 CTTTTATTACCTCTTTTGATTTTCTAAT
1 CTTTTATTACCTCTTTTGATTTTCTAAT
* *
15810 -TTTT-TTACCCTTTTTTGATTTT-TGAT
1 CTTTTATTA-CCTCTTTTGATTTTCTAAT
15836 CTTTT
1 CTTTT
15841 CTATCTCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.14, C:0.15, G:0.05, T:0.66
Consensus pattern (28 bp):
CTTTTATTACCTCTTTTGATTTTCTAAT
Found at i:19307 original size:27 final size:27
Alignment explanation
Indices: 19268--19329 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
19258 ATTTACTTCC
*
19268 CATTTTGGTCATTTACATGTCCGGGGG
1 CATTTTGGTCATTTACATGTCCAGGGG
* * *
19295 TATTTTGGTCATTTGCATGTCTAGGGG
1 CATTTTGGTCATTTACATGTCCAGGGG
19322 CATTTTGG
1 CATTTTGG
19330 ACACTTCAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.15, C:0.15, G:0.29, T:0.42
Consensus pattern (27 bp):
CATTTTGGTCATTTACATGTCCAGGGG
Found at i:26629 original size:15 final size:14
Alignment explanation
Indices: 26609--26646 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
26599 AAATGGTTGC
26609 TTTGTTTTGTTTCAG
1 TTTGTTTTGTTTC-G
26624 TTTGTTTTGTTTCG
1 TTTGTTTTGTTTCG
*
26638 TTTGCTTTG
1 TTTGTTTTG
26647 ATGTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.03, C:0.08, G:0.21, T:0.68
Consensus pattern (14 bp):
TTTGTTTTGTTTCG
Found at i:28478 original size:13 final size:13
Alignment explanation
Indices: 28460--28485 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28450 CATATTCCAT
28460 TCATTCTTTATTC
1 TCATTCTTTATTC
28473 TCATTCTTTATTC
1 TCATTCTTTATTC
28486 AATATTACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (13 bp):
TCATTCTTTATTC
Found at i:29253 original size:21 final size:20
Alignment explanation
Indices: 29210--29263 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
29200 AAGCCAGATC
29210 ACAAAGAAAA-AAAAACAAAA
1 ACAAA-AAAACAAAAACAAAA
*
29230 ACAAAAAAACAAACAACAACA
1 ACAAAAAAACAAA-AACAAAA
*
29251 ACAACAAAACAAA
1 ACAAAAAAACAAA
29264 GAAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 4 0.13
20 8 0.27
21 18 0.60
ACGTcount: A:0.80, C:0.19, G:0.02, T:0.00
Consensus pattern (20 bp):
ACAAAAAAACAAAAACAAAA
Found at i:30995 original size:69 final size:67
Alignment explanation
Indices: 30922--31053 Score: 219
Period size: 69 Copynumber: 1.9 Consensus size: 67
30912 TCCACAAACC
*
30922 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGTGCTTTTCCATA
1 AAACTAGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACA--TGCTTTTCCATA
30987 AGCA
64 AGCA
* *
30991 AAACTAGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCAAGCAGCATGCTTTTCCATA
1 AAACTAGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGCTTTTCCATA
31054 GGCCAAGTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 12 0.20
69 48 0.80
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (67 bp):
AAACTAGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGCTTTTCCATAAG
CA
Found at i:31205 original size:69 final size:69
Alignment explanation
Indices: 31094--31230 Score: 229
Period size: 69 Copynumber: 2.0 Consensus size: 69
31084 TTCCAAGACT
31094 AAACTCGTTTCAATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
1 AAACTCGTTTCAATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
31159 AGCC
66 AGCC
* * * * *
31163 AAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCACCCAAGCAACATGGGTTTTTCCATA
1 AAACTCGTTTCAATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
31228 AGC
66 AGC
31231 TAAGTTCATT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (69 bp):
AAACTCGTTTCAATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
AGCC
Found at i:31210 original size:172 final size:173
Alignment explanation
Indices: 30922--31337 Score: 665
Period size: 172 Copynumber: 2.4 Consensus size: 173
30912 TCCACAAACC
* * *
30922 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACATGTGCTTTTCCATA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACAAGGGCTTTTCCACA
* * *
30987 AGCAAAACTAGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCAAGCAGCAT-GCTTTTCC
66 AGCCAAACTAGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCACCCAAGCAACATGGCTTTTCC
*
31051 ATAGGCCAAGTTCATATCCATATGAATTCAGTCTTCCAAGACT
131 ATAAGCCAAGTTCATATCCATATGAATTCAGTCTTCCAAGACT
* *
31094 AAACTCGTTTCAATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACAAGGGCTTTTCCACA
* *
31159 AGCCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCACCCAAGCAACATGGGTTTTTC
66 AGCCAAACTAGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCACCCAAGCAACAT-GGCTTTTC
* *
31224 CATAAGCTAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
130 CATAAGCCAAGTTCATATCCATATGAATTCAGTCTTCCAAGACT
* *
31268 AAACTCGTTTCCATACGAGTCAGTTCAAACCTTGGTTCCATCCAAGCCACATA-GGCTTTTCCAC
1 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACA-AGGGCTTTTCCAC
31332 AAGCCA
65 AAGCCA
31338 CTGTTCGTTT
Statistics
Matches: 224, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
172 112 0.50
174 111 0.50
175 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (173 bp):
AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCAACAAGGGCTTTTCCACA
AGCCAAACTAGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCACCCAAGCAACATGGCTTTTCC
ATAAGCCAAGTTCATATCCATATGAATTCAGTCTTCCAAGACT
Found at i:31243 original size:69 final size:69
Alignment explanation
Indices: 31094--31246 Score: 216
Period size: 69 Copynumber: 2.2 Consensus size: 69
31084 TTCCAAGACT
* *
31094 AAACTCGTTTCAATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
1 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
31159 AGCC
66 AGCC
* * * * *
31163 AAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCACCCAAGCAACATGGGTTTTTCCATA
1 AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
*
31228 AGCT
66 AGCC
**
31232 AAGTTCATTTCCATA
1 AAACTCATTTCCATA
31247 TGAATTCAGT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 75 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (69 bp):
AAACTCATTTCCATACGAGTCAGTTCAAGCCTTGGTTCCACCCAAGCAACAAGGGCTTTTCCACA
AGCC
Found at i:31416 original size:35 final size:35
Alignment explanation
Indices: 31369--31558 Score: 319
Period size: 35 Copynumber: 5.4 Consensus size: 35
31359 ATTACCATCT
31369 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAA-
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAC
*
31403 TCCAGATGACTCGGTGTAGCATCTTCAAAGATGAAC
1 T-CAGATGACTCGGTGTAGCATCTTCAAAGTTGAAC
*
31439 TCAGATGACTCGGTGTAGCATCTTCAAAGATGAAC
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAC
31474 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAC
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAC
*
31509 TCGGATGACTCGGTGTAGCATCTTCAAAGTTGAAC
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAC
**
31544 TTGGATGACTCGGTG
1 TCAGATGACTCGGTG
31559 CTTTACTTCT
Statistics
Matches: 150, Mismatches: 4, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
34 1 0.01
35 148 0.99
36 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (35 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAC
Found at i:34817 original size:41 final size:40
Alignment explanation
Indices: 34772--34899 Score: 132
Period size: 41 Copynumber: 3.1 Consensus size: 40
34762 ATTCAATCGG
* *
34772 GTCCCTAATTTAGGCTGTTATTTATTCATTGACTCAATTTT
1 GTCCCTAATTTAGG-TATTATTTATTCATTGATTCAATTTT
* * * * * *
34813 GTCCCTGATCTAAGGTAATATTTGTTGATTGATTCAATTAT
1 GTCCCTAAT-TTAGGTATTATTTATTCATTGATTCAATTTT
*
34854 GTCCCTAATTTAGAGTAATT-TTTATTTATTGATTCAATTTT
1 GTCCCTAATTTAG-GT-ATTATTTATTCATTGATTCAATTTT
34895 GTCCC
1 GTCCC
34900 GGATTTAGAA
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
40 3 0.04
41 61 0.87
42 6 0.09
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (40 bp):
GTCCCTAATTTAGGTATTATTTATTCATTGATTCAATTTT
Found at i:34906 original size:41 final size:40
Alignment explanation
Indices: 34792--34924 Score: 146
Period size: 41 Copynumber: 3.4 Consensus size: 40
34782 TAGGCTGTTA
* * * *
34792 TTTATTCATTGACTCAATTTTGTCCCTGATCTAAGGTAATA
1 TTTATTTATTGATTCAATTTTGTCCCTGATTTAA-GTAATT
* * * *
34833 TTTGTTGATTGATTCAATTATGTCCCTAATTTAGAGTAATT
1 TTTATTTATTGATTCAATTTTGTCCCTGATTTA-AGTAATT
*
34874 TTTATTTATTGATTCAATTTTGTCCCGGATTT-AG-AATT
1 TTTATTTATTGATTCAATTTTGTCCCTGATTTAAGTAATT
34912 TTTATTT-TTGATT
1 TTTATTTATTGATT
34925 TATGCGGCCT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
37 6 0.08
38 11 0.14
39 2 0.03
41 59 0.75
42 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (40 bp):
TTTATTTATTGATTCAATTTTGTCCCTGATTTAAGTAATT
Found at i:39652 original size:60 final size:58
Alignment explanation
Indices: 39588--39702 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 58
39578 TTTAGCAATC
* *
39588 CTCCATCAATTTAACATTAGTTTGTCATTTGCAAAAATGTTTTATTAGTTGCATTTAGAA
1 CTCCATCAATTTAACATTAG-TAGTCATTTGCAAAAATGTTTT-TGAGTTGCATTTAGAA
* *
39648 CTCCATCAATTTAACATTAGTAGTCGTTTGCAAAAATGTTTTTGAGTTGCGTTTA
1 CTCCATCAATTTAACATTAGTAGTCATTTGCAAAAATGTTTTTGAGTTGCATTTA
39703 CAATATAAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 11 0.22
59 20 0.39
60 20 0.39
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (58 bp):
CTCCATCAATTTAACATTAGTAGTCATTTGCAAAAATGTTTTTGAGTTGCATTTAGAA
Found at i:42084 original size:41 final size:41
Alignment explanation
Indices: 42038--42257 Score: 350
Period size: 41 Copynumber: 5.4 Consensus size: 41
42028 TTTTTATCTC
42038 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
**
42079 TGCAATTTAGTCCCTGATTTAAGATTCTAACTACTATTTGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
*
42120 TGCAATTTAGTCCCTGATTCAAGATTCTATTTACTATTTGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
*
42161 TGCAATTTAGTCCCTGATTTAAGATTCTTTTTACTATTTGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
* * * *
42202 TGCAATTTAGTCACTGATTTAGGATTTTAGTTACTATTTGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
* *
42243 TTCAATTTGGTCCCT
1 TGCAATTTAGTCCCT
42258 AGTTTTAGAA
Statistics
Matches: 164, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 164 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (41 bp):
TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGA
Found at i:42288 original size:82 final size:82
Alignment explanation
Indices: 42038--42290 Score: 260
Period size: 82 Copynumber: 3.1 Consensus size: 82
42028 TTTTTATCTC
* * * *
42038 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGATGCAATTTAGTCCCTGATTTAAGA
1 TGCAATTTAGTCACTGATTCAAGATTCTAGTTACTATTTGATGCAATTTAGTCCCTGATTTAAAA
** * *
42103 TTC-TAACTACTATTTGA
66 TTCAT-GTTACAAATTGA
* * *
42120 TGCAATTTAGTCCCTGATTCAAGATTCTATTTACTATTTGATGCAATTTAGTCCCTGATTTAAGA
1 TGCAATTTAGTCACTGATTCAAGATTCTAGTTACTATTTGATGCAATTTAGTCCCTGATTTAAAA
* * * *
42185 TTCTTTTTACTATTTGA
66 TTCATGTTACAAATTGA
* * * * * *
42202 TGCAATTTAGTCACTGATTTAGGATTTTAGTTACTATTTGATTCAATTTGGTCCCTAGTTTTAGA
1 TGCAATTTAGTCACTGATTCAAGATTCTAGTTACTATTTGATGCAATTTAGTCCCT-GATTTA-A
*
42267 AATTGATGTTA-AAATTG-
64 AATTCATGTTACAAATTGA
42284 TGCAATT
1 TGCAATT
42291 AGATACTTGA
Statistics
Matches: 151, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
82 133 0.88
83 10 0.07
84 8 0.05
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (82 bp):
TGCAATTTAGTCACTGATTCAAGATTCTAGTTACTATTTGATGCAATTTAGTCCCTGATTTAAAA
TTCATGTTACAAATTGA
Found at i:42288 original size:123 final size:123
Alignment explanation
Indices: 42038--42290 Score: 332
Period size: 123 Copynumber: 2.1 Consensus size: 123
42028 TTTTTATCTC
*
42038 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGATGCAATTTAGTCCCTGATTTAAGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGATGCAATTTAGTCACTGATTTAAGA
* * * *
42103 TTCTAACTACTATTTGATGCAATTTAGTCCCTGATTCAAGATTCTATTTACTATTTGA
66 TTCTAACTACTATTTGATGCAATTTAGTCCCTGATTCAAAATTCGATTTACAAATTGA
* *
42161 TGCAATTTAGTCCCTGATTTAAGATTCTTTTTACTATTTGATGCAATTTAGTCACTGATTTAGGA
1 TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGATGCAATTTAGTCACTGATTTAAGA
* ** * * * *
42226 TTTTAGTTACTATTTGATTCAATTTGGTCCCTAGTTTTAGAAATT-GATGTTA-AAATTG-
66 TTCTAACTACTATTTGATGCAATTTAGTCCCT-GATTCA-AAATTCGAT-TTACAAATTGA
42284 TGCAATT
1 TGCAATT
42291 AGATACTTGA
Statistics
Matches: 113, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
123 96 0.85
124 10 0.09
125 7 0.06
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (123 bp):
TGCAATTTAGTCCCTGATTTAAGATTCTATTTACTATTTGATGCAATTTAGTCACTGATTTAAGA
TTCTAACTACTATTTGATGCAATTTAGTCCCTGATTCAAAATTCGATTTACAAATTGA
Found at i:45720 original size:30 final size:30
Alignment explanation
Indices: 45670--45729 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
45660 CATCTTCAAG
*
45670 TCCACGATAAGTCCTTGGCGCATCATTCCC
1 TCCACGATAAGTCCTTGGCGCATCACTCCC
*
45700 TCCATGATAAG-CCTTGGGCGCATCACTCCC
1 TCCACGATAAGTCCTT-GGCGCATCACTCCC
45730 AACAACCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.25
Consensus pattern (30 bp):
TCCACGATAAGTCCTTGGCGCATCACTCCC
Found at i:46129 original size:18 final size:18
Alignment explanation
Indices: 46106--46140 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
46096 AACAAAAATT
46106 AAGTTGAATTCGGATTAG
1 AAGTTGAATTCGGATTAG
*
46124 AAGTTGAGTTCGGATTA
1 AAGTTGAATTCGGATTA
46141 TTTGGTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (18 bp):
AAGTTGAATTCGGATTAG
Found at i:47670 original size:15 final size:15
Alignment explanation
Indices: 47650--47699 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
47640 AAGCAAATCC
47650 AAAAGAAGATTTTGG
1 AAAAGAAGATTTTGG
* * **
47665 AAAAGAAGGTAATTCC
1 AAAAGAAGAT-TTTGG
47681 AAAAGAAGATTTTGG
1 AAAAGAAGATTTTGG
47696 AAAA
1 AAAA
47700 TAAAGATACC
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.22
Consensus pattern (15 bp):
AAAAGAAGATTTTGG
Found at i:47682 original size:31 final size:30
Alignment explanation
Indices: 47646--47728 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 30
47636 TCTTAAGCAA
*
47646 ATCCAAAAGAAGATTTTGGAAAAG-AAGGT
1 ATCCAAAAGAAGATTTTGGAAAAGAAAGAT
*
47675 AATTCCAAAAGAAGATTTTGGAAAATAAAGAT
1 -A-TCCAAAAGAAGATTTTGGAAAAGAAAGAT
*
47707 ACCCAAAAGAAGATTTTGGAAA
1 ATCCAAAAGAAGATTTTGGAAA
47729 TTAATAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
30 21 0.44
31 23 0.48
32 4 0.08
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (30 bp):
ATCCAAAAGAAGATTTTGGAAAAGAAAGAT
Found at i:60122 original size:30 final size:30
Alignment explanation
Indices: 60086--60148 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
60076 TCTTCAAGGG
*
60086 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATAATGCG-CCAAGGACTTATCAT
*
60116 GGAGGGAATAATGCGGCAAGGACTTATCAT
1 GGAGGGAATAATGCGCCAAGGACTTATCAT
60146 GGA
1 GGA
60149 CTTGAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.17
30 25 0.83
ACGTcount: A:0.30, C:0.16, G:0.35, T:0.19
Consensus pattern (30 bp):
GGAGGGAATAATGCGCCAAGGACTTATCAT
Found at i:70853 original size:19 final size:18
Alignment explanation
Indices: 70820--70855 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
70810 TTAAGATAAT
70820 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
70838 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
70856 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.