Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020665.1 Corchorus olitorius cultivar O-4 contig20698, 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: 93206
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:11803 original size:17 final size:17
Alignment explanation
Indices: 11781--11814 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11771 AATTTTCCTA
*
11781 TGACAACTATACATGCT
1 TGACAACTATAAATGCT
11798 TGACAACTATAAATGCT
1 TGACAACTATAAATGCT
11815 CCTTGACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (17 bp):
TGACAACTATAAATGCT
Found at i:11821 original size:20 final size:19
Alignment explanation
Indices: 11776--11821 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 19
11766 AATTCAATTT
*
11776 TCCTATGACAACTATACATG
1 TCCT-TGACAACTATAAATG
11796 --CTTGACAACTATAAATG
1 TCCTTGACAACTATAAATG
11813 CTCCTTGAC
1 -TCCTTGAC
11822 TACAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
17 14 0.64
18 2 0.09
20 6 0.27
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (19 bp):
TCCTTGACAACTATAAATG
Found at i:14500 original size:31 final size:31
Alignment explanation
Indices: 14456--14524 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
14446 AAAAAATGAG
* *
14456 TCAGGGA-TCCAATTGCTCAATTAACTCCACT
1 TCAGGGACTCCAATTACTC-ACTAACTCCACT
* *
14487 TCAGGGACT-CAATTACTCACTAAGTTCACT
1 TCAGGGACTCCAATTACTCACTAACTCCACT
14517 TCAGGGAC
1 TCAGGGAC
14525 CCATTTGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 17 0.52
31 15 0.45
32 1 0.03
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (31 bp):
TCAGGGACTCCAATTACTCACTAACTCCACT
Found at i:19319 original size:122 final size:123
Alignment explanation
Indices: 19095--19454 Score: 425
Period size: 122 Copynumber: 2.9 Consensus size: 123
19085 TATATATACT
* * * * * * *
19095 ATACCGACGTTTGTAAATGTCGGAACAAGTTCTTCATATCATTTGATTTCGATGTATTCCGACAT
1 ATACCAACGTTTGCAAAAGTCGG-A-AAGTCCTTTACATCATTTGATTTCGACGTATTCCGACAT
* * *
19160 TTGTAAGCATTGGTATAGATAATATATCGTGGCATTTATTAAACGTCGCTATAGAACACA
64 TTGTAAGCGTTGGTATAGATATTATATCGTGGCATTTATTAAACGTCACTATAGAACACA
* *
19220 ATACCAACGTTTGCAAAAGTCGG-AAGTCCTTTACATCATTTGATTTCGACGTATGCCGATATTT
1 ATACCAACGTTTGCAAAAGTCGGAAAGTCCTTTACATCATTTGATTTCGACGTATTCCGACATTT
* * * *
19284 GTAAGCGTTGGTATAGATATTATATCGTGGGATTTATTAAACATTACTATAGAACACT
66 GTAAGCGTTGGTATAGATATTATATCGTGGCATTTATTAAACGTCACTATAGAACACA
* * * * * * *
19342 ATACCGATGTTTGCAAATGTCGGAACAAGTTCTTTACATCATTTGATTTCGACATATTTCAACAT
1 ATACCAACGTTTGCAAAAGTCGG-A-AAGTCCTTTACATCATTTGATTTCGACGTATTCCGACAT
* * * * *
19407 TTGTAAGCGTTGTTATAGATGTTATATCATGACATTTGTTAAACGTCA
64 TTGTAAGCGTTGGTATAGATATTATATCGTGGCATTTATTAAACGTCA
19455 TTTTAAAATA
Statistics
Matches: 199, Mismatches: 33, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
122 106 0.53
125 93 0.47
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (123 bp):
ATACCAACGTTTGCAAAAGTCGGAAAGTCCTTTACATCATTTGATTTCGACGTATTCCGACATTT
GTAAGCGTTGGTATAGATATTATATCGTGGCATTTATTAAACGTCACTATAGAACACA
Found at i:19449 original size:125 final size:125
Alignment explanation
Indices: 19092--19486 Score: 472
Period size: 125 Copynumber: 3.2 Consensus size: 125
19082 CAATATATAT
* * * *
19092 ACTATACCGACGTTTGTAAATGTCGGAACAAGTTCTTCATATCATTTGATTTCGATGTATTCCGA
1 ACTATACCGACGTTTGCAAATGTCGGAACAAGTTCTTTACATCATTTGATTTCGACGTATTCCGA
* * * *
19157 CATTTGTAAGCATTGGTATAGATAATATATCGTGGCATTTATTAAACGTCGCTATAGAAC
66 CATTTGTAAGCGTTGGTATAGATATTATATCGTGGCATTTATTAAACATCACTATAGAAC
* * * * *
19217 ACAATACCAACGTTTGCAAAAGTCGG---AAGTCCTTTACATCATTTGATTTCGACGTATGCCGA
1 ACTATACCGACGTTTGCAAATGTCGGAACAAGTTCTTTACATCATTTGATTTCGACGTATTCCGA
* * *
19279 TATTTGTAAGCGTTGGTATAGATATTATATCGTGGGATTTATTAAACATTACTATAGAAC
66 CATTTGTAAGCGTTGGTATAGATATTATATCGTGGCATTTATTAAACATCACTATAGAAC
* * * *
19339 ACTATACCGATGTTTGCAAATGTCGGAACAAGTTCTTTACATCATTTGATTTCGACATATTTCAA
1 ACTATACCGACGTTTGCAAATGTCGGAACAAGTTCTTTACATCATTTGATTTCGACGTATTCCGA
* * * * * * * * * *
19404 CATTTGTAAGCGTTGTTATAGATGTTATATCATGACATTTGTTAAACGTCATTTTAAAAT
66 CATTTGTAAGCGTTGGTATAGATATTATATCGTGGCATTTATTAAACATCACTATAGAAC
* * *
19464 ATTATACCCACGTTTACAAATGT
1 ACTATACCGACGTTTGCAAATGT
19487 TGACACTTGA
Statistics
Matches: 225, Mismatches: 42, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
122 106 0.47
125 119 0.53
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (125 bp):
ACTATACCGACGTTTGCAAATGTCGGAACAAGTTCTTTACATCATTTGATTTCGACGTATTCCGA
CATTTGTAAGCGTTGGTATAGATATTATATCGTGGCATTTATTAAACATCACTATAGAAC
Found at i:24255 original size:12 final size:12
Alignment explanation
Indices: 24224--24256 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
24214 AAAAAAATAA
24224 AATAAAATAAAT
1 AATAAAATAAAT
24236 AA-ATAAATAAAT
1 AATA-AAATAAAT
24248 AATAAAATA
1 AATAAAATA
24257 GAAAGGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 1 0.05
12 17 0.89
13 1 0.05
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAAAATAAAT
Found at i:24278 original size:24 final size:23
Alignment explanation
Indices: 24251--24318 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
24241 AATAAATAAT
* *
24251 AAAATAGAAAGGAAAAAATAAGAA
1 AAAAAAGAAAGGAAAAAAGAAG-A
* *
24275 AAAAAAGAAAAGAAAAAGGAAGA
1 AAAAAAGAAAGGAAAAAAGAAGA
* *
24298 GAAAAAGAAAGGGAAAAAGAA
1 AAAAAAGAAAGGAAAAAAGAA
24319 TATAAGGAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 18 0.50
24 18 0.50
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (23 bp):
AAAAAAGAAAGGAAAAAAGAAGA
Found at i:24290 original size:12 final size:12
Alignment explanation
Indices: 24251--24318 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
24241 AATAAATAAT
* *
24251 AAAATAGAAAGG
1 AAAAAAGAAAAG
*
24263 AAAAAATAAGAA-
1 AAAAAAGAA-AAG
24275 AAAAAAGAAAAG
1 AAAAAAGAAAAG
* *
24287 AAAAAGGAAGAG
1 AAAAAAGAAAAG
*
24299 -AAAAAGAAAGG
1 AAAAAAGAAAAG
*
24310 GAAAAAGAA
1 AAAAAAGAA
24319 TATAAGGAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 10 0.23
12 33 0.75
13 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:27321 original size:18 final size:18
Alignment explanation
Indices: 27290--27327 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
27280 TCTTCATTGA
*
27290 AAATCACTTCAATTCTTC
1 AAATCACTTCAATTCATC
27308 AAAT-ACTTCAAATTCATC
1 AAATCACTTC-AATTCATC
27326 AA
1 AA
27328 GTTCAGAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATCACTTCAATTCATC
Found at i:27836 original size:126 final size:127
Alignment explanation
Indices: 27640--27877 Score: 442
Period size: 126 Copynumber: 1.9 Consensus size: 127
27630 TTTGGGCTCA
27640 AAAGGAGTTCACTACTATTGTCTTTCAAAGGGTAGGCTTTTTAGGCTAAGAGGGGTAATCCTAAA
1 AAAGGAGTTCACTACTATTGTCTTTCAAAGGGTAGGCTTTTTAGGCTAAGAGGGGTAATCCTAAA
*
27705 CGCATGAATTTTCAATTCAATGAATACCAAAAATCGAATGAGCATGTATATATTTCGCCTCG
66 CGCATGAATTTTCAATTCAATGAATACCAAAAATCAAATGAGCATGTATATATTTCGCCTCG
*
27767 AAAGG-GTTCACTACTATTGTCTTTCAAAGGGTAGGCTTTTTAGGCTAAGAGGGGTAATCTTAAA
1 AAAGGAGTTCACTACTATTGTCTTTCAAAGGGTAGGCTTTTTAGGCTAAGAGGGGTAATCCTAAA
*
27831 TGCATGAATTTTCAATTCAATGAATACCAAAAATCAAATGAGCATGT
66 CGCATGAATTTTCAATTCAATGAATACCAAAAATCAAATGAGCATGT
27878 CGCCTCGAAA
Statistics
Matches: 108, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
126 103 0.95
127 5 0.05
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (127 bp):
AAAGGAGTTCACTACTATTGTCTTTCAAAGGGTAGGCTTTTTAGGCTAAGAGGGGTAATCCTAAA
CGCATGAATTTTCAATTCAATGAATACCAAAAATCAAATGAGCATGTATATATTTCGCCTCG
Found at i:36042 original size:2 final size:2
Alignment explanation
Indices: 36035--36061 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36025 TCTTTCCCTA
36035 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 A
36062 AAATATCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37793 original size:14 final size:15
Alignment explanation
Indices: 37768--37802 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
37758 AATTTTTATA
*
37768 CATATAAGCTATGAG
1 CATATGAGCTATGAG
37783 C-TATGAGCTATGAG
1 CATATGAGCTATGAG
37797 CATATG
1 CATATG
37803 CATAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (15 bp):
CATATGAGCTATGAG
Found at i:57839 original size:36 final size:37
Alignment explanation
Indices: 57769--57842 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
57759 ATACATGAGT
57769 TAGCCACTTAGTGGTAAGCATCAATGAATTGATGTAA
1 TAGCCACTTAGTGGTAAGCATCAATGAATTGATGTAA
*
57806 TAGCCACTTAGTGGTAAGCAT-GATGAATTGATGTAA
1 TAGCCACTTAGTGGTAAGCATCAATGAATTGATGTAA
57842 T
1 T
57843 TATCTGGTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 15 0.42
37 21 0.58
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (37 bp):
TAGCCACTTAGTGGTAAGCATCAATGAATTGATGTAA
Found at i:62483 original size:109 final size:109
Alignment explanation
Indices: 62292--62501 Score: 384
Period size: 109 Copynumber: 1.9 Consensus size: 109
62282 CTATTATATA
*
62292 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGTACAAATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACAAATACCAAACAATA
62357 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
* *
62401 TATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATA
1 TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACAAATACCAAACAATA
*
62466 CAAAGTGCAATGAACTATTGGATTTAAAGAAAAATA
66 CAAAATGCAATGAACTATTGGATTTAAAGAAAAATA
62502 GAAGTACCAA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 97 1.00
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.32
Consensus pattern (109 bp):
TATTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACAAATACCAAACAATA
CAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
Found at i:64277 original size:40 final size:40
Alignment explanation
Indices: 64187--64503 Score: 410
Period size: 40 Copynumber: 8.0 Consensus size: 40
64177 TTTAAAAACT
* *
64187 TTGATGGGATCTTTCCCT-AATTGAAAGCTTTGACAAAGAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAG-C
* *
64227 -TGATTGGATCTTTCCCTAAATTGAAGACTTTGAAAAAGC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGC
* * * *
64266 TCGATGTGATCTTTCCCTTAATTGAAAACTTTGAAAAAAAC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTG-AAAAAGC
* * *
64307 TGGACGGGATCATTCCCT-AATTGAAAACTTTGAAAAA-C
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGC
* *
64345 TTGGACGGGATCTTTCCCTAAATTGAAAACTTTGAAAATGC
1 TT-GATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGC
* *
64386 TTGATGGGATTTTTCCCTAAATCGAAAACTTTGAAAAAGC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGC
* * *
64426 TTGATGGGATTTTTCCCTAAATCGAAATCTTTGAAAAAGC
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGC
64466 TTGATGGGATCTTTCCCTAAATTGAAAA-TTTGAAAAAG
1 TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAG
64504 ATTCTTTTCG
Statistics
Matches: 246, Mismatches: 25, Indels: 13
0.87 0.09 0.05
Matches are distributed among these distances:
38 2 0.01
39 47 0.19
40 174 0.71
41 23 0.09
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (40 bp):
TTGATGGGATCTTTCCCTAAATTGAAAACTTTGAAAAAGC
Found at i:64553 original size:18 final size:18
Alignment explanation
Indices: 64514--64554 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
64504 ATTCTTTTCG
**
64514 ATTTTGAATTTTGAAATT
1 ATTTTGAATTTTGAAAAC
*
64532 ATTTTGGATTTTGAAAAC
1 ATTTTGAATTTTGAAAAC
64550 ATTTT
1 ATTTT
64555 TATTTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTTGAATTTTGAAAAC
Found at i:67133 original size:75 final size:75
Alignment explanation
Indices: 66990--67139 Score: 185
Period size: 75 Copynumber: 2.0 Consensus size: 75
66980 ACAAGGGCCT
* * * *
66990 CGACTCCTCCTGGGCGCCCACATGGTTGCCTTGAGCACCAATGTGGTTTGCCTTAAGACCCAGCT
1 CGACTCCACCTGGGCGCCCACATGGTTG-CTTGAGCACCAATGTGATTTGCCTGAACACCCAGCT
67055 AGGCAGTGTCC
65 AGGCAGTGTCC
* * * * *
67066 CGACTCCACCTGGGTGCCCACATGGTTTG-TTGAGGACCCATGTGATTTGCCTGATCACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGG-TTGCTTGAGCACCAATGTGATTTGCCTGAACACCCAGCT
*
67130 AGGCTGTGTC
65 AGGCAGTGTC
67140 ATGGTTCGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
75 37 0.59
76 23 0.37
77 3 0.05
ACGTcount: A:0.17, C:0.31, G:0.27, T:0.25
Consensus pattern (75 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCTTGAGCACCAATGTGATTTGCCTGAACACCCAGCTA
GGCAGTGTCC
Found at i:67207 original size:24 final size:24
Alignment explanation
Indices: 67162--67207 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
67152 TTGGACATGT
**
67162 CTTCTTGCCTTGAACTCATCTTTG
1 CTTCTTGCCTTGAAAACATCTTTG
67186 CTTCTTTGCCTTGAAAAC-TCTT
1 CTTC-TTGCCTTGAAAACATCTT
67208 AGCAATCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.15, C:0.28, G:0.11, T:0.46
Consensus pattern (24 bp):
CTTCTTGCCTTGAAAACATCTTTG
Found at i:76839 original size:32 final size:32
Alignment explanation
Indices: 76793--76859 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
76783 GATTCATGGG
*
76793 TTAAACTCTCTTTTATTTCATGATCTTGATTT
1 TTAAACTCTATTTTATTTCATGATCTTGATTT
*
76825 TTAAACTCTATTTTATTTTATGATCTTGATTT
1 TTAAACTCTATTTTATTTCATGATCTTGATTT
76857 TTA
1 TTA
76860 TTGATTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.24, C:0.12, G:0.06, T:0.58
Consensus pattern (32 bp):
TTAAACTCTATTTTATTTCATGATCTTGATTT
Found at i:78742 original size:42 final size:42
Alignment explanation
Indices: 78696--78776 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 42
78686 AACAACCGGT
*
78696 GATGGGCGGCTTGAGTGGGGGAAATGAAA-AATGGATGGTGGC
1 GATGGGCGGCTTGAGTCGGGGAAAT-AAACAATGGATGGTGGC
78738 GATGGGCGGCTTGAGTCGGGGAAATAAACAATGGATGGT
1 GATGGGCGGCTTGAGTCGGGGAAATAAACAATGGATGGT
78777 TTCGGGGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.27, C:0.09, G:0.44, T:0.20
Consensus pattern (42 bp):
GATGGGCGGCTTGAGTCGGGGAAATAAACAATGGATGGTGGC
Found at i:80881 original size:1 final size:1
Alignment explanation
Indices: 80875--80902 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
80865 AGTCAATGGC
80875 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
80903 ATGGGATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:81551 original size:14 final size:14
Alignment explanation
Indices: 81532--81561 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
81522 CTACAACCAA
*
81532 AAAATGCTTCTTAG
1 AAAATGCTTCTAAG
81546 AAAATGCTTCTAAG
1 AAAATGCTTCTAAG
81560 AA
1 AA
81562 TTGGAAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (14 bp):
AAAATGCTTCTAAG
Found at i:83465 original size:23 final size:24
Alignment explanation
Indices: 83435--83500 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
83425 GAATATTAAA
83435 ATATATATA-ATTAATTATATATT
1 ATATATATATATTAATTATATATT
83458 ATATATATATATATAA-TA-ATATT
1 ATATATATATAT-TAATTATATATT
* * *
83481 AGATATCTATACTAATTATA
1 ATATATATATATTAATTATA
83501 ATGTGAGAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 3 0.08
23 25 0.69
24 5 0.14
25 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (24 bp):
ATATATATATATTAATTATATATT
Found at i:83501 original size:25 final size:24
Alignment explanation
Indices: 83426--83502 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 24
83416 GAATCGACCG
*
83426 AATATTAAAATATATATAATTAATTAT
1 AATATT-AGATATATAT-A-TAATTAT
* *
83453 -ATATTATATATATATAT-ATAAT
1 AATATTAGATATATATATAATTAT
*
83475 AATATTAGATATCTATACTAATTAT
1 AATATTAGATATATATA-TAATTAT
83500 AAT
1 AAT
83503 GTGAGAACCT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 4 0.10
23 15 0.36
24 2 0.05
25 16 0.38
26 5 0.12
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (24 bp):
AATATTAGATATATATATAATTAT
Found at i:85682 original size:16 final size:17
Alignment explanation
Indices: 85661--85692 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
85651 GAAATTGCGT
85661 TTTATTTTTCT-TTTTC
1 TTTATTTTTCTATTTTC
85677 TTTATTTTTCTATTTT
1 TTTATTTTTCTATTTT
85693 AATTTGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Found at i:91124 original size:34 final size:37
Alignment explanation
Indices: 91085--91154 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
91075 TCCGCGCCAA
91085 GCAGCA-A-GCCGCTGCTGCTGCCT-AGCCCGCGCGC
1 GCAGCACAGGCCGCTGCTGCTGCCTCAGCCCGCGCGC
91119 GCAGCAGCAGGCCGCTGCTGCTGCCTCAGCCCGCGC
1 GCAGCA-CAGGCCGCTGCTGCTGCCTCAGCCCGCGC
91155 ATGAGGCAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
34 6 0.19
36 1 0.03
37 16 0.50
38 9 0.28
ACGTcount: A:0.11, C:0.44, G:0.33, T:0.11
Consensus pattern (37 bp):
GCAGCACAGGCCGCTGCTGCTGCCTCAGCCCGCGCGC
Found at i:92918 original size:11 final size:11
Alignment explanation
Indices: 92902--92926 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
92892 AGAAAATTGT
92902 TTGTTTTTGGA
1 TTGTTTTTGGA
92913 TTGTTTTTGGA
1 TTGTTTTTGGA
92924 TTG
1 TTG
92927 ATTATTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (11 bp):
TTGTTTTTGGA
Done.