Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016572.1 Corchorus olitorius cultivar O-4 contig16605, 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: 147681
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1052 original size:129 final size:131
Alignment explanation
Indices: 911--1161 Score: 382
Period size: 130 Copynumber: 1.9 Consensus size: 131
901 AATATATTTT
* * * * *
911 AAAAATTTTAATATATTTAAGTTTTTT-AATTAAATTAGT-AATTGATAAAAATAAAATAGGTAT
1 AAAAATTCTAATATATATAA-TTTTTTCAATTAAAATAATAAAATGATAAAAATAAAATAGGTAT
*
974 AAGGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAGTTGAGT-AAACTATAAAAACATATT
65 AAAGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACATATT
1038 AA
130 AA
* * *
1040 AAAAATTCTAATATATATAATTTTTTCAATTAAAATAATAAAATGGTAAAAATTAAATAGTTATA
1 AAAAATTCTAATATATATAATTTTTTCAATTAAAATAATAAAATGATAAAAATAAAATAGGTATA
*
1105 AAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
66 AAGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
1162 GTCTAAACAA
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
128 6 0.06
129 28 0.26
130 64 0.59
131 11 0.10
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (131 bp):
AAAAATTCTAATATATATAATTTTTTCAATTAAAATAATAAAATGATAAAAATAAAATAGGTATA
AAGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAACATATTA
A
Found at i:2074 original size:14 final size:13
Alignment explanation
Indices: 2055--2093 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2045 AAATTGTAAA
2055 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
2068 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
2082 ATTTAAAAAATT
1 ATTTAAAAAATT
2094 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:4278 original size:19 final size:19
Alignment explanation
Indices: 4237--4278 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
4227 AATTTACCCT
* *
4237 TAATATATTTTTTTCCTTT
1 TAATATATTTTTTTACTTA
4256 TAAT-TATTTTCTTTACTTA
1 TAATATATTTT-TTTACTTA
4275 TAAT
1 TAAT
4279 GCCAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATATATTTTTTTACTTA
Found at i:10900 original size:20 final size:20
Alignment explanation
Indices: 10872--10956 Score: 80
Period size: 20 Copynumber: 4.1 Consensus size: 20
10862 CAAAGCGGAG
*
10872 CAGAAAACGGACAGCGGAAT
1 CAGACAACGGACAGCGGAAT
*
10892 CAGACAACGGACAGCGGAAAA
1 CAGACAACGGACAGCGG-AAT
* * *
10913 CAGACAGCAGACAACGGAAT
1 CAGACAACGGACAGCGGAAT
* *
10933 CACGGATAACGGACAGCAGAAT
1 CA--GACAACGGACAGCGGAAT
10955 CA
1 CA
10957 TCAAGAATAC
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
20 20 0.39
21 16 0.31
22 15 0.29
ACGTcount: A:0.45, C:0.24, G:0.27, T:0.05
Consensus pattern (20 bp):
CAGACAACGGACAGCGGAAT
Found at i:10948 original size:29 final size:28
Alignment explanation
Indices: 10892--10952 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
10882 ACAGCGGAAT
10892 CAGACAACGGACAGCGGAAAACAGACAG
1 CAGACAACGGACAGCGGAAAACAGACAG
* *
10920 CAGACAACGGAATCA-CGGATAACGGACAG
1 CAGACAACGG-A-CAGCGGAAAACAGACAG
10949 CAGA
1 CAGA
10953 ATCATCAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 10 0.34
29 17 0.59
30 2 0.07
ACGTcount: A:0.44, C:0.25, G:0.28, T:0.03
Consensus pattern (28 bp):
CAGACAACGGACAGCGGAAAACAGACAG
Found at i:11018 original size:28 final size:28
Alignment explanation
Indices: 10978--11049 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
10968 GGAGCATCAT
** *
10978 GTCAAGGGTAGAATACG-GTACCAAACAG
1 GTCAAGGACAGAATACGAG-ACAAAACAG
*
11006 GTCAAGGACAGAACACGAGACAAAACAG
1 GTCAAGGACAGAATACGAGACAAAACAG
11034 GTCAAGGACAGAATAC
1 GTCAAGGACAGAATAC
11050 TGGATCGGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 37 0.97
29 1 0.03
ACGTcount: A:0.44, C:0.19, G:0.26, T:0.10
Consensus pattern (28 bp):
GTCAAGGACAGAATACGAGACAAAACAG
Found at i:11227 original size:13 final size:14
Alignment explanation
Indices: 11209--11244 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
11199 TCAACTATCA
11209 AAAGTCAACAG-TC
1 AAAGTCAACAGATC
11222 AAAGTCAAC-GATC
1 AAAGTCAACAGATC
11235 AAAGTCAACA
1 AAAGTCAACA
11245 CTAACGTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 20 0.95
ACGTcount: A:0.50, C:0.22, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAGTCAACAGATC
Found at i:12488 original size:2 final size:2
Alignment explanation
Indices: 12481--12519 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12471 CCTTTAGGGA
12481 AT AT AT 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 AT AT AT A
12520 CTAAATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13148 original size:37 final size:37
Alignment explanation
Indices: 13093--13164 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
13083 AATGTGAAAG
*
13093 CATTTATTGACCATAAAATCATGTATTATGTATTTCA
1 CATTCATTGACCATAAAATCATGTATTATGTATTTCA
13130 CATTCATTGACCATAAAATCATGTATTATGTATTT
1 CATTCATTGACCATAAAATCATGTATTATGTATTT
13165 ACAAAGAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (37 bp):
CATTCATTGACCATAAAATCATGTATTATGTATTTCA
Found at i:20027 original size:3 final size:3
Alignment explanation
Indices: 20019--20053 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
20009 GAAAGAGTGA
20019 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
20054 AAAAAAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:23369 original size:2 final size:2
Alignment explanation
Indices: 23362--23390 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
23352 AACACCACAC
23362 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23391 ATCTTAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23383 original size:13 final size:13
Alignment explanation
Indices: 23365--23392 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
23355 ACCACACTAT
23365 ATATATATATATA
1 ATATATATATATA
23378 ATATATATATATA
1 ATATATATATATA
23391 AT
1 AT
23393 CTTAATGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:37500 original size:15 final size:15
Alignment explanation
Indices: 37480--37535 Score: 103
Period size: 15 Copynumber: 3.7 Consensus size: 15
37470 TGATGACTGT
37480 TGGGCAGTGGGGTGC
1 TGGGCAGTGGGGTGC
37495 TGGGCAGTGGGGTGC
1 TGGGCAGTGGGGTGC
*
37510 TGGGCAGTGTGGTGC
1 TGGGCAGTGGGGTGC
37525 TGGGCAGTGGG
1 TGGGCAGTGGG
37536 AGTTTCTTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.07, C:0.12, G:0.59, T:0.21
Consensus pattern (15 bp):
TGGGCAGTGGGGTGC
Found at i:38721 original size:26 final size:25
Alignment explanation
Indices: 38668--38756 Score: 101
Period size: 25 Copynumber: 3.6 Consensus size: 25
38658 CCCATTAACC
38668 AAAAACAGAAAGTTAGATACTGATA
1 AAAAACAGAAAGTTAGATACTGATA
* *
38693 AAAAACAGAAAGTTAGATGCTTATAA
1 AAAAACAGAAAGTTAGATACTGAT-A
* * *
38719 AAAAACAGAAAATTATAAACTTG-T-
1 AAAAACAGAAAGTTAGATAC-TGATA
38743 AAAAACAGAAAGTT
1 AAAAACAGAAAGTT
38757 TGAGTACCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
24 13 0.24
25 22 0.41
26 18 0.33
27 1 0.02
ACGTcount: A:0.57, C:0.08, G:0.13, T:0.21
Consensus pattern (25 bp):
AAAAACAGAAAGTTAGATACTGATA
Found at i:39787 original size:15 final size:15
Alignment explanation
Indices: 39767--39826 Score: 75
Period size: 15 Copynumber: 4.0 Consensus size: 15
39757 TAGGCTGAGA
* *
39767 TGCATTAGAAGGCCC
1 TGCATGAGATGGCCC
*
39782 TGCATTAGATGGCCC
1 TGCATGAGATGGCCC
* *
39797 TACATGAGATGGCTC
1 TGCATGAGATGGCCC
39812 TGCATGAGATGGCCC
1 TGCATGAGATGGCCC
39827 CGTAACAGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (15 bp):
TGCATGAGATGGCCC
Found at i:39855 original size:18 final size:18
Alignment explanation
Indices: 39832--39872 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
39822 GGCCCCGTAA
39832 CAGATGGCCCTACCCCAG
1 CAGATGGCCCTACCCCAG
39850 CAGATGGCCCTACCCCAG
1 CAGATGGCCCTACCCCAG
39868 CAGAT
1 CAGAT
39873 TCATTATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.41, G:0.22, T:0.12
Consensus pattern (18 bp):
CAGATGGCCCTACCCCAG
Found at i:40642 original size:35 final size:35
Alignment explanation
Indices: 40596--40674 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
40586 TACATTAGAT
40596 ATGCTCAAACATAGTCACAAAGCAAAATCAGAAAC
1 ATGCTCAAACATAGTCACAAAGCAAAATCAGAAAC
40631 ATGCTCAAACATAGTCACAAAGCAAAATCAGAAAC
1 ATGCTCAAACATAGTCACAAAGCAAAATCAGAAAC
40666 ATGCTCAAA
1 ATGCTCAAA
40675 TCTAACAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.51, C:0.23, G:0.11, T:0.15
Consensus pattern (35 bp):
ATGCTCAAACATAGTCACAAAGCAAAATCAGAAAC
Found at i:45387 original size:30 final size:30
Alignment explanation
Indices: 45351--45413 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
45341 CGTCTCCGGT
45351 GGTTAAAACTTCTGACTATTCGAGTAAAGA
1 GGTTAAAACTTCTGACTATTCGAGTAAAGA
45381 GGTTAAAACTTCTGACTATTCGAGTAAAGA
1 GGTTAAAACTTCTGACTATTCGAGTAAAGA
45411 GGT
1 GGT
45414 CTTGAGTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (30 bp):
GGTTAAAACTTCTGACTATTCGAGTAAAGA
Found at i:50229 original size:6 final size:7
Alignment explanation
Indices: 50212--50236 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
50202 ATCATTTCAA
50212 AAAAAAT
1 AAAAAAT
50219 AAAAAAT
1 AAAAAAT
50226 AAAAAAT
1 AAAAAAT
50233 AAAA
1 AAAA
50237 TTGATGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:57415 original size:22 final size:22
Alignment explanation
Indices: 57389--57431 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
57379 AAGACCATTC
57389 AAATGTTTCAACTAAAGGGTTT
1 AAATGTTTCAACTAAAGGGTTT
*
57411 AAATGTTTTAACTAAAGGGTT
1 AAATGTTTCAACTAAAGGGTT
57432 GTTAAGGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (22 bp):
AAATGTTTCAACTAAAGGGTTT
Found at i:62569 original size:6 final size:6
Alignment explanation
Indices: 62558--62582 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
62548 GCAGTCTTCC
62558 TTCCTT TTCCTT TTCCTT TTCCTT T
1 TTCCTT TTCCTT TTCCTT TTCCTT T
62583 CGATTTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TTCCTT
Found at i:68284 original size:44 final size:45
Alignment explanation
Indices: 68212--68306 Score: 138
Period size: 44 Copynumber: 2.1 Consensus size: 45
68202 CCCCTTTTAC
*
68212 AACAATATATATAAGCTAAGCCTAAATCTAAAGTTCACTCAA-AA
1 AACAGTATATATAAGCTAAGCCTAAATCTAAAGTTCACTCAACAA
* * *
68256 AACAGTATATATAATCTAGGCCTTAATCTAAAGTTCACTCAAGCAA
1 AACAGTATATATAAGCTAAGCCTAAATCTAAAGTTCACTCAA-CAA
68302 AACAG
1 AACAG
68307 GGTCAAAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 38 0.84
46 7 0.16
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.25
Consensus pattern (45 bp):
AACAGTATATATAAGCTAAGCCTAAATCTAAAGTTCACTCAACAA
Found at i:73623 original size:24 final size:24
Alignment explanation
Indices: 73593--73642 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
73583 CAAAAAAAGA
*
73593 AAAATGCAGAGAAGAACAGAGAAG
1 AAAATGCAGAGAAAAACAGAGAAG
* *
73617 AAAATGCAGATAAAAACAGAGGAG
1 AAAATGCAGAGAAAAACAGAGAAG
73641 AA
1 AA
73643 CAGGACTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.60, C:0.08, G:0.26, T:0.06
Consensus pattern (24 bp):
AAAATGCAGAGAAAAACAGAGAAG
Found at i:73775 original size:211 final size:204
Alignment explanation
Indices: 73410--73799 Score: 568
Period size: 211 Copynumber: 1.9 Consensus size: 204
73400 TAAAAGAAGG
* *
73410 GAAGAAAATGCAGATAAAAACAGAGAAGAAAGACTAAACAAAAAAAGTTGAAATACTTTAACGGT
1 GAAGAAAATGCAGATAAAAACAGAGAAGAAAGACTAAACAAAAAAAGATGAAATACTTCAACGGT
* *
73475 TAAAATCTTCCTTATACTACCTTAAAAACAATCTATAGAGGAGATTACTAAGGCCTCCAACGCAC
66 TAAAATCTTCCTTATACTACCTTAAAAACAATCTATAGAGGAGATTACTAAAGCCTCCAACCCAC
* * * * *
73540 AAAAATGTTAGACAAGACCAGAGGTATAATAT-GAAAAAAAGAA-CAAAAAAAGAAAAATGCAGA
131 AAAAATGTTAAACAAAAACAGAGGTAGAACATGGAAAAAAA-AATCAAAAAAAGAAAAATGCAGA
73603 GAAGAACAGA
195 GAAGAACAGA
*
73613 GAAGAAAATGCAGATAAAAACAGAGGAGAACAGGACTAAACAAAATAAAGATGAAATACTTCAAC
1 GAAGAAAATGCAGATAAAAACAGAGAAGAA-A-GACTAAACAAAA-AAAGATGAAATACTTCAAC
* * *
73678 GGTTAAAATCTTCGTTATAGTACCCTTAACAACAATCAATCTATAGAGGAGATTACTAAAGCCTT
63 GGTTAAAATCTTCCTTATACTA-CCTT-A-AA-AA-CAATCTATAGAGGAGATTACTAAAGCCTC
73743 CAACCCACAAAAATGTTAAACAAAAACAGAGGTAGAACATGGAAAAAAAAATCAAAA
123 CAACCCACAAAAATGTTAAACAAAAACAGAGGTAGAACATGGAAAAAAAAATCAAAA
73800 TATTAACAAG
Statistics
Matches: 164, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
203 29 0.18
204 1 0.01
205 12 0.07
206 37 0.23
207 4 0.02
208 1 0.01
209 2 0.01
210 2 0.01
211 63 0.38
212 13 0.08
ACGTcount: A:0.52, C:0.15, G:0.16, T:0.18
Consensus pattern (204 bp):
GAAGAAAATGCAGATAAAAACAGAGAAGAAAGACTAAACAAAAAAAGATGAAATACTTCAACGGT
TAAAATCTTCCTTATACTACCTTAAAAACAATCTATAGAGGAGATTACTAAAGCCTCCAACCCAC
AAAAATGTTAAACAAAAACAGAGGTAGAACATGGAAAAAAAAATCAAAAAAAGAAAAATGCAGAG
AAGAACAGA
Found at i:75002 original size:7 final size:7
Alignment explanation
Indices: 74990--75016 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
74980 TTTTTGGTAC
74990 TGGACAG
1 TGGACAG
74997 TGGACAG
1 TGGACAG
75004 TGGACAG
1 TGGACAG
75011 TGGACA
1 TGGACA
75017 CTGGTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.41, T:0.15
Consensus pattern (7 bp):
TGGACAG
Found at i:78872 original size:44 final size:42
Alignment explanation
Indices: 78798--78881 Score: 123
Period size: 44 Copynumber: 2.0 Consensus size: 42
78788 ATTTTTTTTC
*
78798 CAAAAAACAAAGATATATAGATATAGATTTGATTATAAATTT
1 CAAAAAAAAAAGATATATAGATATAGATTTGATTATAAATTT
* *
78840 CAAAATAAAAAAGATATATTTGATATATATTTGATTATAAAT
1 CAAAA-AAAAAAGATATA-TAGATATAGATTTGATTATAAAT
78882 GGTTTACTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 5 0.14
43 11 0.30
44 21 0.57
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (42 bp):
CAAAAAAAAAAGATATATAGATATAGATTTGATTATAAATTT
Found at i:78950 original size:24 final size:24
Alignment explanation
Indices: 78923--78970 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
78913 TATATAGTAA
78923 TAATATGAATTCCATTAATAATCG
1 TAATATGAATTCCATTAATAATCG
*
78947 TAATATGAATTTCATTAATAATCG
1 TAATATGAATTCCATTAATAATCG
78971 AAATCAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (24 bp):
TAATATGAATTCCATTAATAATCG
Found at i:90626 original size:19 final size:20
Alignment explanation
Indices: 90602--90657 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
90592 GTTTAGCAAA
90602 TGTACAGATGAGATTA-CAC
1 TGTACAGATGAGATTAGCAC
* * *
90621 TGTACATATTAGATTAGTTAC
1 TGTACAGATGAGATTAG-CAC
90642 TGTACAGATGAGATTA
1 TGTACAGATGAGATTA
90658 TTAGAACAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 14 0.47
21 16 0.53
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (20 bp):
TGTACAGATGAGATTAGCAC
Found at i:98269 original size:97 final size:95
Alignment explanation
Indices: 98085--98277 Score: 332
Period size: 97 Copynumber: 2.0 Consensus size: 95
98075 GAGATAAGGC
98085 TAAGTGTTCAGAGCAGGCAGATTCTAATAAGTAGTTTAGAGCATGATTTTCATTTTAAGGATCAA
1 TAAGTGTTCAGAGCAGGCAGATTCTAATAAGTAGTTTAGAGCATGATTTTCATTTTAAGGATCAA
*
98150 TCATTCCGAGTCCTTTCACTAGAATCAGAT
66 TCATTCCAAGTCCTTTCACTAGAATCAGAT
* * *
98180 TAAGTGTTCAGAGCAGGCGGATTCTAATAAGTTGTCTTATAGCATGATTTTCATTTTCAAGGATC
1 TAAGTGTTCAGAGCAGGCAGATTCTAATAAGTAGT-TTAGAGCATGATTTTCATTTT-AAGGATC
98245 AATCATTCCAAGTCCTTTCACTAGAATCAGAT
64 AATCATTCCAAGTCCTTTCACTAGAATCAGAT
98277 T
1 T
98278 CTCCATACTA
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 33 0.36
96 20 0.22
97 39 0.42
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (95 bp):
TAAGTGTTCAGAGCAGGCAGATTCTAATAAGTAGTTTAGAGCATGATTTTCATTTTAAGGATCAA
TCATTCCAAGTCCTTTCACTAGAATCAGAT
Found at i:98895 original size:77 final size:78
Alignment explanation
Indices: 98746--98903 Score: 282
Period size: 77 Copynumber: 2.0 Consensus size: 78
98736 TCATGATTCC
* *
98746 CACTCTACAATATGGAATATACTGCCATCTGATGGAATAAATCATTCCAAGAATGGCTTGGTACA
1 CACTCTACAATATGGAATATACTGCCATCTGATGGAATAAATCATACCAAGAATGGCTTGGAACA
98811 GATCCATGCCATA
66 GATCCATGCCATA
*
98824 CACTCTACAATATGGAATATACTGCCGTCTGATGG-ATAAATCATACCAAGAATGGCTTGGAACA
1 CACTCTACAATATGGAATATACTGCCATCTGATGGAATAAATCATACCAAGAATGGCTTGGAACA
98888 GATCCATGCCATA
66 GATCCATGCCATA
98901 CAC
1 CAC
98904 ACCACGGATA
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
77 43 0.56
78 34 0.44
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (78 bp):
CACTCTACAATATGGAATATACTGCCATCTGATGGAATAAATCATACCAAGAATGGCTTGGAACA
GATCCATGCCATA
Found at i:103350 original size:62 final size:59
Alignment explanation
Indices: 103223--103361 Score: 170
Period size: 62 Copynumber: 2.3 Consensus size: 59
103213 TATACATTTG
** * * *
103223 AAAATCAAATTCTGTTAACAAAATCTGATCTTAGTTTTACAAGATATACATTTGAGAATT
1 AAAATCAAATTCTGTT-ACAAAATCTGATCTTACCTTTACAAGATATACAATAGAAAATT
* * *
103283 AAAATCAAATTCTGTTACAGAATTTGATTTTACCTTTACAAGATAATATACAATAGAAAATT
1 AAAATCAAATTCTGTTACAAAATCTGATCTTACCTTTACAAG---ATATACAATAGAAAATT
103345 AAAATCAAATTCTGTTA
1 AAAATCAAATTCTGTTA
103362 AAGTATAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 21 0.31
60 16 0.24
62 31 0.46
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.36
Consensus pattern (59 bp):
AAAATCAAATTCTGTTACAAAATCTGATCTTACCTTTACAAGATATACAATAGAAAATT
Found at i:110826 original size:29 final size:30
Alignment explanation
Indices: 110754--110829 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
110744 TCGTTTGAGA
* *
110754 GGGGCAAAACGTCCAAAATTGAGAGTTTAG
1 GGGGCAAAACGTCCAAAATTGAGAATTCAG
* *
110784 GGGGCAAAATGTCCAAAATTGA-AATTCAT
1 GGGGCAAAACGTCCAAAATTGAGAATTCAG
110813 GGGGCAAAACGTCCAAA
1 GGGGCAAAACGTCCAAA
110830 CGCTACAAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 20 0.49
30 21 0.51
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.18
Consensus pattern (30 bp):
GGGGCAAAACGTCCAAAATTGAGAATTCAG
Found at i:124934 original size:31 final size:30
Alignment explanation
Indices: 124896--124972 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
124886 TTAATGCCCT
*
124896 TTTTGCCCCCTGAACTTTTATGATTTT-GACG
1 TTTTGCCCCCTGAACTTTTA--ATTTTGGACA
*
124927 TTTTGCCCCCTAAAC-TTTAATTTTGGACA
1 TTTTGCCCCCTGAACTTTTAATTTTGGACA
*
124956 TTTTGCCCCTTGAACTT
1 TTTTGCCCCCTGAACTT
124973 GCAATTTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 5 0.12
29 16 0.40
30 5 0.12
31 14 0.35
ACGTcount: A:0.18, C:0.25, G:0.13, T:0.44
Consensus pattern (30 bp):
TTTTGCCCCCTGAACTTTTAATTTTGGACA
Found at i:125060 original size:31 final size:32
Alignment explanation
Indices: 125017--125096 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
125007 TATATTGCTG
*
125017 ACATGGCATTGCCACGTGGCA-TTTTGGTCCA
1 ACATGGCATTGCCACATGGCATTTTTGGTCCA
*
125048 ACATAGCATTGCCACATGGCATTTTTGGTCCA
1 ACATGGCATTGCCACATGGCATTTTTGGTCCA
*
125080 ACGTGGCATTGCCACAT
1 ACATGGCATTGCCACAT
125097 TAGCAATACC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 19 0.43
32 25 0.57
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.29
Consensus pattern (32 bp):
ACATGGCATTGCCACATGGCATTTTTGGTCCA
Found at i:143324 original size:32 final size:31
Alignment explanation
Indices: 143288--143406 Score: 118
Period size: 32 Copynumber: 3.8 Consensus size: 31
143278 TGATTGAGGG
*
143288 CAAAATTTCAACTCATTTAATGCAAAT-AAGGC
1 CAAAATTTCAA-TCATTAAATGCAAATCAA-GC
*
143320 CAAAATTTCAATTCATTAAATGCAAATCAAGT
1 CAAAATTTCAA-TCATTAAATGCAAATCAAGC
* * *
143352 CAAAATTGCAATCCATTAAATGCAAAACAAGA
1 CAAAATTTCAAT-CATTAAATGCAAATCAAGC
* *
143384 CAAAATTACAA--ATTAATTGCAAA
1 CAAAATTTCAATCATTAAATGCAAA
143407 AAAAAACCAA
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
29 11 0.14
31 1 0.01
32 63 0.82
33 2 0.03
ACGTcount: A:0.50, C:0.17, G:0.08, T:0.26
Consensus pattern (31 bp):
CAAAATTTCAATCATTAAATGCAAATCAAGC
Found at i:144939 original size:15 final size:14
Alignment explanation
Indices: 144916--144945 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
144906 ATAAAAATTA
144916 AATATTTTTATTTT
1 AATATTTTTATTTT
144930 AATATATTTTATTTT
1 AATAT-TTTTATTTT
144945 A
1 A
144946 TTGAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:145212 original size:14 final size:14
Alignment explanation
Indices: 145177--145203 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
145167 TCCACTAGCA
145177 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
145191 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
145204 TTTTTTTTTG
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:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:146969 original size:3 final size:3
Alignment explanation
Indices: 146961--146987 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
146951 AGATGAGGTG
146961 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
146988 AAAAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:147142 original size:10 final size:10
Alignment explanation
Indices: 147103--147154 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
147093 GCCCTAGCCC
147103 AAAGAAAAAA
1 AAAGAAAAAA
*
147113 AAACAAAAAA
1 AAAGAAAAAA
147123 AAATGAAATAAA
1 AAA-GAAA-AAA
*
147135 AAAGAATAAGA
1 AAAGAA-AAAA
*
147146 AAGGAAAAA
1 AAAGAAAAA
147155 GGAAGAAGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 14 0.41
11 13 0.38
12 7 0.21
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.06
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:147365 original size:28 final size:29
Alignment explanation
Indices: 147303--147367 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 29
147293 AAGTTACAAT
* *
147303 TTTACCCTTGGACAGGTAAAATTACTAAA
1 TTTACCCTTGAACAGGTAAAATTACGAAA
* * *
147332 -TCACCCTT-AACATGTTAAATTACGAAA
1 TTTACCCTTGAACAGGTAAAATTACGAAA
147359 TTTACCCTT
1 TTTACCCTT
147368 TTAAAGTGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (29 bp):
TTTACCCTTGAACAGGTAAAATTACGAAA
Done.