Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017025.1 Corchorus olitorius cultivar O-4 contig17058, 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: 127187
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3228 original size:19 final size:18
Alignment explanation
Indices: 3195--3230 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3185 TGGAAATAAT
3195 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
3213 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
3231 TAAATCTTCA
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:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:5180 original size:25 final size:26
Alignment explanation
Indices: 5118--5179 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 26
5108 TCTTTATTAA
* *
5118 TTGCTATAGTTTAGATTTAATTTACT
1 TTGCTTTATTTTAGATTTAATTTACT
*
5144 TTGCTTTATTTTAG-TTTAA-TTGCT
1 TTGCTTTATTTTAGATTTAATTTACT
*
5168 TTTCTTTATTTT
1 TTGCTTTATTTT
5180 TGCTATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 15 0.47
25 5 0.16
26 12 0.38
ACGTcount: A:0.19, C:0.08, G:0.10, T:0.63
Consensus pattern (26 bp):
TTGCTTTATTTTAGATTTAATTTACT
Found at i:12741 original size:84 final size:84
Alignment explanation
Indices: 12600--12764 Score: 312
Period size: 84 Copynumber: 2.0 Consensus size: 84
12590 CTTTATAGAG
*
12600 GGTGTCAACAACCCTAGGTGCCGCCCATGGGGAGAATTCGGCCTATGTTTGTAAGTTTTCCTAAG
1 GGTGTCAACAACCCTAGGTGCCGCCCAAGGGGAGAATTCGGCCTATGTTTGTAAGTTTTCCTAAG
12665 CCTCTCATGGATTTGGGAA
66 CCTCTCATGGATTTGGGAA
*
12684 GGTGTCCACAACCCTAGGTGCCGCCCAAGGGGAGAATTCGGCCTATGTTTGTAAGTTTTCCTAAG
1 GGTGTCAACAACCCTAGGTGCCGCCCAAGGGGAGAATTCGGCCTATGTTTGTAAGTTTTCCTAAG
12749 CCTCTCATGGATTTGG
66 CCTCTCATGGATTTGG
12765 AAAAATCCAT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (84 bp):
GGTGTCAACAACCCTAGGTGCCGCCCAAGGGGAGAATTCGGCCTATGTTTGTAAGTTTTCCTAAG
CCTCTCATGGATTTGGGAA
Found at i:17022 original size:18 final size:18
Alignment explanation
Indices: 16979--17023 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
16969 TAAATCCATG
* *
16979 GAATTTTGCAAAAATTTT
1 GAATTTTTCGAAAATTTT
16997 GAATTTTTCGAAAATTTT
1 GAATTTTTCGAAAATTTT
*
17015 GGATTTTTC
1 GAATTTTTC
17024 ATGCATATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (18 bp):
GAATTTTTCGAAAATTTT
Found at i:19290 original size:11 final size:10
Alignment explanation
Indices: 19274--19326 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
19264 GAAGTTCGTG
19274 ATTGAAGACTT
1 ATTGAAGA-TT
*
19285 ATTGAAGATA
1 ATTGAAGATT
19295 ATTTGAAGA-T
1 A-TTGAAGATT
19305 -TTGAAGATT
1 ATTGAAGATT
19314 ATTGAAGAATT
1 ATTGAAG-ATT
19325 AT
1 AT
19327 CTCAAGAGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 8 0.22
11 20 0.56
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.38
Consensus pattern (10 bp):
ATTGAAGATT
Found at i:19310 original size:19 final size:18
Alignment explanation
Indices: 19286--19321 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19276 TGAAGACTTA
19286 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
19305 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
19322 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:19922 original size:12 final size:12
Alignment explanation
Indices: 19905--19930 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19895 TTTAGATTTA
19905 TTCTTCTAGTTT
1 TTCTTCTAGTTT
19917 TTCTTCTAGTTT
1 TTCTTCTAGTTT
19929 TT
1 TT
19931 AGGCAAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (12 bp):
TTCTTCTAGTTT
Found at i:21966 original size:23 final size:23
Alignment explanation
Indices: 21940--21984 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
21930 TGGATCTTTA
21940 TTATGATTTATATGCTATGATTG
1 TTATGATTTATATGCTATGATTG
21963 TTATGATTTATATGCTATGATT
1 TTATGATTTATATGCTATGATT
21985 TGATTGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.53
Consensus pattern (23 bp):
TTATGATTTATATGCTATGATTG
Found at i:22875 original size:16 final size:15
Alignment explanation
Indices: 22837--22878 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
22827 ACAAAGGTTG
22837 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
22852 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
22867 ACTAGAAAACAA
1 AC-AGAAAACAA
22879 AACAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:28702 original size:34 final size:35
Alignment explanation
Indices: 28649--28719 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 35
28639 CTTCGATGCA
*
28649 AAACACAAAACAAACTTTTTTTTTCAAAACGACGC
1 AAACACAAAACAAACTTTTTTTTTCAAAAAGACGC
**
28684 AAACACAAAATTAA-TTTTTTTTTCAAAAAGACGC
1 AAACACAAAACAAACTTTTTTTTTCAAAAAGACGC
28718 AA
1 AA
28720 GCTAAAAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 21 0.64
35 12 0.36
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.28
Consensus pattern (35 bp):
AAACACAAAACAAACTTTTTTTTTCAAAAAGACGC
Found at i:29126 original size:16 final size:15
Alignment explanation
Indices: 29088--29126 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
29078 ACAAAGGTTG
29088 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
29103 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
29118 ACTAGAAAA
1 AC-AGAAAA
29127 ACAAAGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.67, C:0.13, G:0.08, T:0.13
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:39058 original size:19 final size:19
Alignment explanation
Indices: 39013--39049 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39003 AATAATAATA
*
39013 AATAGATTAAAATTAAATG
1 AATAAATTAAAATTAAATG
39032 AATAAATTAAAATTAAAT
1 AATAAATTAAAATTAAAT
39050 TGTATAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AATAAATTAAAATTAAATG
Found at i:46331 original size:29 final size:29
Alignment explanation
Indices: 46289--46348 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
46279 AGTCACTTGA
46289 CGGGCGCTTCGGGGGTGCCGATCCTTCCC
1 CGGGCGCTTCGGGGGTGCCGATCCTTCCC
46318 CGGGCGCTTCGGGGGTGCCGATCCTTCCC
1 CGGGCGCTTCGGGGGTGCCGATCCTTCCC
46347 CG
1 CG
46349 AGCGTAACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.03, C:0.38, G:0.38, T:0.20
Consensus pattern (29 bp):
CGGGCGCTTCGGGGGTGCCGATCCTTCCC
Found at i:50615 original size:60 final size:61
Alignment explanation
Indices: 50542--50670 Score: 206
Period size: 60 Copynumber: 2.1 Consensus size: 61
50532 ATCACTTGCA
* *
50542 TTGTATTTCAGTTTTGGATTTTCTTGCTCAGATTTTCTTATGATTGTAGTGATCAAAATT-
1 TTGTATTTCAGTTTTGGATTTTCTTGCTCAGATTTTCTCATGATTATAGTGATCAAAATTG
* *
50602 TTGTATTTCAGTTTTGGGTTTTCTTGTTCAGATTTTCTCATGATTATAGTGATCAAAATTG
1 TTGTATTTCAGTTTTGGATTTTCTTGCTCAGATTTTCTCATGATTATAGTGATCAAAATTG
*
50663 TTGCATTT
1 TTGTATTT
50671 GTTTCTTTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
60 56 0.89
61 7 0.11
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (61 bp):
TTGTATTTCAGTTTTGGATTTTCTTGCTCAGATTTTCTCATGATTATAGTGATCAAAATTG
Found at i:51322 original size:13 final size:12
Alignment explanation
Indices: 51289--51315 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
51279 AAATCAAGTG
51289 AAAAAAATGAAA
1 AAAAAAATGAAA
51301 AAAAAAATGAAA
1 AAAAAAATGAAA
51313 AAA
1 AAA
51316 GGAAATGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAAAATGAAA
Found at i:56243 original size:22 final size:24
Alignment explanation
Indices: 56203--56252 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
56193 ATTATTTAAA
*
56203 TTTTCCATTTTTTTATCTTATTCT
1 TTTTCCATTTTCTTATCTTATTCT
* *
56227 TTTTCC-TTTTCTT-TCTTCTTTT
1 TTTTCCATTTTCTTATCTTATTCT
56249 TTTT
1 TTTT
56253 TTTTACCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 11 0.48
23 6 0.26
24 6 0.26
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTCCATTTTCTTATCTTATTCT
Found at i:56245 original size:7 final size:6
Alignment explanation
Indices: 56213--56302 Score: 58
Period size: 6 Copynumber: 14.5 Consensus size: 6
56203 TTTTCCATTT
* * * *
56213 TTTTATC TTATTC TTTTTC CTTTTC TTTCTTC TTTTTTT TTTTTAC CTTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTT-TTC -TTTTTC TTTTT-C TTTTTC
* * *
56265 CTTTTC -CTTTC TTTTT- TTTTTC TTCTTC TTTTCTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT-TC TTT
56303 CACTTGGGCC
Statistics
Matches: 66, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
5 9 0.14
6 37 0.56
7 17 0.26
8 3 0.05
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:56295 original size:27 final size:26
Alignment explanation
Indices: 56226--56303 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 26
56216 TATCTTATTC
*
56226 TTTTTCCTTTTCTTTCTTCTTT-TTTT
1 TTTTTCCTTTTCTTT-TCCTTTCTTTT
56252 TTTTTACCTTTTCCTTTTCCTTTCTTTT
1 TTTTT-CCTTTT-CTTTTCCTTTCTTTT
*
56280 TTTTTTCTTCTTCTTTTCTCTTTC
1 TTTTTCCTT-TTCTTTTC-CTTTC
56304 ACTTGGGCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
26 5 0.11
27 20 0.44
28 20 0.44
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTCCTTTTCTTTTCCTTTCTTTT
Found at i:56296 original size:33 final size:31
Alignment explanation
Indices: 56210--56302 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 31
56200 AAATTTTCCA
*
56210 TTTTTTTATCTTATTCTTTTTCCTTTTCTTTCT
1 TTTTTTTTTCTT-TTC-TTTTCCTTTTCTTTCT
56243 TCTTTTTTTT-TTTTACCTTTTCCTTTTCCTTTCT
1 T-TTTTTTTTCTTTT--CTTTTCCTTTT-CTTTCT
56277 TTTTTTTTTCTTCTTCTTTTCTCTTT
1 TTTTTTTTTCTT-TTCTTTTC-CTTT
56303 CACTTGGGCC
Statistics
Matches: 52, Mismatches: 1, Indels: 13
0.79 0.02 0.20
Matches are distributed among these distances:
32 2 0.04
33 27 0.52
34 21 0.40
35 2 0.04
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.76
Consensus pattern (31 bp):
TTTTTTTTTCTTTTCTTTTCCTTTTCTTTCT
Found at i:60769 original size:6 final size:6
Alignment explanation
Indices: 60743--60781 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
60733 ATTTAATGTA
*
60743 AAAATT AAAAAT AATAA-T AAAATT AAAATT AAAATT AAA
1 AAAATT AAAATT AA-AATT AAAATT AAAATT AAAATT AAA
60782 TATGCAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 2 0.07
6 26 0.87
7 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (6 bp):
AAAATT
Found at i:67524 original size:59 final size:59
Alignment explanation
Indices: 67423--67996 Score: 663
Period size: 59 Copynumber: 9.8 Consensus size: 59
67413 TAAAGCAGGG
** * * * *
67423 TTTTTGAAAC-AAAACTCTCGAAAAGAGACCTCAAACAAGATTTAAAAATGAAACAATA
1 TTTTTGAAACAAAAACTCTCGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
* * *
67481 TTTTTGAAACAAAAAGTCTCGACCAGAGACCTCGAACAGGATTTTGAAATGAAACAAGA
1 TTTTTGAAACAAAAACTCTCGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
* * *
67540 TATTTTGAAACAGAAACTCTCGACTAGAGACCTCAAATAGGATTTTAAAATGAAACAAGA
1 T-TTTTGAAACAAAAACTCTCGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
* * ** * * *
67600 TATTTGAAACAGAAACTCTTAACTAGAGACCTCGAACAGGATTTAAAAACGTAACAAGA
1 TTTTTGAAACAAAAACTCTCGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
* * * * * *
67659 TATTTGAAACGAAAACTCTAGACTAGAGACCTCAAACAAGATTTTGAAATGAAACAAGA
1 TTTTTGAAACAAAAACTCTCGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
*** * *
67718 TTTTT-AATTGATAACTCTCGAC-CGAAGACCTCGAACAGGATTTTAAAATGAAACAAGA
1 TTTTTGAAACAAAAACTCTCGACTAG-AGACCTCGAACAGGATTTTAAAATGAAACAAGA
* * * * *
67776 TTTTTTGAAACAGAAACTCTCGACTAGAGATCTTGAACATGATTTTAAAATGAAACGAGA
1 -TTTTTGAAACAAAAACTCTCGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
* *
67836 TATTTGAAACAGAAACTCTCGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
1 TTTTTGAAACAAAAACTCTCGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
*** * *
67895 TTTTT-AATTGAAAACTCTCGACTAGAGACCTTGAACAGGATTTTAAAATGAAACGAGA
1 TTTTTGAAACAAAAACTCTCGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
**** *
67953 -TTTTGATTTGAAAACTCTCGACCAGAGACCTCGAACAGGATTTT
1 TTTTTGAAACAAAAACTCTCGACTAGAGACCTCGAACAGGATTTT
67997 TGAAATAAGA
Statistics
Matches: 443, Mismatches: 66, Indels: 14
0.85 0.13 0.03
Matches are distributed among these distances:
57 5 0.01
58 136 0.31
59 207 0.47
60 94 0.21
61 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (59 bp):
TTTTTGAAACAAAAACTCTCGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
Found at i:67839 original size:236 final size:235
Alignment explanation
Indices: 67424--67996 Score: 808
Period size: 236 Copynumber: 2.4 Consensus size: 235
67414 AAAGCAGGGT
** * *
67424 TTTTGAAAC-AAAACTCTCGAAAAGAGACCTCAAACAAGATTTAAAAATGAAACAATATTTTTGA
1 TTTTGAAACGAAAACTCTCGACTAGAGACCTCAAACAAGATTTTAAAATGAAACAAGATTTTT-A
*** * *
67488 AACAAAAAGTCTCGACCAGAGACCTCGAACAGGATTTTGAAATGAAACAAGATATTTTGAAACAG
65 ATTGAAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAATGAAACAAGATATTTTGAAACAG
*
67553 AAACTCTCGACTAGAGACCTCAAATAGGATTTTAAAATGAAACAAGATATTTGAAACAGAAACTC
130 AAACTCTCGACTAGAGACCTCAAACAGGATTTTAAAATGAAACAAGATATTTGAAACAGAAACTC
* *
67618 TTAACTAGAGACCTCGAACAGGATTTAAAAACGTAACAAGA
195 TCAACTAGAGACCTCGAACAGGATTTAAAAACGAAACAAGA
* *
67659 TATTTGAAACGAAAACTCTAGACTAGAGACCTCAAACAAGATTTTGAAATGAAACAAGATTTTTA
1 T-TTTGAAACGAAAACTCTCGACTAGAGACCTCAAACAAGATTTTAAAATGAAACAAGATTTTTA
* *
67724 ATTGATAACTCTCGACC-GAAGACCTCGAACAGGATTTTAAAATGAAACAAGATTTTTTGAAACA
65 ATTGAAAACTCTCGACCAG-AGACCTCGAACAGGATTTTAAAATGAAACAAGATATTTTGAAACA
* ** * *
67788 GAAACTCTCGACTAGAGATCTTGAACATGATTTTAAAATGAAACGAGATATTTGAAACAGAAACT
129 GAAACTCTCGACTAGAGACCTCAAACAGGATTTTAAAATGAAACAAGATATTTGAAACAGAAACT
* * *
67853 CTCGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
194 CTCAACTAGAGACCTCGAACAGGATTTAAAAACGAAACAAGA
* ** ** * * * *
67895 TTTTTAATTGAAAACTCTCGACTAGAGACCTTGAACAGGATTTTAAAATGAAACGAGATTTTGAT
1 TTTTGAAACGAAAACTCTCGACTAGAGACCTCAAACAAGATTTTAAAATGAAACAAGATTTTTAA
67960 TTGAAAACTCTCGACCAGAGACCTCGAACAGGATTTT
66 TTGAAAACTCTCGACCAGAGACCTCGAACAGGATTTT
67997 TGAAATAAGA
Statistics
Matches: 298, Mismatches: 36, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
235 89 0.30
236 162 0.54
237 47 0.16
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (235 bp):
TTTTGAAACGAAAACTCTCGACTAGAGACCTCAAACAAGATTTTAAAATGAAACAAGATTTTTAA
TTGAAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAATGAAACAAGATATTTTGAAACAGA
AACTCTCGACTAGAGACCTCAAACAGGATTTTAAAATGAAACAAGATATTTGAAACAGAAACTCT
CAACTAGAGACCTCGAACAGGATTTAAAAACGAAACAAGA
Found at i:68400 original size:115 final size:115
Alignment explanation
Indices: 68198--68428 Score: 453
Period size: 115 Copynumber: 2.0 Consensus size: 115
68188 CTTCTCAAAA
68198 ACACACTTTGGATATGCTTTAATGATGACTCCCTTTTATGAAATATATGCCCCTCATTGAGTACT
1 ACACACTTTGGATATGCTTTAATGATGACTCCCTTTTATGAAATATATGCCCCTCATTGAGTACT
68263 TGCACCACAAGAATCTCATTTTTACTTCCAATGTGAACTTCCCAGATTAT
66 TGCACCACAAGAATCTCATTTTTACTTCCAATGTGAACTTCCCAGATTAT
*
68313 ACACACTTTGGATATTCTTTAATGATGACTCCCTTTTATGAAATATATGCCCCTCATTGAGTACT
1 ACACACTTTGGATATGCTTTAATGATGACTCCCTTTTATGAAATATATGCCCCTCATTGAGTACT
68378 TGCACCACAAGAATCTCATTTTTACTTCCAATGTGAACTTCCCAGATTAT
66 TGCACCACAAGAATCTCATTTTTACTTCCAATGTGAACTTCCCAGATTAT
68428 A
1 A
68429 ATGAAATTAA
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (115 bp):
ACACACTTTGGATATGCTTTAATGATGACTCCCTTTTATGAAATATATGCCCCTCATTGAGTACT
TGCACCACAAGAATCTCATTTTTACTTCCAATGTGAACTTCCCAGATTAT
Found at i:69062 original size:38 final size:38
Alignment explanation
Indices: 69015--69093 Score: 117
Period size: 37 Copynumber: 2.1 Consensus size: 38
69005 TTTCTTTTTA
*
69015 TTTCTCTTTTTCCGACCTTTTTCTATTTTAGG-CCAAGTT
1 TTTCTCTTTTT-CGACCTCTTTCTATTTTAGGTCC-AGTT
69054 TTTC-CTTTTTCGACCTCTTTCTATTTTAGGTCCAGTT
1 TTTCTCTTTTTCGACCTCTTTCTATTTTAGGTCCAGTT
69091 TTT
1 TTT
69094 TTCCCTTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
37 26 0.68
38 8 0.21
39 4 0.11
ACGTcount: A:0.11, C:0.23, G:0.10, T:0.56
Consensus pattern (38 bp):
TTTCTCTTTTTCGACCTCTTTCTATTTTAGGTCCAGTT
Found at i:74555 original size:9 final size:9
Alignment explanation
Indices: 74541--74571 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
74531 TCTTCTCCAT
74541 AGACCTTGA
1 AGACCTTGA
74550 AGACCTTGA
1 AGACCTTGA
*
74559 AGACTTTGA
1 AGACCTTGA
74568 AGAC
1 AGAC
74572 ATGGAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (9 bp):
AGACCTTGA
Found at i:83091 original size:26 final size:27
Alignment explanation
Indices: 83040--83091 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
83030 TAGATCTTAT
83040 TACATCACCAAATATCTACTTGTCCAG
1 TACATCACCAAATATCTACTTGTCCAG
*
83067 TACATCATCAAATA-CTACTTGTCCA
1 TACATCACCAAATATCTACTTGTCCA
83092 CTACTCCCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.31
Consensus pattern (27 bp):
TACATCACCAAATATCTACTTGTCCAG
Found at i:91123 original size:15 final size:16
Alignment explanation
Indices: 91090--91129 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
91080 TTACTTTGCT
91090 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
91106 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
91121 TTGCTTTCT
1 TTGTTTTCT
91130 TTCAACATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:100596 original size:29 final size:29
Alignment explanation
Indices: 100554--100611 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
100544 CTAAGCAAAT
100554 ATGGGACCAACTTAAACATTAAAAAGGAC
1 ATGGGACCAACTTAAACATTAAAAAGGAC
100583 ATGGGACCAACTTAAACATTAAAAAGGAC
1 ATGGGACCAACTTAAACATTAAAAAGGAC
100612 CAATGACTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (29 bp):
ATGGGACCAACTTAAACATTAAAAAGGAC
Found at i:102509 original size:19 final size:18
Alignment explanation
Indices: 102485--102520 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
102475 TGAAGACTTA
102485 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
102504 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
102521 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:111763 original size:43 final size:41
Alignment explanation
Indices: 111629--111773 Score: 157
Period size: 41 Copynumber: 3.5 Consensus size: 41
111619 CAACTTCAAC
** * **
111629 GTGACAACTTCCAGTGTCAAATACTAAT-TTAATTTACCGGA
1 GTGACAACTTCTGGTGTCAAAGA-TAATATTAATTTACCAAA
* * *
111670 GCGACAACTTCTAGTGTCAAAGATAATATTAATTTACCAAC
1 GTGACAACTTCTGGTGTCAAAGATAATATTAATTTACCAAA
* * *
111711 TTGACAACTTCTGGTGTCAAAGGTAATTTTAATTTTTACCAAA
1 GTGACAACTTCTGGTGTCAAAGATAATATTAA--TTTACCAAA
111754 GTGACAACTTCTGGTGTCAA
1 GTGACAACTTCTGGTGTCAA
111774 TCAAATTTTA
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 57 0.65
43 27 0.31
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (41 bp):
GTGACAACTTCTGGTGTCAAAGATAATATTAATTTACCAAA
Found at i:123631 original size:5 final size:5
Alignment explanation
Indices: 123621--123645 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
123611 GTAGCAAGGC
123621 AGGGG AGGGG AGGGG AGGGG AGGGG
1 AGGGG AGGGG AGGGG AGGGG AGGGG
123646 GCCAATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (5 bp):
AGGGG
Done.