Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020983.1 Corchorus olitorius cultivar O-4 contig21016, 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: 56694
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1860 original size:85 final size:84
Alignment explanation
Indices: 1761--1930 Score: 268
Period size: 85 Copynumber: 2.0 Consensus size: 84
1751 TAATTAAATT
*
1761 AGTAATATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTT
*
1826 TAGTTGAGTAAAACTATAAA
66 T-GTTGACTAAAACTATAAA
* * *
1846 AGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTATATTTAATTAAATAAAAATAGAGTTTT
1 AGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTT
* *
1911 TTTTTACTAAAACTATAAA
66 TGTTGACTAAAACTATAAA
1930 A
1 A
1931 ATTTAAGCAA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
84 16 0.21
85 62 0.79
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (84 bp):
AGTAAAATCGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTT
TGTTGACTAAAACTATAAA
Found at i:5782 original size:11 final size:11
Alignment explanation
Indices: 5766--5800 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5756 TTTTTCTGTT
5766 TTTTGTTTTTG
1 TTTTGTTTTTG
*
5777 TTTTGTTTTCG
1 TTTTGTTTTTG
*
5788 TTTTGATTTTG
1 TTTTGTTTTTG
5799 TT
1 TT
5801 GCGCTGTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.03, C:0.03, G:0.17, T:0.77
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:6890 original size:126 final size:126
Alignment explanation
Indices: 6665--6916 Score: 495
Period size: 126 Copynumber: 2.0 Consensus size: 126
6655 TTTACGTTGG
6665 GATTTCTGCTGCAATGAGTAAGTTGATTGAGCCAAGATTATGTCTATCTTTATGGTCATTTCCTA
1 GATTTCTGCTGCAATGAGTAAGTTGATTGAGCCAAGATTATGTCTATCTTTATGGTCATTTCCTA
6730 TGCTTTTTGGTATTTTTATGTGTGGTTATGCTCTATTTTGCAAGTATTTGTGATTTTAGGT
66 TGCTTTTTGGTATTTTTATGTGTGGTTATGCTCTATTTTGCAAGTATTTGTGATTTTAGGT
*
6791 GATTTCTGTTGCAATGAGTAAGTTGATTGAGCCAAGATTATGTCTATCTTTATGGTCATTTCCTA
1 GATTTCTGCTGCAATGAGTAAGTTGATTGAGCCAAGATTATGTCTATCTTTATGGTCATTTCCTA
6856 TGCTTTTTGGTATTTTTATGTGTGGTTATGCTCTATTTTGCAAGTATTTGTGATTTTAGGT
66 TGCTTTTTGGTATTTTTATGTGTGGTTATGCTCTATTTTGCAAGTATTTGTGATTTTAGGT
6917 CTTGAAGAGA
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 125 1.00
ACGTcount: A:0.20, C:0.11, G:0.21, T:0.48
Consensus pattern (126 bp):
GATTTCTGCTGCAATGAGTAAGTTGATTGAGCCAAGATTATGTCTATCTTTATGGTCATTTCCTA
TGCTTTTTGGTATTTTTATGTGTGGTTATGCTCTATTTTGCAAGTATTTGTGATTTTAGGT
Found at i:12270 original size:30 final size:30
Alignment explanation
Indices: 12201--12323 Score: 174
Period size: 30 Copynumber: 4.1 Consensus size: 30
12191 AAAAAACTTA
* *
12201 AACAAGCCTCTAATTGAAACAATCACACAT
1 AACAAGCCTCAAATTGAAACAATCAAACAT
*
12231 AATCAAGCCTCAAATTGTAACAATCAAACAT
1 AA-CAAGCCTCAAATTGAAACAATCAAACAT
*
12262 AACAAGCCTCAAATTGTAACAATCAAACAT
1 AACAAGCCTCAAATTGAAACAATCAAACAT
* * *
12292 TACAAGCCTCAAACTGAAACAAACAAACAT
1 AACAAGCCTCAAATTGAAACAATCAAACAT
12322 AA
1 AA
12324 TCAGCCCCCA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
30 57 0.68
31 27 0.32
ACGTcount: A:0.50, C:0.24, G:0.07, T:0.19
Consensus pattern (30 bp):
AACAAGCCTCAAATTGAAACAATCAAACAT
Found at i:12283 original size:17 final size:17
Alignment explanation
Indices: 12234--12283 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
12224 CACACATAAT
12234 CAAGCCTCAAATTGTAA
1 CAAGCCTCAAATTGTAA
**
12251 CAA---TCAAA-CATAA
1 CAAGCCTCAAATTGTAA
12264 CAAGCCTCAAATTGTAA
1 CAAGCCTCAAATTGTAA
12281 CAA
1 CAA
12284 TCAAACATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
13 6 0.24
14 5 0.20
16 5 0.20
17 9 0.36
ACGTcount: A:0.48, C:0.24, G:0.08, T:0.20
Consensus pattern (17 bp):
CAAGCCTCAAATTGTAA
Found at i:15092 original size:51 final size:50
Alignment explanation
Indices: 15033--15307 Score: 322
Period size: 50 Copynumber: 5.5 Consensus size: 50
15023 GGTCAGCTTC
* * * *
15033 TTCGAACTGTCTTCCGATTCAATCAT-AAAGGATCGTCTTCCGATCAACTTT
1 TTCGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGAT-TA-TCT
* * * * * *
15084 TTCAAACTGTCTTCCAATTCAATCTTAGAAGGACCATCTTCTGCTTATCT
1 TTCGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGATTATCT
* *
15134 TTCGAACTGTCCTCCAATTCAATCTTAAAAGGA-CTGTCTTCCGCTTATCT
1 TTCGAACTGTCTTCCAATTCAATCTTAAAAGGATC-GTCTTCCGATTATCT
* * *
15184 TT-GAATTGTCTTCCAATTCAATTTTAAAAGGATCGTCTTCCGATTATCC
1 TTCGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGATTATCT
* * *
15233 TTCGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCTGCTTATCC
1 TTCGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGATTATCT
* *
15283 TTCGAATTGTCTTCCAATTCCATCT
1 TTCGAACTGTCTTCCAATTCAATCT
15308 CGGATGAAGT
Statistics
Matches: 194, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
49 43 0.22
50 114 0.59
51 24 0.12
52 13 0.07
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (50 bp):
TTCGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGATTATCT
Found at i:15215 original size:99 final size:100
Alignment explanation
Indices: 15032--15307 Score: 324
Period size: 99 Copynumber: 2.8 Consensus size: 100
15022 CGGTCAGCTT
* * * * * ** * *
15032 CTTCGAACTGTCTTCCGATTCAATCAT-AAAGGATCGTCTTCCGATCAACTTTTTCAAACTGTCT
1 CTTCGAACTGTCCTCCAATTCAATCTTAAAAGGATCGTCTTCCGCT-TA-TCCTTCGAATTGTCT
* * *
15096 TCCAATTCAATCTTAGAAGGACCATCTTCTGCTTATC
64 TCCAATTCAATCTTAAAAGGACCATCTTCCGATTATC
* *
15133 TTTCGAACTGTCCTCCAATTCAATCTTAAAAGGA-CTGTCTTCCGCTTAT-CTTTGAATTGTCTT
1 CTTCGAACTGTCCTCCAATTCAATCTTAAAAGGATC-GTCTTCCGCTTATCCTTCGAATTGTCTT
* * *
15196 CCAATTCAATTTTAAAAGGATCGTCTTCCGATTATC
65 CCAATTCAATCTTAAAAGGACCATCTTCCGATTATC
* *
15232 CTTCGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCTGCTTATCCTTCGAATTGTCTTC
1 CTTCGAACTGTCCTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATCCTTCGAATTGTCTTC
*
15297 CAATTCCATCT
66 CAATTCAATCT
15308 CGGATGAAGT
Statistics
Matches: 149, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
99 84 0.56
100 25 0.17
101 25 0.17
102 15 0.10
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.38
Consensus pattern (100 bp):
CTTCGAACTGTCCTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATCCTTCGAATTGTCTTC
CAATTCAATCTTAAAAGGACCATCTTCCGATTATC
Found at i:15265 original size:149 final size:150
Alignment explanation
Indices: 15031--15307 Score: 387
Period size: 149 Copynumber: 1.9 Consensus size: 150
15021 CCGGTCAGCT
* **
15031 TCTTCGAACTGTCTTCCGATTCAATCATAAAGGATCGTCTTCCGATCAACTTTTTCAAACTGTCT
1 TCTTCGAACTGTCTTCCAATTCAATCATAAAGGATCGTCTTCCGATCAACTCCTTCAAACTGTCT
* *
15096 TCCAATTCAATCTTAGAAGGACCATCTTCTGCTTATCTTTCGAACTGTCCTCCAATTCAATCTTA
66 TCCAATTCAATCTTAAAAGGACCATCTTCTGCTTATCCTTCGAACTGTCCTCCAATTCAATCTTA
15161 AAAGGACTGTCTTCCGCTTA
131 AAAGGACTGTCTTCCGCTTA
* * ** * *
15181 TCTTTGAATTGTCTTCCAATTCAATTTTAAAAGGATCGTCTTCCGAT-TA-TCCTTCGAACTGTC
1 TCTTCGAACTGTCTTCCAATTCAATCAT-AAAGGATCGTCTTCCGATCAACTCCTTCAAACTGTC
* * * * *
15244 TTCCAATTCAATCTTAAAAGGATCGTCTTCTGCTTATCCTTCGAATTGTCTTCCAATTCCATCT
65 TTCCAATTCAATCTTAAAAGGACCATCTTCTGCTTATCCTTCGAACTGTCCTCCAATTCAATCT
15308 CGGATGAAGT
Statistics
Matches: 110, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
149 68 0.62
150 24 0.22
151 18 0.16
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.38
Consensus pattern (150 bp):
TCTTCGAACTGTCTTCCAATTCAATCATAAAGGATCGTCTTCCGATCAACTCCTTCAAACTGTCT
TCCAATTCAATCTTAAAAGGACCATCTTCTGCTTATCCTTCGAACTGTCCTCCAATTCAATCTTA
AAAGGACTGTCTTCCGCTTA
Found at i:16371 original size:15 final size:15
Alignment explanation
Indices: 16337--16374 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
16327 AGGCTTAGTG
*
16337 TTTTTCTTTCTTTTC
1 TTTTTTTTTCTTTTC
16352 TTTTTTTTTCTTTT-
1 TTTTTTTTTCTTTTC
16366 TATTTTTTT
1 T-TTTTTTT
16375 AGGCATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTCTTTTC
Found at i:23545 original size:15 final size:15
Alignment explanation
Indices: 23525--23556 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
23515 GATTCTTAAG
*
23525 ATATACATGTAGTTA
1 ATATACAGGTAGTTA
23540 ATATACAGGTAGTTA
1 ATATACAGGTAGTTA
23555 AT
1 AT
23557 GAATAATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (15 bp):
ATATACAGGTAGTTA
Found at i:23883 original size:20 final size:20
Alignment explanation
Indices: 23858--23900 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
23848 CTCAGAATCA
23858 GAATCAGAATAAAACGAAAT
1 GAATCAGAATAAAACGAAAT
23878 GAATCAGAATAAAACGAAAT
1 GAATCAGAATAAAACGAAAT
23898 GAA
1 GAA
23901 GTGGTCTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.60, C:0.09, G:0.16, T:0.14
Consensus pattern (20 bp):
GAATCAGAATAAAACGAAAT
Found at i:26376 original size:141 final size:141
Alignment explanation
Indices: 25886--26776 Score: 1067
Period size: 141 Copynumber: 6.2 Consensus size: 141
25876 TCTCTACTCA
* * *
25886 GAGTTTGCGTTTGTAAGACCTCTGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * *
25951 CCTCCGGGTATCATCTCATTTCATCAAATTT-TTAATCAAAGTTGCGTTTAAGTTTAAAAAAAAA
66 CCTCCGGGTATCACCTCATTTCATC-AATTTGTTAATCAAAGCTGCGTTTAAGTTT--CAAAAAA
26015 CCTTGCTCAAGGTC
128 CCTTGCTCAAGGTC
* * * *
26029 GAGTTTGCATTTGTAAGACCTCTGGGCAAGACTTCAGAAACCTTCGGGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * *
26094 CCTCTGGGTATCATCC-CATTTCATCAAGTTT-TTAATCAAAGTTGCATTTAAGTTTCAAAATCA
66 CCTCCGGGTATCA-CCTCATTTCATCAA-TTTGTTAATCAAAGCTGCGTTTAAGTTTC--AA--A
*
26157 AAACCTTGCTCAAAGTC
125 AAACCTTGCTCAAGGTC
* * *
26174 GAGTTCGCATTTGTAAAACCTCCGGGCACGATTTCATAAACCTCCGGGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * *
26239 CCTCCGGGTATCACCTTACTTCATCAATTTGTTAATCAAAGCTGCGTTTAAATTTCAAAAAACCT
66 CCTCCGGGTATCACCTCATTTCATCAATTTGTTAATCAAAGCTGCGTTTAAGTTTCAAAAAACCT
26304 TGCTCAAGGTC
131 TGCTCAAGGTC
* * * * * *
26315 GAGTTTGCATTTGTAAAACCTCCGGGCACGATTTTAGAAACATGCGGGTACTAATTTTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * * *
26380 CCTCTGGGTATCACCTTACTTCATCAATTTGTTAATCAAAGCCGCGTTTAAGTTTCAAAAAACCT
66 CCTCCGGGTATCACCTCATTTCATCAATTTGTTAATCAAAGCTGCGTTTAAGTTTCAAAAAACCT
*
26445 TTCTCAAGGTC
131 TGCTCAAGGTC
* *
26456 GAGTTTGCATTTGTAAGACCTCCGGGCACGACTTCAGAAACCTCCAGGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* *
26521 CCTCCGGGTATCACCTCATTTCATCAAGTTGTTAATCGAAA-CT--GTGTAAGTTTCAAAAAAAA
66 CCTCCGGGTATCACCTCATTTCATCAATTTGTTAATC-AAAGCTGCGTTTAAGTTTC-----AAA
*
26583 AAACTTTGCTCAAGGTC
125 AAACCTTGCTCAAGGTC
* * * * * * *
26600 AAGTTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAATCTACGGGTATTAATTCTTATGAAC
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * * ** * *
26665 CCCCCAGGTATCATCTCATTTCATC-ATGTTGTTAATCAAATTTGCGTTTAAATTTCAATAAACC
66 CCTCCGGGTATCACCTCATTTCATCAAT-TTGTTAATCAAAGCTGCGTTTAAGTTTCAAAAAACC
26729 TTGCTCAAGGTCTTTACTC
130 TTGCTCAAGG-------TC
26748 AGAGTTTGCATTTGTAAGACCTCCGGGCA
1 -GAGTTTGCATTTGTAAGACCTCCGGGCA
26777 TTCCATATTT
Statistics
Matches: 652, Mismatches: 70, Indels: 46
0.85 0.09 0.06
Matches are distributed among these distances:
139 10 0.02
141 254 0.39
142 5 0.01
143 115 0.18
144 112 0.17
145 118 0.18
146 9 0.01
148 2 0.00
149 27 0.04
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (141 bp):
GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
CCTCCGGGTATCACCTCATTTCATCAATTTGTTAATCAAAGCTGCGTTTAAGTTTCAAAAAACCT
TGCTCAAGGTC
Found at i:26737 original size:426 final size:427
Alignment explanation
Indices: 25886--26740 Score: 1182
Period size: 426 Copynumber: 2.0 Consensus size: 427
25876 TCTCTACTCA
* * * * *
25886 GAGTTTGCGTTTGTAAGACCTCTGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAAACCTCCGGGCACAATTTCAGAAACATCCGGGTACTAATTCTGATAAAT
* * **
25951 CCTCCGGGTATCATCTCATTTCATCAAATTTTTAATCAAAGTTGCGTTTAAGTTTAAAAAAAAAC
66 CCTCCGGGTATCACCTCACTTCATCAAATTTTTAATCAAAGCCGCGTTTAAGTTT-AAAAAAAAC
* * *
26016 CTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCTGGGCAAGACTTCAGAAACCTTCGGGTATT
130 CTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCAAGACTTCAGAAACCTCCAGGTATT
* * * *
26081 AATTCTGATAAATCCTCTGGGTATCATCCCATTTCATCAAGTTTTTAATCAAAGTTGCATTTAAG
195 AATTCTGATAAATCCTCCGGGTATCATCCCATTTCATCAAGTTGTTAATCAAAGCTG-ATGTAAG
** * * *
26146 TTTCAAAATCAAAACCTTGCTCAAAGTCGAGTTCGCATTTGTAAAACCTCCGGGCACGATTTCAT
259 TTTCAAAAAAAAAACCTTGCTCAAAGTCAAGTTCGCATTTGTAAAACCTCCGGGCACCATTTCAG
* * * * *
26211 AAACCTCCGGGTATTAATTCTGATAAATCCTCCGGGTATCACCTTACTTCATCAATTTGTTAATC
324 AAACCTACGGGTATTAATTCTGATAAACCCCCCAGGTATCACCTCACTTCATCAATTTGTTAATC
26276 AAAGCTGCGTTTAAATTTCAAAAAACCTTGCTCAAGGTC
389 AAAGCTGCGTTTAAATTTCAAAAAACCTTGCTCAAGGTC
* * * *
26315 GAGTTTGCATTTGTAAAACCTCCGGGCACGATTTTAGAAACATGCGGGTACTAATTTTGATAAAT
1 GAGTTTGCATTTGTAAAACCTCCGGGCACAATTTCAGAAACATCCGGGTACTAATTCTGATAAAT
* * *
26380 CCTCTGGGTATCACCTTACTTCATC-AATTTGTTAATCAAAGCCGCGTTTAAGTTT-CAAAAAAC
66 CCTCCGGGTATCACCTCACTTCATCAAATTT-TTAATCAAAGCCGCGTTTAAGTTTAAAAAAAAC
* *
26443 CTTTCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACGACTTCAGAAACCTCCAGGTATT
130 CTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCAAGACTTCAGAAACCTCCAGGTATT
26508 AATTCTGATAAATCCTCCGGGTATCA-CCTCATTTCATCAAGTTGTTAATCGAAA-CTG-TGTAA
195 AATTCTGATAAATCCTCCGGGTATCATCC-CATTTCATCAAGTTGTTAATC-AAAGCTGATGTAA
* * * *
26570 GTTTCAAAAAAAAAAACTTTGCTCAAGGTCAAGTTTGCATTTGTAAGACCTCCGGGCACCATTTC
258 GTTTC-AAAAAAAAAACCTTGCTCAAAGTCAAGTTCGCATTTGTAAAACCTCCGGGCACCATTTC
* * * * *
26635 AGAAATCTACGGGTATTAATTCTTATGAACCCCCCAGGTATCATCTCATTTCATC-ATGTTGTTA
322 AGAAACCTACGGGTATTAATTCTGATAAACCCCCCAGGTATCACCTCACTTCATCAAT-TTGTTA
** *
26699 ATCAAATTTGCGTTTAAATTTCAATAAACCTTGCTCAAGGTC
386 ATCAAAGCTGCGTTTAAATTTCAAAAAACCTTGCTCAAGGTC
26741 TTTACTCAGA
Statistics
Matches: 374, Mismatches: 47, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
425 11 0.03
426 142 0.38
427 114 0.30
428 8 0.02
429 99 0.26
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (427 bp):
GAGTTTGCATTTGTAAAACCTCCGGGCACAATTTCAGAAACATCCGGGTACTAATTCTGATAAAT
CCTCCGGGTATCACCTCACTTCATCAAATTTTTAATCAAAGCCGCGTTTAAGTTTAAAAAAAACC
TTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCAAGACTTCAGAAACCTCCAGGTATTA
ATTCTGATAAATCCTCCGGGTATCATCCCATTTCATCAAGTTGTTAATCAAAGCTGATGTAAGTT
TCAAAAAAAAAACCTTGCTCAAAGTCAAGTTCGCATTTGTAAAACCTCCGGGCACCATTTCAGAA
ACCTACGGGTATTAATTCTGATAAACCCCCCAGGTATCACCTCACTTCATCAATTTGTTAATCAA
AGCTGCGTTTAAATTTCAAAAAACCTTGCTCAAGGTC
Found at i:26738 original size:285 final size:283
Alignment explanation
Indices: 25886--26776 Score: 1096
Period size: 285 Copynumber: 3.1 Consensus size: 283
25876 TCTCTACTCA
* * *
25886 GAGTTTGCGTTTGTAAGACCTCTGGGCACAATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * *
25951 CCTCCGGGTATCATCTCATTTCATCAAATTTTTAATCAAAGTTGCGTTTAAGTTT-AAAAAAAAA
66 CCTCCGGGTATCACCTCATTTCATCAAATTGTTAATCAAAGCT-CGTTTAAGTTTCAAAAAAAAA
* * * *
26015 CCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCTGGGCAAGACTTCAGAAACCTTCGGGTAT
130 CCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAA-CTACGGGTAT
* * * * *
26080 TAATTCTGATAAATCCTCTGGGTATCATCCCATTTCATCAAGTTTTTAATCAAAGTTGCATTTAA
194 TAATTCTTATAAATCCTCTGGGTATCATCTCATTTCATCATGTTGTTAATCAAAGTTGCGTTTAA
*
26145 GTTTCAAAATCAAAACCTTGCTCAAAGTC
259 GTTTC--AAT--AAACCTTGCTCAAGGTC
* * *
26174 GAGTTCGCATTTGTAAAACCTCCGGGCACGATTTCATAAACCTCCGGGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* * * *
26239 CCTCCGGGTATCACCTTACTTCATCAATTTGTTAATCAAAGCTGCGTTTAAATTTC---AAAAAA
66 CCTCCGGGTATCACCTCATTTCATCAAATTGTTAATCAAAGCT-CGTTTAAGTTTCAAAAAAAAA
* * * *
26301 CCTTGCTCAAGGTCGAGTTTGCATTTGTAAAACCTCCGGGCACGATTTTAGAAACATGCGGGTAC
130 CCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAAC-TACGGGTAT
* * * **
26366 TAATT-TTGATAAATCCTCTGGGTATCACCTTACTTCATCAAT-TTGTTAATCAAAGCCGCGTTT
194 TAATTCTT-ATAAATCCTCTGGGTATCATCTCATTTCATC-ATGTTGTTAATCAAAGTTGCGTTT
* *
26429 AAGTTTCAAAAAACCTTTCTCAAGGTC
257 AAGTTTCAATAAACCTTGCTCAAGGTC
* *
26456 GAGTTTGCATTTGTAAGACCTCCGGGCACGACTTCAGAAACCTCCAGGTATTAATTCTGATAAAT
1 GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
* *
26521 CCTCCGGGTATCACCTCATTTCATCAAGTTGTTAATCGAAA-CT-GTGTAAGTTTCAAAAAAAAA
66 CCTCCGGGTATCACCTCATTTCATCAAATTGTTAATC-AAAGCTCGTTTAAGTTTC--AAAAAAA
* * *
26584 AACTTTGCTCAAGGTCAAGTTTGCATTTGTAAGACCTCCGGGCACCATTTCAGAAATCTACGGGT
128 AACCTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAA-CTACGGGT
* * * ** *
26649 ATTAATTCTTATGAACCCCCCAGGTATCATCTCATTTCATCATGTTGTTAATCAAATTTGCGTTT
192 ATTAATTCTTATAAATCCTCTGGGTATCATCTCATTTCATCATGTTGTTAATCAAAGTTGCGTTT
*
26714 AAATTTCAATAAACCTTGCTCAAGGTCTTTACTC
257 AAGTTTCAATAAACCTTGCTCAAGG-------TC
26748 AGAGTTTGCATTTGTAAGACCTCCGGGCA
1 -GAGTTTGCATTTGTAAGACCTCCGGGCA
26777 TTCCATATTT
Statistics
Matches: 518, Mismatches: 64, Indels: 37
0.84 0.10 0.06
Matches are distributed among these distances:
280 9 0.02
282 111 0.21
283 3 0.01
284 4 0.01
285 132 0.25
286 121 0.23
287 1 0.00
288 107 0.21
292 2 0.00
293 28 0.05
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (283 bp):
GAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACCTCCGGGTATTAATTCTGATAAAT
CCTCCGGGTATCACCTCATTTCATCAAATTGTTAATCAAAGCTCGTTTAAGTTTCAAAAAAAAAC
CTTGCTCAAGGTCGAGTTTGCATTTGTAAGACCTCCGGGCACGATTTCAGAAACTACGGGTATTA
ATTCTTATAAATCCTCTGGGTATCATCTCATTTCATCATGTTGTTAATCAAAGTTGCGTTTAAGT
TTCAATAAACCTTGCTCAAGGTC
Found at i:26866 original size:37 final size:37
Alignment explanation
Indices: 26820--26933 Score: 104
Period size: 37 Copynumber: 3.0 Consensus size: 37
26810 TCAATATGTG
*
26820 TTTTAATCCTGCTCAGGATCATTTTTTTACCAGTCAA
1 TTTTAATCCTGCTCAGGATCATTTCTTTACCAGTCAA
* ** * * ** *
26857 TTTTTATCCTATTCATGATCATTGCTTTATTAGTC-G
1 TTTTAATCCTGCTCAGGATCATTTCTTTACCAGTCAA
*
26893 TTTTCAAAATCCTGCTCAGGATCGTTTCTTTACCAGTCAA
1 TTTT---AATCCTGCTCAGGATCATTTCTTTACCAGTCAA
26933 T
1 T
26934 CAATGTCAAA
Statistics
Matches: 55, Mismatches: 18, Indels: 5
0.71 0.23 0.06
Matches are distributed among these distances:
36 4 0.07
37 27 0.49
39 23 0.42
40 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (37 bp):
TTTTAATCCTGCTCAGGATCATTTCTTTACCAGTCAA
Found at i:26994 original size:40 final size:39
Alignment explanation
Indices: 26939--27037 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 39
26929 TCAATCAATG
* *
26939 TCAAAATCCTATTCAGGATCATTGCTTTATCAT-TTAATT
1 TCAAAATCCCATTCAGGATCATTGCCTTATC-TGTTAATT
*
26978 TCAAAAATCCCATTCAGGATCATTGCCTTATCTGTTGATT
1 TC-AAAATCCCATTCAGGATCATTGCCTTATCTGTTAATT
*
27018 TCAACATCCCATTCAGGATC
1 TCAAAATCCCATTCAGGATC
27038 CTGAGTTAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
39 20 0.37
40 34 0.63
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.37
Consensus pattern (39 bp):
TCAAAATCCCATTCAGGATCATTGCCTTATCTGTTAATT
Found at i:28995 original size:3 final size:3
Alignment explanation
Indices: 28987--29049 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
28977 CCCTGCCTCA
28987 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29035 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
29050 TTCTTAAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:31364 original size:18 final size:20
Alignment explanation
Indices: 31343--31382 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 20
31333 TTAGGTTGAA
*
31343 ATTTTGTTT-AT-TTTTTTT
1 ATTTTGTTTGATATTTTTCT
31361 A-TTTGTTTGATATTTTTCT
1 ATTTTGTTTGATATTTTTCT
31380 ATT
1 ATT
31383 AAACCTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 7 0.39
20 1 0.06
ACGTcount: A:0.15, C:0.03, G:0.07, T:0.75
Consensus pattern (20 bp):
ATTTTGTTTGATATTTTTCT
Found at i:31365 original size:17 final size:19
Alignment explanation
Indices: 31345--31382 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31335 AGGTTGAAAT
*
31345 TTTGTTT-AT-TTTTTTTA
1 TTTGTTTGATATTTTTCTA
31362 TTTGTTTGATATTTTTCTA
1 TTTGTTTGATATTTTTCTA
31381 TT
1 TT
31383 AAACCTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 2 0.11
19 9 0.50
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.76
Consensus pattern (19 bp):
TTTGTTTGATATTTTTCTA
Found at i:33390 original size:30 final size:30
Alignment explanation
Indices: 33321--33465 Score: 193
Period size: 30 Copynumber: 4.8 Consensus size: 30
33311 CCAAAATTGA
* *
33321 AACAAGCCTCCAATTGAAACAATCACACAT
1 AACAAGCCTCAAATTGAAACAATCAAACAT
*
33351 AATCAAGCCTCAAATTGTAACAATCAAACAT
1 AA-CAAGCCTCAAATTGAAACAATCAAACAT
*
33382 AACAAGCCTCAAATTGTAACAATCAAACAT
1 AACAAGCCTCAAATTGAAACAATCAAACAT
*
33412 AACAAGCCTCAAATTGAAACAAACAAACAT
1 AACAAGCCTCAAATTGAAACAATCAAACAT
* *
33442 AATC-AGCCTCCAAATAGCAACAAT
1 AA-CAAGCCT-CAAATTGAAACAAT
33466 TGAAAAAAAA
Statistics
Matches: 104, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
30 65 0.62
31 39 0.38
ACGTcount: A:0.50, C:0.26, G:0.07, T:0.18
Consensus pattern (30 bp):
AACAAGCCTCAAATTGAAACAATCAAACAT
Found at i:33403 original size:17 final size:17
Alignment explanation
Indices: 33354--33433 Score: 59
Period size: 17 Copynumber: 5.2 Consensus size: 17
33344 CACACATAAT
33354 CAAGCCTCAAATTGTAA
1 CAAGCCTCAAATTGTAA
**
33371 CAA---TCAAA-CATAA
1 CAAGCCTCAAATTGTAA
33384 CAAGCCTCAAATTGTAA
1 CAAGCCTCAAATTGTAA
**
33401 CAA---TCAAA-CATAA
1 CAAGCCTCAAATTGTAA
*
33414 CAAGCCTCAAATTGAAA
1 CAAGCCTCAAATTGTAA
33431 CAA
1 CAA
33434 ACAAACATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 16
0.65 0.13 0.23
Matches are distributed among these distances:
13 12 0.26
14 10 0.22
16 10 0.22
17 14 0.30
ACGTcount: A:0.50, C:0.24, G:0.07, T:0.19
Consensus pattern (17 bp):
CAAGCCTCAAATTGTAA
Found at i:33456 original size:61 final size:62
Alignment explanation
Indices: 33321--33465 Score: 199
Period size: 61 Copynumber: 2.4 Consensus size: 62
33311 CCAAAATTGA
* * *
33321 AACAAGCCTCC-AATTGAAACAATCACACATAATCAAGCCTCAAATTGTAACAATCAAACAT
1 AACAAGCCTCCAAATTGAAACAATCAAACATAATCAAGCCTCAAATTGAAACAAACAAACAT
*
33382 AACAAGCCT-CAAATTGTAACAATCAAACATAA-CAAGCCTCAAATTGAAACAAACAAACAT
1 AACAAGCCTCCAAATTGAAACAATCAAACATAATCAAGCCTCAAATTGAAACAAACAAACAT
* *
33442 AATC-AGCCTCCAAATAGCAACAAT
1 AA-CAAGCCTCCAAATTGAAACAAT
33466 TGAAAAAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
60 34 0.45
61 41 0.55
ACGTcount: A:0.50, C:0.26, G:0.07, T:0.18
Consensus pattern (62 bp):
AACAAGCCTCCAAATTGAAACAATCAAACATAATCAAGCCTCAAATTGAAACAAACAAACAT
Found at i:46369 original size:6 final size:6
Alignment explanation
Indices: 46358--46383 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
46348 CGAATATAGC
46358 AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AA
46384 CACAATCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:48379 original size:26 final size:26
Alignment explanation
Indices: 48323--48380 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
48313 TGATAACTAC
*
48323 TAAAATAAATTCTAGTATTATAGTAT
1 TAAATTAAATTCTAGTATTATAGTAT
48349 TAAATTAAATTCTAGTATTATAGTAT
1 TAAATTAAATTCTAGTATTATAGTAT
48375 TAAATT
1 TAAATT
48381 GCTAAAATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (26 bp):
TAAATTAAATTCTAGTATTATAGTAT
Found at i:48878 original size:21 final size:21
Alignment explanation
Indices: 48838--48883 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
48828 AAATAGCGAT
*
48838 TAAAAACAAAAGCAATTAAAC
1 TAAAAACAAAAGCAAGTAAAC
*
48859 TAAAAAC-AAAGCAAAGTAAAT
1 TAAAAACAAAAGC-AAGTAAAC
48880 TAAA
1 TAAA
48884 TCTAAACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.67, C:0.11, G:0.07, T:0.15
Consensus pattern (21 bp):
TAAAAACAAAAGCAAGTAAAC
Found at i:55588 original size:15 final size:17
Alignment explanation
Indices: 55568--55605 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
55558 CGCTCAAATG
55568 TCGGGTC-ATT-TGGGT
1 TCGGGTCAATTCTGGGT
55583 TCGGGTCAATTCTGGGT
1 TCGGGTCAATTCTGGGT
55600 T-GGGTC
1 TCGGGTC
55606 GTTTTCGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.08, C:0.16, G:0.39, T:0.37
Consensus pattern (17 bp):
TCGGGTCAATTCTGGGT
Done.