Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014896.1 Corchorus olitorius cultivar O-4 contig14929, 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: 81953
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:14756 original size:7 final size:7
Alignment explanation
Indices: 14744--14781 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
14734 ACCGACCGCC
14744 TAATATA
1 TAATATA
14751 TAATATA
1 TAATATA
14758 TAATATA
1 TAATATA
*
14765 TATTTATA
1 TA-ATATA
14773 TAATATA
1 TAATATA
14780 TA
1 TA
14782 CAATATAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TAATATA
Found at i:15813 original size:13 final size:13
Alignment explanation
Indices: 15795--15823 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
15785 TGACTTGTGA
15795 GTTGATGATAATT
1 GTTGATGATAATT
15808 GTTGATGATAATT
1 GTTGATGATAATT
15821 GTT
1 GTT
15824 TCAGAATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (13 bp):
GTTGATGATAATT
Found at i:20868 original size:19 final size:20
Alignment explanation
Indices: 20844--20883 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20834 TGAGTTAGAG
20844 TTTAA-TTAATTTAATAATT
1 TTTAATTTAATTTAATAATT
* *
20863 TTTAATTTAGTTTAGTAATT
1 TTTAATTTAATTTAATAATT
20883 T
1 T
20884 AATTTTAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTAATTTAATTTAATAATT
Found at i:21212 original size:35 final size:35
Alignment explanation
Indices: 21184--21668 Score: 316
Period size: 35 Copynumber: 14.0 Consensus size: 35
21174 AGTAAGACCG
**
21184 TAATCAACTTAATTCAAGGTAATTAAGTAAGTCTT
1 TAATCAACTTAATTCAAGGTAATTAAGTAAGTCAA
* * * * *
21219 TAGTCTACTTAATTAAAGGTAATTAGGTAATTCAA
1 TAATCAACTTAATTCAAGGTAATTAAGTAAGTCAA
* **
21254 TAAGT-AACTTGATTC-AGAGTAA-T---TAAGTCTT
1 TAA-TCAACTTAATTCAAG-GTAATTAAGTAAGTCAA
* * * * *
21285 TAGTCTACTTAATTTAGGGTAATTAAGTAATTCAA
1 TAATCAACTTAATTCAAGGTAATTAAGTAAGTCAA
* * * * **
21320 T-TTGCAGCTTAATTCAGGGTAATTAAGTAAATCTT
1 TAAT-CAACTTAATTCAAGGTAATTAAGTAAGTCAA
* * *
21355 TAGTCAACTTAGTTCATGGTAATTAAGTAAGT-AA
1 TAATCAACTTAATTCAAGGTAATTAAGTAAGTCAA
* * **
21389 TTAATCAGCTTAATTCAGGGTAATTTAAGTAAGTCTT
1 -TAATCAACTTAATTCAAGGTAA-TTAAGTAAGTCAA
* * * * *
21426 TAGTCAACTTAATTTAGGGTAATTAAGTAATTCAG
1 TAATCAACTTAATTCAAGGTAATTAAGTAAGTCAA
* * * *
21461 TAGGT-AACTTAATTCAGGGTAATTAAGTAATTCAG
1 TA-ATCAACTTAATTCAAGGTAATTAAGTAAGTCAA
* * * *
21496 TAGTCAACTTAATT-TAGGATAATTAAGGAAATCAA
1 TAATCAACTTAATTCAAGG-TAATTAAGTAAGTCAA
* *
21531 TAAGT-AACTTAATT-AAGGGAGATCAAGTAAGTCAA
1 TAA-TCAACTTAATTCAAGGTA-ATTAAGTAAGTCAA
*
21566 TAAGT-AATTTAATTCAAGGTAATTAAGTAAGTC-A
1 TAA-TCAACTTAATTCAAGGTAATTAAGTAAGTCAA
*
21600 TAATCAACTTAATTCATGGTAATTAAGTAAGT-AA
1 TAATCAACTTAATTCAAGGTAATTAAGTAAGTCAA
* * * * *
21634 TTAATTAGCTTAATTTAGGGTAGTTAAGTAAGTCA
1 -TAATCAACTTAATTCAAGGTAATTAAGTAAGTCA
21669 TATGGCCAAA
Statistics
Matches: 357, Mismatches: 70, Indels: 45
0.76 0.15 0.10
Matches are distributed among these distances:
30 1 0.00
31 18 0.05
32 2 0.01
33 1 0.00
34 39 0.11
35 256 0.72
36 40 0.11
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (35 bp):
TAATCAACTTAATTCAAGGTAATTAAGTAAGTCAA
Found at i:21383 original size:70 final size:70
Alignment explanation
Indices: 21188--21672 Score: 434
Period size: 70 Copynumber: 7.0 Consensus size: 70
21178 AGACCGTAAT
* * * * *
21188 CAACTTAATTCAAGGTAATTAAGTAAGTCTTTAGTCTACTTAATTAAAGGTAATTAGGTAATTCA
1 CAACTTAATTCAGGGTAATTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAGTAATTCA
*
21253 ATAAG
66 ATATG
* * * *
21258 TAACTTGATTCAGAGTAA-T---TAAGTCTTTAGTCTACTTAATTTAGGGTAATTAAGTAATTCA
1 CAACTTAATTCAGGGTAATTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAGTAATTCA
*
21319 ATTTG
66 ATATG
* * * * * *
21324 CAGCTTAATTCAGGGTAATTAAGTAAATCTTTAGTCAACTTAGTTCATGGTAATTAAGTAAGT-A
1 CAACTTAATTCAGGGTAATTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAGTAATTCA
21388 ATTAAT-
66 A-T-ATG
*
21394 CAGCTTAATTCAGGGTAATTTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAGTAATTC
1 CAACTTAATTCAGGGTAA-TTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAGTAATTC
* *
21459 AGTAGG
65 AATATG
* * ** * * *
21465 TAACTTAATTCAGGGTAATTAAGTAATTCAGTAGTCAACTTAATTTAGGATAATTAAGGAAATCA
1 CAACTTAATTCAGGGTAATTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAGTAATTCA
*
21530 ATAAG
66 ATATG
* * * * * * * * *
21535 TAACTTAATTAAGGG-AGATCAAGTAAGTCAATAAGT-AATTTAATTCAAGGTAATTAAGTAAGT
1 CAACTTAATTCAGGGTA-ATTAAGTAAGTC-TTTAGTCAACTTAATTTAGGGTAATTAAGTAATT
21598 C-ATAAT-
64 CAAT-ATG
* ** * * * * *
21604 CAACTTAATTCATGGTAATTAAGTAAGTAATTAATTAGCTTAATTTAGGGTAGTTAAGTAAGTC-
1 CAACTTAATTCAGGGTAATTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAGTAATTCA
21668 ATATG
66 ATATG
21673 GCCAAAAAAA
Statistics
Matches: 339, Mismatches: 61, Indels: 31
0.79 0.14 0.07
Matches are distributed among these distances:
66 56 0.17
67 1 0.00
68 6 0.02
69 53 0.16
70 160 0.47
71 62 0.18
72 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (70 bp):
CAACTTAATTCAGGGTAATTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAGTAATTCA
ATATG
Found at i:21473 original size:141 final size:137
Alignment explanation
Indices: 21189--21629 Score: 439
Period size: 141 Copynumber: 3.2 Consensus size: 137
21179 GACCGTAATC
* * * * *
21189 AACTTAATTCAAGGTAATTAAGTAAGTCTTTAGTCTACTTAATTAAAGGTAATTAGGTAATTCAA
1 AACTTAATTCAGGGTAATTAAGTAAATCTTTAGTCAACTTAATT-AAGGTAATTAAGTAAATCAA
* * *
21254 TAAGTAACTTGATTCAGAGTAA-T---TAAGTCTTTAGTCTACTTAATTTAGGGTAATTAAGTAA
65 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAGTAA
* *
21315 TTCAATTTGC
130 TTC-A-TAGT
* * * *
21325 AGCTTAATTCAGGGTAATTAAGTAAATCTTTAGTCAACTTAGTTCATGGTAATTAAGTAAGT-AA
1 AACTTAATTCAGGGTAATTAAGTAAATCTTTAGTCAACTTAATT-AAGGTAATTAAGTAAATCAA
*
21389 TTAA-TCAGCTTAATTCAGGGTAATTTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAG
65 -TAAGT-AACTTAATTCAGGGTAA-TTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAG
21453 TAATTCAGTAGGT
127 TAATTCA-TA-GT
* ** * *
21466 AACTTAATTCAGGGTAATTAAGTAATTCAGTAGTCAACTTAATTTAGGATAATTAAGGAAATCAA
1 AACTTAATTCAGGGTAATTAAGTAAATCTTTAGTCAACTTAATTAAGG-TAATTAAGTAAATCAA
* * * * * * *
21531 TAAGTAACTTAATTAAGGG-AGATCAAGTAAGTCAATAAGT-AATTTAATTCAAGGTAATTAAGT
65 TAAGTAACTTAATTCAGGGTA-ATTAAGTAAGTC-TTTAGTCAACTTAATTTAGGGTAATTAAGT
* *
21594 AAGTCATAAT
128 AATTCATAGT
*
21604 CAACTTAATTCATGGTAATTAAGTAA
1 -AACTTAATTCAGGGTAATTAAGTAA
21630 GTAATTAATT
Statistics
Matches: 255, Mismatches: 36, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
135 3 0.01
136 70 0.27
138 2 0.01
139 26 0.10
140 40 0.16
141 111 0.44
142 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (137 bp):
AACTTAATTCAGGGTAATTAAGTAAATCTTTAGTCAACTTAATTAAGGTAATTAAGTAAATCAAT
AAGTAACTTAATTCAGGGTAATTAAGTAAGTCTTTAGTCAACTTAATTTAGGGTAATTAAGTAAT
TCATAGT
Found at i:21493 original size:18 final size:18
Alignment explanation
Indices: 21435--21495 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
21425 TTAGTCAACT
*
21435 TAATTTAGGGTAATTAAG
1 TAATTCAGGGTAATTAAG
*
21453 TAATTCAGTAGGTAACT---
1 TAATTCAG--GGTAATTAAG
21470 TAATTCAGGGTAATTAAG
1 TAATTCAGGGTAATTAAG
21488 TAATTCAG
1 TAATTCAG
21496 TAGTCAACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
15 6 0.17
17 8 0.23
18 15 0.43
20 6 0.17
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.36
Consensus pattern (18 bp):
TAATTCAGGGTAATTAAG
Found at i:21914 original size:59 final size:58
Alignment explanation
Indices: 21819--21960 Score: 187
Period size: 59 Copynumber: 2.4 Consensus size: 58
21809 AATTAAGTTA
* * *
21819 TAATTAAGTTAGTTAAGAAGTAAAAAGGGTAATCAGTTATAGTTGGCTTAATTAAGGG
1 TAATTAAGTTAATTAAGAAGTAAAAAGGGTAATCAGTAATAATTGGCTTAATTAAGGG
* * *
21877 TAATTAAGTTAAATAAGAAGTTGAAAA-GGTAAGTCAGTAATAATTGGCTTAATTTAGGG
1 TAATTAAGTTAATTAAGAAG-TAAAAAGGGTAA-TCAGTAATAATTGGCTTAATTAAGGG
* *
21936 TAATTGAGTTAATTAAGAAATAAAA
1 TAATTAAGTTAATTAAGAAGTAAAA
21961 GGTTTCAGAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
58 27 0.38
59 45 0.62
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (58 bp):
TAATTAAGTTAATTAAGAAGTAAAAAGGGTAATCAGTAATAATTGGCTTAATTAAGGG
Found at i:24174 original size:41 final size:41
Alignment explanation
Indices: 24003--24175 Score: 131
Period size: 40 Copynumber: 4.3 Consensus size: 41
23993 TAAGTTTCTA
* * **
24003 AAATCAGGGGCCAAATTGCATTAAACAATGTATAGCATCCT
1 AAATCAGGGACAAAATTGCATTAAACAAAATATAGCATCCT
* *
24044 AAATCAGGGACAAAATTGCATTAAATAGTAAATA-A--ATCTT
1 AAATCAGGGACAAAATTGCATTAAACA--AAATATAGCATCCT
* * *** * **
24084 GAATCAGGGACTAAGCCGCA-TAAATCAAAA-ACAAAATCCT
1 AAATCAGGGACAAAATTGCATTAAA-CAAAATATAGCATCCT
* *
24124 AGATCAGGGACAAAATTGCATCAAACAAAATATAGCATCCT
1 AAATCAGGGACAAAATTGCATTAAACAAAATATAGCATCCT
*
24165 AAATTAGGGAC
1 AAATCAGGGAC
24176 CATGTTGAAC
Statistics
Matches: 99, Mismatches: 25, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
37 1 0.01
38 4 0.04
39 4 0.04
40 43 0.43
41 43 0.43
42 1 0.01
43 3 0.03
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.21
Consensus pattern (41 bp):
AAATCAGGGACAAAATTGCATTAAACAAAATATAGCATCCT
Found at i:24718 original size:10 final size:10
Alignment explanation
Indices: 24703--24727 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
24693 AGAAGAACCG
24703 AGGGATCCAT
1 AGGGATCCAT
24713 AGGGATCCAT
1 AGGGATCCAT
24723 AGGGA
1 AGGGA
24728 AAAAGAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (10 bp):
AGGGATCCAT
Found at i:26436 original size:43 final size:43
Alignment explanation
Indices: 26370--26463 Score: 161
Period size: 43 Copynumber: 2.2 Consensus size: 43
26360 TAAATAAAAC
* * *
26370 GCAACAATACTAAATTACTAAATGAAGTTAAGCCATGACATAT
1 GCAAAAATACTAAATTACTAAATGAAGTTAAGCCATAAAATAT
26413 GCAAAAATACTAAATTACTAAATGAAGTTAAGCCATAAAATAT
1 GCAAAAATACTAAATTACTAAATGAAGTTAAGCCATAAAATAT
26456 GCAAAAAT
1 GCAAAAAT
26464 GCCAAAGGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (43 bp):
GCAAAAATACTAAATTACTAAATGAAGTTAAGCCATAAAATAT
Found at i:26598 original size:27 final size:27
Alignment explanation
Indices: 26560--26617 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
26550 AGTGGACTTA
26560 AAATGACCAAAATACCCCTGAATATAC
1 AAATGACCAAAATACCCCTGAATATAC
* *
26587 AAATGACCAAAATGCCCCTGAATGTAC
1 AAATGACCAAAATACCCCTGAATATAC
26614 AAAT
1 AAAT
26618 TAGGACTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.24, G:0.10, T:0.19
Consensus pattern (27 bp):
AAATGACCAAAATACCCCTGAATATAC
Found at i:26762 original size:10 final size:10
Alignment explanation
Indices: 26747--26772 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
26737 ACCGCCAATT
26747 TCGGTTTCGG
1 TCGGTTTCGG
26757 TCGGTTTCGG
1 TCGGTTTCGG
26767 TCGGTT
1 TCGGTT
26773 ATATTTGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.42
Consensus pattern (10 bp):
TCGGTTTCGG
Found at i:30755 original size:184 final size:183
Alignment explanation
Indices: 30446--30809 Score: 719
Period size: 184 Copynumber: 2.0 Consensus size: 183
30436 ACAGAGCTTT
30446 GAACAATGCCATTTCAATATACTGTTATCACTTGCACTATTTTTAATCATGAAAAATGGTGCACA
1 GAACAATGCCATTTCAATATACTGTTATCACTTGCACTATTTTTAATCATGAAAAATGGTGCACA
30511 CATTTTAACATGTTGAATTGCCTATGCTGAAAATTGAAATCTGGGTAATGCATGGACTATGATAA
66 CATTTTAACATGTTGAATTGCCTATGCTGAAAATTGAAATCTGGGTAATGCATGGACTATGATAA
30576 ACTATAATTCTAATAAACAAAAAAAATAGAATTGTTCTGTTTGGTTTCCAGTAA
131 ACTATAATTCTAATAAAC-AAAAAAATAGAATTGTTCTGTTTGGTTTCCAGTAA
30630 GAACAATGCCATTTCAATATACTGTTATCACTTGCACTATTTTTAATCATGAAAAATGGTGCACA
1 GAACAATGCCATTTCAATATACTGTTATCACTTGCACTATTTTTAATCATGAAAAATGGTGCACA
30695 CATTTTAACATGTTGAATTGCCTATGCTGAAAATTGAAATCTGGGTAATGCATGGACTATGATAA
66 CATTTTAACATGTTGAATTGCCTATGCTGAAAATTGAAATCTGGGTAATGCATGGACTATGATAA
30760 ACTATAATTCTAATAAACAAAAAAATAGAATTGTTCTGTTTGGTTTCCAG
131 ACTATAATTCTAATAAACAAAAAAATAGAATTGTTCTGTTTGGTTTCCAG
30810 GAAAATCAAA
Statistics
Matches: 180, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
183 32 0.18
184 148 0.82
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (183 bp):
GAACAATGCCATTTCAATATACTGTTATCACTTGCACTATTTTTAATCATGAAAAATGGTGCACA
CATTTTAACATGTTGAATTGCCTATGCTGAAAATTGAAATCTGGGTAATGCATGGACTATGATAA
ACTATAATTCTAATAAACAAAAAAATAGAATTGTTCTGTTTGGTTTCCAGTAA
Found at i:31965 original size:27 final size:27
Alignment explanation
Indices: 31913--31965 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
31903 CAGCCCTAGT
* * *
31913 ACAAATGATCAAAATGCCCTTTGGTGC
1 ACAAATGACCAAAATGCCCATGGGTGC
31940 ACAAATGACCAAAATGCCCATGGGTG
1 ACAAATGACCAAAATGCCCATGGGTG
31966 ATCCTAATGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (27 bp):
ACAAATGACCAAAATGCCCATGGGTGC
Found at i:34364 original size:527 final size:526
Alignment explanation
Indices: 33479--34533 Score: 1851
Period size: 527 Copynumber: 2.0 Consensus size: 526
33469 CAGACTTCTC
*
33479 AAGCCCAAGGTTCTGCAGATTTGATGGATGAGGATGATTGTGGTGATGCAATGCAGCTGTTCATG
1 AAGCCCAAGGTTCTGCAGATTTGATGGATGAGGATGATTGTGGTGATGCAATGCAACTGTTCATG
* *
33544 AAACATCAAAGGATAAGTTTGTTTCTATTTAGTCTACTTCAAATTGATTGATATTCTTATTTTGC
66 AAACATCAAAGGATAAGTTTGTTTCCAATTAGTCTACTTCAAATTGATTGATATTCTTATTTTGC
*
33609 TTTCAATAGACTAATGTACTTTTCTCTTTTTCATGTAAGGAATTTGGTTTACAAGCAAACAAGAC
131 TTTCAATAGACTAATGTACTTTTCTCTTTTTCATGTAAGGAACTTGGTTTACAAGCAAACAAGAC
33674 TAAGTTGGACATATACTTGCAAGAGGAAATGAAGCAAGAAGGAGCTGCGTTTGATGTGCTTGCAT
196 TAAGTTGGACATATACTTGCAAGAGGAAATGAAGCAAGAAGGAGCTGCGTTTGATGTGCTTGCAT
* * *
33739 GGTGGAAATTGAATGGTCTAAGGTTCCCCATACTGTCTTGCCTTGCGAAGGATGTGCTTGTTGTT
261 GGTGGAAATTGAATGGTCTAAGGTTCCCCATACTGTCTTGCCTTGAGAAAGATGTGCTTGCTGTT
*
33804 CCAGTCTCAACGGTTGCTTCTGAATCAGCTTTCAGCACTGGTGCTAGAGTGTTTGATGTCGAAGC
326 CCAGTCTCAACGGTTGCTTCTGAATCAGCTTTCAGCACTGGTGCAAGAGTGTTTGATGTCGAAGC
*
33869 AGCCTCAATGTTAAGATGGTTCAAGCTCTAATTTATGATCAAGATTTGTTGAAGGGCTCATGTGA
391 AGCCTCAATGTTAAGATGGTTCAAGCTCTAATCTATGATCAAGATTTGTTGAAGGGCTCATGTGA
*
33934 ATTTGACCCGGAAGCAGAGAGTAATGACCAAACAGAGATGGACGAAGTTTTTCTAGGTAATGATT
456 ATTTGACCCGGAAGCAGAGAGTAATGACCAAACAGAGATGGACGAAGTTTGTCTAGGTAATGATT
33999 ATTAAGA
521 ATT-AGA
* *
34006 AAGCCCAAGGTTCTTCAGATTTGATGGATGAGGATGATTGTGGTGCTGCAATGCAACTGTTCATG
1 AAGCCCAAGGTTCTGCAGATTTGATGGATGAGGATGATTGTGGTGATGCAATGCAACTGTTCATG
* *
34071 AAGCATCAAAGGGTAAGTTTGTTTCCAATTAGTCTACTTCAAATTGATTGATATTCTTATTTTGC
66 AAACATCAAAGGATAAGTTTGTTTCCAATTAGTCTACTTCAAATTGATTGATATTCTTATTTTGC
* *
34136 TGTT-AATAGACTATTGTACTTTTCTCTTTTTCATGTAAGGAACTTGGTTTACAAGCTAACAAGA
131 T-TTCAATAGACTAATGTACTTTTCTCTTTTTCATGTAAGGAACTTGGTTTACAAGCAAACAAGA
*
34200 CTGAGTTGGACATATACTTGCAAGAGGAAATGAAGCAAGAAGGAGCTGCGTTTGATGTGCTTGCA
195 CTAAGTTGGACATATACTTGCAAGAGGAAATGAAGCAAGAAGGAGCTGCGTTTGATGTGCTTGCA
34265 TGGTGGAAATTGAATGGTCTAAGGTTCCCCATACTGTCTTGCCTTGAGAAAGATGTGCTTGCTGT
260 TGGTGGAAATTGAATGGTCTAAGGTTCCCCATACTGTCTTGCCTTGAGAAAGATGTGCTTGCTGT
*
34330 TCCAGTCTCAACGGTTGCTTCTGAATCAGCTTTCAGCACTGGTGGAAGAGTGTTTGATGTCGAAG
325 TCCAGTCTCAACGGTTGCTTCTGAATCAGCTTTCAGCACTGGTGCAAGAGTGTTTGATGTCGAAG
* * *
34395 CAGCCTTAATGTTAAGATGGTTCAAGCTCTAATCTGTGGTCAAGATTTGTTGAAGGGCTCATGTG
390 CAGCCTCAATGTTAAGATGGTTCAAGCTCTAATCTATGATCAAGATTTGTTGAAGGGCTCATGTG
* * ***
34460 AATTTGACCCGGAAGCAGATATTAATGACCAAACAGAGATGTTTGAAGTTTGTCTAGGTAATGAT
455 AATTTGACCCGGAAGCAGAGAGTAATGACCAAACAGAGATGGACGAAGTTTGTCTAGGTAATGAT
34525 TATTAGA
520 TATTAGA
34532 AA
1 AA
34534 CCCTTGCAAT
Statistics
Matches: 501, Mismatches: 26, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
526 5 0.01
527 494 0.99
528 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (526 bp):
AAGCCCAAGGTTCTGCAGATTTGATGGATGAGGATGATTGTGGTGATGCAATGCAACTGTTCATG
AAACATCAAAGGATAAGTTTGTTTCCAATTAGTCTACTTCAAATTGATTGATATTCTTATTTTGC
TTTCAATAGACTAATGTACTTTTCTCTTTTTCATGTAAGGAACTTGGTTTACAAGCAAACAAGAC
TAAGTTGGACATATACTTGCAAGAGGAAATGAAGCAAGAAGGAGCTGCGTTTGATGTGCTTGCAT
GGTGGAAATTGAATGGTCTAAGGTTCCCCATACTGTCTTGCCTTGAGAAAGATGTGCTTGCTGTT
CCAGTCTCAACGGTTGCTTCTGAATCAGCTTTCAGCACTGGTGCAAGAGTGTTTGATGTCGAAGC
AGCCTCAATGTTAAGATGGTTCAAGCTCTAATCTATGATCAAGATTTGTTGAAGGGCTCATGTGA
ATTTGACCCGGAAGCAGAGAGTAATGACCAAACAGAGATGGACGAAGTTTGTCTAGGTAATGATT
ATTAGA
Found at i:35134 original size:643 final size:644
Alignment explanation
Indices: 34006--35240 Score: 2125
Period size: 643 Copynumber: 1.9 Consensus size: 644
33996 ATTATTAAGA
* * *
34006 AAGCCCAAGGTTCTTCAGATTTGATGGATGAGGATGATTGTGGTGCTGCAATGCAACTGTTCATG
1 AAGCCCAAGGTTCTGCAGATTTGATGGATGAGGATGATTGTGGTGATGCAATGCAACTATTCATG
34071 AAGCATCAAAGGGTAAGTTTGTTTCCAATTAGTCTACTTCAAATTGATTGATATTCTTATTTTGC
66 AAGCATCAAAGGGTAAGTTTGTTTCCAATTAGTCTACTTCAAATTGATTGATATTCTTATTTTGC
* *
34136 TGTTAATAGACTATTGTACTTTTCTCTTTTTCATGTAAGGAACTTGGTTTACAAGCTAACAAGAC
131 TGTTAATAGACTAATGTACTTTTCTCTTTTTCATGTAAGGAACTTGGTTTACAAGCAAACAAGAC
34201 TGAGTTGGACATATACTTGCAAGAGGAAATGAAGCAAGAAGGAGCTGCGTTTGATGTGCTTGCAT
196 TGAGTTGGACATATACTTGCAAGAGGAAATGAAGCAAGAAGGAGCTGCGTTTGATGTGCTTGCAT
34266 GGTGGAAATTGAATGGTCTAAGGTTCCCCATACTGTCTTGCCTTGAGAAAGATGTGCTTGCTGTT
261 GGTGGAAATTGAATGGTCTAAGGTTCCCCATACTGTCTTGCCTTGAGAAAGATGTGCTTGCTGTT
34331 CCAGTCTCAACGGTTGCTTCTGAATCAGCTTTCAGCACTGGTGGAAGAGTGTTTGATGTCGAAGC
326 CCAGTCTCAACGGTTGCTTCTGAATCAGCTTTCAGCACTGGTGGAAGAGTGTTTGATGTCGAAGC
* * *
34396 AGCCTTAATGTTAAGATGGTTCAAGCTCTAATCTGTGGTCAAGATTTGTTGAAGGGCTCATGTGA
391 AGCCTCAATGTTAAGATGGTTCAAGCTCTAATCTGTGGTCAAGATTGGTTGAAGAGCTCATGTGA
* * * * ***
34461 ATTTGACCCGGAAGCAGATATTAATGACCAAACAGAGATGTTTGAAGTTTGTCTAGGTAATGATT
456 ATTCGAACCGGAAGCAGAGAGTAATGACCAAACAGAGATGGACGAAGTTTGTCTAGGTAATGATT
* **
34526 ATT-AGAAACCCTTGCAATTTATTTATGTCAATTTCATTTGGTTATTTTAAG-ATTTCATGAGTT
521 ATTAAG-AACCCTTGCAATTTATTTATGTCAATTTCATTAGGTTATTTTAAGTATTTCACAAGTT
34589 TTAACTTTATAGGAGAGCCCAAGGATCTGAAAAAAGGGTGTGATGCTTCACAAACTTCTC
585 TTAACTTTATAGGAGAGCCCAAGGATCTGAAAAAAGGGTGTGATGCTTCACAAACTTCTC
* * *
34649 AAGCCGAAGGTTCTGCAGATTTGATGGATGAGGATGATTGTGTTGATGCAATGCAGCTATTCATG
1 AAGCCCAAGGTTCTGCAGATTTGATGGATGAGGATGATTGTGGTGATGCAATGCAACTATTCATG
* *
34714 AAGCATCAAAGGGTAAGTTTGTTTCTATTTAGTCTACTTCAAATTGATTGATATTCTTATTTTGC
66 AAGCATCAAAGGGTAAGTTTGTTTCCAATTAGTCTACTTCAAATTGATTGATATTCTTATTTTGC
* *
34779 T-TTCAATAGACTAATGTACTTTTCTCTTTTTCTTGTAAGGAATTTGGTTTACAAGCAAACAAGA
131 TGTT-AATAGACTAATGTACTTTTCTCTTTTTCATGTAAGGAACTTGGTTTACAAGCAAACAAGA
*
34843 TTGAGTTGGACATATACTTGCAAGAGGAAATGAAGCAAGAAGGAGCTGCGTTTGATGTGCTTGCA
195 CTGAGTTGGACATATACTTGCAAGAGGAAATGAAGCAAGAAGGAGCTGCGTTTGATGTGCTTGCA
* *
34908 TGGTGGAAATTGAATGGTCTAAGGTTCCCCATACTGTCTTGCCTTGCGAAGGATGTGCTTGCTGT
260 TGGTGGAAATTGAATGGTCTAAGGTTCCCCATACTGTCTTGCCTTGAGAAAGATGTGCTTGCTGT
*
34973 TCCAGTCTCAACGGTTGCTTCTGAATCAGCTTTCAGTACTGGTGGAAGAGTGTTTGATGTCGAAG
325 TCCAGTCTCAACGGTTGCTTCTGAATCAGCTTTCAGCACTGGTGGAAGAGTGTTTGATGTCGAAG
*
35038 CAGCCTCAATGTTAAGATGGTTCATGCTCTAATCTGTGGTCAAGATTGGTTGAAGAGCTCATGTG
390 CAGCCTCAATGTTAAGATGGTTCAAGCTCTAATCTGTGGTCAAGATTGGTTGAAGAGCTCATGTG
* *
35103 AATTCGAACCGGAAGCAGAGAGTATTGACCAAACAGAGATGGACGAAGTTTGTGTAGGTAATGAT
455 AATTCGAACCGGAAGCAGAGAGTAATGACCAAACAGAGATGGACGAAGTTTGTCTAGGTAATGAT
* *
35168 TATTAAGAACCCTTGCAATTTATTTATGTCAATTTCATTAGGTTATTTTCAGTTTTTCACAAGTT
520 TATTAAGAACCCTTGCAATTTATTTATGTCAATTTCATTAGGTTATTTTAAGTATTTCACAAGTT
35233 TTAACTTT
585 TTAACTTT
35241 GTTTTTTTTT
Statistics
Matches: 555, Mismatches: 34, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
642 2 0.00
643 534 0.96
644 19 0.03
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (644 bp):
AAGCCCAAGGTTCTGCAGATTTGATGGATGAGGATGATTGTGGTGATGCAATGCAACTATTCATG
AAGCATCAAAGGGTAAGTTTGTTTCCAATTAGTCTACTTCAAATTGATTGATATTCTTATTTTGC
TGTTAATAGACTAATGTACTTTTCTCTTTTTCATGTAAGGAACTTGGTTTACAAGCAAACAAGAC
TGAGTTGGACATATACTTGCAAGAGGAAATGAAGCAAGAAGGAGCTGCGTTTGATGTGCTTGCAT
GGTGGAAATTGAATGGTCTAAGGTTCCCCATACTGTCTTGCCTTGAGAAAGATGTGCTTGCTGTT
CCAGTCTCAACGGTTGCTTCTGAATCAGCTTTCAGCACTGGTGGAAGAGTGTTTGATGTCGAAGC
AGCCTCAATGTTAAGATGGTTCAAGCTCTAATCTGTGGTCAAGATTGGTTGAAGAGCTCATGTGA
ATTCGAACCGGAAGCAGAGAGTAATGACCAAACAGAGATGGACGAAGTTTGTCTAGGTAATGATT
ATTAAGAACCCTTGCAATTTATTTATGTCAATTTCATTAGGTTATTTTAAGTATTTCACAAGTTT
TAACTTTATAGGAGAGCCCAAGGATCTGAAAAAAGGGTGTGATGCTTCACAAACTTCTC
Found at i:36203 original size:24 final size:24
Alignment explanation
Indices: 36185--36232 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
36175 TGAATTGTGG
36185 ATAGGATGATATTAAGAATAATAA
1 ATAGGATGATATTAAGAATAATAA
*
36209 ATAGGATGATATTAAGAAGAATAA
1 ATAGGATGATATTAAGAATAATAA
36233 GCTAGGTTGT
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:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (24 bp):
ATAGGATGATATTAAGAATAATAA
Found at i:48391 original size:13 final size:13
Alignment explanation
Indices: 48366--48399 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
48356 ATTTCATTAA
48366 GAAAAATGC-TTT
1 GAAAAATGCTTTT
48378 GAAAAATGCTTTT
1 GAAAAATGCTTTT
48391 G-AAAATGCT
1 GAAAAATGCT
48400 CCCATGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (13 bp):
GAAAAATGCTTTT
Found at i:67671 original size:89 final size:89
Alignment explanation
Indices: 67561--67737 Score: 264
Period size: 89 Copynumber: 2.0 Consensus size: 89
67551 CTTGCTTAGA
* *
67561 ACAATAAGAGTACTTCCAACCTCTACAAGGAGAAAAATATTCTACTATTTGGATGGAGCATTTAG
1 ACAATAAGAGTACTTCCAACCTCTACAAGGAGAAAAATATTCTACTACTTGGATGAAGCATTTAG
* *
67626 ATATTGAGTACGCTTTGATTAGCG
66 ATATTGAGGACGCTTTAATTAGCG
* * * * *
67650 ACAATAAGAGTGCTTTCAACCTCTACAAGGAGAAAAATATTCTGCTGCTTGGATGAAGCATTTGG
1 ACAATAAGAGTACTTCCAACCTCTACAAGGAGAAAAATATTCTACTACTTGGATGAAGCATTTAG
*
67715 ATATTGAGGCCGCTTTAATTAGC
66 ATATTGAGGACGCTTTAATTAGC
67738 AGCAATGAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 78 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (89 bp):
ACAATAAGAGTACTTCCAACCTCTACAAGGAGAAAAATATTCTACTACTTGGATGAAGCATTTAG
ATATTGAGGACGCTTTAATTAGCG
Found at i:70156 original size:17 final size:17
Alignment explanation
Indices: 70134--70166 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
70124 TGATTAGTAT
70134 TTTAATTTG-AATTATTG
1 TTTAA-TTGCAATTATTG
70151 TTTAATTGCAATTATT
1 TTTAATTGCAATTATT
70167 TAATCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (17 bp):
TTTAATTGCAATTATTG
Found at i:71338 original size:19 final size:19
Alignment explanation
Indices: 71314--71368 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
71304 TCACAACCAT
71314 AAATGAAATGTATAAAATG
1 AAATGAAATGTATAAAATG
*
71333 AAATGAAATTGTAAAAAAATG
1 AAATGAAA-TGT-ATAAAATG
*
71354 -AATGAAATGTTTAAA
1 AAATGAAATGTATAAA
71369 CAAAGACGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.10
19 11 0.35
20 10 0.32
21 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (19 bp):
AAATGAAATGTATAAAATG
Found at i:71368 original size:21 final size:21
Alignment explanation
Indices: 71314--71361 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
71304 TCACAACCAT
*
71314 AAATGAAA-TGT-ATAAAATG
1 AAATGAAATTGTAAAAAAATG
71333 AAATGAAATTGTAAAAAAATG
1 AAATGAAATTGTAAAAAAATG
71354 -AATGAAAT
1 AAATGAAAT
71362 GTTTAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 8 0.31
20 11 0.42
21 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (21 bp):
AAATGAAATTGTAAAAAAATG
Found at i:78785 original size:38 final size:37
Alignment explanation
Indices: 78705--78785 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
78695 TTAAAAAAAA
* * *
78705 AGGACAAGTCCTGCCCAGGACTTGACAACTCCTACCT
1 AGGACTAGTCCTGCCCAAGACTTGACAACTCCTACCC
* *
78742 GGGACTAGTCCTGCCCAAGACTTGGACAACTCCTGCCC
1 AGGACTAGTCCTGCCCAAGACTT-GACAACTCCTACCC
78780 AGGACT
1 AGGACT
78786 TGTTGCGGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 20 0.54
38 17 0.46
ACGTcount: A:0.25, C:0.35, G:0.22, T:0.19
Consensus pattern (37 bp):
AGGACTAGTCCTGCCCAAGACTTGACAACTCCTACCC
Found at i:80925 original size:39 final size:39
Alignment explanation
Indices: 80868--80945 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
80858 AAGTCCCGAT
**
80868 CTTTTTTCTTTCCGCTCTTCTCTGCCTCCATAGTTAGGG
1 CTTTTTTCTTTCAACTCTTCTCTGCCTCCATAGTTAGGG
*
80907 CTTTTTTCTTTCAACTCTTCTTTGCCTCCATAGTTAGGG
1 CTTTTTTCTTTCAACTCTTCTCTGCCTCCATAGTTAGGG
80946 TTTCAAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.10, C:0.28, G:0.14, T:0.47
Consensus pattern (39 bp):
CTTTTTTCTTTCAACTCTTCTCTGCCTCCATAGTTAGGG
Found at i:81262 original size:2 final size:2
Alignment explanation
Indices: 81257--81281 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
81247 TGATTATATA
81257 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
81282 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:81286 original size:2 final size:2
Alignment explanation
Indices: 81281--81311 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
81271 TGTGTGTGTG
81281 TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
81312 AGTCTAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:81590 original size:21 final size:21
Alignment explanation
Indices: 81566--81632 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
81556 GTAATATAAA
81566 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
* ** *
81587 TAATTAAATGTAATA-ATAC-T
1 TAA-TAACTAAAATACTTACAT
*
81607 ATAATAACTAAAACACTTACAT
1 -TAATAACTAAAATACTTACAT
81629 TAAT
1 TAAT
81633 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 8 0.24
21 16 0.48
22 9 0.27
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (21 bp):
TAATAACTAAAATACTTACAT
Done.