Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024748.1 Corchorus olitorius cultivar O-4 contig24781, 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: 98016
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:2391 original size:30 final size:29
Alignment explanation
Indices: 2348--2404 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
2338 TTAGGATTAG
2348 TTATTTATGCTTTAATTTTCAA-TTTCTT
1 TTATTTATGCTTTAATTTTCAAGTTTCTT
2376 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTAT-TTATG-CTTTAATTTTCAAGTTTC
2405 ATTAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.61
Consensus pattern (29 bp):
TTATTTATGCTTTAATTTTCAAGTTTCTT
Found at i:3948 original size:19 final size:18
Alignment explanation
Indices: 3924--3959 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3914 TGAAGACTTA
3924 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
3943 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
3960 ATTATTTTCA
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:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:7012 original size:48 final size:46
Alignment explanation
Indices: 6938--7070 Score: 131
Period size: 48 Copynumber: 2.8 Consensus size: 46
6928 AGCGTACCAA
* * * * *
6938 TCAATTTTGTCCAAAAATAGATAAAAAGAGCAATGAAAATTAAATAT
1 TCAATTTTGTCTAAAAATTGAGAAAAAGAGCAA-GAAAAATAAAGAT
* * *
6985 TCAATTTTGTCTTAAAAATTGAGAAAAAGGTGCGAGAAAAATAAAGGT
1 TCAATTTTGTC-TAAAAATTGAGAAAAA-GAGCAAGAAAAATAAAGAT
* * *
7033 TCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGGAAA
1 TCAATTTTGT-CTAAAAATTGAGAAAAAGAGCAAGAAA
7071 TGTAAAACAT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
47 19 0.26
48 49 0.68
49 4 0.06
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (46 bp):
TCAATTTTGTCTAAAAATTGAGAAAAAGAGCAAGAAAAATAAAGAT
Found at i:7398 original size:32 final size:31
Alignment explanation
Indices: 7347--7409 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
7337 ATGAACAAGA
*
7347 TTGAAAAATAAAAATGAAAGCTCTGAGGCTTG
1 TTGAAAAATAAAAATGAAAGCACT-AGGCTTG
*
7379 TTGAAAAATGATAAA-GAAAGCACTAGGCTTG
1 TTGAAAAAT-AAAAATGAAAGCACTAGGCTTG
7410 ATTGTTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 7 0.25
32 17 0.61
33 4 0.14
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (31 bp):
TTGAAAAATAAAAATGAAAGCACTAGGCTTG
Found at i:19066 original size:24 final size:24
Alignment explanation
Indices: 19033--19078 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
19023 TGGACTTGAA
*
19033 GATGACCATGGAGAGCATGGAGAG
1 GATGACCATGGACAGCATGGAGAG
* *
19057 GATGAGCATGGACTGCATGGAG
1 GATGACCATGGACAGCATGGAG
19079 GCATGAAGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.13, G:0.41, T:0.15
Consensus pattern (24 bp):
GATGACCATGGACAGCATGGAGAG
Found at i:24082 original size:52 final size:52
Alignment explanation
Indices: 24024--24140 Score: 184
Period size: 52 Copynumber: 2.2 Consensus size: 52
24014 AATTCAATTT
*
24024 AAGTTTTCAAAGTATTCAATCTAAG-TCTTTTTCAAATTGGGAAAGTTCCCATC
1 AAGTTTTCAAAGTATTCAAT-TAAGCTCTTTTT-AAAATGGGAAAGTTCCCATC
*
24077 -AGTTTTCAAAGTATTCAATTTAGCTCTTTTTAAAATGGGAAAGTTCCCATC
1 AAGTTTTCAAAGTATTCAATTAAGCTCTTTTTAAAATGGGAAAGTTCCCATC
24128 AAGTTTTCAAAGT
1 AAGTTTTCAAAGT
24141 TTTTAAAATG
Statistics
Matches: 60, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
51 22 0.37
52 38 0.63
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (52 bp):
AAGTTTTCAAAGTATTCAATTAAGCTCTTTTTAAAATGGGAAAGTTCCCATC
Found at i:24153 original size:37 final size:37
Alignment explanation
Indices: 24103--24208 Score: 149
Period size: 37 Copynumber: 2.9 Consensus size: 37
24093 AATTTAGCTC
24103 TTTTTAAAATGGGAAAGTTCCCATCAAGTTTTCAAAG
1 TTTTTAAAATGGGAAAGTTCCCATCAAGTTTTCAAAG
* **
24140 TTTTTAAAATGGGAAAGTTCCCATCAAGTCTTCATGG
1 TTTTTAAAATGGGAAAGTTCCCATCAAGTTTTCAAAG
* * * *
24177 TTTTCAAATTGGGAATGTTCCCATCAGGTTTT
1 TTTTTAAAATGGGAAAGTTCCCATCAAGTTTT
24209 AGTTTTCAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (37 bp):
TTTTTAAAATGGGAAAGTTCCCATCAAGTTTTCAAAG
Found at i:24872 original size:21 final size:21
Alignment explanation
Indices: 24833--24873 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
24823 AACTCTTTTA
*
24833 ATGGAAATCTTGATAGAACAT
1 ATGGAAATCTTCATAGAACAT
24854 ATGGAAATCTTCCAT-GAACA
1 ATGGAAATCTT-CATAGAACA
24874 CTTCTTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (21 bp):
ATGGAAATCTTCATAGAACAT
Found at i:27285 original size:40 final size:41
Alignment explanation
Indices: 27223--27418 Score: 168
Period size: 40 Copynumber: 4.7 Consensus size: 41
27213 GGAAAAGGAG
* *
27223 CAACACCTTCCGATGAGAAAGGGCAG-ACTAGGAATTTAGA
1 CAACACCTTCCGATGAGGAAGGGCAGAACTAGGAATTTAAA
* * *
27263 CAACACCTTCCGGTGAGGAAGGGCA-AACTGGGAAAAGTGAACTTAGA
1 CAACACCTTCCGATGAGGAAGGGCAGAACT------AG-GAATTTAAA
* * *
27310 CAACACCTTCCGATGAGAAAGGG-TGAACTGGGAATTTAAA
1 CAACACCTTCCGATGAGGAAGGGCAGAACTAGGAATTTAAA
* * *
27350 CAACACCTTCCGATGAGGAAGGGC-GAATTGGGAAGTTAAA
1 CAACACCTTCCGATGAGGAAGGGCAGAACTAGGAATTTAAA
* * *
27390 CAACACCTACCGGTGGGGAAGGGCA-AACT
1 CAACACCTTCCGATGAGGAAGGGCAGAACT
27419 GGGTAAATTG
Statistics
Matches: 129, Mismatches: 16, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
40 93 0.72
41 1 0.01
46 2 0.02
47 33 0.26
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.16
Consensus pattern (41 bp):
CAACACCTTCCGATGAGGAAGGGCAGAACTAGGAATTTAAA
Found at i:27369 original size:87 final size:87
Alignment explanation
Indices: 27223--27383 Score: 252
Period size: 87 Copynumber: 1.9 Consensus size: 87
27213 GGAAAAGGAG
* *
27223 CAACACCTTCCGATGAGAAAGGGCAGACTAGGAATTTAGACAACACCTTCCGGTGAGGAAGGGCA
1 CAACACCTTCCGATGAGAAAGGGCAGACTAGGAATTTAAACAACACCTTCCGATGAGGAAGGGCA
27288 AACTGGGAAAAGTGAACTTAGA
66 AACTGGGAAAAGTGAACTTAGA
* *
27310 CAACACCTTCCGATGAGAAAGGG-TGAACTGGGAATTTAAACAACACCTTCCGATGAGGAAGGGC
1 CAACACCTTCCGATGAGAAAGGGCAG-ACTAGGAATTTAAACAACACCTTCCGATGAGGAAGGGC
* *
27374 GAATTGGGAA
65 AAACTGGGAA
27384 GTTAAACAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
86 1 0.01
87 66 0.99
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (87 bp):
CAACACCTTCCGATGAGAAAGGGCAGACTAGGAATTTAAACAACACCTTCCGATGAGGAAGGGCA
AACTGGGAAAAGTGAACTTAGA
Found at i:27484 original size:41 final size:41
Alignment explanation
Indices: 27438--27731 Score: 285
Period size: 41 Copynumber: 7.2 Consensus size: 41
27428 GGACAAAGGC
27438 AACAACACCTCCCGATGAGGAAGGGCAAATTGGTAAATGCT
1 AACAACACCTCCCGATGAGGAAGGGCAAATTGGTAAATGCT
* ** * * * * *
27479 TACAACACCTTTCGATGAGGAATGGCGAACTGGACAAAGGC-
1 AACAACACCTCCCGATGAGGAAGGGCAAATTGG-TAAATGCT
* *
27520 AACAACACCTCCCGATGCGGAAGGGCAAATTGGT-AATACT
1 AACAACACCTCCCGATGAGGAAGGGCAAATTGGTAAATGCT
* * * * * *
27560 GACAACACCTTCCGATGAGGAAGGGAAAACTGG-ACAAAGGT
1 AACAACACCTCCCGATGAGGAAGGGCAAATTGGTA-AATGCT
*
27601 AACAACACCTCCCGATGAGGAAGGGCAAATTGGT-AATACT
1 AACAACACCTCCCGATGAGGAAGGGCAAATTGGTAAATGCT
* * * * * * *
27641 GACAACACCTTCCGAGGAGGAAGGGAAAACTGG-ACAAAGGT
1 AACAACACCTCCCGATGAGGAAGGGCAAATTGGTA-AATGCT
*
27682 AACAACACCTCCCGATGAGGAAGGGCAAATTGGT-AATACT
1 AACAACACCTCCCGATGAGGAAGGGCAAATTGGTAAATGCT
*
27722 GACAACACCT
1 AACAACACCT
27732 TCTGATCGGT
Statistics
Matches: 195, Mismatches: 50, Indels: 17
0.74 0.19 0.06
Matches are distributed among these distances:
39 3 0.02
40 71 0.36
41 116 0.59
42 5 0.03
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.15
Consensus pattern (41 bp):
AACAACACCTCCCGATGAGGAAGGGCAAATTGGTAAATGCT
Found at i:27613 original size:81 final size:81
Alignment explanation
Indices: 27427--27733 Score: 515
Period size: 81 Copynumber: 3.8 Consensus size: 81
27417 CTGGGTAAAT
* * *
27427 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAAATGCTTACAACACCTTTC
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGT-AATACTGACAACACCTTCC
* **
27492 GATGAGGAATGGCGAAC
65 GATGAGGAAGGGAAAAC
*
27509 TGGACAAAGGCAACAACACCTCCCGATGCGGAAGGGCAAATTGGTAATACTGACAACACCTTCCG
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAACACCTTCCG
27574 ATGAGGAAGGGAAAAC
66 ATGAGGAAGGGAAAAC
*
27590 TGGACAAAGGTAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAACACCTTCCG
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAACACCTTCCG
*
27655 AGGAGGAAGGGAAAAC
66 ATGAGGAAGGGAAAAC
*
27671 TGGACAAAGGTAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAACACCTTC
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAACACCTTC
27734 TGATCGGTCG
Statistics
Matches: 215, Mismatches: 10, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
81 171 0.80
82 44 0.20
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.15
Consensus pattern (81 bp):
TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGTAATACTGACAACACCTTCCG
ATGAGGAAGGGAAAAC
Found at i:29304 original size:10 final size:9
Alignment explanation
Indices: 29289--29335 Score: 51
Period size: 10 Copynumber: 4.9 Consensus size: 9
29279 TTGAGATAAT
29289 TCTTCAATA
1 TCTTCAATA
29298 GTCTTCAA-A
1 -TCTTCAATA
29307 TCTTCAATTA
1 TCTTCAA-TA
29317 TCTTCAATAAA
1 TCTTCAAT--A
29328 TCTTCAAT
1 TCTTCAAT
29336 CACGAACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 7 0.21
9 2 0.06
10 15 0.45
11 9 0.27
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (9 bp):
TCTTCAATA
Found at i:29310 original size:18 final size:18
Alignment explanation
Indices: 29289--29323 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29279 TTGAGATAAT
29289 TCTTCAA-TAGTCTTCAAA
1 TCTTCAATTA-TCTTCAAA
29307 TCTTCAATTATCTTCAA
1 TCTTCAATTATCTTCAA
29324 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.43
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:31559 original size:10 final size:9
Alignment explanation
Indices: 31544--31590 Score: 51
Period size: 10 Copynumber: 4.9 Consensus size: 9
31534 TTGAGATAAT
31544 TCTTCAATA
1 TCTTCAATA
31553 GTCTTCAA-A
1 -TCTTCAATA
31562 TCTTCAATTA
1 TCTTCAA-TA
31572 TCTTCAATAAA
1 TCTTCAAT--A
31583 TCTTCAAT
1 TCTTCAAT
31591 CACGAACTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 7 0.21
9 2 0.06
10 15 0.45
11 9 0.27
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (9 bp):
TCTTCAATA
Found at i:31567 original size:18 final size:18
Alignment explanation
Indices: 31544--31578 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31534 TTGAGATAAT
31544 TCTTCAA-TAGTCTTCAAA
1 TCTTCAATTA-TCTTCAAA
31562 TCTTCAATTATCTTCAA
1 TCTTCAATTATCTTCAA
31579 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.43
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:31954 original size:41 final size:41
Alignment explanation
Indices: 31815--31964 Score: 135
Period size: 41 Copynumber: 3.7 Consensus size: 41
31805 TTGGCTCGAT
* *
31815 CACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAA
1 CACCTCCCGATGAGGAAGGGAAAACTGGACAAAGGCAACAA
* * * * * * *
31856 CAACTCCTGAAGAGGATGGGAAAATTGGTA-ATA--CTGACAA
1 CACCTCCCGATGAGGAAGGGAAAACTGG-ACAAAGGC-AACAA
* *
31896 GACCTTCCGATGAGGAAGGGAAAACTGGACAAAGGCAACAA
1 CACCTCCCGATGAGGAAGGGAAAACTGGACAAAGGCAACAA
* **
31937 CACCTCCCGATGGGGAAGGCCAAACTGG
1 CACCTCCCGATGAGGAAGGGAAAACTGG
31965 GAATTGTTAA
Statistics
Matches: 81, Mismatches: 23, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
39 2 0.02
40 27 0.33
41 50 0.62
42 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.28, T:0.13
Consensus pattern (41 bp):
CACCTCCCGATGAGGAAGGGAAAACTGGACAAAGGCAACAA
Found at i:32354 original size:50 final size:50
Alignment explanation
Indices: 32293--32416 Score: 137
Period size: 49 Copynumber: 2.5 Consensus size: 50
32283 AAAACCAATC
* * * *
32293 TTTATTCACAAATTACTTAAAAATTCTACCTTT-T-CCTCAAAGATTACACT
1 TTTATTTACAAATTACTTAAAAATTC-A-ATTTCTAACTCAAAGATGACACT
* * *
32343 TTTATTTACAAATTACTTAAAAA-ACAATTTCTAACTCAAAGGTGACATT
1 TTTATTTACAAATTACTTAAAAATTCAATTTCTAACTCAAAGATGACACT
*
32392 TTTATTTACAAATTACCTAAAAATT
1 TTTATTTACAAATTACTTAAAAATT
32417 TAATCCTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
47 3 0.05
48 2 0.03
49 35 0.56
50 22 0.35
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (50 bp):
TTTATTTACAAATTACTTAAAAATTCAATTTCTAACTCAAAGATGACACT
Found at i:48532 original size:18 final size:19
Alignment explanation
Indices: 48499--48534 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
48489 TGAAGACTTA
48499 TTGAAGACAAATTGAAGAT
1 TTGAAGACAAATTGAAGAT
*
48518 TTGAAGAC-CATTGAAGA
1 TTGAAGACAAATTGAAGA
48535 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.25
Consensus pattern (19 bp):
TTGAAGACAAATTGAAGAT
Found at i:58562 original size:110 final size:111
Alignment explanation
Indices: 58369--58581 Score: 374
Period size: 110 Copynumber: 1.9 Consensus size: 111
58359 ACACCAAAGC
* *
58369 ATAATTTATAACCCAAACTCACCCTTAAATATAAATAAGCATAATTTATAAGTAAACTTAAGACC
1 ATAATTTATAACCCAAACTCACCCTTAAATATAAATAAGCATAATTTATAAGCAAAATTAAGACC
* *
58434 CTGACACCAACATTCCT-AATCAAATGACCTATCTTTGTAAGCATA
66 CTAACACCAACATTCCTAAATCAAATGACCCATCTTTGTAAGCATA
*
58479 ATAATTTATAACCCAAACTCACCCTTAAATATAAATAAGCATAATTTATAAGCAAAATTAAGGCC
1 ATAATTTATAACCCAAACTCACCCTTAAATATAAATAAGCATAATTTATAAGCAAAATTAAGACC
58544 CTAACACCAACATTCCTAAATCAAATGACCCATCTTTG
66 CTAACACCAACATTCCTAAATCAAATGACCCATCTTTG
58582 AATCAACAAT
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 78 0.80
111 19 0.20
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.28
Consensus pattern (111 bp):
ATAATTTATAACCCAAACTCACCCTTAAATATAAATAAGCATAATTTATAAGCAAAATTAAGACC
CTAACACCAACATTCCTAAATCAAATGACCCATCTTTGTAAGCATA
Found at i:64886 original size:17 final size:17
Alignment explanation
Indices: 64838--64887 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
64828 TATTTTATTT
64838 GATTGTTTTAAGAAAAA
1 GATTGTTTTAAGAAAAA
** *
64855 G--T-TCCTAAAAAAAA
1 GATTGTTTTAAGAAAAA
64869 GATTGTTTTAAGAAAAA
1 GATTGTTTTAAGAAAAA
64886 GA
1 GA
64888 ATAAAGAGCT
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
14 10 0.42
15 1 0.04
16 1 0.04
17 12 0.50
ACGTcount: A:0.50, C:0.04, G:0.16, T:0.30
Consensus pattern (17 bp):
GATTGTTTTAAGAAAAA
Found at i:67902 original size:19 final size:18
Alignment explanation
Indices: 67869--67904 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
67859 TTGAAATAAT
67869 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
67887 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
67905 TGAGTCATCA
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:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:71608 original size:19 final size:18
Alignment explanation
Indices: 71584--71624 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
71574 AGTTTTAGAT
71584 TTAATTTAGTTTTGCTTTA
1 TTAATTT-GTTTTGCTTTA
*
71603 TTAA-TTGTTTTTCTTTA
1 TTAATTTGTTTTGCTTTA
71620 -TAATT
1 TTAATT
71625 GGTATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 11 0.55
18 2 0.10
19 4 0.20
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (18 bp):
TTAATTTGTTTTGCTTTA
Found at i:71625 original size:16 final size:17
Alignment explanation
Indices: 71592--71625 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
71582 ATTTAATTTA
71592 GTTTTGCTTTATTAATT
1 GTTTTGCTTTATTAATT
*
71609 GTTTTTCTTTA-TAATT
1 GTTTTGCTTTATTAATT
71625 G
1 G
71626 GTATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.65
Consensus pattern (17 bp):
GTTTTGCTTTATTAATT
Found at i:77407 original size:41 final size:41
Alignment explanation
Indices: 77362--77439 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
77352 CATAAATCAA
***
77362 AAATAAAA-TCCTAAATCAGGGGTGAAATTGAATCAATAAAT
1 AAATAAAACT-CTAAATCAGGGACAAAATTGAATCAATAAAT
**
77403 AAATATTACTCTAAATCAGGGACAAAATTGAATCAAT
1 AAATAAAACTCTAAATCAGGGACAAAATTGAATCAAT
77440 TAACAAATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 30 0.97
42 1 0.03
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.26
Consensus pattern (41 bp):
AAATAAAACTCTAAATCAGGGACAAAATTGAATCAATAAAT
Found at i:79787 original size:31 final size:30
Alignment explanation
Indices: 79651--79828 Score: 158
Period size: 31 Copynumber: 5.8 Consensus size: 30
79641 ACGGTGTCCG
* *
79651 ACGTGGCATGCCACGTGTACAAAAAGCGAC
1 ACGTGGCACGCCACGTGTACAAAAAGTGAC
* * **
79681 ATGTGGCACGTCACGTGTACCAAAAAGCAAC
1 ACGTGGCACGCCACGTGTA-CAAAAAGTGAC
* *
79712 ATGTGGCACGCCACGTGTACCAAAAGGTGAC
1 ACGTGGCACGCCACGTGTA-CAAAAAGTGAC
* ** * *
79743 ACATATCACGCCATGTGTACCCAAAAGTGAC
1 ACGTGGCACGCCACGTGTA-CAAAAAGTGAC
* * *
79774 ACGTGGCATGCCATGTGTTTCAAAAAGTGAC
1 ACGTGGCACGCCACGTG-TACAAAAAGTGAC
* *
79805 ACGTGGCATGCCACGTGCACAAAA
1 ACGTGGCACGCCACGTGTACAAAA
79829 GGATACGTGC
Statistics
Matches: 122, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
30 21 0.17
31 100 0.82
32 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (30 bp):
ACGTGGCACGCCACGTGTACAAAAAGTGAC
Found at i:83176 original size:27 final size:26
Alignment explanation
Indices: 83100--83176 Score: 102
Period size: 28 Copynumber: 2.9 Consensus size: 26
83090 TAGGGTCATC
*
83100 CAGGGGCATTTTGATCA-TTTGCACT
1 CAGGGGCATTTTGGTCATTTTGCACT
**
83125 CAAAGGCATTTTGGTCATTTGTGCACT
1 CAGGGGCATTTTGGTCATTT-TGCACT
83152 CAGGGGGCATTTTGGTCATTTTGCA
1 CA-GGGGCATTTTGGTCATTTTGCA
83177 TGCTCTAGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
25 14 0.32
26 2 0.05
27 12 0.27
28 16 0.36
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.36
Consensus pattern (26 bp):
CAGGGGCATTTTGGTCATTTTGCACT
Found at i:91074 original size:26 final size:27
Alignment explanation
Indices: 91022--91127 Score: 83
Period size: 26 Copynumber: 3.9 Consensus size: 27
91012 TTAAGAGTGT
* ** *
91022 ACTT-AAAATGATCAACGTGCCCATGA
1 ACTTGAAAATGACCAAAATGCCCCTGA
*
91048 ACTT-AAAATGACCAAAATGTCCCTGA
1 ACTTGAAAATGACCAAAATGCCCCTGA
* *
91074 A-TATGCAAATGACTAAAATGCCCCTAGA
1 ACT-TGAAAATGACCAAAATGCCCCT-GA
* *
91102 TTCTTGAGAATGACCAAAATGCCCCT
1 -ACTTGAAAATGACCAAAATGCCCCT
91128 AGTTGATCCT
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
25 1 0.02
26 23 0.37
27 17 0.27
28 2 0.03
29 19 0.30
30 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (27 bp):
ACTTGAAAATGACCAAAATGCCCCTGA
Found at i:91428 original size:35 final size:35
Alignment explanation
Indices: 91382--91637 Score: 372
Period size: 35 Copynumber: 7.3 Consensus size: 35
91372 CGAGTTCATA
*
91382 TTGAAAATGCTACACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
91417 TTGAAGATGCTACACCGAGTCATCTAAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* *
91452 TTGAAGATGCTACACCGAGTCATCCGAGA-TCATTT
1 TTGAAGATGCTACACCGAGTCATCTGA-ATTCATCT
* * *
91487 TTGAAGATGCCACACCGAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
91522 TTGAAGATGTTACACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* *
91557 TTGAAGATGCTACACCGAGTCATCCGAGA-TCATTT
1 TTGAAGATGCTACACCGAGTCATCTGA-ATTCATCT
* *
91592 TTGAAGATGCTACACCGAGTCATCTGGATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
91627 TTGAAGATGCT
1 TTGAAGATGCT
91638 TTGAAAAATA
Statistics
Matches: 196, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
34 2 0.01
35 192 0.98
36 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
Found at i:91564 original size:105 final size:105
Alignment explanation
Indices: 91382--91637 Score: 458
Period size: 105 Copynumber: 2.4 Consensus size: 105
91372 CGAGTTCATA
* * *
91382 TTGAAAATGCTACACCGAGTCATCTGAATTCATCTTTGAAGATGCTACACCGAGTCATCTAAATT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACTTTGAAGATGCTACACCGAGTCATCTAAATT
91447 CATCTTTGAAGATGCTACACCGAGTCATCCGAGATCATTT
66 CATCTTTGAAGATGCTACACCGAGTCATCCGAGATCATTT
* * *
91487 TTGAAGATGCCACACCGAGTCATCTGGATTCAACTTTGAAGATGTTACACCGAGTCATCTGAATT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACTTTGAAGATGCTACACCGAGTCATCTAAATT
91552 CATCTTTGAAGATGCTACACCGAGTCATCCGAGATCATTT
66 CATCTTTGAAGATGCTACACCGAGTCATCCGAGATCATTT
91592 TTGAAGATGCTACACCGAGTCATCTGGATTCAACTTTGAAGATGCT
1 TTGAAGATGCTACACCGAGTCATCTGGATTCAACTTTGAAGATGCT
91638 TTGAAAAATA
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 143 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (105 bp):
TTGAAGATGCTACACCGAGTCATCTGGATTCAACTTTGAAGATGCTACACCGAGTCATCTAAATT
CATCTTTGAAGATGCTACACCGAGTCATCCGAGATCATTT
Found at i:92145 original size:50 final size:50
Alignment explanation
Indices: 92087--92235 Score: 199
Period size: 50 Copynumber: 3.0 Consensus size: 50
92077 CTTAAATGCC
* * * * *
92087 CTTTGAAAAACAAATTTTGATCTTGGACTCACAATTGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* *
92137 CTTTGAAAAGCGAATTTTGATCTTGAACTCTCAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
* * * *
92187 TTTTGAAAAGCGAATTTTGATCTTGAACTCATAAATGCAAAGAAATCTT
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTT
92236 GTTATAAAAC
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 86 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATCTTA
Found at i:92838 original size:5 final size:5
Alignment explanation
Indices: 92822--92895 Score: 66
Period size: 5 Copynumber: 14.6 Consensus size: 5
92812 TCAATTCTCT
92822 TTTGA TTTTGA TTTGA TTTGA TTTTTGA TTTTGA TTTGA TTT-- TTTGA
1 TTTGA -TTTGA TTTGA TTTGA --TTTGA -TTTGA TTTGA TTTGA TTTGA
*
92869 -TTGA CTTTGA TTTGA TTT-T TTTGA TTT
1 TTTGA -TTTGA TTTGA TTTGA TTTGA TTT
92896 TTTTTATTGT
Statistics
Matches: 59, Mismatches: 2, Indels: 15
0.78 0.03 0.20
Matches are distributed among these distances:
3 3 0.05
4 7 0.12
5 29 0.49
6 15 0.25
7 5 0.08
ACGTcount: A:0.16, C:0.01, G:0.16, T:0.66
Consensus pattern (5 bp):
TTTGA
Found at i:92847 original size:23 final size:21
Alignment explanation
Indices: 92821--92896 Score: 100
Period size: 23 Copynumber: 3.5 Consensus size: 21
92811 ATCAATTCTC
92821 TTTTGATTTTGATTTGATTTGAT
1 TTTTGATTTTGATTTGATTT--T
92844 TTTTGATTTTGATTTGATTTT
1 TTTTGATTTTGATTTGATTTT
*
92865 TTGATTGACTTTGATTTGA-TTT
1 TT--TTGATTTTGATTTGATTTT
92887 TTTTGATTTT
1 TTTTGATTTT
92897 TTTTATTGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
20 7 0.14
21 3 0.06
22 5 0.10
23 34 0.69
ACGTcount: A:0.16, C:0.01, G:0.16, T:0.67
Consensus pattern (21 bp):
TTTTGATTTTGATTTGATTTT
Done.