Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019053.1 Corchorus olitorius cultivar O-4 contig19086, 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: 70917
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:592 original size:133 final size:133
Alignment explanation
Indices: 354--624 Score: 524
Period size: 133 Copynumber: 2.0 Consensus size: 133
344 AATTTATTTT
*
354 AAGGGGGGTAGAGCTGTGATACTCGTCCCTAGTTATTAAGTTCACTAGACTAAGATCATCATTTA
1 AAGGGGGGTAGAGCTGTGATACTCGTCCCTAGTTATTAAGTTCACTAGACTAAGATAATCATTTA
*
419 CTAAGGAAGTAATTGTTGTAATGGAAGTCAAATTGAAACAATATAGAAGTAATTAGCAATTTGAA
66 CTAAGGAAGTAATTGTTGTAATGGAAGTCAAATTGAAACAATATAAAAGTAATTAGCAATTTGAA
484 AAG
131 AAG
487 AAGGGGGGTAGAGCTGTGATACTCGTCCCTAGTTATTAAGTTCACTAGACTAAGATAATCATTTA
1 AAGGGGGGTAGAGCTGTGATACTCGTCCCTAGTTATTAAGTTCACTAGACTAAGATAATCATTTA
552 CTAAGGAAGTAATTGTTGTAATGGAAGTCAAATTGAAACAATATAAAAGTAATTAGCAATTTGAA
66 CTAAGGAAGTAATTGTTGTAATGGAAGTCAAATTGAAACAATATAAAAGTAATTAGCAATTTGAA
617 AAG
131 AAG
620 AAGGG
1 AAGGG
625 TTGAATTGAA
Statistics
Matches: 136, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 136 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (133 bp):
AAGGGGGGTAGAGCTGTGATACTCGTCCCTAGTTATTAAGTTCACTAGACTAAGATAATCATTTA
CTAAGGAAGTAATTGTTGTAATGGAAGTCAAATTGAAACAATATAAAAGTAATTAGCAATTTGAA
AAG
Found at i:6012 original size:12 final size:13
Alignment explanation
Indices: 5996--6028 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5986 TTCTATTAAT
5996 TTTTTCTTTTGAG
1 TTTTTCTTTTGAG
*
6009 TTTTTGTTTTGA-
1 TTTTTCTTTTGAG
6021 TTTTTCTT
1 TTTTTCTT
6029 GAAAGTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.06, C:0.06, G:0.12, T:0.76
Consensus pattern (13 bp):
TTTTTCTTTTGAG
Found at i:7505 original size:29 final size:29
Alignment explanation
Indices: 7455--7748 Score: 326
Period size: 29 Copynumber: 10.2 Consensus size: 29
7445 TCTTAATTGA
**
7455 TCATTTTTGCTTA-CCAAGGGGCATTTTGG
1 TCATTTTTGCACATCCAA-GGGCATTTTGG
* * *
7484 TCATATTTGCACGTCCATGGGCATTTTGG
1 TCATTTTTGCACATCCAAGGGCATTTTGG
* *
7513 TCATTTTTGCACATCTAGGGGCATTTTGG
1 TCATTTTTGCACATCCAAGGGCATTTTGG
* *
7542 TCATTTTTGCGCATCCAAGGGCATTATGG
1 TCATTTTTGCACATCCAAGGGCATTTTGG
** * * *
7571 TCATTTTTGCATGTCCAGGGGCAGTTTGA
1 TCATTTTTGCACATCCAAGGGCATTTTGG
** *
7600 TCATTTTTGTGCATCCAAGGGCATTTT-T
1 TCATTTTTGCACATCCAAGGGCATTTTGG
* *
7628 TTATGTTTGCACATCCAAGGGCATTTTGG
1 TCATTTTTGCACATCCAAGGGCATTTTGG
*
7657 TCATATTTGCACATCCAAGGGCATTTTGG
1 TCATTTTTGCACATCCAAGGGCATTTTGG
* * *
7686 TCATTTTTTCACGTCCAGGGGCATTTTGG
1 TCATTTTTGCACATCCAAGGGCATTTTGG
* *
7715 TCACTTTTGCACAT-CTAGGGCA-TTTGG
1 TCATTTTTGCACATCCAAGGGCATTTTGG
7742 TCATTTT
1 TCATTTT
7749 GCATACTCTG
Statistics
Matches: 219, Mismatches: 44, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
27 11 0.05
28 29 0.13
29 176 0.80
30 3 0.01
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (29 bp):
TCATTTTTGCACATCCAAGGGCATTTTGG
Found at i:9662 original size:12 final size:12
Alignment explanation
Indices: 9645--9670 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9635 CACTTAGGAC
9645 AGTTGTCATTTT
1 AGTTGTCATTTT
9657 AGTTGTCATTTT
1 AGTTGTCATTTT
9669 AG
1 AG
9671 GCATAAAAAG
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:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (12 bp):
AGTTGTCATTTT
Found at i:12266 original size:14 final size:14
Alignment explanation
Indices: 12232--12267 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
12222 TCACTTAGAC
*
12232 TTACATCTAGCATT
1 TTACATTTAGCATT
12246 TTACATTTAGCATT
1 TTACATTTAGCATT
12260 TTACATTT
1 TTACATTT
12268 TGCCGCCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.50
Consensus pattern (14 bp):
TTACATTTAGCATT
Found at i:24221 original size:35 final size:35
Alignment explanation
Indices: 24175--24246 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
24165 TATAGTTTGT
24175 CAAGTTATCATAACATTCTTTTGTATATGTTCATG
1 CAAGTTATCATAACATTCTTTTGTATATGTTCATG
24210 CAAGTTATCATAACATTCTTTTGTATATGTTCATG
1 CAAGTTATCATAACATTCTTTTGTATATGTTCATG
24245 CA
1 CA
24247 TCCGTCTTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.44
Consensus pattern (35 bp):
CAAGTTATCATAACATTCTTTTGTATATGTTCATG
Found at i:26397 original size:72 final size:72
Alignment explanation
Indices: 26278--26417 Score: 178
Period size: 72 Copynumber: 1.9 Consensus size: 72
26268 ATCTGGACTA
* *
26278 TGAGCAAAGGAATGATGAGTTTTAATCAAAATTTTCAAAAAATCAGTTTTAATCAAAACTATGAT
1 TGAGCAAAGGAATGACGAGTTTTAATCAAAATTTTC--AAAATCAGTTTTAATCAAAACAATGAT
26343 TTCGAGCTG
64 TTCGAGCTG
**
26352 TGAGC-AAGGAATGACG-GTTTTAATCAAAAGGTGTTTC-AAATCAGTTTTGGTCAAAACAATGA
1 TGAGCAAAGGAATGACGAGTTTTAATCAAAA--T-TTTCAAAATCAGTTTTAATCAAAACAATGA
26414 TTTC
63 TTTC
26418 AAGATGACTG
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
72 39 0.66
73 10 0.17
74 6 0.10
75 4 0.07
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (72 bp):
TGAGCAAAGGAATGACGAGTTTTAATCAAAATTTTCAAAATCAGTTTTAATCAAAACAATGATTT
CGAGCTG
Found at i:27262 original size:5 final size:5
Alignment explanation
Indices: 27254--27325 Score: 56
Period size: 5 Copynumber: 13.6 Consensus size: 5
27244 AAAGAGAAAA
* **
27254 AAATC AAATC AAAGTC -AACC AAAAA AAATC AAATC AAAATC AAAAATC
1 AAATC AAATC AAA-TC AAATC AAATC AAATC AAATC -AAATC --AAATC
*
27302 AAATT AAATC AAATC AAAATC AAA
1 AAATC AAATC AAATC -AAATC AAA
27326 AGAGAATTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
4 1 0.02
5 36 0.65
6 12 0.22
7 6 0.11
ACGTcount: A:0.65, C:0.17, G:0.01, T:0.17
Consensus pattern (5 bp):
AAATC
Found at i:27312 original size:10 final size:11
Alignment explanation
Indices: 27253--27325 Score: 64
Period size: 10 Copynumber: 6.8 Consensus size: 11
27243 AAAAGAGAAA
27253 AAAATCAAATC
1 AAAATCAAATC
* *
27264 AAAGTC-AACC
1 AAAATCAAATC
*
27274 AAAA-AAAATC
1 AAAATCAAATC
27284 -AAATCAAAATC
1 AAAATC-AAATC
27295 AAAAATCAAAT-
1 -AAAATCAAATC
*
27306 TAAATCAAATC
1 AAAATCAAATC
27317 AAAATCAAA
1 AAAATCAAA
27326 AGAGAATTGA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
9 3 0.06
10 18 0.38
11 18 0.38
12 4 0.08
13 5 0.10
ACGTcount: A:0.66, C:0.16, G:0.01, T:0.16
Consensus pattern (11 bp):
AAAATCAAATC
Found at i:28011 original size:50 final size:50
Alignment explanation
Indices: 27914--28011 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 50
27904 GAAGATTTAC
* * * ** **
27914 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCTCTTTTCAA
1 AATAAGATTGCACTCCATTTGTGAGACCAAGACCAAAAGCCGATTTTCAA
*
27964 AATAAGATTGCACTCCATTTGTGAGACCAAGACCAAAGGCCGATTTTC
1 AATAAGATTGCACTCCATTTGTGAGACCAAGACCAAAAGCCGATTTTC
28012 GAAAGGCATT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (50 bp):
AATAAGATTGCACTCCATTTGTGAGACCAAGACCAAAAGCCGATTTTCAA
Found at i:28368 original size:25 final size:28
Alignment explanation
Indices: 28340--28405 Score: 86
Period size: 25 Copynumber: 2.5 Consensus size: 28
28330 AATTCAAGGA
28340 CAAA-TCAAGAAGAGCAAAGA-T-GAAG
1 CAAAGTCAAGAAGAGCAAAGATTCGAAG
*
28365 CAAAGCCAAGAA-AGCAAAGATTCGAAG
1 CAAAGTCAAGAAGAGCAAAGATTCGAAG
28392 CAACAGTCAAGAAG
1 CAA-AGTCAAGAAG
28406 TTTTCAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 12 0.35
26 7 0.21
27 7 0.21
28 8 0.24
ACGTcount: A:0.53, C:0.17, G:0.23, T:0.08
Consensus pattern (28 bp):
CAAAGTCAAGAAGAGCAAAGATTCGAAG
Found at i:28849 original size:50 final size:50
Alignment explanation
Indices: 28612--28832 Score: 415
Period size: 50 Copynumber: 4.4 Consensus size: 50
28602 CCATCCGAAT
28612 ACATAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCA
28662 ACATAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCA
*
28712 ACATAGGCTTTTGCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCA
28762 ACATAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCA
1 ACATAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCA
* *
28812 ACACATGCTTTTCCACAAGCC
1 ACATAGGCTTTTCCACAAGCC
28833 ACATCCGTTT
Statistics
Matches: 167, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 167 1.00
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.28
Consensus pattern (50 bp):
ACATAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCA
Found at i:28937 original size:50 final size:50
Alignment explanation
Indices: 28861--29067 Score: 360
Period size: 50 Copynumber: 4.1 Consensus size: 50
28851 TGCATTACCT
28861 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
*
28911 TTTTAAGATTGAATTGGTAGAGAGTTCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
* *
28961 TTTTAAGATTGAATTGGTAGACAATCCAAAGGATAAGCGGGAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
*
29011 TTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 -TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
*
29062 TCTTAA
1 TTTTAA
29068 TATGTTAGAT
Statistics
Matches: 148, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
50 101 0.68
51 47 0.32
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.27
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCC
Found at i:29045 original size:101 final size:100
Alignment explanation
Indices: 28861--29067 Score: 360
Period size: 101 Copynumber: 2.1 Consensus size: 100
28851 TGCATTACCT
* *
28861 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTGAATT
1 TTTTAAGATTGAATTGGTAGACAATCCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTGAATT
* *
28926 GGTAGAGAGTTCAAAGGATAAGCGGGAGACGGTCC
66 GGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
28961 TTTTAAGATTGAATTGGTAGACAATCCAAAGGATAAGCGGGAGACGGTCCTTTTTAAGATTGAAT
1 TTTTAAGATTGAATTGGTAGACAATCCAAAGGATAAGCGGGAGACGGTCC-TTTTAAGATTGAAT
29026 TGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
65 TGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
*
29062 TCTTAA
1 TTTTAA
29068 TATGTTAGAT
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 48 0.48
101 53 0.52
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.27
Consensus pattern (100 bp):
TTTTAAGATTGAATTGGTAGACAATCCAAAGGATAAGCGGGAGACGGTCCTTTTAAGATTGAATT
GGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:29407 original size:27 final size:28
Alignment explanation
Indices: 29334--29413 Score: 101
Period size: 29 Copynumber: 2.9 Consensus size: 28
29324 TTAGGATTAC
29334 CTAGGGGCATTTTGGTCATTTTCAAAAAT
1 CTAGGGGCATTTTGGTCATTTT-AAAAAT
* * *
29363 CTAGGGGCATTTTAGTCATTTGT-ATATT
1 CTAGGGGCATTTTGGTCATTT-TAAAAAT
29391 C-AGGGGCATTTTGGTCATTTTAA
1 CTAGGGGCATTTTGGTCATTTTAA
29414 GTCCACGCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 1 0.02
27 19 0.42
28 4 0.09
29 20 0.44
30 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (28 bp):
CTAGGGGCATTTTGGTCATTTTAAAAAT
Found at i:34106 original size:15 final size:16
Alignment explanation
Indices: 34073--34112 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
34063 TTACTTTGCT
34073 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
34089 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
34104 TTGCTTTCT
1 TTGTTTTCT
34113 TTCAACCTCT
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:34322 original size:21 final size:22
Alignment explanation
Indices: 34298--34339 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
34288 TTTGCCTCAT
34298 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATGCCATG
* *
34319 GCATTCGTTCATGCATTCCAT
1 GCATTCATTCATGCATGCCAT
34340 TAAACCTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (22 bp):
GCATTCATTCATGCATGCCATG
Found at i:36459 original size:19 final size:19
Alignment explanation
Indices: 36419--36464 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
36409 TCCCCGATTT
* *
36419 AAAAAAAAGAGATAAATGA
1 AAAAAAAAGAGAAAAAAGA
36438 AAAAAAAAGA-AAAAAAGA
1 AAAAAAAAGAGAAAAAAGA
36456 AAAAGAAAA
1 AAAA-AAAA
36465 TGGAAAAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (19 bp):
AAAAAAAAGAGAAAAAAGA
Found at i:37602 original size:50 final size:50
Alignment explanation
Indices: 37505--37606 Score: 125
Period size: 50 Copynumber: 2.0 Consensus size: 50
37495 AATAAGAAGC
* * **
37505 TTTACAATAAAATTGCTTTCCATTTGTGAGTCCACGGTCAAAATTCGCTT
1 TTTACAATAAAATTGCATTCCATTTGTGAGACCACGACCAAAATTCGCTT
* * *
37555 TTTATAATAAGATTGCATTCCATTTGTGAGACCGA-GACCAAAGTTCGCTT
1 TTTACAATAAAATTGCATTCCATTTGTGAGACC-ACGACCAAAATTCGCTT
37605 TT
1 TT
37607 CGAAGGGCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 43 0.98
51 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (50 bp):
TTTACAATAAAATTGCATTCCATTTGTGAGACCACGACCAAAATTCGCTT
Found at i:38406 original size:87 final size:87
Alignment explanation
Indices: 38294--38511 Score: 357
Period size: 87 Copynumber: 2.5 Consensus size: 87
38284 TTCAAGGCAA
*
38294 CAATCAAGAAGTTTTAATCACAACATCAGACTTAGAGTTATTCTTCAAGTTTTCAAAGTTGACCG
1 CAATCAAGAAGTTTTAATCACAACATCAGACTTAGAGTTATTCTTCAAGTTATCAAAGTTGACCG
*
38359 GAAATTGGTCCTCTTTCATCAT
66 CAAATTGGTCCTCTTTCATCAT
** * *
38381 CAATCAAGAAGTTTTAATCACAACATCAGACTCGGAGTTATTTTTCAAGTTATCAAAGTTGATCG
1 CAATCAAGAAGTTTTAATCACAACATCAGACTTAGAGTTATTCTTCAAGTTATCAAAGTTGACCG
38446 CAAATTGGTCCTCTTTCATCAT
66 CAAATTGGTCCTCTTTCATCAT
*
38468 CAATCAAGAAGTTTTAATCACAACATCAGA-TTCCGAGTTATTCT
1 CAATCAAGAAGTTTTAATCACAACATCAGACTT-AGAGTTATTCT
38512 CGAAAGGTAT
Statistics
Matches: 121, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
86 1 0.01
87 120 0.99
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (87 bp):
CAATCAAGAAGTTTTAATCACAACATCAGACTTAGAGTTATTCTTCAAGTTATCAAAGTTGACCG
CAAATTGGTCCTCTTTCATCAT
Found at i:38712 original size:69 final size:69
Alignment explanation
Indices: 38598--38766 Score: 275
Period size: 69 Copynumber: 2.4 Consensus size: 69
38588 AATGTTTTGA
* * *
38598 CTTTTCCATAAGTCAAACTCGTTTCCATACGAGTTAGTTTCAGCCTTGGTTTCAACCAAGCCACA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAGTTTAAGCCTTGGTTTCAACCAAGCCACA
38663 TAGG
66 TAGG
* *
38667 CTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTTAGTTTAAGCCTTGGTTTCATCCAAGCCACA
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAGTTTAAGCCTTGGTTTCAACCAAGCCACA
38732 TAGG
66 TAGG
* *
38736 CTTTTCCACAACCCAAATTCGTTTCCATACG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACG
38767 GTGCATTACC
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 92 1.00
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.31
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGTTAGTTTAAGCCTTGGTTTCAACCAAGCCACA
TAGG
Found at i:38921 original size:91 final size:91
Alignment explanation
Indices: 38765--38954 Score: 292
Period size: 91 Copynumber: 2.1 Consensus size: 91
38755 CGTTTCCATA
* *
38765 CGGTGCATTACCTTTTTCAAGATCGGACTCGGTGAGATCGGTGCAGCAAATCTTCAAATGTATCA
1 CGGTGCATTACCATTTTCAAGATCGGACTCGGTGAGATCGGTGCAACAAATCTTCAAATGTATCA
* *
38830 GGTTGATTCGGTGAATCAAGTTAATG
66 GGGTGATTCGGTGAATCAAGTCAATG
* * *
38856 CGGTGCATTACCATTTTCAAGATTGGACTTGGTGAGCTCGGTGCAACAAATCTTCAAATAG-ATC
1 CGGTGCATTACCATTTTCAAGATCGGACTCGGTGAGATCGGTGCAACAAATCTTCAAAT-GTATC
*
38920 AGGGTGTTTCGGTGAATCAAGTCAATG
65 AGGGTGATTCGGTGAATCAAGTCAATG
38947 CGGTGCAT
1 CGGTGCAT
38955 CTCTTCAAAG
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 89 0.99
92 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (91 bp):
CGGTGCATTACCATTTTCAAGATCGGACTCGGTGAGATCGGTGCAACAAATCTTCAAATGTATCA
GGGTGATTCGGTGAATCAAGTCAATG
Found at i:51041 original size:30 final size:29
Alignment explanation
Indices: 51005--51069 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
50995 GCAATTGCAC
51005 AAATTCAACAAAAACAAAAACTGCAACACT
1 AAATTCAACAAAAA-AAAAACTGCAACACT
* * * * *
51035 AAATTCAACCAAGAGAAAATTGCAGCACT
1 AAATTCAACAAAAAAAAAACTGCAACACT
51064 AAATTC
1 AAATTC
51070 CCAATCCATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.54, C:0.22, G:0.08, T:0.17
Consensus pattern (29 bp):
AAATTCAACAAAAAAAAAACTGCAACACT
Found at i:55455 original size:14 final size:15
Alignment explanation
Indices: 55436--55464 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55426 TTAAATATCA
55436 CAATTAA-CAAAAAT
1 CAATTAATCAAAAAT
55450 CAATTAATCAAAAAT
1 CAATTAATCAAAAAT
55465 AAATCAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (15 bp):
CAATTAATCAAAAAT
Found at i:57818 original size:22 final size:22
Alignment explanation
Indices: 57792--57833 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
57782 ACTTTCCCAT
*
57792 TTTGAAAACATGAAGTGAACAC
1 TTTGAAAACATGAAGGGAACAC
*
57814 TTTGAAAACCTGAAGGGAAC
1 TTTGAAAACATGAAGGGAAC
57834 CTTCCCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (22 bp):
TTTGAAAACATGAAGGGAACAC
Found at i:58615 original size:10 final size:10
Alignment explanation
Indices: 58600--58624 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
58590 CTTCGAACTT
58600 TAATTAAAAC
1 TAATTAAAAC
58610 TAATTAAAAC
1 TAATTAAAAC
58620 TAATT
1 TAATT
58625 TATTCATATT
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (10 bp):
TAATTAAAAC
Found at i:62944 original size:19 final size:19
Alignment explanation
Indices: 62908--62947 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
62898 TTTCTCTGTT
*
62908 TTCTGCCCTCCACGTCAGA
1 TTCTGCCCTCCACATCAGA
*
62927 TTCTGCCCTCCATATCAGA
1 TTCTGCCCTCCACATCAGA
62946 TT
1 TT
62948 TTCTCTTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.38, G:0.12, T:0.33
Consensus pattern (19 bp):
TTCTGCCCTCCACATCAGA
Found at i:68741 original size:72 final size:72
Alignment explanation
Indices: 68654--68798 Score: 220
Period size: 72 Copynumber: 2.0 Consensus size: 72
68644 GTTATAATTG
* * *
68654 TGTTTGGGGACTTTGATATAGATGACTCTGTGTTGTAAATGTGTTTGAGGACTTT-GAAATAGAA
1 TGTTTGGGGACTTTGATATAGATGACTCTGTGTTATAAATGTATTTGAGGACTTTAGAAAGAGAA
68718 GTGCCCC
66 GTGCCCC
* *
68725 TGTTTGGGGGACTTTGATATAGATGCCTCTGTGTTATAATTGTATTTGAGGACTTTAGAAAGAGA
1 TGTTT-GGGGACTTTGATATAGATGACTCTGTGTTATAAATGTATTTGAGGACTTTAGAAAGAGA
*
68790 ATTGCCCC
65 AGTGCCCC
68798 T
1 T
68799 ATGTTATAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 5 0.08
72 46 0.70
73 15 0.23
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (72 bp):
TGTTTGGGGACTTTGATATAGATGACTCTGTGTTATAAATGTATTTGAGGACTTTAGAAAGAGAA
GTGCCCC
Done.