Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021781.1 Corchorus olitorius cultivar O-4 contig21814, 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: 49797
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:592 original size:43 final size:43
Alignment explanation
Indices: 545--673 Score: 258
Period size: 43 Copynumber: 3.0 Consensus size: 43
535 GGATGGGATC
545 AGTTGGCCTAAATTAAACACATATTTTACAACCACTGAGAATA
1 AGTTGGCCTAAATTAAACACATATTTTACAACCACTGAGAATA
588 AGTTGGCCTAAATTAAACACATATTTTACAACCACTGAGAATA
1 AGTTGGCCTAAATTAAACACATATTTTACAACCACTGAGAATA
631 AGTTGGCCTAAATTAAACACATATTTTACAACCACTGAGAATA
1 AGTTGGCCTAAATTAAACACATATTTTACAACCACTGAGAATA
674 TTCTCATATG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 86 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (43 bp):
AGTTGGCCTAAATTAAACACATATTTTACAACCACTGAGAATA
Found at i:958 original size:41 final size:44
Alignment explanation
Indices: 913--997 Score: 104
Period size: 41 Copynumber: 2.0 Consensus size: 44
903 TTAAAGATAC
*
913 AAAATTTATATATATTGACTTTTA-ATTT-TAATTATTT-TATT
1 AAAATTTATATATATTGAATTTTATATTTATAATTATTTCTATT
* * * *
954 AAAATTTGTATTTATTTAATTTTATCTTTATAATTATTTCTATT
1 AAAATTTATATATATTGAATTTTATATTTATAATTATTTCTATT
998 CAATGTTGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 20 0.56
42 3 0.08
43 9 0.25
44 4 0.11
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (44 bp):
AAAATTTATATATATTGAATTTTATATTTATAATTATTTCTATT
Found at i:10956 original size:47 final size:44
Alignment explanation
Indices: 10904--11002 Score: 144
Period size: 47 Copynumber: 2.2 Consensus size: 44
10894 GAATACAGAA
*
10904 AATTGAAGGAAGTTTTTTTACCAAAAAAGAGAGAGAAAAAAAGAAAG
1 AATTGAAGGAAGTTTTTCTACC-AAAAA-AGAGA-AAAAAAAGAAAG
* *
10951 AATTGAAGGAAGTTTTTCTACCAAAAAAGAGAAAAAGAAGAATG
1 AATTGAAGGAAGTTTTTCTACCAAAAAAGAGAAAAAAAAGAAAG
10995 AATTGAAG
1 AATTGAAG
11003 CAGTTGGAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
44 18 0.37
45 5 0.10
46 5 0.10
47 21 0.43
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.20
Consensus pattern (44 bp):
AATTGAAGGAAGTTTTTCTACCAAAAAAGAGAAAAAAAAGAAAG
Found at i:11461 original size:2 final size:2
Alignment explanation
Indices: 11445--11480 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
11435 TTTAATTTAT
11445 TA TA CTA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11481 ATTTGTGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:26061 original size:288 final size:290
Alignment explanation
Indices: 25542--26103 Score: 756
Period size: 288 Copynumber: 1.9 Consensus size: 290
25532 TAGATTATCG
* * * *
25542 GGTTTCATACCTCAAGAAGTTGGATTCTTGACATCTCTTTCCCAGCTTTATTTGTATGGAAACAA
1 GGTTTCATACCTCAACAACTTGGATTCTTGACATCTCTTTCCCAGCTCTATTTGAATGGAAACAA
* * *
25607 TTTAACAGGTCCAATCCCAACTTCAATGATGGGAAACTTGAGCAACCTAAATGTTCTTTATCTTC
66 TTTAACAGGCCCAATCCCAACTTC-ATGATGGGAAACTTGACCAACCTAAATGCTCTTTATCTTC
* ** * * * * * *
25672 ATAGCAACAAACTCTCGGGTTCCATTCCTCGAGAGATTGGATTATTAAGATCTATTCAAGATCTT
130 ATACCAACAAACTCTCGGCCTCCATTCCTCAACAGATTGGATTACTAACATCCATTCAAGAGCTT
* ** * *
25737 GACTTTTCAATAAATAGCCTCACTGGCAGTATTCCTCATGGAATAGGAAATTTGAGTAACTTGTT
195 GACTTCTCAATAAATAGCCTCACTGGCAGTATTCCTCATCAAATAGGAAATTTGACTAACTTGTC
*
25802 TTATCTTAGTCTTTCGAGAAACAACCTGTCT
260 TGATCTTAGTCTTTCGAGAAACAACCTGTCT
**
25833 GGTTTCATACCTCAACAACTTGGATTCTTGACATCTCTTTCCTTGCTCTATTTGAATGGAAACAA
1 GGTTTCATACCTCAACAACTTGGATTCTTGACATCTCTTTCCCAGCTCTATTTGAATGGAAACAA
* **
25898 TTTAACAGGCCCAATCCCAACTTC-T-ATTGGAAACTTGACCAACAC-ACTTGCTCTTTATCTTC
66 TTTAACAGGCCCAATCCCAACTTCATGATGGGAAACTTGACCAAC-CTAAATGCTCTTTATCTTC
* * *
25960 GTACCAACAAACTCTCTGGCCT-CATTCCTCAACAGATTGGGTTGCTAACATCCATTCAAGAGCT
130 ATACCAACAAACTCTC-GGCCTCCATTCCTCAACAGATTGGATTACTAACATCCATTCAAGAGCT
* *
26024 TGACTTCTCACA-AAATTGCCTCACTGGCAGTATTCCTCATCAAATAGGAAATTTGACTAATTTG
194 TGACTTCTCA-ATAAATAGCCTCACTGGCAGTATTCCTCATCAAATAGGAAATTTGACTAACTTG
*
26088 TCTGCTCTTAGTCTTT
258 TCTGATCTTAGTCTTT
26104 TGGACAACAG
Statistics
Matches: 235, Mismatches: 33, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
288 147 0.63
289 6 0.03
291 82 0.35
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (290 bp):
GGTTTCATACCTCAACAACTTGGATTCTTGACATCTCTTTCCCAGCTCTATTTGAATGGAAACAA
TTTAACAGGCCCAATCCCAACTTCATGATGGGAAACTTGACCAACCTAAATGCTCTTTATCTTCA
TACCAACAAACTCTCGGCCTCCATTCCTCAACAGATTGGATTACTAACATCCATTCAAGAGCTTG
ACTTCTCAATAAATAGCCTCACTGGCAGTATTCCTCATCAAATAGGAAATTTGACTAACTTGTCT
GATCTTAGTCTTTCGAGAAACAACCTGTCT
Found at i:34643 original size:28 final size:28
Alignment explanation
Indices: 34579--34653 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 28
34569 TCCAGCGTCT
* **
34579 AAGGGCAAAATTGTAA-TTTAGCCAATT
1 AAGGGCAAAATAGTAATTTTAGCCAACC
* * *
34606 AGGGGTAAAATAGTAATTTTAGCCGACC
1 AAGGGCAAAATAGTAATTTTAGCCAACC
* *
34634 AAGGGCAAAACAATAATTTT
1 AAGGGCAAAATAGTAATTTT
34654 GACATCTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
27 13 0.35
28 24 0.65
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (28 bp):
AAGGGCAAAATAGTAATTTTAGCCAACC
Found at i:35238 original size:5 final size:5
Alignment explanation
Indices: 35224--35285 Score: 65
Period size: 5 Copynumber: 12.4 Consensus size: 5
35214 ATTTCATTTC
*
35224 TTATT ATTATT TTA-- TTATT TTATT TTATT TTAAT TTATT TTATTT TTATT
1 TTATT -TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTA-TT TTATT
* *
35274 TTCTT TTCTT TT
1 TTATT TTATT TT
35286 CCTTTTCTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
3 3 0.06
5 37 0.74
6 10 0.20
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:35285 original size:15 final size:15
Alignment explanation
Indices: 35238--35295 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
35228 TATTATTTTA
*
35238 TTATTTTATTTTATT
1 TTATTTTCTTTTATT
* *
35253 TTAATTTATTTTATTT
1 TTATTTTCTTTTA-TT
*
35269 TTATTTTCTTTTCTT
1 TTATTTTCTTTTATT
*
35284 TTCCTTTTCTTT
1 TT-ATTTTCTTT
35296 CTTTTCTCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 16 0.44
16 20 0.56
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTATTTTCTTTTATT
Found at i:35296 original size:15 final size:16
Alignment explanation
Indices: 35272--35301 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35262 TTTATTTTTA
35272 TTTTCTTTTCTTTTCC
1 TTTTCTTTTCTTTTCC
35288 TTTTC-TTTCTTTTC
1 TTTTCTTTTCTTTTC
35302 TCTTCTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCTTTTCTTTTCC
Found at i:35363 original size:5 final size:5
Alignment explanation
Indices: 35353--35399 Score: 55
Period size: 5 Copynumber: 10.0 Consensus size: 5
35343 CCTCAGCCAC
* *
35353 CTTTT CTTTT CTTTC CTTTT CTTTT CTTTT -TTTT -TTTG CTTTT -TTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
35400 TTATTCAGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
4 11 0.30
5 26 0.70
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (5 bp):
CTTTT
Found at i:35387 original size:15 final size:15
Alignment explanation
Indices: 35354--35400 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
35344 CTCAGCCACC
**
35354 TTTTCTTTTCTTTCC
1 TTTTCTTTTCTTTTT
35369 TTTTCTTTTC-TTTT
1 TTTTCTTTTCTTTTT
*
35383 TTTT-TTTGCTTTTT
1 TTTTCTTTTCTTTTT
35397 TTTT
1 TTTT
35401 TATTCAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 4 0.14
14 14 0.50
15 10 0.36
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTCTTTTT
Found at i:35394 original size:13 final size:12
Alignment explanation
Indices: 35354--35401 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
35344 CTCAGCCACC
*
35354 TTTTCTTTTCTT
1 TTTTTTTTTCTT
35366 TCCTTTTCTTTTCTT
1 T--TTTT-TTTTCTT
35381 TTTTTTTTTGCTT
1 TTTTTTTTT-CTT
35394 TTTTTTTT
1 TTTTTTTT
35402 ATTCAGTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.16
13 15 0.48
14 3 0.10
15 8 0.26
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:35881 original size:17 final size:17
Alignment explanation
Indices: 35859--35894 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
35849 TCTTAAAAGG
35859 AACAAGTTCTAATTCAA
1 AACAAGTTCTAATTCAA
35876 AACAAGTTCTAATTCAA
1 AACAAGTTCTAATTCAA
35893 AA
1 AA
35895 ATATACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (17 bp):
AACAAGTTCTAATTCAA
Found at i:39611 original size:6 final size:6
Alignment explanation
Indices: 39600--39644 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
39590 CTCAATTCGA
*
39600 ATATGT ATATGT ATAAGT ATATGT ATATGT -TATGT ATATGT ATAT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATAT
39645 ACTATCAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (6 bp):
ATATGT
Found at i:39899 original size:21 final size:22
Alignment explanation
Indices: 39874--39923 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
39864 TTATCGAAAA
39874 TCATAGGAAGATTA-CAAAATT
1 TCATAGGAAGATTATCAAAATT
** *
39895 TCATAGTTAGATTATCAAAGTT
1 TCATAGGAAGATTATCAAAATT
39917 TCATAGG
1 TCATAGG
39924 GGTACAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATAGGAAGATTATCAAAATT
Found at i:39918 original size:22 final size:21
Alignment explanation
Indices: 39882--39922 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
39872 AATCATAGGA
39882 AGATTACAAAATTTCATAGTT
1 AGATTACAAAATTTCATAGTT
*
39903 AGATTATCAAAGTTTCATAG
1 AGATTA-CAAAATTTCATAG
39923 GGGTACAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (21 bp):
AGATTACAAAATTTCATAGTT
Found at i:40280 original size:22 final size:22
Alignment explanation
Indices: 40211--40398 Score: 109
Period size: 22 Copynumber: 8.5 Consensus size: 22
40201 ACAATCAAAC
* *
40211 CAAAATTACATAGT-AAGGTTAT
1 CAAAATTTCATAGTGTA-GTTAT
* * *
40233 CAAAATTTCATAGTGTTGTAAC
1 CAAAATTTCATAGTGTAGTTAT
*
40255 CAAAATTTCAT-GTGGAGATTAT
1 CAAAATTTCATAGTGTAG-TTAT
40277 CAAAACTTT-ATAGTGTAGTTAT
1 CAAAA-TTTCATAGTGTAGTTAT
* ** *
40299 CAAAATTTTATACAG-AGGTTAC
1 CAAAATTTCATAGTGTA-GTTAT
* * *
40321 CAAAATTTCTTAG-GGAGGTTAA
1 CAAAATTTCATAGTGTA-GTTAT
* *
40343 CAAAATTTCATA-CGAAGGTTAT
1 CAAAATTTCATAGTGTA-GTTAT
** * *
40365 TGAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGTGTAGTTAT
40387 CAAAATTTCATA
1 CAAAATTTCATA
40399 AGAAGGTTAA
Statistics
Matches: 128, Mismatches: 29, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
21 9 0.07
22 110 0.86
23 9 0.07
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGTGTAGTTAT
Found at i:40325 original size:44 final size:44
Alignment explanation
Indices: 40225--40415 Score: 133
Period size: 44 Copynumber: 4.4 Consensus size: 44
40215 ATTACATAGT
* * * * **
40225 AAGGTTATCAAAATTTCATAGTGTTGTAACCAAAATTTCAT-GTG
1 AAGGTTACCAAAATTT-ATAGTGTAGTTATCAAAATTTCATACAG
* * * *
40269 GAGATTATCAAAACTTTATAGTGTAGTTATCAAAATTTTATACAG
1 AAGGTTACCAAAA-TTTATAGTGTAGTTATCAAAATTTCATACAG
* * *
40314 -AGGTTACCAAAATTTCTTAG-GGAGGTTAACAAAATTTCATAC-G
1 AAGGTTACCAAAATTT-ATAGTGTA-GTTATCAAAATTTCATACAG
** * *
40357 AAGGTTATTGAAATTTTATAGTGTGGTTATCAAAATTTCATA-AG
1 AAGGTTA-CCAAAATTTATAGTGTAGTTATCAAAATTTCATACAG
*
40401 AAGGTTA-AAAAATTT
1 AAGGTTACCAAAATTT
40416 TCAGAGAGAG
Statistics
Matches: 116, Mismatches: 23, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
42 6 0.05
43 6 0.05
44 93 0.80
45 11 0.09
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (44 bp):
AAGGTTACCAAAATTTATAGTGTAGTTATCAAAATTTCATACAG
Found at i:40503 original size:20 final size:21
Alignment explanation
Indices: 40226--40518 Score: 91
Period size: 22 Copynumber: 13.4 Consensus size: 21
40216 TTACATAGTA
*
40226 AGGTTATCAAAATTTCATAGTG
1 AGGTTATCAAAATTT-ATAGGG
** * *
40248 TTGTAACCAAAATTTCAT-GTGG
1 AGGTTATCAAAATTT-ATAG-GG
* *
40270 AGATTATCAAAACTTTATAGTGT
1 AGGTTATCAAAA-TTTATAG-GG
**
40293 A-GTTATCAAAATTTTATACAG
1 AGGTTATCAAAA-TTTATAGGG
* *
40314 AGGTTACCAAAATTTCTTAGGG
1 AGGTTATCAAAATTT-ATAGGG
* * *
40336 AGGTTAACAAAATTTCATACGA
1 AGGTTATCAAAATTT-ATAGGG
* * *
40358 AGGTTATTGAAATTTTATAGTG
1 AGGTTA-TCAAAATTTATAGGG
* * *
40380 TGGTTATCAAAATTTCATAAGA
1 AGGTTATCAAAATTT-ATAGGG
* *
40402 AGGTTA-AAAAATTTTCAGAGAGAGTG
1 AGGTTATCAAAA-TTT---ATAG-G-G
*
40428 AGGTTATCAAAA-CT-T---G
1 AGGTTATCAAAATTTATAGGG
* *
40444 TGCTTATCAAAATTTCATAGGG
1 AGGTTATCAAAATTT-ATAGGG
*
40466 AGGTTATGAAAATTT-TATGGAG
1 AGGTTATCAAAATTTATA-GG-G
*
40488 AGGTTATCAAAATTATATAGAG
1 AGGTTATCAAAATT-TATAGGG
*
40510 AGGATATCA
1 AGGTTATCA
40519 CAGCTTCGTT
Statistics
Matches: 194, Mismatches: 54, Indels: 46
0.66 0.18 0.16
Matches are distributed among these distances:
16 11 0.06
17 1 0.01
19 1 0.01
20 2 0.01
21 18 0.09
22 130 0.67
23 15 0.08
24 4 0.02
25 2 0.01
26 6 0.03
27 4 0.02
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (21 bp):
AGGTTATCAAAATTTATAGGG
Found at i:40657 original size:22 final size:22
Alignment explanation
Indices: 40539--40689 Score: 90
Period size: 22 Copynumber: 6.7 Consensus size: 22
40529 CTCATACGGA
* * *
40539 GGTTTTCAGAATTTCATGGTGT
1 GGTTATCAAAATTTCATAGTGT
40561 GGTTATCAAAATTTTCATATATAGTGT
1 GGTTATCAAAA-TTTC----ATAGTGT
* * **
40588 GATTA-C-CAATTTTGTAGTGT
1 GGTTATCAAAATTTCATAGTGT
* ** * *
40608 GATTATCAAAATTTTCCCACTGA
1 GGTTATCAAAA-TTTCATAGTGT
*
40631 AGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
40653 GGTTATCAAATTTTCACAGTGT
1 GGTTATCAAAATTTCATAGTGT
*
40675 GGTTATCAATATTTC
1 GGTTATCAAAATTTC
40690 TACGTTGGAG
Statistics
Matches: 97, Mismatches: 24, Indels: 16
0.71 0.18 0.12
Matches are distributed among these distances:
20 11 0.11
21 1 0.01
22 50 0.52
23 19 0.20
24 3 0.03
25 2 0.02
26 1 0.01
27 10 0.10
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:40680 original size:44 final size:45
Alignment explanation
Indices: 40602--40689 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 45
40592 ACCAATTTTG
*
40602 TAGTGTGATTATCAAAATTTTCCCACTGAAGTTATCAAAATTTCA
1 TAGTGTGATTATCAAAATTTTCACACTGAAGTTATCAAAATTTCA
* * ** *
40647 TAGTGTGGTTATC-AAATTTTCACAGTGTGGTTATCAATATTTC
1 TAGTGTGATTATCAAAATTTTCACACTGAAGTTATCAAAATTTC
40690 TACGTTGGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 25 0.68
45 12 0.32
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (45 bp):
TAGTGTGATTATCAAAATTTTCACACTGAAGTTATCAAAATTTCA
Found at i:43041 original size:60 final size:61
Alignment explanation
Indices: 42960--43075 Score: 180
Period size: 60 Copynumber: 1.9 Consensus size: 61
42950 GGGTTTAAAG
42960 AAAGAAAAAAAAATGCTCAAATGAAGACCCAACATTACGAAAATTGCTAAAATAAGGGCTC
1 AAAGAAAAAAAAATGCTCAAATGAAGACCCAACATTACGAAAATTGCTAAAATAAGGGCTC
* * * * *
43021 AAAG-AAAAAAAATGTTCAAATTAGGACCCAACATTGCGAAAATTGCTCAAATAAG
1 AAAGAAAAAAAAATGCTCAAATGAAGACCCAACATTACGAAAATTGCTAAAATAAG
43076 TCTGTGCTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 46 0.92
61 4 0.08
ACGTcount: A:0.52, C:0.16, G:0.15, T:0.18
Consensus pattern (61 bp):
AAAGAAAAAAAAATGCTCAAATGAAGACCCAACATTACGAAAATTGCTAAAATAAGGGCTC
Found at i:43194 original size:28 final size:28
Alignment explanation
Indices: 43158--43236 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
43148 TTTTGCAACG
* *
43158 TTGGACCCTTATTTGAGCTTTTTTTTCT
1 TTGGACCCTTATTTGAACATTTTTTTCT
* *
43186 TTGGGCCCTGATTTGAACATTTTTTTCT
1 TTGGACCCTTATTTGAACATTTTTTTCT
*
43214 TTAGACCCTTATTT-AATCATTTT
1 TTGGACCCTTATTTGAA-CATTTT
43237 CGCAAACATT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 2 0.05
28 41 0.95
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.53
Consensus pattern (28 bp):
TTGGACCCTTATTTGAACATTTTTTTCT
Found at i:48018 original size:360 final size:358
Alignment explanation
Indices: 47345--48043 Score: 892
Period size: 360 Copynumber: 1.9 Consensus size: 358
47335 CGCACAAGAC
*
47345 CAAGATAAGACAAATTAGTCAAATTTCCAATTCCACGAGGAATACTGCCAGTGAGGCTATTGTCT
1 CAAGATAAGACAAATTAATCAAATTTCCAATTCCACGAGGAATACTGCCAGTGAGGCTATTGTCT
* *
47410 GATAAGCTAAGCAATTGAATGGATCTTAACAAGCCAATCTGGCTAGGAATTGGACCAGAGAGTTT
66 GACAAGCTAAGCAATTGAATGGATCTTAACAAGCCAATCT-GCTAGGAATGGGACCAGAGAGTTT
*
47475 GTTCGAAGAAAGAGAAAGAAAAAGTATGTTGGTCAAGTTTCCAATAGAAGTTGGGATTGGACCAG
130 GTTCCAAGAAAGAGAAAGAAAAAGTATGTTGGTCAAGTTTCCAATAGAAGTTGGGATTGGACCAG
* * * * * *
47540 TTAAATTGTTTTCTTGCAAATCAAGCTGGGAAAGAGCGGTTAGAAATCCAATTTCTTGTGGTATG
195 TTAAATTGTTTTC-TACAAATAAAGCTGGGAAAGAGAGGTCAGAAATCCAAGTTCTTGAGGTATG
** * * **** * * **
47605 TTACCCGACAACTTGTTTTCCCAGAGATGAAGATAAGACAAATTAGTCAAATTTCCCAAA-GAAG
259 AAACCAGACAACTTATTGGAACAAAGATCAAGATAAGACAAATTACACAAATTT-CCAAAGGAAG
47669 GAGGGATCCTACCCGACAACTTGTTTCCCCATAAAA
323 GAGGGATCCTACCCGACAACTTGTTTCCCCATAAAA
* * * * *
47705 CAAGA-AATGACAAATTAATCAAATTTCCTATTCCATGAGGAATACTGCCAGTGAGGTTGTTTTC
1 CAAGATAA-GACAAATTAATCAAATTTCCAATTCCACGAGGAATACTGCCAGTGAGGCTATTGTC
**
47769 TGACAAG-TCAAGCTTTTGAATGGATCTTAACAAGCCAATCT-CTTGAGGAATGGGACCAGAGAG
65 TGACAAGCT-AAGCAATTGAATGGATCTTAACAAGCCAATCTGC-T-AGGAATGGGACCAGAGAG
* * * * *
47832 TTTGTTCCTATAAAGATAGAGAAAAAGTATGTTGGTCAAGTTTCCTATAGAAGTTGGGATTGGAC
127 TTTGTTCCAAGAAAGAGAAAGAAAAAGTATGTTGGTCAAGTTTCCAATAGAAGTTGGGATTGGAC
* *
47897 CAGTTAAATTGTTTATGC-ACAAATAAAGCTGGGAGAGAGATGTCA-ATAATCCAAGTTCTTGAG
192 CAGTTAAATTGTTT-T-CTACAAATAAAGCTGGGAAAGAGAGGTCAGA-AATCCAAGTTCTTGAG
* *
47960 GTATGAAACCAGACAA-TCTATTGGAACAAAGGTCAAGA-AATGACAAGTTACACAAATTTCCAA
254 GTATGAAACCAGACAACT-TATTGGAACAAAGATCAAGATAA-GACAAATTACACAAATTTCCAA
48023 AGGAAGGAGGGATCCTACCCG
317 AGGAAGGAGGGATCCTACCCG
48044 TCAGGATATT
Statistics
Matches: 291, Mismatches: 38, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
358 1 0.00
359 13 0.04
360 275 0.95
361 1 0.00
362 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (358 bp):
CAAGATAAGACAAATTAATCAAATTTCCAATTCCACGAGGAATACTGCCAGTGAGGCTATTGTCT
GACAAGCTAAGCAATTGAATGGATCTTAACAAGCCAATCTGCTAGGAATGGGACCAGAGAGTTTG
TTCCAAGAAAGAGAAAGAAAAAGTATGTTGGTCAAGTTTCCAATAGAAGTTGGGATTGGACCAGT
TAAATTGTTTTCTACAAATAAAGCTGGGAAAGAGAGGTCAGAAATCCAAGTTCTTGAGGTATGAA
ACCAGACAACTTATTGGAACAAAGATCAAGATAAGACAAATTACACAAATTTCCAAAGGAAGGAG
GGATCCTACCCGACAACTTGTTTCCCCATAAAA
Found at i:48211 original size:72 final size:72
Alignment explanation
Indices: 48072--48214 Score: 184
Period size: 72 Copynumber: 2.0 Consensus size: 72
48062 AGTCAAGGTG
* * * *
48072 GATGAGTTTGGTAAGATTACCAATTGGTGATGGAATATTTCCAGAAGGAGTGTTAGAACTAAGAT
1 GATGAGTTTGGGAAGATTACCAATTGGTGATGGAATATTTCCAGAAGGAGAGTTAGAAATAAAAT
48137 CAAGATA
66 CAAGATA
* *
48144 GATGAGTTTGGGAAGATTACCAATTTGTGGA-GGAATGTTTCCAGTAA-GAGAGTTA-AAATAAA
1 GATGAGTTTGGGAAGATTACCAATTGGT-GATGGAATATTTCCAG-AAGGAGAGTTAGAAAT-AA
48206 AATCAAGAT
63 AATCAAGAT
48215 GAGTAAGGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
71 3 0.05
72 55 0.89
73 4 0.06
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.29
Consensus pattern (72 bp):
GATGAGTTTGGGAAGATTACCAATTGGTGATGGAATATTTCCAGAAGGAGAGTTAGAAATAAAAT
CAAGATA
Done.