Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012514.1 Corchorus capsularis cultivar CVL-1 contig12535, 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: 77177
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1441 original size:31 final size:29
Alignment explanation
Indices: 1346--1443 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 29
1336 TGGTTAGATA
* *
1346 CTCAATTTGGTCCTAAACCTTTGAGGAA-ATG
1 CTCAATTTAGTCCTAAACCTTT-A--AACCTG
* *
1377 CTCAATTTGGTCCTAAACCTTTAAACCTA
1 CTCAATTTAGTCCTAAACCTTTAAACCTG
*
1406 CTCAATTTAGTACC-AAACGTTTCAAAACCTG
1 CTCAATTTAGT-CCTAAACCTTT--AAACCTG
1437 CTCAATT
1 CTCAATT
1444 CCGTCCTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
28 2 0.03
29 18 0.31
30 3 0.05
31 35 0.60
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (29 bp):
CTCAATTTAGTCCTAAACCTTTAAACCTG
Found at i:3350 original size:37 final size:37
Alignment explanation
Indices: 3309--3386 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
3299 GCTAAATCAC
3309 TTGATTTTTAATTATTAATCACACATATAATCAATAT
1 TTGATTTTTAATTATTAATCACACATATAATCAATAT
3346 TTGATTTTTAATTATTAATCACACATATAATCAATAT
1 TTGATTTTTAATTATTAATCACACATATAATCAATAT
3383 TTGA
1 TTGA
3387 CGTGTAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (37 bp):
TTGATTTTTAATTATTAATCACACATATAATCAATAT
Found at i:3395 original size:37 final size:37
Alignment explanation
Indices: 3317--3395 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
3307 ACTTGATTTT
** *
3317 TAATTATTAATCACACATATAATCAATATTTGATTTT
1 TAATTATTAATCACACATATAATCAATATTTGACGTG
3354 TAATTATTAATCACACATATAATCAATATTTGACGTG
1 TAATTATTAATCACACATATAATCAATATTTGACGTG
3391 TAATT
1 TAATT
3396 TAGACTCGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (37 bp):
TAATTATTAATCACACATATAATCAATATTTGACGTG
Found at i:5852 original size:32 final size:32
Alignment explanation
Indices: 5787--5864 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 32
5777 GGAAGGAACT
*
5787 AAATACCAATCAAG---TTTTTTTTGGCATCA
1 AAATACCAATCAAGTTTTTTTTTTTGGCAACA
5816 AAATACCAATCAAGTTTTTTTTTTTTGGCAAC-
1 AAATACCAATCAAG-TTTTTTTTTTTGGCAACA
5848 AAATACCAATCAAGTTT
1 AAATACCAATCAAGTTT
5865 AGTTTTGGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 14 0.32
31 3 0.07
32 14 0.32
33 13 0.30
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (32 bp):
AAATACCAATCAAGTTTTTTTTTTTGGCAACA
Found at i:11693 original size:21 final size:21
Alignment explanation
Indices: 11661--11700 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
11651 AAAATGTAGA
*
11661 ATAAACAAGGTGGTAAAGATC
1 ATAAACAAGGTGGGAAAGATC
11682 ATAAA-AATGGTGGGAAAGA
1 ATAAACAA-GGTGGGAAAGA
11701 AAATGGGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.50, C:0.05, G:0.28, T:0.17
Consensus pattern (21 bp):
ATAAACAAGGTGGGAAAGATC
Found at i:13800 original size:37 final size:37
Alignment explanation
Indices: 13747--13820 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
13737 CTTGTCTACA
*
13747 GACCTTTGATTTCCTATTATTTCCTTTTCTAAGATGT
1 GACCTTTGATTTCCTATTATTTCCTTTTCTAAAATGT
*
13784 GACCTTTG-TTTACCTATTGTTTCCTTTTCTAAAATGT
1 GACCTTTGATTT-CCTATTATTTCCTTTTCTAAAATGT
13821 AATCTATAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 3 0.09
37 31 0.91
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (37 bp):
GACCTTTGATTTCCTATTATTTCCTTTTCTAAAATGT
Found at i:14868 original size:22 final size:22
Alignment explanation
Indices: 14842--14888 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
14832 ATTTATTCAT
14842 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
14864 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
14886 TAT
1 TAT
14889 ATAGTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:14884 original size:11 final size:11
Alignment explanation
Indices: 14842--14884 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
14832 ATTTATTCAT
*
14842 TATTAATTAAC
1 TATTAATTAGC
*
14853 TATTAATTAGA
1 TATTAATTAGC
14864 TATTAATTAGC
1 TATTAATTAGC
14875 TATTAATTAG
1 TATTAATTAG
14885 ATATATAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:27259 original size:23 final size:21
Alignment explanation
Indices: 27177--27248 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
27167 GACAAGATGA
27177 GAGCTATAGGTTGTCTCACGT
1 GAGCTATAGGTTGTCTCACGT
* * *
27198 GAGCTATAGGTTGCCTCAAGC
1 GAGCTATAGGTTGTCTCACGT
27219 GAGCTATAGGTTGTCTCACGT
1 GAGCTATAGGTTGTCTCACGT
27240 GAGCTATAG
1 GAGCTATAG
27249 TGGTTATCTC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
GAGCTATAGGTTGTCTCACGT
Found at i:27342 original size:21 final size:21
Alignment explanation
Indices: 27313--27404 Score: 148
Period size: 21 Copynumber: 4.4 Consensus size: 21
27303 GACAAGGTGA
27313 GAGCTATAGGTTGTCTCACGT
1 GAGCTATAGGTTGTCTCACGT
*
27334 GAGTTATAGGTTGTCTCACGT
1 GAGCTATAGGTTGTCTCACGT
* *
27355 GAGCTATAGGTTGTCTCAAGC
1 GAGCTATAGGTTGTCTCACGT
*
27376 GAGCTATAGGTTGTCTCATGT
1 GAGCTATAGGTTGTCTCACGT
27397 GAGCTATA
1 GAGCTATA
27405 ATGGTTATCT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (21 bp):
GAGCTATAGGTTGTCTCACGT
Found at i:27364 original size:136 final size:138
Alignment explanation
Indices: 27130--27384 Score: 406
Period size: 136 Copynumber: 1.9 Consensus size: 138
27120 CAATTACCAT
27130 TGTCTTGCCACAAAGTGGACCTTTTATAAATAATAAAGACAAGATGAGAGCTATAGGTTGTCTCA
1 TGTCTTGCCACAAAGTGGACCTTTTATAAATAATAAAGACAAGATGAGAGCTATAGGTTGTCTCA
* *
27195 CGTGAGCTATAGGTTGCCTCAAGCGAGCTATAGGTTGTCTCACGTGAGCTATAGTGGTTATCTCA
66 CGTGAGCTATAGGTTGCCTCAAGCGAGCTATAGGTTGTCTCAAGCGAGCTATAGTGGTTATCTCA
27260 ATCACCTA
131 ATCACCTA
* * * *
27268 TGTCTTGCCACAAGGTGGA-C-TTTGTAAATAATGAAGACAAGGTGAGAGCTATAGGTTGTCTCA
1 TGTCTTGCCACAAAGTGGACCTTTTATAAATAATAAAGACAAGATGAGAGCTATAGGTTGTCTCA
* * * *
27331 CGTGAGTTATAGGTTGTCTCACGTGAGCTATAGGTTGTCTCAAGCGAGCTATAG
66 CGTGAGCTATAGGTTGCCTCAAGCGAGCTATAGGTTGTCTCAAGCGAGCTATAG
27385 GTTGTCTCAT
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
136 88 0.82
137 1 0.01
138 18 0.17
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (138 bp):
TGTCTTGCCACAAAGTGGACCTTTTATAAATAATAAAGACAAGATGAGAGCTATAGGTTGTCTCA
CGTGAGCTATAGGTTGCCTCAAGCGAGCTATAGGTTGTCTCAAGCGAGCTATAGTGGTTATCTCA
ATCACCTA
Found at i:27525 original size:70 final size:69
Alignment explanation
Indices: 27413--27596 Score: 282
Period size: 70 Copynumber: 2.7 Consensus size: 69
27403 TAATGGTTAT
* * * *
27413 CTCAATCACCTATGTCTTGCCACAAGGTGGA-C-TTTGTAATAGTAAAGAAAAGGTGAGAGACAT
1 CTCAATCACCAATGCCTTGCCACAAAGTGGACCTTTTGTAATAGTAAAGAAAAGGTAAGAGACAT
27476 AATG
66 AATG
*
27480 CTCAATCATCCAATGCCTTGCCACAAAGTGGACCTTTTGTAATAGTAAAGACAAGGTAAGAGACA
1 CTCAATCA-CCAATGCCTTGCCACAAAGTGGACCTTTTGTAATAGTAAAGAAAAGGTAAGAGACA
27545 TAATG
65 TAATG
* *
27550 CTCAATTACCATTGCCTTGCCACAAAGTGGACCTTTTGTAATAGTAA
1 CTCAATCACCAATGCCTTGCCACAAAGTGGACCTTTTGTAATAGTAA
27597 GAAGGAAACC
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
67 8 0.07
68 20 0.19
69 39 0.36
70 40 0.37
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (69 bp):
CTCAATCACCAATGCCTTGCCACAAAGTGGACCTTTTGTAATAGTAAAGAAAAGGTAAGAGACAT
AATG
Found at i:32308 original size:6 final size:6
Alignment explanation
Indices: 32273--32318 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
32263 AGGGAGGAAA
* * *
32273 GAAATG GAAA-G GAAA-G GAAATG GCAAGG GAAAGG GAAAGG GAAAGG
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG
32319 AAATAGGGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
5 10 0.28
6 26 0.72
ACGTcount: A:0.50, C:0.02, G:0.43, T:0.04
Consensus pattern (6 bp):
GAAAGG
Found at i:33911 original size:30 final size:30
Alignment explanation
Indices: 33877--33939 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
33867 ATGGAAAACT
* *
33877 ATTGATATAGAACTAAGTGATAAAGAAAAA
1 ATTGAAATAGAACTAAATGATAAAGAAAAA
* *
33907 ATTGAAATAGAACTAAATGATAGAGAAACA
1 ATTGAAATAGAACTAAATGATAAAGAAAAA
33937 ATT
1 ATT
33940 TAAACAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.56, C:0.05, G:0.16, T:0.24
Consensus pattern (30 bp):
ATTGAAATAGAACTAAATGATAAAGAAAAA
Found at i:51617 original size:2 final size:2
Alignment explanation
Indices: 51606--51643 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
51596 CTTTAGCTTT
51606 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51644 GTATGTATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54406 original size:3 final size:3
Alignment explanation
Indices: 54400--54426 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54390 GCAGCGGCGG
54400 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
54427 AGCGAAGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:63229 original size:13 final size:14
Alignment explanation
Indices: 63211--63240 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
63201 CAGTCTTCCC
63211 TTTTTCCTTTT-TT
1 TTTTTCCTTTTCTT
63224 TTTTTCCTTTTCTT
1 TTTTTCCTTTTCTT
63238 TTT
1 TTT
63241 GGGTTTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCCTTTTCTT
Found at i:64714 original size:3 final size:3
Alignment explanation
Indices: 64706--64734 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
64696 CACAATCTTG
64706 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
64735 TACCAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:69000 original size:12 final size:13
Alignment explanation
Indices: 68978--69014 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
68968 AGTATATTTT
68978 TGGAAAATGGAGA
1 TGGAAAATGGAGA
*
68991 T-GACAATGGAG-
1 TGGAAAATGGAGA
69002 TGGAAAATGGAGA
1 TGGAAAATGGAGA
69015 ACATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 1 0.05
12 18 0.90
13 1 0.05
ACGTcount: A:0.43, C:0.03, G:0.38, T:0.16
Consensus pattern (13 bp):
TGGAAAATGGAGA
Found at i:71858 original size:333 final size:325
Alignment explanation
Indices: 71164--72681 Score: 977
Period size: 334 Copynumber: 4.6 Consensus size: 325
71154 TCTAACTCAG
* * * *
71164 TCTCAGCAACATTGGATTTAAGAATTTGTTTTAATGAGCATCTAAATCTTGTCTT-GATTTAATT
1 TCTCAGCCACATTGGATTTAAGGATTTGTTTT--TAAGCATCTGAATCTTGT-TTCGATTTAATT
* * * * * *
71228 AGAAATTAATTTAGAAAAAAAAAAGAAATACGATATTAAAAGCGTAAAAAGCTCTCCAATTTTTT
63 AGAAATTAATTT-G-GAAAAATATGAAAAACGATATTAAAAGCGTAAAAA-C-CTTCAATATTTT
* * * * *
71293 TGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGGCAAAAATAAAGGAGAA-A--TATTGGCT
124 T-GCTTTGAATTATATATTTTTTATGAGTATTTTAGTCAAAAATTAAGGA-AATATCTTTTGGGT
** * * ***** * * **
71354 -AA---AAACGACAATTCATCA-CGGTTTTCATGTACTAACAATTCATCACGGTTTTTAGCTAAA
187 CAATTTTTAC-AAAATT--TTAGCAAAAATCATGTACT-A-TA-TCA-CA-GTTTTTTAATTAAA
* * * * * * * **
71414 AATGAGTTCCGGGGA-CCCAGCTCAATTTTGCATGATTTTTTGCT-CCGAGACTAATTGAAATAT
244 AACGCGTTTC-GAGACCCCAACTCAGTTTTGCATGATTTTTTG-TGCCGACACTCCTTGAAATAT
71477 CTATATTCATCTAATAAAA
307 CTATATTCATCTAATAAAA
*
71496 TCTCAGCCACATTGGATTTAGGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
1 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTA--AGCATCTGAATCTTGTTTCGATTTAATTA
* *
71561 GAAATTAATTTGGAAAAATA-GGAAAACGATGTTAGAAA-CGTCAAAAACTCTTCAATATTTTTG
64 GAAATTAATTTGGAAAAATATGAAAAACGATATTA-AAAGCGT-AAAAAC-CTTCAATATTTTTG
* *
71624 CTGTTGAATTATATATTTTTTATGAGTATTTTAGTCAAAAATTTAGGAAATATCTTTCGGGTCAA
126 CT-TTGAATTATATATTTTTTATGAGTATTTTAGTCAAAAATTAAGGAAATATCTTTTGGGTCAA
* ** * * *
71689 TTTTTACAAAATTTTATCTGAAATCGTGTAGGTAATAACCATTACAG-TTTTTAATTAAAAA-GC
190 TTTTTACAAAATTTTAGCAAAAATCATGTA-CT-AT----ATCACAGTTTTTTAATTAAAAACGC
* * * * * * * * *
71752 G-TTCTGGGGCCCTAACTCTGTTTTGCATGATTTTTTGTGCCAATACTCCTTGAGATATCCATGT
249 GTTTC-GAGACCCCAACTCAGTTTTGCATGATTTTTTGTGCCGACACTCCTTGAAATATCTATAT
* * *
71816 TAATCAAATCAAA
313 TCATCTAATAAAA
* * * *
71829 TCTCAGCTACATTGGATTTAAGAATTTGTTTCTAAAAGCATCTGAATCTTGTTTCGATTTAATTG
1 TCTCAGCCACATTGGATTTAAGGATTTGTTT-T-TAAGCATCTGAATCTTGTTTCGATTTAATTA
** * * ** * * *
71894 GAAATTAATTCAGAATAATATGAAAAACGATATTAAAAGCGATTTAAGTCCTCCAATCTTTTTGG
64 GAAATTAATTTGGAAAAATATGAAAAACGATATTAAAAGCG--TAAAAACCTTCAATATTTTTGC
* * * * * *
71959 TATTAAATTATTTATATTTTATGAGTAGTTTA-TCCAAAAATTAAGGAAAAAAT-TTTTGAGTCA
127 T-TTGAATTATATATTTTTTATGAGTATTTTAGT-CAAAAATTAAGG-AAATATCTTTTGGGTCA
* * ** *
72022 TTTTTTTTTTCAAAATTCCAGCAAAAATCATGTACTATATCACAGTTTTTTTACTTAAAAACGCG
189 ---ATTTTTACAAAATTTTAGCAAAAATCATGTACTATATCACAG-TTTTTTAATTAAAAACGCG
** * * *
72087 TTTCGAGACCCCGGCTCAGTTTTGCATGATTTTTGGTGTCGGCACTCCTTGAAATATCTATATTC
250 TTTCGAGACCCCAACTCAGTTTTGCATGATTTTTTGTGCCGACACTCCTTGAAATATCTATATTC
72152 ATCTAATAAAA
315 ATCTAATAAAA
* * * *
72163 TTTGAGCCACATTGCATTTAAGGATTTGTTTTT-A-C-T-T-AATCTTGTTTTGATTTAATTAGA
1 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTAAGCATCTGAATCTTGTTTCGATTTAATTAGA
*
72223 AATTAATTCTGAAAAAATATGAAAAACGATATTAAAAGCGTAAAAAGCCCTTCAATATTTTTGCC
66 AATTAATT-TGGAAAAATATGAAAAACGATATTAAAAGCGTAAAAA--CCTTCAATATTTTTG-C
* * *
72288 TTTGAATTATATATTTTTTATGAGTATTAT-GGCTAAAAATTAATGAAATATCTTTTGGGTCAAT
127 TTTGAATTATATATTTTTTATGAGTATTTTAGTC-AAAAATTAAGGAAATATCTTTTGGGTCAAT
* * * * * * * *** *
72352 TTTTGCAAAATTTTAGGAGAAATCGTATAATA-ATCATCACGATTTTTGGCTAAAAACGCGTTCC
191 TTTTACAAAATTTTAGCAAAAATCATGTACTATATCA-CA-GTTTTTTAATTAAAAACGCGTTTC
* *** * * * * *
72416 GGGA-CCCGGTTTAATTTTGAATGATTTTTTGCGCCGAGACTCCTTGAAATATCTATATTCATCT
254 GAGACCCCAACTCAGTTTTGCATGATTTTTTGTGCCGACACTCCTTGAAATATCTATATTCATCT
**
72480 AACCAAA
319 AATAAAA
** *
72487 TC-CTAG-C-C-----A--T-----TTT-TTTACAAGCATCTGAATCATGTTTC-ATTTTAATTA
1 TCTC-AGCCACATTGGATTTAAGGATTTGTTTTTAAGCATCTGAATCTTGTTTCGA-TTTAATTA
* * * * * * *
72535 GAAATTAATTCGGAAAAATAGGAAAAACGATATTAGAAGCATGAAAAGTCCTTCAATCTTTTCGG
64 GAAATTAATTTGGAAAAATATGAAAAACGATATTAAAAGCGT-AAAA-ACCTTCAATATTTT-TG
* * * * *
72600 CGTTGAATTATATATTTTTTATGAGTATTGT-GACTAAAAA-TAGAGGAAAAATATTTTGGGTCA
126 CTTTGAATTATATATTTTTTATGAGTATTTTAGTC-AAAAATTA-AGGAAATATCTTTTGGGTCA
* *
72663 ATTTTTGCAAAATATTAGC
189 ATTTTTACAAAATTTTAGC
72682 CGAAATCGTG
Statistics
Matches: 950, Mismatches: 179, Indels: 133
0.75 0.14 0.11
Matches are distributed among these distances:
309 3 0.00
310 4 0.00
311 1 0.00
312 3 0.00
313 112 0.12
314 32 0.03
315 1 0.00
317 1 0.00
322 1 0.00
323 1 0.00
324 63 0.07
325 48 0.05
326 4 0.00
327 35 0.04
328 86 0.09
329 43 0.05
330 46 0.05
331 10 0.01
332 76 0.08
333 148 0.16
334 177 0.19
335 23 0.02
336 6 0.01
337 25 0.03
338 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (325 bp):
TCTCAGCCACATTGGATTTAAGGATTTGTTTTTAAGCATCTGAATCTTGTTTCGATTTAATTAGA
AATTAATTTGGAAAAATATGAAAAACGATATTAAAAGCGTAAAAACCTTCAATATTTTTGCTTTG
AATTATATATTTTTTATGAGTATTTTAGTCAAAAATTAAGGAAATATCTTTTGGGTCAATTTTTA
CAAAATTTTAGCAAAAATCATGTACTATATCACAGTTTTTTAATTAAAAACGCGTTTCGAGACCC
CAACTCAGTTTTGCATGATTTTTTGTGCCGACACTCCTTGAAATATCTATATTCATCTAATAAAA
Found at i:72835 original size:21 final size:20
Alignment explanation
Indices: 72781--72839 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
72771 GGAAATGTTG
*
72781 TCACTATTTGGTGTAATGAT
1 TCACTATTAGGTGTAATGAT
* *
72801 TC-CTTTTAGGTGTAATGGT
1 TCACTATTAGGTGTAATGAT
*
72820 ATCACTATTAGATGTAATGA
1 -TCACTATTAGGTGTAATGA
72840 AGTTTCAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 14 0.45
20 4 0.13
21 13 0.42
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.42
Consensus pattern (20 bp):
TCACTATTAGGTGTAATGAT
Done.