Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022436.1 Corchorus olitorius cultivar O-4 contig22469, 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: 40579
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:8013 original size:3 final size:3
Alignment explanation
Indices: 8007--8037 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
7997 AAGAAGAAGA
*
8007 AGG AGG AGG AGG CGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
8038 AAGTAGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:8172 original size:18 final size:18
Alignment explanation
Indices: 8132--8174 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
8122 TCCTATTGCT
8132 GTTTT-TTTTCAGATCCA
1 GTTTTGTTTTCAGATCCA
*
8149 GGTTTGTTTTCAGATCCA
1 GTTTTGTTTTCAGATCCA
*
8167 TTTTTGTT
1 GTTTTGTT
8175 CTCTTAGCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.56
Consensus pattern (18 bp):
GTTTTGTTTTCAGATCCA
Found at i:17853 original size:29 final size:30
Alignment explanation
Indices: 17800--17883 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 30
17790 CAAATTCACA
* *
17800 CATGGCACGTGTC-CTTTTTATGTAC-GAGG
1 CATGCCACGTGTCACTTTTT-GGTACAGAGG
* *
17829 CATGCCATGTGTCACTTTTTGGTACATGTGG
1 CATGCCACGTGTCACTTTTTGGTACA-GAGG
* *
17860 CGTGTCACGTGTCACTTTTTGGTA
1 CATGCCACGTGTCACTTTTTGGTA
17884 TACGTGGCGT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
29 15 0.33
30 6 0.13
31 24 0.53
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.38
Consensus pattern (30 bp):
CATGCCACGTGTCACTTTTTGGTACAGAGG
Found at i:17875 original size:31 final size:31
Alignment explanation
Indices: 17831--17914 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
17821 GTACGAGGCA
* *
17831 TGCCATGTGTCACTTTTTGGTACATGTGGCG
1 TGCCACGTGTCACTTTTTGGTACACGTGGCG
* *
17862 TGTCACGTGTCACTTTTTGGTATACGTGGCG
1 TGCCACGTGTCACTTTTTGGTACACGTGGCG
* * *
17893 TGCCACATATCGCTTTTTGGTA
1 TGCCACGTGTCACTTTTTGGTA
17915 TACATGGCAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.14, C:0.20, G:0.26, T:0.39
Consensus pattern (31 bp):
TGCCACGTGTCACTTTTTGGTACACGTGGCG
Found at i:21298 original size:21 final size:21
Alignment explanation
Indices: 21273--21355 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
21263 TATCTTAGAT
21273 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
21294 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
21315 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
21337 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
21356 TTATTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:21306 original size:25 final size:25
Alignment explanation
Indices: 21275--21323 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21265 TCTTAGATAT
*
21275 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
21300 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
21324 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:22988 original size:1 final size:1
Alignment explanation
Indices: 22982--23015 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
22972 TTAGCATTAG
22982 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
23016 ATCTTGAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26114 original size:42 final size:42
Alignment explanation
Indices: 26055--26139 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
26045 GTTCATCAAT
26055 TGTTGGCTAAATGCTACTAATTAGACTATTCCCTAATCTGGC
1 TGTTGGCTAAATGCTACTAATTAGACTATTCCCTAATCTGGC
26097 TGTTGGCTAAATGCTACTAATTAGACTATTCCCTAATCTGGC
1 TGTTGGCTAAATGCTACTAATTAGACTATTCCCTAATCTGGC
26139 T
1 T
26140 TGTGATTCTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.36
Consensus pattern (42 bp):
TGTTGGCTAAATGCTACTAATTAGACTATTCCCTAATCTGGC
Found at i:26345 original size:99 final size:97
Alignment explanation
Indices: 26173--26460 Score: 334
Period size: 99 Copynumber: 3.0 Consensus size: 97
26163 ATATAAACAC
* * * * *
26173 ATGAATGAAATCTGTT-TT-TCCTCGAATGTCGGGTCTAGTGGAAGGAG-TTCAAAATCCTTTTA
1 ATGAATAAAATATGTTATTCTCCTCAAATGTCGGGTCTAGTGGAAGGAGCTT-GAAACCCTTTTA
* *
26235 AGCAAGATTTTTATGCATTTTGGTCCTTCTAGTA
65 AACAAGGTTTTTATGCATTTTGGTCCTT-TAGTA
* * *
26269 ATGAATGAAATATTTTTTTCCTCCTCAAATGTCGGGTCTAGTGGAAGGAGCTTGAAACCCTTTTA
1 ATGAATAAAATATGTTATT-CTCCTCAAATGTCGGGTCTAGTGGAAGGAGCTTGAAACCCTTTTA
26334 AACAAGGTTTTTATGCATTTTGGTCCCTTTAGTA
65 AACAAGGTTTTTATGCATTTTGGT-CCTTTAGTA
* * * * *
26368 ATGAATAAAATCTGTTATTCT--TCAAATGTTGGATCTAGTGGAAGGAACTCGAAACCCTTTTAT
1 ATGAATAAAATATGTTATTCTCCTCAAATGTCGGGTCTAGTGGAAGGAGCTTGAAACCCTTTTA-
* *
26431 AAGCAATGTGTTTATGCATTTTGGTCCTTT
65 AA-CAAGGTTTTTATGCATTTTGGTCCTTT
26461 TAGGCTTTTA
Statistics
Matches: 168, Mismatches: 17, Indels: 13
0.85 0.09 0.07
Matches are distributed among these distances:
96 51 0.30
97 9 0.05
98 22 0.13
99 80 0.48
100 6 0.04
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (97 bp):
ATGAATAAAATATGTTATTCTCCTCAAATGTCGGGTCTAGTGGAAGGAGCTTGAAACCCTTTTAA
ACAAGGTTTTTATGCATTTTGGTCCTTTAGTA
Found at i:30173 original size:96 final size:96
Alignment explanation
Indices: 29960--30225 Score: 345
Period size: 98 Copynumber: 2.7 Consensus size: 96
29950 TAAACACATA
* ** ** *
29960 TCGGGTCTAGTGGAAGGAGCTCAAAACCCTTTTAAGCAAATTGTTTATGCATTTTGGTCCTTTTA
1 TCGGGTCTAGTGGAAGGAACTCGGAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCTTTAA
*
30025 GTATAATGAATGGAATCTATTCTTCCTCAAATG
66 G--TAATGAATGAAATCTATTCTTCCTCAAATG
* * *
30058 TAGGGTCTAATGGAAGGAACTCGGAACCCTTTTAAGCAAGGTGTTTATACATTTTGGTCCTTTAA
1 TCGGGTCTAGTGGAAGGAACTCGGAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCTTTAA
*
30123 GTAATGAATGAAATCTGTTCTTCCTCAAATG
66 GTAATGAATGAAATCTATTCTTCCTCAAATG
* * * * *
30154 TCGGGTTTAGTGGAAGGAACTTGCGTACCCTTTTAAGTAAGGTGTTTATGCATTTTTGTCCTTTT
1 TCGGGTCTAGTGGAAGGAACTCG-GAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCC-TTT
30219 AA-TAATG
64 AAGTAATG
30226 TTCAACACAA
Statistics
Matches: 147, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
96 47 0.32
97 38 0.26
98 62 0.42
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (96 bp):
TCGGGTCTAGTGGAAGGAACTCGGAACCCTTTTAAGCAAGGTGTTTATGCATTTTGGTCCTTTAA
GTAATGAATGAAATCTATTCTTCCTCAAATG
Found at i:30475 original size:2 final size:2
Alignment explanation
Indices: 30457--30499 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
30447 GGAAATAGAC
* *
30457 AT AT AC AT AT GT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30497 AT A
1 AT A
30500 ACCTCACTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:31367 original size:19 final size:21
Alignment explanation
Indices: 31329--31369 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31319 ATTCCACGCT
*
31329 AGCCCACACAAAAGGGCACAA
1 AGCCCACACAAAAGGACACAA
31350 AGCCCACA-AAAA-GACACAA
1 AGCCCACACAAAAGGACACAA
31369 A
1 A
31370 ATACACTGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.54, C:0.32, G:0.15, T:0.00
Consensus pattern (21 bp):
AGCCCACACAAAAGGACACAA
Found at i:31905 original size:96 final size:96
Alignment explanation
Indices: 31731--31908 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
31721 ATATAAACAC
* * * * * *
31731 ATGAATGAAATCTGTTCTTCCTCGAATGTTGGGTCCAGTGGAAGGAACTCGAAACCCTTTTGAGC
1 ATGAATGAAATCTGTACTTCCTCAAATGTCGGGTCCAGTGGAAGGAACTCGAAACCCTTCTAAAC
**
31796 AAGGTGTTCATGCATTTTGGTCGTTTTAGTA
66 AAGGCATTCATGCATTTTGGTCGTTTTAGTA
* *
31827 ATGAATGAAATC-GATACTTCCTCAAATGTCGGGTCTAGTGGAAGGAATTCGAAACCCTTCTAAA
1 ATGAATGAAATCTG-TACTTCCTCAAATGTCGGGTCCAGTGGAAGGAACTCGAAACCCTTCTAAA
*
31891 CAAGGCATTTATGCATTT
65 CAAGGCATTCATGCATTT
31909 AGGTAGTGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
95 1 0.01
96 69 0.99
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (96 bp):
ATGAATGAAATCTGTACTTCCTCAAATGTCGGGTCCAGTGGAAGGAACTCGAAACCCTTCTAAAC
AAGGCATTCATGCATTTTGGTCGTTTTAGTA
Found at i:36702 original size:330 final size:328
Alignment explanation
Indices: 35985--37650 Score: 1722
Period size: 330 Copynumber: 5.0 Consensus size: 328
35975 ACCATGATGA
35985 TAAAAA-TGA-CCTGAAAGATTTTTCCTCAATTTTT-GACAAAAATACTCATAATATATATATAT
1 TAAAAATTGATCC-GAAAGATTTTTCCTCAATTTTTAG-CAAAAATACTCATAA-A-A-ATATAT
** * * * * * * * *
36047 AATTCAACCCCAAAAATATTGGAGGG-CTTTCATGCTTTTAATATCATTTTTCATATTTTTTCTG
61 AATTCAA-CATAAAAAAATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTATCTG
*
36111 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATTCTTAAATCCAAT
125 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAAT
* * *
36176 GT-GCTTGAGATCTGATTAGATGAATAAAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCA
190 GTGGC-TGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCA
* *
36240 AAACAGAGCCGTGGCCCTGGAACGTGTTTTTAGCCAAAAACCGTGAT-G--GGTACACGATTTTG
254 AAACAGAGCCG-GGCCC-GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTGGTACACGATTTCG
36302 GCTAAAATTTTG
317 GCTAAAATTTTG
* * * *
36314 CAAAAATTGATCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATT
1 TAAAAATTGATCCGAAAGATTTTTCCTCAATTTTTAGCAAAAATACTCAT-AAAAATATATAATT
* * * * ** *
36379 CGAGATAAAAAACATTGACGGGATTTTAACGCTTCTAATATTATTTTTGCTATTTCTATCTGAAT
65 CAACATAAAAAA-ATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCCTATTT-TATCTGAAT
* * * * *
36444 TAATTTCTAATTAAATCAAAATAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCTAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTG
* * * *
36509 GCTGAGATTTGCTTAGATGAATATAGATATTTCAAAGAGTCTTGGCACCAAAAATCATGCAAAAT
193 GCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAAC
* * * * *
36574 TGAGCCGGGCCTCGGAACGCGTTTTTAGCTGAAAAA-CATGATGGTTGGTACAAGATTTCGACTA
258 AGAGCCGGGCC-CGGAACGCGTTTTTAGC-CAAAAACCGTGATGGTTGGTACACGATTTCGGCTA
*
36638 AACTTTTG
321 AAATTTTG
* * **
36646 TAAAAATTGATCTGAAAGATTTTTCCTCAATTTATATAAAAAATACTCATAAAATATATATAATT
1 TAAAAATTGATCCGAAAGATTTTTCCTCAATTTTTAGCAAAAATACTCATAAAA-ATATATAATT
* ** * * *
36711 CAATTC-CAAAAAAA-TGAAAGCCATTTTCACGCTTTTAATATCGTTTTTCCTATTTTATTTCCA
65 CAA--CATAAAAAAATTG-AAGGGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTATCT-GA
** *
36774 AGTTAATTGATATTTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAAT
126 A-TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAAT
* * * * *
36839 GTGGTTGAGATTTGGTTAGATGAAGAAAGATATTTCAAGGAG-CCT-CCACGTCAAAAATCATGC
190 GTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTTGGCAC--CAAAAATCATGC
* * * *
36902 AAAACAAAGTCGTGGCCCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC
253 AAAACAGAGCCG-GG-CCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTGGTACACGATTTC
* *
36967 GGCTTAATTTTTG
316 GGCTAAAATTTTG
* * * * * *
36980 TAAAAATTGACCCGAAAGATATTTCCTTAATTTTTGGCTAAAATACTCATAAAAAATATTTAATT
1 TAAAAATTGATCCGAAAGATTTTTCCTCAATTTTTAGCAAAAATACTCAT-AAAAATATATAATT
* * * * *
37045 CAACATCAAAAAGATTGAAGGGTTTTTAATGCTTCTAATATTGTTTTTCCTACTTTTATCTGAAT
65 CAACAT-AAAAAAATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTATCTGAAT
* * * * *
37110 TAATTTCTAAATAAATCGAAACAAGATTCAGATGCTCGTAAGAACAAATCCTTATATCCAATATG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTG
* * * * * * * *
37175 GCTGAAATTTGGTTTGACG--TATAGATATTTCAAGGAGACTTGGCACCAAAAATCATACGAAAC
193 GCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAAC
* * * * * *
37238 TGAACCGGACGTCGTAACGCGTTTTTAG-CAAAAACCGTGATGGTTAGTTACA--ATTTCGGCTA
258 AGAGCCGGGC-CCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTT-GGTACACGATTTCGGCTA
37300 AAATTTTG
321 AAATTTTG
* * * *
37308 CAAAAATTGGTCAGAAAGATTTTTCCTCAATTTCTAGCAAAAATACTCATAAAAAATATATAATT
1 TAAAAATTGATCCGAAAGATTTTTCCTCAATTTTTAGCAAAAATACTCAT-AAAAATATATAATT
* **** * **
37373 CAATGC-CAAAAAAATTGAAAACCTTTTTCACGCTTCTAATATCGGTTTTCCTATTTTATTTCCA
65 CAA--CATAAAAAAATTG-AAGGGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTA--TCTG
* * * **
37437 AATTGATTGCTATTTAAATCGAAACAAGATTCAGATAAACGTAAAAACAAATCCTTAAATCCAAT
125 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAAT
* * * * * *
37502 GTGGCTGAGATCTGATTAAATGAA-AAAGATATTTCAAGGAGTCTCGGTGA-TAAAAGTCATGCA
190 GTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTTGG-CACCAAAAATCATGCA
* * *
37565 AAACAGAGCCATGGCCCTGGAACGCGTTTTTAGCC-AAAACCGTGATGGTTAGTACACGACTTCG
254 AAACAGAGCC-GGGCCC-GGAACGCGTTTTTAGCCAAAAACCGTGATGGTTGGTACACGATTTCG
37629 GCTAAAATTTT-
317 GCTAAAATTTTG
37640 TCAAAAATTGA
1 T-AAAAATTGA
37651 CCCGTGGCCC
Statistics
Matches: 1096, Mismatches: 194, Indels: 90
0.79 0.14 0.07
Matches are distributed among these distances:
327 5 0.00
328 107 0.10
329 101 0.09
330 265 0.24
331 96 0.09
332 146 0.13
333 224 0.20
334 137 0.12
335 15 0.01
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (328 bp):
TAAAAATTGATCCGAAAGATTTTTCCTCAATTTTTAGCAAAAATACTCATAAAAATATATAATTC
AACATAAAAAAATTGAAGGGATTTTCACGCTTCTAATATCGTTTTTCCTATTTTATCTGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTGGCT
GAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACAGA
GCCGGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTGGTACACGATTTCGGCTAAAATT
TTG
Found at i:37403 original size:663 final size:660
Alignment explanation
Indices: 35997--37654 Score: 2239
Period size: 663 Copynumber: 2.5 Consensus size: 660
35987 AAAATGACCT
* *
35997 GAAAGATTTTTCCTCAATTTTTGACAAAAATACTCATAATATATATATATAATTCAACCCCAAAA
1 GAAAGATTTTTCCTCAATTTTAG-CAAAAATACTCATAA-A-ATATATATAATTCAATCCCAAAA
* * * * * * * * * *
36062 ATATTGGAGGGC-TTTCATGCTTTTAATATCATTTTTCATA-TTT-TTTCTGAATTAATTTCTAA
63 AAATTGAAAGCCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTATTTC-CAATTAATTGCTAT
* *
36124 TTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATTCTTAAATCCAATGTGCTTGAGATCT
127 TTAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATCT
* *
36189 GATTAGATGAATAAAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACAGAGCCGTGG
192 GATTAGATGAA-AAAGATATTTCAAGGAGTCTC-CCGTCAAAAATCATGCAAAACAGAGCCGTGG
* * *
36254 CCCTGGAACGTGTTTTTAGCCAAAAACCGTGATGG---GTACACGATTTTGGCTAAAATTTTGCA
255 CCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAATTTTTGCA
* *
36316 AAAATTGATCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCG
320 AAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCA
* * *
36381 AGATAAAAAACATTGACGGGATTTTAACGCTTCTAATATTATTTTTGCTATTTCTATCTGAATTA
385 ACATAAAAAACATTGAAGGGATTTTAACGCTTCTAATATTATTTTTCCTATTTCTATCTGAATTA
* * * * *
36446 ATTTCTAATTAAATCAAAATAAGATTCTGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGC
450 ATTTCTAAATAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGC
* * * * *
36511 TGAGATTTGCTTAGATGAATATAGATATTTCAAAGAGTCTTGGCACCAAAAATCATGCAAAATTG
515 TGAAATTTGCTTAGACG-ATATAGATATTTCAAAGAGACTTGGCACCAAAAATCATACAAAACTG
* * *
36576 AGCCGGGCCTCGGAACGCGTTTTTAGCTGAAAAACATGATGGTTGGTACAAGATTTCGACTAAAC
579 AACCGGACCTCGGAACGCGTTTTTAGC-GAAAAACATGATGGTTGGTACAAGATTTCGACTAAAA
* *
36641 TTTTGTAAAAATTGATCT
643 TTTTGCAAAAATTGATCA
** *
36659 GAAAGATTTTTCCTCAATTTATATAAAAAATACTCATAAAATATATATAATTCAATTCCAAAAAA
1 GAAAGATTTTTCCTCAATTT-TAGCAAAAATACTCATAAAATATATATAATTCAATCCCAAAAAA
*
36724 A-TGAAAGCCATTTTCACGCTTTTAATATCGTTTTTCCTATTTTATTTCCAAGTTAATTGATATT
65 ATTGAAAGCC-TTTTCACGCTTTTAATATCGTTTTTCCTATTTTATTTCCAA-TTAATTGCTATT
*
36788 TAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTG
128 TAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATCTG
* * * *
36853 GTTAGATGAAGAAAGATATTTCAAGGAGCCTCCACGTCAAAAATCATGCAAAACAAAGTCGTGGC
193 ATTAGATGAA-AAAGATATTTCAAGGAGTCTCC-CGTCAAAAATCATGCAAAACAGAGCCGTGGC
* * * *
36918 CCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTTAATTTTTGTAA
256 CCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAATTTTTGCAA
* *
36983 AAATTGACCCGAAAGATATTTCCTTAATTTTTGGCTAAAATACTCATAAAAAATATTTAATTCAA
321 AAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAA
* * * * *
37048 CATCAAAAAGATTGAAGGGTTTTTAATGCTTCTAATATTGTTTTTCCTACTTT-TATCTGAATTA
386 CATAAAAAACATTGAAGGGATTTTAACGCTTCTAATATTATTTTTCCTA-TTTCTATCTGAATTA
* * *
37112 ATTTCTAAATAAATCGAAACAAGATTCAGATGCTCGTAAGAACAAATCCTTATATCCAATATGGC
450 ATTTCTAAATAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGC
* * * *
37177 TGAAATTTGGTTTGACG-TATAGATATTTCAAGGAGACTTGGCACCAAAAATCATACGAAACTGA
515 TGAAATTTGCTTAGACGATATAGATATTTCAAAGAGACTTGGCACCAAAAATCATACAAAACTGA
* * * * *
37241 ACCGGACGTCGTAACGCGTTTTTAGC-AAAAACCGTGATGGTTAGTTAC-A-ATTTCGGCTAAAA
580 ACCGGACCTCGGAACGCGTTTTTAGCGAAAAA-CATGATGGTT-GGTACAAGATTTCGACTAAAA
*
37303 TTTTGCAAAAATTGGTCA
643 TTTTGCAAAAATTGATCA
* *
37321 GAAAGATTTTTCCTCAATTTCTAGCAAAAATACTCATAAAAAATATATAATTCAATGCCAAAAAA
1 GAAAGATTTTTCCTCAATTT-TAGCAAAAATACTCATAAAATATATATAATTCAATCCCAAAAAA
* * * *
37386 ATTGAAAACCTTTTTCACGCTTCTAATATCGGTTTTCCTATTTTATTTCCAAATTGATTGCTATT
65 ATTGAAAGCC-TTTTCACGCTTTTAATATCGTTTTTCCTATTTTATTTCC-AATTAATTGCTATT
** *
37451 TAAATCGAAACAAGATTCAGATAAACGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATCTG
128 TAAATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATCTG
* * * *
37516 ATTAAATGAAAAAGATATTTCAAGGAGTCT-CGGTGATAAAAGTCATGCAAAACAGAGCCATGGC
193 ATTAGATGAAAAAGATATTTCAAGGAGTCTCCCGTCA-AAAA-TCATGCAAAACAGAGCCGTGGC
*
37580 CCTGGAACGCGTTTTTAGCC-AAAACCGTGATGGTTAGTACACGACTTCGGCTAAAATTTTT-CA
256 CCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT-AAATTTTTGCA
37643 AAAATTGACCCG
320 AAAATTGACCCG
37655 TGGCCCTGGA
Statistics
Matches: 877, Mismatches: 101, Indels: 37
0.86 0.10 0.04
Matches are distributed among these distances:
659 5 0.01
660 26 0.03
661 75 0.09
662 194 0.22
663 297 0.34
664 70 0.08
666 207 0.24
667 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (660 bp):
GAAAGATTTTTCCTCAATTTTAGCAAAAATACTCATAAAATATATATAATTCAATCCCAAAAAAA
TTGAAAGCCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTATTTCCAATTAATTGCTATTTAA
ATCGAAACAAGATTCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATCTGATT
AGATGAAAAAGATATTTCAAGGAGTCTCCCGTCAAAAATCATGCAAAACAGAGCCGTGGCCCTGG
AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAATTTTTGCAAAAATT
GACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACATAA
AAAACATTGAAGGGATTTTAACGCTTCTAATATTATTTTTCCTATTTCTATCTGAATTAATTTCT
AAATAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAAAT
TTGCTTAGACGATATAGATATTTCAAAGAGACTTGGCACCAAAAATCATACAAAACTGAACCGGA
CCTCGGAACGCGTTTTTAGCGAAAAACATGATGGTTGGTACAAGATTTCGACTAAAATTTTGCAA
AAATTGATCA
Found at i:37712 original size:80 final size:79
Alignment explanation
Indices: 37576--37735 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 79
37566 AACAGAGCCA
37576 TGGCCCTGGAACGCGTTTTTAGCCAAAACCGTGATGGTTAGTACACGACTTCGGCTAAAATTTTT
1 TGGCCCTGGAACGCGTTTTTAGCCAAAACCGTGATGGTTAGTACACGACTTCGGCTAAAATTTTT
37641 CAAAAATTGACCCG
66 CAAAAATTGACCCG
37655 TGGCCCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGACTTCGGCTAAAATTTT
1 TGGCCCTGGAACGCGTTTTTAGCC-AAAACCGTGATGGTTAGTACACGACTTCGGCTAAAATTTT
37720 TCAAAAATTGACCCG
65 TCAAAAATTGACCCG
37735 T
1 T
37736 AAGATATTTC
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 24 0.30
80 56 0.70
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (79 bp):
TGGCCCTGGAACGCGTTTTTAGCCAAAACCGTGATGGTTAGTACACGACTTCGGCTAAAATTTTT
CAAAAATTGACCCG
Found at i:37993 original size:123 final size:121
Alignment explanation
Indices: 37850--38091 Score: 342
Period size: 123 Copynumber: 2.0 Consensus size: 121
37840 TTTATCTGAA
* *
37850 TTAATTTCTAATTAAATCAAAAT-AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATG
1 TTAATTTCTAATTAAATC-AAATCAAGATTCAGATGCTCGAAAAAACAAATCCTTAAATCAAATA
* * *
37914 TGGCTGAGATTTGCTTAGATGAATATAGATATTTCAAAGAGTCTTGGCACCAAAAATTC
65 TGACTGAGATTTGCTTAGATG--TATAGATAATTCAAAGAGACTTGGCACCAAAAATTC
* *
37973 TTAATTTCTAATTAAATCAAATCAAGATTCAGATGCTCGAAAAAACAAATCCTTAAGTCCAATAT
1 TTAATTTCTAATTAAATCAAATCAAGATTCAGATGCTCGAAAAAACAAATCCTTAAATCAAATAT
* * * * *
38038 GACTGAGATTTGGTTAGATGTTTATATAATTCAAGGAGACTTGGCGCCAAAAAT
66 GACTGAGATTTGCTTAGATGTATAGATAATTCAAAGAGACTTGGCACCAAAAAT
38092 CATGCAAAAC
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
121 28 0.26
122 4 0.04
123 74 0.70
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (121 bp):
TTAATTTCTAATTAAATCAAATCAAGATTCAGATGCTCGAAAAAACAAATCCTTAAATCAAATAT
GACTGAGATTTGCTTAGATGTATAGATAATTCAAAGAGACTTGGCACCAAAAATTC
Found at i:39450 original size:331 final size:332
Alignment explanation
Indices: 38847--39632 Score: 1299
Period size: 332 Copynumber: 2.4 Consensus size: 332
38837 AAAGAAAAAA
* * *
38847 GTTAGTACACGATTTTGGCTAAAATTTTGCAAAAATTGACCCGAAAG-TTTTTTCAACAATCTTT
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAAGATTTTTTCCACAATCTTT
* * * * * * *
38911 GGCCAAAATACTTATAGAATATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGTTTC
66 GGCGAAAACAATTATTGAAAAGA-ATAATTCAACGCCAAAAAGATTGAAGGG-TTTTCACGCTTC
*
38976 TAATATCGATTTTCCTATATGTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTTTGATGC
129 TAATATCGATTTTCCTATAAGTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTTTGATGC
* * *
39041 TCGTAAAATCAAATCCTTAAATTCAATTTGGATGAGATTTGGTTAGATGAATATAGATATGTCAA
194 TCGTAAAATCAAATCCTTAAATTCAATTTGGATGAGATTTCGTTAGATAAAAATAGATATGTCAA
*
39106 GGAGTCTCGGGGCCATAAATCATTAAAAACTGAGCCGGGG-TCCGGAACGCGTTTTTAGCCAAAT
259 GGAGTCTCGGGGCCATAAACCATTAAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAA-
39170 ACC-GTGATG
323 ACCAGTGATG
* *
39179 GTTAGTACACGATTTCGGCTATAATTTTGCAAAAATTGACCTAAAAGATTTTTTCCACAATCTTT
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAAGATTTTTTCCACAATCTTT
*
39244 GGCGAAAACAATTATTGAAAAGAATAATTCAACGCCAAATAGATTGAAGGGTTTTCACGCTTCTA
66 GGCGAAAACAATTATTGAAAAGAATAATTCAACGCCAAAAAGATTGAAGGGTTTTCACGCTTCTA
39309 ATATCGATTTTCCTATAAGTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTTTGATGCTC
131 ATATCGATTTTCCTATAAGTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTTTGATGCTC
**
39374 GTAAAATCAAATCCTTAAATTCAATTTGGATGAGATTTCGTTAGATAAAAATAGATATGTCAATT
196 GTAAAATCAAATCCTTAAATTCAATTTGGATGAGATTTCGTTAGATAAAAATAGATATGTCAAGG
*
39439 AGTCTCGGGGCCATAAACCATTAAAAACTTAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAACC
261 AGTCTCGGGGCCATAAACCATTAAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAACC
39504 AGTGATG
326 AGTGATG
39511 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAAGATTTTTTCCACAATCTTT
1 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAAGATTTTTTCCACAATCTTT
* * *
39576 GGTGAAAACATTTATTGAAAAGAATAATTCAACGCCAAAAAAATTGAAGGGGTTTTC
66 GGCGAAAACAATTATTGAAAAGAATAATTCAACGCCAAAAAGATTGAA-GGGTTTTC
39633 CACAATCTTT
Statistics
Matches: 423, Mismatches: 27, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
331 176 0.42
332 206 0.49
333 41 0.10
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (332 bp):
GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAAGATTTTTTCCACAATCTTT
GGCGAAAACAATTATTGAAAAGAATAATTCAACGCCAAAAAGATTGAAGGGTTTTCACGCTTCTA
ATATCGATTTTCCTATAAGTTTCCGAATTAATTTCTGATTAAATCGAAACATGATTTTGATGCTC
GTAAAATCAAATCCTTAAATTCAATTTGGATGAGATTTCGTTAGATAAAAATAGATATGTCAAGG
AGTCTCGGGGCCATAAACCATTAAAAACTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAACC
AGTGATG
Found at i:39683 original size:40 final size:40
Alignment explanation
Indices: 39628--39704 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
39618 ATTGAAGGGG
*
39628 TTTTCCACAATCTTTGGCCAAAACACTAATAGAATATGTA
1 TTTTCCACAATCTTTGGCAAAAACACTAATAGAATATGTA
*
39668 TTTTCCACAATCTTTGGCAAAAACACTTATAGAATAT
1 TTTTCCACAATCTTTGGCAAAAACACTAATAGAATAT
39705 ATATAATTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (40 bp):
TTTTCCACAATCTTTGGCAAAAACACTAATAGAATATGTA
Done.