Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019072.1 Corchorus olitorius cultivar O-4 contig19105, 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: 75013
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2952 original size:2 final size:2
Alignment explanation
Indices: 2945--2974 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2935 AATTTTATTG
2945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2975 GTGAGATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4740 original size:29 final size:31
Alignment explanation
Indices: 4708--4769 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
4698 TTTGTTCTTG
*
4708 TACTCA-AAAAGCGA-TCAATTTAGTTCATA
1 TACTCACAAAAGCGAGTCAATTTAGTCCATA
* **
4737 TACTTACAAAATTGAGTCAATTTAGTCCATA
1 TACTCACAAAAGCGAGTCAATTTAGTCCATA
4768 TA
1 TA
4770 TCCAACAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 5 0.19
30 6 0.22
31 16 0.59
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (31 bp):
TACTCACAAAAGCGAGTCAATTTAGTCCATA
Found at i:8363 original size:35 final size:35
Alignment explanation
Indices: 8317--8386 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
8307 AGCAATATTT
8317 CATTTTCAAAATCAATTTAAATCATCATCATATAA
1 CATTTTCAAAATCAATTTAAATCATCATCATATAA
**
8352 CATTTTCAAAATCAATTTAGTTCATCATCATATAA
1 CATTTTCAAAATCAATTTAAATCATCATCATATAA
8387 TTATTCTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.17, G:0.01, T:0.39
Consensus pattern (35 bp):
CATTTTCAAAATCAATTTAAATCATCATCATATAA
Found at i:30039 original size:25 final size:25
Alignment explanation
Indices: 30011--30059 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
30001 ACCCGATATT
30011 CAAAATTTTGCTCTAACTAATCCAA
1 CAAAATTTTGCTCTAACTAATCCAA
30036 CAAAATTTTGCTCTAACTAATCCA
1 CAAAATTTTGCTCTAACTAATCCA
30060 GTTCGACCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (25 bp):
CAAAATTTTGCTCTAACTAATCCAA
Found at i:35838 original size:30 final size:30
Alignment explanation
Indices: 35803--35896 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
35793 CTTATTTTCT
35803 TTTTTAATTATACTTTGCTGTATTTTAAGA
1 TTTTTAATTATACTTTGCTGTATTTTAAGA
* * **
35833 TTTTT-ATCCATA-TGTTCCCT-TATTTT--CT
1 TTTTTAAT-TATACT-TT-GCTGTATTTTAAGA
*
35861 TTTTTAATTATACTTTGTTGTATTTTAAGA
1 TTTTTAATTATACTTTGCTGTATTTTAAGA
35891 TTTTTA
1 TTTTTA
35897 TCCATATGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 16
0.65 0.12 0.22
Matches are distributed among these distances:
27 1 0.02
28 16 0.34
29 6 0.13
30 22 0.47
31 2 0.04
ACGTcount: A:0.22, C:0.10, G:0.07, T:0.61
Consensus pattern (30 bp):
TTTTTAATTATACTTTGCTGTATTTTAAGA
Found at i:35883 original size:58 final size:58
Alignment explanation
Indices: 35789--35906 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
35779 TTACCCTTTT
35789 TTCCCTTATTTTCTTTTTTAATTATACTTTGCTGTATTTTAAGATTTTTATCCATATG
1 TTCCCTTATTTTCTTTTTTAATTATACTTTGCTGTATTTTAAGATTTTTATCCATATG
*
35847 TTCCCTTATTTTCTTTTTTAATTATACTTTGTTGTATTTTAAGATTTTTATCCATATG
1 TTCCCTTATTTTCTTTTTTAATTATACTTTGCTGTATTTTAAGATTTTTATCCATATG
35905 TT
1 TT
35907 TTAGTATTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (58 bp):
TTCCCTTATTTTCTTTTTTAATTATACTTTGCTGTATTTTAAGATTTTTATCCATATG
Found at i:50892 original size:3 final size:3
Alignment explanation
Indices: 50854--50912 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
50844 AGCAATAGGG
* * * * * *
50854 CAT CAA CAT CAA CAT CAG CAG CAT CTT CAT CTT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
50902 CAT CAT CAT CA
1 CAT CAT CAT CA
50913 AAGAAAGGAG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.34, C:0.34, G:0.03, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:51821 original size:31 final size:31
Alignment explanation
Indices: 51742--51821 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
51732 AAATCGCGAT
*
51742 AATTTGCCCCATGAATTTCTAAATACAGAAC
1 AATTTGCCCCATGAATTTCCAAATACAGAAC
* * * *
51773 AATATACCTCATGAATTTCCAAATTCA-AGAC
1 AATTTGCCCCATGAATTTCCAAATACAGA-AC
*
51804 AATTTGCCCCATCAATTT
1 AATTTGCCCCATGAATTT
51822 TTTAAATTTA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 1 0.03
31 38 0.97
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (31 bp):
AATTTGCCCCATGAATTTCCAAATACAGAAC
Found at i:55965 original size:327 final size:326
Alignment explanation
Indices: 53249--57294 Score: 2668
Period size: 327 Copynumber: 12.3 Consensus size: 326
53239 AATTCAACTA
** * * * *
53249 AAATTTTCCAAAAATTGACCCAAAATATTTTTTCTCGATTTCTAG-CGAAAATACTCATAAAAAT
1 AAATTTTGAAAAAATTGACCCAAAATATTTTTCCTCAATTT-TTGTCTAAAATACTCATAAAAA-
* * ** * * * ** * *
53313 ATATATAATTTAACACCAAAAA-AACGAAAGCCTTTTTCACGCTTTTTATATTATTTTCCCCATT
64 ATATATAATTCAACGCCAAAAAGATTGAAGGGC-TTTTCACGCTTTTAATATCGTTTT--TCATA
** * * *** *
53377 TTATTTCCAAATTAATTTCTGATTAAATCAAAACAAGATTTAGAAATTCGTAAAAACAAATCCTT
126 TT-TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT-AAAA-AAATCCAT
* * * * * *
53442 AAATACAATGTGGTTGAGATTTGGTTAGATGAATATAGATATATTTTAAGGAGTCTTGGCGCCAA
188 AAATCCAATGTGGCTGAGATTTGATTAGATGAATATAG--ATATTTCAAGGATTCTTGACGCCAA
* * * ** *
53507 AAATCATGCAAAACTGACCCAGGACCCCGGAAA-GCGTTTTTAGCCAAAAAACAATGACG--A-T
251 AAATCATGCAAAACTGACCCGGGGCCCC-GAAACGCTTTTTTAGCC-AAAAACCGTGATGTTAGT
53568 ACACGATTTCGGCT
314 A-ACGATTTCGGCT
* * * * * *
53582 AAAATTTTGCAAAAATTAACCCGAAATATTTTT-CTCAATTTTTAG-CCACAATACTCATTAAAA
1 -AAATTTTGAAAAAATTGACCCAAAATATTTTTCCTCAATTTTT-GTCTAAAATACTCATAAAAA
* * ** *
53645 ATATATAATTCAACGCCAAAAAGATT---GGGCTTCTCACGCTTCTAATATAATTTTTCCTATTT
64 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTT
* * * * * * *
53707 TT-TCAAATTAATTTCTAATTAAATTGAAACATGATTCAAATGCTCGCAAAACAAATCCTTAAAT
129 TTCT-GAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAA-AAATCCATAAAT
* * * * *
53771 -CAAGTGTGGCTAAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTT-TTGCCACCAAAAAT
192 CCAA-TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGA-TTCTTGACGCCAAAAAT
** * * *
53834 CATGTC-AAACTGATTCGGAGCCCC-AGAACGCGTTTTTAGCCAAAAAAACTGTGATG---GTAC
255 CATG-CAAAACTGACCCGGGGCCCCGA-AACGCTTTTTTAGCC--AAAAACCGTGATGTTAGTA-
*
53894 ACGATTTCGTCT
315 ACGATTTCGGCT
* * * * * * * ** *
53906 AAAATTTTGTAAAAATTGACCCGAAATATTTTGT-CTCAATTTTAGGCCACAACACTGGT-AAAT
1 -AAATTTTGAAAAAATTGACCCAAAATATTTT-TCCTCAATTTTTGTCTAAAATACTCATAAAAA
* * * ** **
53969 ATATATAATTCAACACCAAAAAGAATGGAGGATTTTTCACATTTTTAATATCGTTTTTCATATAT
64 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTC--ATAT
* *
54034 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA-GCCTCGTAAAAATAAATCCTTA
127 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATG-CTCGT-AAAA-AAATCCATA
* * * * * ** * *
54098 GATTCAATGTGGTTGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCAATGCAAAAAA
189 AATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTTGACGCCAAAAA
* * * * * * *
54163 TTATGCAAAACTAAGCTGGGGCCTCGAAACGCGTTTTTAGCCAAAAACCGTGATAGTTAGCACAC
254 TCATGCAAAACTGACCCGGGGCCCCGAAACGCTTTTTTAGCCAAAAACCGTGAT-GTTAGTA-AC
54228 GATTTCGGCT
317 GATTTCGGCT
* * *
54238 AAAATTTT-ACAAAAATTGACCCAAAAAATTTTTCCGACAATTTTTGGCTAAAATACTCATAATA
1 -AAATTTTGA-AAAAATTGACCCAAAATATTTTTCC-TCAATTTTTGTCTAAAATACTCATAA-A
* * * * ** *
54302 TATATATATAAAATTTAATGCCAAAAAGATTGGAGAACTTTTCACGCTTTTAATATTGTTTTT-A
62 -A-A-ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCA
* * * *
54366 CTATTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCATAAAAGACAAATT
124 -TATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT-AAA-A-AAATC
* * * * * * * * *
54431 CTTAAATCCAATGTTGCTGATATTTGATTAAATGAATATGGATATCTCAAAGAGTCTTGGCGCCA
185 CATAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTTGACGCCA
** * * **
54496 AAAATCATGCAAAACTGAGTCGGGGTCCCGAAACACGATTTTAGCCAAAAACCGTGATGATTA-T
250 AAAATCATGCAAAACTGACCCGGGGCCCCGAAACGCTTTTTTAGCCAAAAACCGTGATG-TTAGT
54560 CAA--A---C-G--
314 -AACGATTTCGGCT
* * * * * *
54566 --A--TT-------TTG--CCAAAGT-TATTTCCTCAATTTTTAG-CCACAATACTCATTAAAAT
1 AAATTTTGAAAAAATTGACCCAAAATATTTTTCCTCAATTTTT-GTCTAAAATACTCATAAAAAA
* * * * * *
54616 TATCTAATTCAATGCCAATAAGATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTC----TTA
65 TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTT
* * * * ** * *
54677 T-T--ATT--TTTC----GAAATCGAAACATGATTCAGATGCTTGTTTTAGAAATCCTTAAATCC
130 TCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG-TAAAAAAATCCATAAATCC
* * * * *
54733 AATGTGGCCGAGATTTGGTTAGATGAATATAGATGTTTCAAGGAGTC-TCAGCGCCAAAAATCAT
194 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTTGA-CGCCAAAAATCAT
* * * * * *
54797 GCAACACTGTA-CCGGGACCCC-AGAACGCGTTTTTAGCAGAAAAAAGAAAACGTAAATTTCGAC
258 GCAAAACTG-ACCCGGGGCCCCGA-AACGCTTTTTTAGC-----CAA-AAACCGT-GA--T-G--
* *
54860 TAACGTACACGATTTCAGCT
309 TTA-GTA-ACGATTTCGGCT
* ** *
54880 AATATTCTGCAAAACTTTGA-CCAGAATTATTTTTCCTCAATTTTTGTCTAAAATACTCATAAAA
1 AA-ATTTTG-AAAAAATTGACCCA-AAATATTTTTCCTCAATTTTTGTCTAAAATACTCATAAAA
* * * **
54944 AATATATATTTCAATGCCAAAAAGATTGCAGAACTTTTCACGCTTTTAATATCGTTTTTCATATT
63 AATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATT
* * * * * * *
55009 TTTTTTAATTAATTTCAAATTAAATCAAAACGAGATTCATATGCTCGTAAAAACACATCC-TAAA
128 TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAA-A-ATCCAT-AA
* * * * ** *
55073 ATGCAATGTAGCTGAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTCAACGGCAAAAAT
190 ATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTTGACGCCAAAAAT
* ** ** * * * *
55138 CATACAAAACTGAGTCGAAGCCCCGAAAACACGTTTTTAGCAAAAAAAAAAAATCGTGATGGTTA
255 CATGCAAAACTGACCCGGGGCCCCG-AAACGCTTTTTTAGC------CAAAAACCGTGAT-GTTA
55203 GTACACGATTTCGGCT
312 GTA-ACGATTTCGGCT
* * * * * *
55219 AAATTTTTGCAAAAAA-T-AACCAGAAAAACTTTTCCTTAATTTTTGTCTAAAATGCTCATGAAA
1 AAA-TTTTG-AAAAAATTGACCCA-AAATATTTTTCCTCAATTTTTGTCTAAAATACTCATAAAA
* * * * * * * *
55282 TATATATAATTTAACGTCAAAAATATTGGAGGACTTTTTACGCTTTTCATATCGTTTTTCATATT
63 AATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-T
* * **
55347 TTTTTTGAAAATTAATTTGTAATTAAATCGAAACAAGATACAGATGCTCGTAAAAACAAAT-CAT
127 TTTTCTG--AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT-AAAA-AAATCCA-
* * * * *
55411 TAAATGCAATATGGATGAGATTTGATTAGATTAATAT-GAATATCTCAAGGATTCTT-AGCGCCA
187 TAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAG-ATATTTCAAGGATTCTTGA-CGCCA
* * * * * * *
55474 AAAATCATGCAAAACTGACCTGGGGCCCTGGAATGCGTTTTTAGCCAAAAACTGTGATGATTTAT
250 AAAATCATGCAAAACTGACCCGGGGCCCCGAAACGCTTTTTTAGCCAAAAACCGTGATG--TTAG
55539 TACACGATTTCGGCT
313 TA-ACGATTTCGGCT
* * * * *
55554 AACATTTTGCAAAAATTGACCAAAAAAAATATTTCCTCAATTTTTAG-CTAAAATACTTATAAAA
1 AA-ATTTTGAAAAAATTGACC-CAAAATATTTTTCCTCAATTTTT-GTCTAAAATACTCATAAAA
* * * * * * * * *
55618 AAAATATTATTCATCGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCTTTTTTCCTACT
63 AATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-T
* * *
55683 TTTTCTGAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTTGTAAAAAAATCCATAATT
127 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAAATCCATAAAT
* * * *
55748 CCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTGC-ATGATTTTTGACTCCAAAAATC
192 CCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT-CAAGGATTCTTGACGCCAAAAATC
* ** *
55812 ATGCAAAACTGACCCGGGGTCCCGAAACGCTTTTTGGTA-AAAAAAACCGTTATGTTA-T-ACGA
256 ATGCAAAACTGACCCGGGGCCCCGAAACGCTTTTT--TAGCCAAAAACCGTGATGTTAGTAACGA
55874 TTTCGGCT
319 TTTCGGCT
* *
55882 AATATTTTGAAAAAATTGACCCAAAATATTTTTCCTCAATTTTTAGTC-ACAATACTTATAAAAA
1 AA-ATTTTGAAAAAATTGACCCAAAATATTTTTCCTCAATTTTT-GTCTAAAATACTCATAAAAA
* * * * *
55946 ATATATAATTCAACGCCAAAAAGATTAAAGGGCTTTTCATGCTTCTAATACCGTTTTTCTTATTT
64 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTC--A-TA
* * * * *
56011 TTGTTTCCGAATTAATTTTTAATTAAAAT-GAAGCATGATTTAGATGCTTGT------A---A-A
126 TT-TTTCTGAATTAATTTCTAATT-AAATCGAAACAAGATTTAGATGCTCGTAAAAAAATCCATA
* *
56065 AA--CAA--TGGCT-AGGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCTG-CGCCAAA
189 AATCCAATGTGGCTGA-GATTTGATTAGATGAATATAGATATTTCAAGGATTCT-TGACGCCAAA
* * * * *
56124 ATTCATTCAAAACTGAACCC--GGCCCCGGAACGCATTTTTAGCCAAAAACCGTGATGATTATTA
252 AATCATGCAAAACTG-ACCCGGGGCCCCGAAACGCTTTTTTAGCCAAAAACCGTGATG-TTAGTA
*
56187 CTCGATTTCGGCT
315 -ACGATTTCGGCT
* *** * * * *
56200 AAAATTTTGTAAAAATTGACATGAAATATATTTCCTCAATTTTTAG-CCATAATACTCA-ATAAA
1 -AAATTTTGAAAAAATTGACCCAAAATATTTTTCCTCAATTTTT-GTCTAAAATACTCATAAAAA
* * ** * *
56263 ATATATAATTCGACACC--AAA-ATTGAAGGGCTTTTCGTGCTTTTAATACCCTTTTTTCATATT
64 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATA-TCGTTTTTCATATT
* *
56325 TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTAAAT
128 TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAA-AAATCCATAAAT
** * * * *
56390 GTAATGTGGCTAAGGTTTTATTAGATGAATATAGATATTTCATGGAGTGTC-TG-CGCCAAAAAT
192 CCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGA-T-TCTTGACGCCAAAAAT
* * * * * *
56453 CATGCAAAACTGAGCTGGGGCCCCAAAACGCGTTTTTAGCTAAAAACTGTGATGGGTTAGTACAC
255 CATGCAAAACTGACCCGGGGCCCCGAAACGCTTTTTTAGCCAAAAACCGTGAT--GTTAGTA-AC
*
56518 GATTTTGGCT
317 GATTTCGGCT
* * **
56528 AAAGTTCTGCAAAAAA-TGTCCCGAAAAT-TTTTTCCTCAATTTTTGGATAAAATACTCATAAAA
1 AAA-TTTTG-AAAAAATTGACCC-AAAATATTTTTCCTCAATTTTTGTCTAAAATACTCATAAAA
* * * *
56591 AATATATAATTTAACGCCAAAACA-ATTGGAGGACTTTTCACGCTTTTAATATCATTTTTCCATA
63 AATATATAATTCAACGCCAAAA-AGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTT-CATA
* * * *
56655 TTTTTCTCAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACAAATTCTTA
126 TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT-AAAA-AAATCCATA
* * * *
56720 AATCCAATGTGGCTGAGATTTGATTAGATGAATAT-GAATATCTCAAGGAGTCTTGGCGCAAAAA
189 AATCCAATGTGGCTGAGATTTGATTAGATGAATATAG-ATATTTCAAGGATTCTTGACGCCAAAA
* * * * ** ** * * * *
56784 ATCAGGCATAACTGAGCCAGGTTCCTAAAACGCATTTTTAGCCAAAAACTGTGATGTTA--CATG
253 ATCATGCAAAACTGACCCGGGGCCCCGAAACGCTTTTTTAGCCAAAAACCGTGATGTTAGTAACG
56847 ATTTCGGCT
318 ATTTCGGCT
* * * ** * *
56856 AAAATTTTGTAAAAATTGAGCCGAAAGGTATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAA
1 -AAATTTTGAAAAAATTGACCCAAAATATTTTTCCTCAATTTTTGTCTAAAATACTCATAAAAAA
* * *
56921 TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTGACG-TTTCTCATATCGTTTTTCCTATTT
65 TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTTTCATATTT
** * * *
56985 TTCCAAATTAAGTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCTTTAAAT
129 TTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAA-AATCC-ATAAAT
* * ** * * *
57050 CTAATGTGACTGAGATTTGATTAGATGAGGATAGATATTTCAAGTAGTCTTGGA-GTCAAAAATC
192 CCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTT-GACGCCAAAAATC
* * * * ** ** * * *
57114 ATGTAAAATTGAGCTGGTACCTAG-AACACTATTTTAGCCAAAAACCGCGATGGTTTGTTAGTAC
256 ATGCAAAACTGACCCGGGGCCCCGAAACGCTTTTTTAGCCAAAAA-C-CG-T-G-ATGTTAGTA-
*
57178 ACAATTTCGGCT
315 ACGATTTCGGCT
* * * *
57190 AAAATTTTGAAAAAATTGACACGAAAGATTTCTT-CTCAATTTTTGACTAAAATACTCAT-AAAA
1 -AAATTTTGAAAAAATTGACCCAAAATATTT-TTCCTCAATTTTTGTCTAAAATACTCATAAAAA
* * * * * *
57253 ATATAAAATTCAACACCAAGAAGATTGGAGGCCTTTTTACGC
64 ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGC
57295 ATTTCTTATT
Statistics
Matches: 2984, Mismatches: 524, Indels: 408
0.76 0.13 0.10
Matches are distributed among these distances:
292 2 0.00
293 91 0.03
294 1 0.00
295 23 0.01
296 1 0.00
298 2 0.00
299 10 0.00
300 1 0.00
301 3 0.00
302 1 0.00
303 2 0.00
304 5 0.00
305 1 0.00
306 2 0.00
308 48 0.02
309 1 0.00
310 5 0.00
311 39 0.01
312 24 0.01
313 10 0.00
314 41 0.01
315 31 0.01
316 58 0.02
317 27 0.01
318 61 0.02
319 3 0.00
320 2 0.00
321 2 0.00
322 5 0.00
323 54 0.02
324 91 0.03
325 68 0.02
326 116 0.04
327 281 0.09
328 197 0.07
329 104 0.03
330 215 0.07
331 32 0.01
332 228 0.08
333 207 0.07
334 148 0.05
335 31 0.01
336 147 0.05
337 116 0.04
338 141 0.05
339 37 0.01
340 17 0.01
341 111 0.04
342 11 0.00
343 25 0.01
344 77 0.03
345 20 0.01
346 8 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (326 bp):
AAATTTTGAAAAAATTGACCCAAAATATTTTTCCTCAATTTTTGTCTAAAATACTCATAAAAAAT
ATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTT
CTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAAATCCATAAATCCAA
TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGATTCTTGACGCCAAAAATCATGCA
AAACTGACCCGGGGCCCCGAAACGCTTTTTTAGCCAAAAACCGTGATGTTAGTAACGATTTCGGC
T
Found at i:57788 original size:15 final size:16
Alignment explanation
Indices: 57770--57799 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
57760 ATAAATAATA
57770 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
57785 ATATTATAATCTAAA
1 ATATTATAATCTAAA
57800 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:58186 original size:21 final size:22
Alignment explanation
Indices: 58126--58223 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
58116 TGAATATTTT
*
58126 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACCACCC
*
58148 TACT-AAATTTTGATAACCACGC
1 TA-TGAAATTTTGATAACCACCC
** *
58170 TATGAAATTTT-ATAACCTTCA
1 TATGAAATTTTGATAACCACCC
* *
58191 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACCC
*
58212 TATGAGATTTTG
1 TATGAAATTTTG
58224 TTAATCTCCC
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
20 5 0.08
21 23 0.38
22 32 0.52
23 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACCC
Found at i:58244 original size:22 final size:22
Alignment explanation
Indices: 58133--58248 Score: 62
Period size: 22 Copynumber: 5.4 Consensus size: 22
58123 TTTTATGAAA
*
58133 TTTTGATAA-CTACCCTACTAA-A
1 TTTTGATAACCT-CCCTA-TAAGT
* * *
58155 TTTTGATAACCACGCTATGAA-A
1 TTTTGATAACCTCCCTAT-AAGT
* * *
58177 TTTT-ATAACCTTCATATGA-T
1 TTTTGATAACCTCCCTATAAGT
* *
58197 TTTTGATAACCTCCCTATGAGA
1 TTTTGATAACCTCCCTATAAGT
* * *
58219 TTTTGTTAATCTCCCTATAATT
1 TTTTGATAACCTCCCTATAAGT
58241 TTTTGATA
1 TTTTGATA
58249 TTATAGTATG
Statistics
Matches: 73, Mismatches: 17, Indels: 8
0.74 0.17 0.08
Matches are distributed among these distances:
20 5 0.07
21 23 0.32
22 44 0.60
23 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTTGATAACCTCCCTATAAGT
Found at i:59373 original size:15 final size:15
Alignment explanation
Indices: 59353--59384 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
59343 GACAAGAAGT
59353 TATCAATACCATACC
1 TATCAATACCATACC
59368 TATCAATACCATACC
1 TATCAATACCATACC
59383 TA
1 TA
59385 GACGGTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (15 bp):
TATCAATACCATACC
Found at i:62063 original size:31 final size:32
Alignment explanation
Indices: 62009--62068 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
61999 TTTGAATATC
* * *
62009 CAAATTTAGGATAATTTGGTCCCTGAATTTTT
1 CAAATATAGGACAATTTGATCCCTGAATTTTT
*
62041 CAAATATAGGACAATTT-ATCCCTTAATT
1 CAAATATAGGACAATTTGATCCCTGAATT
62069 AATGTAGGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 9 0.38
32 15 0.62
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (32 bp):
CAAATATAGGACAATTTGATCCCTGAATTTTT
Found at i:63606 original size:10 final size:10
Alignment explanation
Indices: 63591--63662 Score: 63
Period size: 10 Copynumber: 7.0 Consensus size: 10
63581 TCTAACTAAC
63591 TAAGCTCTAT
1 TAAGCTCTAT
*
63601 TAAGCTCAAT
1 TAAGCTCTAT
*
63611 GAAGCTCTAT
1 TAAGCTCTAT
* * *
63621 AAAACTCTAGC
1 TAAGCTCTA-T
63632 TAAGCTCTAT
1 TAAGCTCTAT
* *
63642 TATGCTCTAGC
1 TAAGCTCTA-T
63653 TAAGCTCTAT
1 TAAGCTCTAT
63663 GATGTGAGAT
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
10 32 0.68
11 15 0.32
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.33
Consensus pattern (10 bp):
TAAGCTCTAT
Found at i:63638 original size:21 final size:21
Alignment explanation
Indices: 63612--63662 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
63602 AAGCTCAATG
63612 AAGCTCTATAAAACTCTAGCT
1 AAGCTCTATAAAACTCTAGCT
* **
63633 AAGCTCTATTATGCTCTAGCT
1 AAGCTCTATAAAACTCTAGCT
63654 AAGCTCTAT
1 AAGCTCTAT
63663 GATGTGAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (21 bp):
AAGCTCTATAAAACTCTAGCT
Found at i:65339 original size:423 final size:424
Alignment explanation
Indices: 64513--65499 Score: 1148
Period size: 428 Copynumber: 2.3 Consensus size: 424
64503 CGCGTTGGCT
* * *
64513 TTTAATTTTGTATT-TTT-TTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTA
1 TTTATTTTTTTATTCTTTGTTT-TATTTGTCCGATTAAGGTGATTCATGTGTCTATTAAAAGGTA
* * ** * ** ** *
64576 ATTTCTTGATCTACAATTTTCATTCAGAACTCAAAAGTCAATTTAAATGTTTTGATTCTAAAAAA
65 ATTTCATGATCTACAACTTTCATGAAGGACTCAAAAG-CAATTTTTATGTTTCAATTCAAAAAAA
* * * * * * * * ***
64641 TGCTTTCGAAATTTTGTGGTTTTGATTGCCGGTTAATTTAATATCGTATACTTTTTTTTCCACAT
129 TGCTTCCGAAATTTGGTCGTTTCGATTGCCGGTTAATTTAACACCATATAATTTTCGATCCACAT
* * * * *
64706 GTCCGATTGAAGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGACTTCCATGAAGG
194 GTCCAATTGAAGTTATT--A-TCTCGGTTAAAAGGTTATTGCATAATCTACGACTTCCATGAAGA
* *
64771 ACCTGAAAGCTAAATTTGATCTAAGAGTTTCGTGAAGGATCCAAAAGGGAATTTTTATGTTTCAA
256 ACCTGAAAGCTAAATTTGATCTAAGAGTTTCATGAAGGATCCAAAAGGGAATTTTTATATTTCAA
* *
64836 GATCTCCATTAACAAACATTTTCTTATTTGGATTATTGATCAAATGACCCTCATACTTTTATACT
321 GATCTCCATTAACAAACATTTTCTTATTTGAATTATTGATCAAATCACCCTCATACTTTTATACT
* *
64901 TTATACTATTTAGTCCTTTACAAATTCTATCTTAATCGC
386 TTATACTACTTAGTCCTTTACAAATTCTATCTTAATCGA
*
64940 TTTATTTTTTTATTCTTTGTTTTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAAGGTAA
1 TTTATTTTTTTATTCTTTGTTTTATTTGTCCGATTAAGGTGATTCATGTGTCTATTAAAAGGTAA
* *
65005 TTTCATGATCTACAACTTTCATGAAGGATTCAAAAGCAAATTTTTATGTTCCAATTCAAAAAAAT
66 TTTCATGATCTACAACTTTCATGAAGGACTCAAAAGC-AATTTTTATGTTTCAATTCAAAAAAAT
* **
65070 GCTTCCTAAATTTGGTCGTTTCGATTGTTGGTCT-ATTTAACACCATATAATTTTCGATCCACAT
130 GCTTCCGAAATTTGGTCGTTTCGATTGCCGGT-TAATTTAACACCATATAATTTTCGATCCACAT
* *
65134 GTCCAATT-AGAGTTA-T-TCTCGGTTAAAAAGGTTATTGTATAATCTACGACTTTCATGAAGAA
194 GTCCAATTGA-AGTTATTATCTCGGTT-AAAAGGTTATTGCATAATCTACGACTTCCATGAAGAA
* * * * *
65196 -CTCGAAAG-TCAATTTGATCTATGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATATTTTAA
257 CCT-GAAAGCTAAATTTGATCTAAGAGTTTCATGAAGGATCCAAAAGGGAATTTTTATATTTCAA
* * *
65259 GATCTCCATTAACAAATATTTTCTTATTTGAATTAGTT-ATCAAATCACCCTCATACTTTTCTAT
321 GATCTCCATTAACAAACATTTTCTTATTTGAATTA-TTGATCAAATCACCCTCATACTTTTATAC
* *
65323 TTTATGCTACTTAGTCCTTTACAAATTCTATCTTACTCGA
385 TTTATACTACTTAGTCCTTTACAAATTCTATCTTAATCGA
* * * * *
65363 TTTAACACTTCATTTTTTTTTCTTTGTTCTATTTGTCCAATTAAGGTAATT-TTGGTGTCTATTA
1 TTT---A--T--TTTTTTATTCTTTGTTTTATTTGTCCGATTAAGGTGATTCAT-GTGTCTATTA
* * * * *
65427 AAAGGTAATTTTATAATCTAAAACTTTCATGAAAGACTCAAAAACTAATTTTTATGTTTCAATTC
58 AAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGC-AATTTTTATGTTTCAATTC
65492 TAAAAAAA
122 -AAAAAAA
65500 GTTTTAAAAT
Statistics
Matches: 476, Mismatches: 67, Indels: 30
0.83 0.12 0.05
Matches are distributed among these distances:
423 152 0.32
424 39 0.08
426 1 0.00
427 15 0.03
428 156 0.33
429 5 0.01
430 101 0.21
431 7 0.01
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (424 bp):
TTTATTTTTTTATTCTTTGTTTTATTTGTCCGATTAAGGTGATTCATGTGTCTATTAAAAGGTAA
TTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAATTTTTATGTTTCAATTCAAAAAAATG
CTTCCGAAATTTGGTCGTTTCGATTGCCGGTTAATTTAACACCATATAATTTTCGATCCACATGT
CCAATTGAAGTTATTATCTCGGTTAAAAGGTTATTGCATAATCTACGACTTCCATGAAGAACCTG
AAAGCTAAATTTGATCTAAGAGTTTCATGAAGGATCCAAAAGGGAATTTTTATATTTCAAGATCT
CCATTAACAAACATTTTCTTATTTGAATTATTGATCAAATCACCCTCATACTTTTATACTTTATA
CTACTTAGTCCTTTACAAATTCTATCTTAATCGA
Found at i:65768 original size:20 final size:19
Alignment explanation
Indices: 65728--65765 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
65718 TATGAATGAA
*
65728 AAAATAGCCACGTGGCATT
1 AAAATAGCCACGTGGAATT
65747 AAAATAGCCACGTGGAATT
1 AAAATAGCCACGTGGAATT
65766 TAATTGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (19 bp):
AAAATAGCCACGTGGAATT
Found at i:65850 original size:22 final size:22
Alignment explanation
Indices: 65825--65868 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
65815 ACCCAAAACC
65825 GTTTAGCTTTTCTTTT-CCTTTT
1 GTTT-GCTTTTCTTTTCCCTTTT
**
65847 GTTTTTTTTTCTTTTCCCTTTT
1 GTTTGCTTTTCTTTTCCCTTTT
65869 CATTTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.02, C:0.18, G:0.07, T:0.73
Consensus pattern (22 bp):
GTTTGCTTTTCTTTTCCCTTTT
Found at i:65874 original size:21 final size:21
Alignment explanation
Indices: 65832--65881 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
65822 ACCGTTTAGC
**
65832 TTTTCTTTTCCTTTTGTTTTT
1 TTTTCTTTTCCTTTTGCATTT
65853 TTTTCTTTTCCCTTTT-CATTT
1 TTTTCTTTT-CCTTTTGCATTT
65874 TTCTTCTT
1 TT-TTCTT
65882 CTTCAACCCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTCCTTTTGCATTT
Found at i:65874 original size:22 final size:21
Alignment explanation
Indices: 65832--65881 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
65822 ACCGTTTAGC
**
65832 TTTTCTTTTCCTTTTGTTTTT
1 TTTTCTTTTCCTTTTCATTTT
65853 TTTTCTTTTCCCTTTTCATTTT
1 TTTTCTTTT-CCTTTTCATTTT
*
65875 TCTTCTT
1 TTTTCTT
65882 CTTCAACCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTCCTTTTCATTTT
Found at i:66890 original size:31 final size:31
Alignment explanation
Indices: 66855--66923 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
66845 AATTTGATTA
66855 CAGGGACTTAATTGCACAATTAATTAATATT
1 CAGGGACTTAATTGCACAATTAATTAATATT
*
66886 CAGGGACTTATTTGCACAATTAATTAATATT
1 CAGGGACTTAATTGCACAATTAATTAATATT
*
66917 CAAGGAC
1 CAGGGAC
66924 CTAAGATGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (31 bp):
CAGGGACTTAATTGCACAATTAATTAATATT
Found at i:71508 original size:51 final size:51
Alignment explanation
Indices: 71432--71533 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
71422 CAAGGTAGTT
71432 GATATAATGTCAAGCATCTAGTGAACTCCAACTCATTAAGGAACTAAAGAA
1 GATATAATGTCAAGCATCTAGTGAACTCCAACTCATTAAGGAACTAAAGAA
*
71483 GATATAATGTCAAGCATCTAGTGAACTCGAACTCATTAAGGAACTAAAGAA
1 GATATAATGTCAAGCATCTAGTGAACTCCAACTCATTAAGGAACTAAAGAA
71534 ACAATATTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (51 bp):
GATATAATGTCAAGCATCTAGTGAACTCCAACTCATTAAGGAACTAAAGAA
Done.