Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019107.1 Corchorus olitorius cultivar O-4 contig19140, 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: 71807
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4450 original size:18 final size:19
Alignment explanation
Indices: 4415--4457 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
4405 ACTCAGACTC
4415 AAACT-AACTGATTCAAAA
1 AAACTGAACTGATTCAAAA
4433 AAACTGAACTGATT-AAAA
1 AAACTGAACTGATTCAAAA
4451 AAACTGA
1 AAACTGA
4458 TCTAAACCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.56, C:0.14, G:0.09, T:0.21
Consensus pattern (19 bp):
AAACTGAACTGATTCAAAA
Found at i:6104 original size:21 final size:20
Alignment explanation
Indices: 6066--6105 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
6056 CAAAAATCCC
*
6066 CGTTAAGTCCTTGCCGTTAT
1 CGTTAAGTACTTGCCGTTAT
*
6086 CGTTATAGTACTTGTCGTTA
1 CGTTA-AGTACTTGCCGTTA
6106 CTTTGCTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (20 bp):
CGTTAAGTACTTGCCGTTAT
Found at i:9176 original size:31 final size:31
Alignment explanation
Indices: 9140--9202 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
9130 ATGACCCTTA
*
9140 AATCCAGCA-GACCCGAGACCCGAATGACCTG
1 AATCCAG-ATGACCCGAAACCCGAATGACCTG
* *
9171 AATCCAGATGAGCCGAAACCCGAATGATCTG
1 AATCCAGATGACCCGAAACCCGAATGACCTG
9202 A
1 A
9203 GAAAATTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.35, C:0.30, G:0.22, T:0.13
Consensus pattern (31 bp):
AATCCAGATGACCCGAAACCCGAATGACCTG
Found at i:9638 original size:13 final size:13
Alignment explanation
Indices: 9620--9645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9610 TAATTTTTTA
9620 AAATTAAAATATT
1 AAATTAAAATATT
9633 AAATTAAAATATT
1 AAATTAAAATATT
9646 TATAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTAAAATATT
Found at i:11467 original size:15 final size:15
Alignment explanation
Indices: 11434--11466 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11424 GATTTCCCCA
11434 TTTTCTTCTTCTTTC
1 TTTTCTTCTTCTTTC
*
11449 TTTTCTTTTTCTTT-
1 TTTTCTTCTTCTTTC
11463 TTTT
1 TTTT
11467 TTAGCTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTCTTCTTTC
Found at i:12033 original size:13 final size:14
Alignment explanation
Indices: 12015--12066 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 14
12005 AGTATATATC
*
12015 ATATTT-TATATTT
1 ATATTTATATAATT
*
12028 ATA-TT-TACAATT
1 ATATTTATATAATT
12040 ATATTTATATAATT
1 ATATTTATATAATT
12054 A-ATTTATATAATT
1 ATATTTATATAATT
12067 TAACTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.29
13 17 0.50
14 7 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATTTATATAATT
Found at i:14565 original size:213 final size:210
Alignment explanation
Indices: 14182--14578 Score: 605
Period size: 213 Copynumber: 1.9 Consensus size: 210
14172 CACGTTTTTT
* * *
14182 TACATGGATAATTATTTGATACACCGGTGGTGTAAATTTTAAATTCCACAAGCGGATTGTGGAGT
1 TACATGGATAATTATTTGATACACCAGCGGTGTAAATTTTAAACTCCACAAGCGGATTGTGGAGT
* * *
14247 TGACACATGTCCATTTTTTGAATTAATTAAGTTTTAAATTTTTCAATCTAGTCCCTAGAGGACAC
66 TGACACATGTCAATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACAC
* * * * *
14312 ATGTCACCCTTCAGGACCCGCTTGTGTAGTCTGCTAAACTCCACCGCCGGTGTATTATATAATTT
131 ATGTCACCCTTCAAGACCCACTTGTGTAATCTGCTAAACTCCACCACCAGTGTATTATATAATTT
14377 GCCTTTTTACATATA
196 GCCTTTTTACATATA
* ** *
14392 TACATAGGGTAATTATTTGATACACCAGCGGTGTAAATTTTGGACTCCACAAGCGGGTTGTGGAG
1 TACAT-GGATAATTATTTGATACACCAGCGGTGTAAATTTTAAACTCCACAAGCGGATTGTGGAG
* *
14457 TTGACACATGTCAATTTCTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTTCCTAAAGGA
65 TTGACACATGTCAA-TT-TTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGA
*
14522 CACATGTCACCCTTCAAGACCCACTTGTGTAATCTGTTAAACTCCACCACCAGTGTA
128 CACATGTCACCCTTCAAGACCCACTTGTGTAATCTGCTAAACTCCACCACCAGTGTA
14579 GTTTGCCATA
Statistics
Matches: 166, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
210 5 0.03
211 65 0.39
212 2 0.01
213 94 0.57
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (210 bp):
TACATGGATAATTATTTGATACACCAGCGGTGTAAATTTTAAACTCCACAAGCGGATTGTGGAGT
TGACACATGTCAATTTTTTGAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAAAGGACAC
ATGTCACCCTTCAAGACCCACTTGTGTAATCTGCTAAACTCCACCACCAGTGTATTATATAATTT
GCCTTTTTACATATA
Found at i:16461 original size:2 final size:2
Alignment explanation
Indices: 16456--16500 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
16446 CATTATCTTC
16456 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16497 AT AT
1 AT AT
16501 CACCCATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:23695 original size:13 final size:13
Alignment explanation
Indices: 23672--23707 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
23662 ATGCAATTTT
*
23672 AACATAAAGCAGAC
1 AACA-AAAGCAAAC
23686 AACAAAAGCAAAC
1 AACAAAAGCAAAC
23699 AACAAAAGC
1 AACAAAAGC
23708 TTCTACTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.64, C:0.22, G:0.11, T:0.03
Consensus pattern (13 bp):
AACAAAAGCAAAC
Found at i:25654 original size:46 final size:47
Alignment explanation
Indices: 25592--25687 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 47
25582 TCCAAGACCT
25592 CCTCTATATCATGGCTAGTCATCTCATGTTATGTAGCAAAACTCCTC
1 CCTCTATATCATGGCTAGTCATCTCATGTTATGTAGCAAAACTCCTC
25639 CCTC-ATATCATGGCTAGTCATCTCATGTTATGTAGCAAAACTCCTC
1 CCTCTATATCATGGCTAGTCATCTCATGTTATGTAGCAAAACTCCTC
25685 CCT
1 CCT
25688 AGTCATCTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 45 0.92
47 4 0.08
ACGTcount: A:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (47 bp):
CCTCTATATCATGGCTAGTCATCTCATGTTATGTAGCAAAACTCCTC
Found at i:25695 original size:34 final size:34
Alignment explanation
Indices: 25652--25721 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
25642 CATATCATGG
25652 CTAGTCATCTCATGTTATGTAGCAAAACTCCTCC
1 CTAGTCATCTCATGTTATGTAGCAAAACTCCTCC
25686 CTAGTCATCTCATGTTATGTAGCAAAACTCCTCC
1 CTAGTCATCTCATGTTATGTAGCAAAACTCCTCC
25720 CT
1 CT
25722 CATATCATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (34 bp):
CTAGTCATCTCATGTTATGTAGCAAAACTCCTCC
Found at i:25739 original size:80 final size:80
Alignment explanation
Indices: 25606--25765 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
25596 TATATCATGG
*
25606 CTAGTCATCTCATGTTATGTAGCAAAACTCCTCCCTCATATCATGGCTAGTCATCTCATGTTATG
1 CTAGTCATCTCATGTTATGTAGCAAAACTCCTCCCTCATATCATGGCTAGTCATCTCATGTTAAG
25671 TAGCAAAACTCCTCC
66 TAGCAAAACTCCTCC
25686 CTAGTCATCTCATGTTATGTAGCAAAACTCCTCCCTCATATCATGGCTAGTCATCTCATGTTAAG
1 CTAGTCATCTCATGTTATGTAGCAAAACTCCTCCCTCATATCATGGCTAGTCATCTCATGTTAAG
25751 TAGCAAAACTCCTCC
66 TAGCAAAACTCCTCC
25766 ACTCAAGTAG
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (80 bp):
CTAGTCATCTCATGTTATGTAGCAAAACTCCTCCCTCATATCATGGCTAGTCATCTCATGTTAAG
TAGCAAAACTCCTCC
Found at i:25819 original size:32 final size:32
Alignment explanation
Indices: 25783--25846 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
25773 TAGTGGTGGG
25783 ACCAGCCTACTGGATCAACGGTAGCAAAACTC
1 ACCAGCCTACTGGATCAACGGTAGCAAAACTC
25815 ACCAGCCTACTGGATCAACGGTAGCAAAACTC
1 ACCAGCCTACTGGATCAACGGTAGCAAAACTC
25847 TTATGTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.19, T:0.16
Consensus pattern (32 bp):
ACCAGCCTACTGGATCAACGGTAGCAAAACTC
Found at i:27951 original size:50 final size:50
Alignment explanation
Indices: 27879--27973 Score: 172
Period size: 50 Copynumber: 1.9 Consensus size: 50
27869 CTACCATTTA
* *
27879 AAACCGTTTGATGTTGATTTGATTTGAATAATAACCGTTGGATATAGTTT
1 AAACCGTTTGATGTGGACTTGATTTGAATAATAACCGTTGGATATAGTTT
27929 AAACCGTTTGATGTGGACTTGATTTGAATAATAACCGTTGGATAT
1 AAACCGTTTGATGTGGACTTGATTTGAATAATAACCGTTGGATAT
27974 GGGTAGTGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (50 bp):
AAACCGTTTGATGTGGACTTGATTTGAATAATAACCGTTGGATATAGTTT
Found at i:39396 original size:17 final size:17
Alignment explanation
Indices: 39374--39416 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
39364 CTGTTGCGTG
*
39374 TCTTTTTTCTT-TTCTTT
1 TCTTTTTTCTTATT-TAT
*
39391 TCTTTTTTGTTATTTAT
1 TCTTTTTTCTTATTTAT
39408 TCTTTTTTC
1 TCTTTTTTC
39417 CTTTATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 20 0.91
18 2 0.09
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (17 bp):
TCTTTTTTCTTATTTAT
Found at i:54788 original size:2 final size:2
Alignment explanation
Indices: 54781--54817 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54771 AGTACTAGTG
54781 TA TA 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 T
54818 TGATTGTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64879 original size:332 final size:328
Alignment explanation
Indices: 60362--64159 Score: 3054
Period size: 331 Copynumber: 11.5 Consensus size: 328
60352 TCATGATGGT
* * *
60362 AAAATTGACCCGAAAGATTTTTCCTCAATTTTT-GACAAAAATACTTATAAAATATATATAATTC
1 AAAATTGA-CCGAAAGATTTTTCCTCAATTTTTAG-CCAAAATACTCATAAAAAATATATAATTC
* * * * *
60426 AACCCCAAAAAGATTGGAGGACTTTTCACGTTTTTAATATCGTTTTT-C-ATTTTTTTAAAATTA
64 AACGCCAAAAAGATTGAAGGGCTTTTCACG-TTTTAATATCGTTTTTCCTATTTTTCT-GAATTA
* * * * *
60489 ATTTCTAATTAAATCGATACAAGATTCAGATGCACATAAAAACAAATCGTTAAATCCAATGTGAC
127 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * *
60554 TGAGATTTTATTAGATGAATAAAGATATTTCAAGGAGTCTTGACGTCAAAAATCATGCAAAAC-A
192 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTA
** ** * * * *
60618 GAGTTGTGGCCTTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAA
257 -AGCCG-GGCCCCGGAACGCGTTTTTAGCAAAAAACCATGATGATTAGTACACGATTTCGGCTAA
*
60683 AATTTTACA
320 AATTTTGCA
* * * * * **
60692 AAAATTGACCCGAAAGATATTTCTTCAATTTTTGGCTAAAATACTCATAAAAAATATATGATTTT
1 AAAATTGA-CCGAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTCA
*** * * * * *
60757 ATATCAAAAAGATTGAAGGGTTTTTAACGCTTCTAATATTGTTTTTCCTATTTCTTTCCGAATTA
65 ACGCCAAAAAGATTGAAGGGCTTTTCACG-TTTTAATATCGTTTTTCCTA-TT-TTTCTGAATTA
* * *
60822 ATTTCCAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGC
127 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* *
60887 TAAGATTTCG-TTAGATGAATATAGATATTTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACT
192 TGAGATTT-GATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
* * * ** * * * *
60951 GAGCCGGACCCCGTAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCAGTTAAA
256 AAGCCGGGCCCCGGAACGCGTTTTTAGCAAAAAACCATGATGATTAGTACACGATTTCGGCTAAA
**
61016 ATTTACCA
321 ATTTTGCA
* * * *
61024 AAAATTGACTCGAAAAATTTTTCCTCGATTTCTAGCGAAAATACTCAT-AAAAATATATAATTCA
1 AAAATTGAC-CGAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTCA
* * * * * * * **
61088 ATGTCAAAAAAAATGAAAGCCTTTTTCACGCTTCTAATATCG-TTTTCCTTATTTTCTTTCCAAA
65 ACGCCAAAAAGATTGAAGGGC-TTTTCACG-TTTTAATATCGTTTTTCC-TA--TT-TTTCTGAA
* * *** * * *
61152 TTAATTTCTAATTAAATCCAAATC-AGATTTAGAAATTTGTAAAAACAAATTCTTAAATACAATG
124 TTAATTTCTAATTAAATCGAAA-CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * *
61216 TAGCTGAGATTTGGTTAGATGAATATAGATATATTTTAAGGAGTCTTGGCGCCAAAAATCATGCA
188 TGGCTGAGATTTGATTAGATGAATATAG--ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCA
* * * ** *** ** ** *
61281 AAACTGACCCAGGACCTTGGAACGCGTTTTTTTTTTTAAAAAAAAACAATGA-TGGTACACGATT
251 AAACTAAGCC-GGGCCCCGGAACGCG---TTTTTAGCAAAAAACCATGATGATTAGTACACGA-T
*
61345 TTCGGCTAAAATTTTGTA
311 TTCGGCTAAAATTTTGCA
* * * *
61363 AAAATTAACCTGAAATATTTTT-CTCAATTTTTAGCCACAATACTCATAAGAAATATATAATTCA
1 AAAATTGACC-GAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTCA
* * * * * *
61427 ACGCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCATTTTGCCTATTTTTTTCAAATTAA
65 ACGCCAAAAAGATTGAAGGGCTTTTCACG-TTTTAATATCGTTTTTCCTATTTTTCT-GAATTAA
* * *
61492 TTTCTAATTAAATCGAAACATGATTCAAATGCTCGCAAAAACAAATCCTTAAAT-CAAGTGTGGC
128 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA-TGTGGC
* * * * * * * * *
61556 TAAGATTTGGTTAAATTAATATAGATATTTCAAGGAGTTTTGCCACAAAAAAT-ATGCAAAACTG
192 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTA
* * * *
61620 ACCCGGGGCTCCGGAACGCGTTTTTAGC-CAAAA-CACTG-TGA-TGGTACACGATTTCGGCTAA
257 AGCC-GGGCCCCGGAACGCGTTTTTAGCAAAAAACCA-TGATGATTAGTACACGATTTCGGCTAA
61681 AATTTTGCA
320 AATTTTGCA
* * * * **
61690 AAAATTGACCCGAAATATTTTGT-CTCGATTTTTAGCCACAACACTCATAAAATTTATATAATTC
1 AAAATTGA-CCGAAAGATTTT-TCCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTC
* * * * * * *
61754 AACACCAAAAAGACTGGAGGACTTTTCACACTTTTAATATCGTTTTACATATTTTTCTGAATTAA
64 AACGCCAAAAAGATTGAAGGGCTTTTCAC-GTTTTAATATCGTTTTTCCTATTTTTCTGAATTAA
*
61819 TTTCTAATTAAATCGAAACAAGATTCAGA-GTCTCGTAAAAACAAATCCTTAAATTCAATGTGGC
128 TTTCTAATTAAATCGAAACAAGATTCAGATG-CTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* ** * *
61883 TGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCAGCACAAAAAATCATGCAAAACTA
192 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTA
** * * *
61948 AGCCCGGGCCTTGAAACGCGTTTTTAG-------CCA--A--A-AAGTACACGATTTTGGCTAAA
257 AG-CCGGGCCCCGGAACGCGTTTTTAGCAAAAAACCATGATGATTAGTACACGATTTCGGCTAAA
62001 ATTTTGCA
321 ATTTTGCA
* * *
62009 AAAATTGACCCGAAA-ATTTTTTCCGACAATTTTTGGCTAAAATACTCATAATATATATATATAT
1 AAAATTGA-CCGAAAGA-TTTTTCC-TCAATTTTTAGCCAAAATACTC---ATA-A-A-A-A-AT
* * ** ** *
62073 ATATAATTTAATGCCAAAAAGATTGAAGAACTTTTCACGCTTTTAATATCGTTTTTATTAATTTT
55 ATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACG-TTTTAATATCGTTTTTCCTATTTTT
* * * * *
62138 CTGAATTAATTTTTAATTAAATCGAAATAAGATTTAGATGCTCATAAAAACAAATTCTTAAATCC
119 CTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* * * * * ** *
62203 AATGTTGCTGATATTTGATTAGATAAATATGGATATCTCAAAAAGTCCTGGCGCCAAAAATCATG
184 AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATG
* * * * * ** * * * *
62268 CAAAACTGAGCCGGGGTCTCGAAACGTGACTTTAGCCAAAAACCGTGATGATTA-TCAAACGAGT
249 CAAAACTAAGCC-GGGCCCCGGAACGCGTTTTTAGCAAAAAACCATGATGATTAGT-ACACGATT
* *
62332 TCGGCTAGAATTTTACA
312 TCGGCTAAAATTTTGCA
* * * *
62349 AAAATTGACTCGAAAG-TTATTTCCTCAATTTTTAGCCACAACACTCATTAAAATTATATAATTC
1 AAAATTGAC-CGAAAGATT-TTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTC
* * * *
62413 AACGCTAATAAGATTGAAGGGTTTTTCATGCTTTTAATATCGTTTTTCCTAAATTTTT-TGAATT
64 AACGCCAAAAAGATTGAAGGGCTTTTCACG-TTTTAATATCGTTTTTCCT--ATTTTTCTGAATT
* * * * * *** *
62477 AATTTTTGATTAAATCGAAATATGATTCAGATGCTTGT-TTTAGAAATCCTTAAATCCAATGTGG
126 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * *** *
62541 CTGAGATTTGGTTAAATGAATATAGATATTTCAAGGAGTCTCAACGCCAAAAATCATGCAACACT
191 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
* * * * *
62606 GTA-CCGAGACCCCGGAACGCGTTTTTAGCAAAAAAAAAAACCGTAATTTCGACTAACGTACACG
256 -AAGCCG-GGCCCCGGAACGCGTTTTTAGC-----AAAAAACCATGA--T-GA-TTA-GTACACG
* *
62670 ATTTCGGCTAATATTTTGTA
309 ATTTCGGCTAAAATTTTGCA
*
62690 AAAATTGACC-AGAAGTATTTTTCCTCAATTTTT-GTCTAAAATACTCATAAAATATATATATAT
1 AAAATTGACCGA-AAG-ATTTTTCCTCAATTTTTAG-CCAAAATACTCAT-AAA-A-A-ATATAT
* * * * * *
62753 ATATTTCAACTCCAAAAAGATTGTAGGACATTTCATGCTTTTAATATCGTTTTTCATATTTTTCT
59 A-A-TTCAACGCCAAAAAGATTGAAGGGCTTTTCACG-TTTTAATATCGTTTTTCCTATTTTTCT
* * * * *
62818 GAATTAATTTCAAAATAAATCAAAACAAGATTCAGATGCTCGTAAAAACACATCCTTAAATGCAA
121 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * * * *
62883 TGTGGCTGAGATTTGATTAGATAAATACAGATATTTCAAGGAGTCTCGACGCCAAAAATAATGCA
186 TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCA
** ** * * * ** ** * * *
62948 GTACTAAGTCAAGG-CCCGAAACGCATTTTTCGCAAAAAAAAAAAACCG-TGA-TACACGATTTT
251 AAACTAAG-CCGGGCCCCGGAACGCGTTTTTAGCAAAAAACCATGA-TGATTAGTACACGATTTC
*
63010 AGCTAAAATTTTGCA
314 GGCTAAAATTTTGCA
* * * * *
63025 AAAAATGACCAAAAAAATTTTTCCTCAATTTTT-GACTAAAATACTCATGAAAATATATATAATT
1 AAAATTGACC-GAAAGATTTTTCCTCAATTTTTAG-CCAAAATACTCAT-AAAAAATATATAATT
* * * * * * *
63089 TAACGGCAAAAAGATTAAAGGACTTTTCACGCTTTTCATATCGTTTTTCATATTTTTGTTGAATT
63 CAACGCCAAAAAGATTGAAGGGCTTTTCACG-TTTTAATATCGTTTTTCCTATTTTT-CTGAATT
* * * * *
63154 AATTTGTAATTAGATCGAAACAAGATACAGATGCTCGTAAAAACAAATCATTAAATGCAATGTGG
126 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * **
63219 ATGAGATTTGATTAGATTAATATGGATATCTCAAGGATTCTTAACGCCAAAAATCATGCAAAACT
191 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT
* * * * * *
63284 AA-CTTGGGGCCCTGGAACGTGTTTTTAG-ACAAAAACCGTGATTATTATTACACGATTTCGGCT
256 AAGC--CGGGCCCCGGAACGCGTTTTTAGCA-AAAAACCATGATGATTAGTACACGATTTCGGCT
*
63347 ACAATTTTGCA
318 AAAATTTTGCA
* * **
63358 AAAATTGACCGAAAAAAATATTTCCTCAATTTTT-GACTTAAATACTCATAAAAAA-ATATAATT
1 AAAATTGACCG--AAAGATTTTTCCTCAATTTTTAG-CCAAAATACTCATAAAAAATATATAATT
* * * * * * *
63421 CATCGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATATCTTTTTTCCTATTTTTTCCGAATT
63 CAACGCCAAAAAGATTGAAGGGCTTTTCACG-TTTTAATATCGTTTTTCCTA-TTTTTCTGAATT
* * *
63486 AATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAA-AATTCCTTAATTCCAATGTGG
126 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * *
63550 CTGAGATTTTATTAGATGAATATAGATATTTGC-ATGATTTTTGGCGCAAAAAATCATGCAAAAT
191 CTGAGATTTGATTAGATGAATATAGATATTT-CAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
* * * ** ** * *
63614 TGACCCGGGGCCCCGGAACGCAG-TTTTGGCAAAAAAAAAAAAATCG-TGATGTTACACGATTTT
255 TAAGCC-GGGCCCCGGAACGC-GTTTTTAGC-AAAAAACCATGAT-GATTA-G-TACACGATTTC
* *
63677 GGCTAATATTTTACA
314 GGCTAAAATTTTGCA
* * * * *
63692 AAAATTGACCCAAAATATTTTTCCTTAACTTTTAGCCACAATACTCATAAAAAATATATAATTCA
1 AAAATTGA-CCGAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTCA
* * * *
63757 ATGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATA-CTGTTTTTTCTTATTTTTTTCTGAAT
65 ACGCCAAAAAGATTGAAGGGCTTTTCACG-TTTTAATATC-G-TTTTTCCTA--TTTTTCTGAAT
* * * **
63821 TAATTTCTAATTAAAACAAAACATGATTCAGATG--C-T---------T--TTAAAAACAA--TG
125 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * * *
63870 GCTGAGATTTGGTTAGATCAATATAGATATTTCAAGGAGTCTCGGCACCAAAAATTATTCAAAAC
190 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC
* * * * * *
63935 TAAACCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGACTAA
255 TAAGCCGGGCCCCGGAACGCGTTTTTAGCAAAAAACCATGATGATTAGTACACGATTTCGGCTAA
64000 AATTTTGCA
320 AATTTTGCA
* * * * *
64009 AAAATTGACCTGAAAGATATTTCCTAAATTTTTAGCCATAATACTCA-ATAAAATATATAATTCG
1 AAAATTGACC-GAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTCA
* * * *
64073 ACGCCAAAAAAATTGAAGGGCTTTTCGAGCG-TTTAATATCATTTTTCATATTTTTTCTTAATTA
65 ACGCCAAAAAGATTGAAGGGCTTTTC-A-CGTTTTAATATCGTTTTTCCTA-TTTTTCTGAATTA
*
64137 ATTTCTAATTAAATAGAAACAAG
127 ATTTCTAATTAAATCGAAACAAG
64160 TTTGGCCAAA
Statistics
Matches: 2811, Mismatches: 528, Indels: 274
0.78 0.15 0.08
Matches are distributed among these distances:
314 32 0.01
315 8 0.00
316 47 0.02
317 62 0.02
318 4 0.00
319 57 0.02
320 36 0.01
321 57 0.02
323 12 0.00
324 1 0.00
325 2 0.00
326 2 0.00
327 142 0.05
328 322 0.11
329 8 0.00
330 148 0.05
331 386 0.14
332 291 0.10
333 321 0.11
334 138 0.05
335 127 0.05
336 144 0.05
337 4 0.00
338 52 0.02
339 105 0.04
340 46 0.02
341 60 0.02
342 5 0.00
343 1 0.00
344 1 0.00
345 12 0.00
346 54 0.02
347 123 0.04
348 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (328 bp):
AAAATTGACCGAAAGATTTTTCCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTCAA
CGCCAAAAAGATTGAAGGGCTTTTCACGTTTTAATATCGTTTTTCCTATTTTTCTGAATTAATTT
CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAAGCC
GGGCCCCGGAACGCGTTTTTAGCAAAAAACCATGATGATTAGTACACGATTTCGGCTAAAATTTT
GCA
Found at i:65285 original size:15 final size:16
Alignment explanation
Indices: 65267--65296 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
65257 ATAAATAATA
65267 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
65282 ATATTATAATCTAAA
1 ATATTATAATCTAAA
65297 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:65574 original size:8 final size:8
Alignment explanation
Indices: 65561--65586 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
65551 TTTTATATAG
65561 TAGTAAGA
1 TAGTAAGA
65569 TAGTAAGA
1 TAGTAAGA
65577 TAGTAAGA
1 TAGTAAGA
65585 TA
1 TA
65587 ATTTCAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (8 bp):
TAGTAAGA
Found at i:71543 original size:2 final size:2
Alignment explanation
Indices: 71536--71560 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71526 TGGTTAAATA
71536 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
71561 GAATTTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71639 original size:340 final size:329
Alignment explanation
Indices: 70169--71802 Score: 1436
Period size: 340 Copynumber: 4.9 Consensus size: 329
70159 CATGATGATC
* * * * * *
70169 AAAA-TGATCCGAAAGATTATTCCTCAATTTTTGGTAAAAATAT-TCATAAAATATATATAA-TC
1 AAAATTGACCCGAAATATTTTTCCTCAATTCTTAGT-AAAATATCT-ATAAAAAATATATAATTC
* * * * * * * *
70231 AACG-CCAGAAAGATCGGAGTACATTGCATGCTTTTAATATCGTTTTTCATATTTTTCTTAATTA
64 AACGACAAAAAAGAT-TGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAATTA
* * *
70295 ATTTCCAATTAAATCGAAACAAGAATCAGATGCACGTAAAAACAAATCCTTAAATCCAATGTGGC
128 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* *
70360 TGAGATTTGATTAGATGAATAAATATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC-A
193 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTA
* * * * *
70424 GAGCCGTGGCCCCGGAACACGTCTTTAGCGAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
258 -AGTCG-GGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
70489 AATTTTGCA
321 AATTTTGCA
* * * * * * * * *
70498 AATATTGATCTGAAAGATATTTCCTCAATTCTTGGCTAAAATACCCATAAAAAATATATAATTCG
1 AAAATTGACCCGAAATATTTTTCCTCAATTCTTAG-TAAAATATCTATAAAAAATATATAATTCA
* * * * * **
70563 ACGTC-AAAAAGATTGAGGGGCTTTTAACGCTTATAATAT--TTTTTCCCATTTTTTGTCCGAAT
65 ACGACAAAAAAGATTGA-GGACTTTTCACGCTTTTAATATCGTTTTT--CATATTTT-TCTAAAT
* * *
70625 TAATTTTTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTCAATCCAATGTG
126 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * ** * * *
70690 GCTGATAATTGGTTAGATGAATATAGATATTTCAAGGAGTCTTAGCACAAAAAATCATGCAAATC
191 GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAAC
* *** * * * *
70755 TGAGTCGGGCCCCGAAACGCGTTTTTAGTTGAAAACCGTGATGATTA-T----TA-TACGGCGAA
256 TAAGTCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
70814 AATTTTGCA
321 AATTTTGCA
* ** *
70823 AAAATTGACCCGAAAGATTTTTTTATCAATT-TCTAGCGAAAATA-CTTATAAAAAATATATAAT
1 AAAATTGACCCGAAATA-TTTTTCCTCAATTCT-TAG-TAAAATATC-TATAAAAAATATATAAT
* * * *
70886 TCAACGCCAAAAAA-ATTGA-AATCTTTTTTCATGCTTCTAATATCGTTTTTTCCGAT-TTTATT
62 TCAACGACAAAAAAGATTGAGGA-C--TTTTCACGCTTTTAATATCG-TTTTT-C-ATATTT-TT
* * * *** * *
70948 CCAAATTAATTTCTGATTAAATCGAAACAAGATTTAGAAATTCGTAAAAACAAATCCTCAAATAC
120 CTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* * * *
71013 AATGTGGCTGAGGTTTGGTTAGATGAATATAGATATATTTTAAGGAGCCAT-GGCGCCAAAAATC
185 AATGTGGCTGAGATTTGATTAGATGAATATAG--ATATTTCAAGGAGTC-TCGGCGCCAAAAATC
* * ***** * * *
71077 ATGCAAAACTGA-TCTGGGACCCC-AGAACGCGTTTTTAGCAAAAAAAAAAAAACGTGATGGTAC
247 ATGCAAAACTAAGTC-GGG-CCCCGA-AACGCGTTTTTAGC-CAAAAACCGTGATG-GTTAGTAC
* *
71140 ATGATTTCGGCTAAAATTTGGCA
307 ACGATTTCGGCTAAAATTTTGCA
* * *
71163 AAAATTGACCCGAAATATTTTTCCTCAATTCTTAGCCATAATA-CTCATAAAATATATATAATTC
1 AAAATTGACCCGAAATATTTTTCCTCAATTCTTAG-TAAAATATCT-ATAAAAAATATATAATTC
* * * * *
71227 AATG-CCAAAAAGATTGAAGGGCTTCTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTA
64 AACGACAAAAAAGATTG-AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAATTA
* *
71291 ATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGC
128 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* *
71356 TGGGATTTAATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTA
193 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTA
* *
71421 AGTCGAGGCCTCGAAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCTAAA
258 AGTCG-GGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAA
71486 ATTTTGCA
322 ATTTTGCA
* * * * * *
71494 AAAACTGATCTGAAATTTTTTTCCTCAATT-TATGGTTAAATAATATATATATATATATATATAT
1 AAAATTGACCCGAAATATTTTTCCTCAATTCT-TAG-T-AA-AATATCTATA-A-A-A-A-ATAT
* *
71558 ATAGAATTTAAC-ACAAAAAAGATTGGAGGACTTTTCACGTTTTTAATATCGTTTTTCATATTTT
57 AT--AATTCAACGACAAAAAAGATT-GAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTT
* * * *
71622 TCTAAATTAATTTCTAATTAAATCGAAATAAGATTTAGTTGCTCGTAAAAATAAATTACC--AAA
119 TCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA-T-CCTTAAA
* * * * * * *
71685 TCCAATGTAGC-GAAGATTTGATAAGATGAATATGGCTATCTCAAAGAGTCTTGGCGCCAAAAAT
182 TCCAATGTGGCTG-AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAAT
*** * * * * *
71749 CATGTGGAAGTTAGTAGGGGCCCCGGAACGCGTTTTTAGCCAAAACCCGTGATG
246 CATGCAAAACTAAGT-CGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATG
71803 TTATT
Statistics
Matches: 1060, Mismatches: 182, Indels: 115
0.78 0.13 0.08
Matches are distributed among these distances:
325 33 0.03
326 47 0.04
327 20 0.02
329 97 0.09
330 60 0.06
331 161 0.15
332 152 0.14
333 68 0.06
334 8 0.01
335 89 0.08
336 5 0.00
337 5 0.00
338 30 0.03
339 47 0.04
340 233 0.22
341 3 0.00
342 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (329 bp):
AAAATTGACCCGAAATATTTTTCCTCAATTCTTAGTAAAATATCTATAAAAAATATATAATTCAA
CGACAAAAAAGATTGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAATTAATT
TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGT
CGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTT
TGCA
Done.