Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017987.1 Corchorus olitorius cultivar O-4 contig18020, 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: 44503
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:2437 original size:18 final size:18
Alignment explanation
Indices: 2414--2451 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2404 CAATTTATAC
2414 ATAGTCACTTTTATTTAA
1 ATAGTCACTTTTATTTAA
2432 ATAGTCACTTTTATTTAA
1 ATAGTCACTTTTATTTAA
2450 AT
1 AT
2452 TATTTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (18 bp):
ATAGTCACTTTTATTTAA
Found at i:2841 original size:11 final size:11
Alignment explanation
Indices: 2820--2851 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
2810 CCTAAAGCAC
2820 AAAAAGCAAAAA
1 AAAAAG-AAAAA
2832 AAAAAGAAAAA
1 AAAAAGAAAAA
2843 AAAAAGAAA
1 AAAAAGAAA
2852 GGAAATTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:4738 original size:18 final size:18
Alignment explanation
Indices: 4715--4751 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4705 TTAAACCAAA
4715 ATGATAATATTTATATAT
1 ATGATAATATTTATATAT
4733 ATGATAATATTTATATAT
1 ATGATAATATTTATATAT
4751 A
1 A
4752 ATAACTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
ATGATAATATTTATATAT
Found at i:4749 original size:16 final size:17
Alignment explanation
Indices: 4715--4761 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
4705 TTAAACCAAA
4715 ATGATAATATTTATATAT
1 ATGATAATA-TTATATAT
4733 ATGATAATATT-TATAT
1 ATGATAATATTATATAT
*
4749 ATAATAACTATTA
1 ATGATAA-TATTA
4762 ATTAACATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 11 0.42
17 6 0.23
18 9 0.35
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
ATGATAATATTATATAT
Found at i:5136 original size:28 final size:28
Alignment explanation
Indices: 5096--5152 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
5086 GAACAATAAA
5096 TTAACATGTGTGATACCTTATCGTCCAT
1 TTAACATGTGTGATACCTTATCGTCCAT
5124 TTAACATGTGTGATACCTTATCGTCCAT
1 TTAACATGTGTGATACCTTATCGTCCAT
5152 T
1 T
5153 GCTGTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (28 bp):
TTAACATGTGTGATACCTTATCGTCCAT
Found at i:8308 original size:992 final size:980
Alignment explanation
Indices: 6598--8429 Score: 2193
Period size: 992 Copynumber: 1.8 Consensus size: 980
6588 AAATTTATAC
*
6598 AATTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATAGTTTTTCATATTCTTTTTC
1 AATTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATAGTTTTTCATATTCTTTTCC
** * * *
6663 AAATTAATTTCTAATTAAATCAAAACATGATTCAAATTCTCATAAAAACAAATCCTTAAATCTAA
66 AAATTAATTTCTAATTAAATCAAAACAAAATTCAAATACTCACAAAAACAAATCCTTAAATCCAA
* * *
6728 TGTGGCTAAGATTTGGGTAGATGAATATGGATATTTCAAGGAGTTTTGCCACAAAAAATCATGCA
131 TGTGGCTAAGATTTGAGTAGATGAATATAGATATTTCAAGGAGTCTTGCCACAAAAAATCATGCA
* *
6793 AAACTGACCTGAGGCCCCAGAACGCGTTTTTAGCGAAAAAACCGTGATGGTACACGATTTTGCTT
196 AAACTGACCTGAGGCCCCAGAACGCGTTTTTAGCGAAAAAACCGTGATGGTACACAATTTGGCTT
**
6858 AAAATTTTGCAAAAATTGTCCCGAAATATTTTTCCTCAATTTTTAGCCACAATACTCATAAATAT
261 AAAATTTTGCAAAAATTGAACCGAAATATTTTTCCTCAATTTTTAGCCACAATACTCATAAATAT
* * * *
6923 ATATAATTCAACTCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCGTATTTTT
326 ATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTT
* *
6988 CTTATTTAATTTCTAATTCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATG
391 CTGAATTAATTTCTAATTCGAAACAAGATTCAGATGCTC-T---AACAAA----TAAA-TCAA-G
* * * *
7053 TGGCTGAGATTTGATTAGATGAGTATAGATATTTCCAGGAGTCTCGGCGCAAAAAAAATCATGCA
446 TGACTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTCGGCGC-AAAAAAATCATGCA
* * * * *
7118 AAACTAAGCCGGGGCCCCGAAATGCGTTTTTAGCCAAAAACCGTGATGTAACGTACACGATTTCA
510 AAACTAAGCCGAGGCCCCGAAACGCGATTTTAGCAAAAAACCATGATGTAACGTACACGATTTCA
* * * *
7183 GCTAAAATTTTACAAAAAATGACCCGAAAATTTTTTCTCAATTTTTGGCTAAAATACTCATAATA
575 GCTAAAATTTTACAAAAAATGACCCGAAAATATTTCCTCAATTTTTAGCCAAAATACTC--AATA
* * ** * *
7248 TATATATATATATATAATTTAACTCCAAAAAGGTTGGTGGACTTTTCACTCTTTTCATATCATTT
638 TATATATATATATATAATTCAACACCAAAAAGGTTGAAGGACTTTTCACGCTTTTAATATCATTT
* * * * *
7313 TTCATATTTTTTCTCAATTAATTTCTAATTAAGTAGAAAGAAGATTCAGATGCTCGTAAAAAGAA
703 TTCATATTTTTTCTCAACTAATTTCTAATCAAATAGAAAGAAGATTCAGATGCCCGTAAAAACAA
* * * *
7378 ATCCTTAAATGCAATGTGGCTGAGA-TTTGATTAGATGAATATGGATATCACAAGGAGTCTTAGT
768 ATCCTTAAATACAATGTGGCTAAGACTAT-ATTAGATGAATATAGATATCACAAGGAGTCTTAGT
7442 GCCAAAAATCATGCAAAAATGACTCAGTTCTTTGGAACGCGTTTTTAGCCAAAAACTGTGATGAT
832 GCCAAAAATCATGCAAAAATGACTCAGTTCTTTGGAACGCGTTTTTAGCCAAAAACTGTGATGAT
7507 TATTACATGATTTCGGCTAATATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGA
897 TATTACATGATTTCGGCTAATATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGA
7572 TAAAATACCCAAAAAAAAT
962 TAAAATACCCAAAAAAAAT
* * * * *
7591 AATTCAACGCCAAAAATATTGAAGGG-TTTTTACGCTTCTAATATCGTTTTTCCTACTT-TTTTC
1 AATTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATAGTTTTTCATA-TTCTTTTC
* * * * *
7654 CAAATTAATTTCTATTTAAATCGAAACAAAATTTAGATACTCGCAAAAACAAATCCTTAAATCCA
65 CAAATTAATTTCTAATTAAATCAAAACAAAATTCAAATACTCACAAAAACAAATCCTTAAATCCA
* * * *** *
7719 ATGTGGCTGAGATTTGATTAGATGAATATAGATTTTTCAAGGAGTCTTGGGGCCAAAAA-CATGC
130 ATGTGGCTAAGATTTGAGTAGATGAATATAGATATTTCAAGGAGTCTTGCCACAAAAAATCATGC
* *
7783 AAAACTGA-CTCGGGGCCCCAGAATGCGTTTTTAAGCGTAAAAAAAAAAAAAAAAAAAAAAACCC
195 AAAACTGACCT-GAGGCCCCAGAACGCGTTTTT-AGCG------------------AAAAAA-CC
*
7847 GTGATGGTACACAATTTCGGC-TAATATTTTGCAAAAATTGAACCGAAATATTTTTCCTCAATTT
239 GTGATGGTACACAATTT-GGCTTAAAATTTTGCAAAAATTGAACCGAAATATTTTTCCTCAATTT
* *
7911 TTAGCCACAATACTCATAAAAAATGTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACG
303 TTAGCCACAATACTCAT---AAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACG
* *
7976 CTTCTAATATTGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCAGA
365 CTTCTAATATCGTTTTTCCTA-TTTTTCTGAATTAATTTCTAA-T---TCGAAACAAGATTCAGA
* * * *
8041 TGCT-T-A-TAA-AAA-CAA-TGACTGTGATTTGGTTAGATGAATATAAATATTTCAAGGATTCT
425 TGCTCTAACAAATAAATCAAGTGACTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCT
* * * *
8100 TGGCGC-CAAAAATCATGCAAAACTGAA-CC-AGGCCTCGGAACGC-ATTTTAGCAAAAAACCAT
490 CGGCGCAAAAAAATCATGCAAAACT-AAGCCGAGGCCCCGAAACGCGATTTTAGCAAAAAACCAT
* * * * *
8161 GAT-TATTA-TTACATGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAA
554 GATGTA--ACGTACACGATTTCAGCTAAAATTTTACAAAAAATGACCCGAAA-ATATTTCCTCAA
* * *
8224 TTTTTAGCCACAATACTC-ATA-A-A-A-A-ATATATAATTCAACACC-AAAAGGATTTAAGGTC
616 TTTTTAGCCAAAATACTCAATATATATATATATATATAATTCAACACCAAAAAGG-TTGAAGGAC
** * * *
8282 TTTTCACGCTTTTAATATTGTTTTTCATATTTTTTCTGAACTAATTTCTAATCAAATCGAAATAA
680 TTTTCACGCTTTTAATATCATTTTTCATATTTTTTCTCAACTAATTTCTAATCAAATAGAAAGAA
8347 GATTCAGATGCCCGTAAAAACAAATCCTTAAATACAATGTGGCTAAGACTATATTAGATGAATAT
745 GATTCAGATGCCCGTAAAAACAAATCCTTAAATACAATGTGGCTAAGACTATATTAGATGAATAT
**
8412 AGATATTTCAAGGAGTCT
810 AGATATCACAAGGAGTCT
8430 CAGCACAAAA
Statistics
Matches: 708, Mismatches: 94, Indels: 75
0.81 0.11 0.09
Matches are distributed among these distances:
990 2 0.00
991 38 0.05
992 284 0.40
993 30 0.04
994 1 0.00
995 1 0.00
996 1 0.00
997 3 0.00
998 2 0.00
999 55 0.08
1000 36 0.05
1001 19 0.03
1002 2 0.00
1003 42 0.06
1005 3 0.00
1007 3 0.00
1010 6 0.01
1011 75 0.11
1012 4 0.01
1013 1 0.00
1014 59 0.08
1015 19 0.03
1016 1 0.00
1017 1 0.00
1019 20 0.03
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (980 bp):
AATTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATAGTTTTTCATATTCTTTTCC
AAATTAATTTCTAATTAAATCAAAACAAAATTCAAATACTCACAAAAACAAATCCTTAAATCCAA
TGTGGCTAAGATTTGAGTAGATGAATATAGATATTTCAAGGAGTCTTGCCACAAAAAATCATGCA
AAACTGACCTGAGGCCCCAGAACGCGTTTTTAGCGAAAAAACCGTGATGGTACACAATTTGGCTT
AAAATTTTGCAAAAATTGAACCGAAATATTTTTCCTCAATTTTTAGCCACAATACTCATAAATAT
ATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTT
CTGAATTAATTTCTAATTCGAAACAAGATTCAGATGCTCTAACAAATAAATCAAGTGACTGAGAT
TTGATTAGATGAATATAAATATTTCAAGGAGTCTCGGCGCAAAAAAATCATGCAAAACTAAGCCG
AGGCCCCGAAACGCGATTTTAGCAAAAAACCATGATGTAACGTACACGATTTCAGCTAAAATTTT
ACAAAAAATGACCCGAAAATATTTCCTCAATTTTTAGCCAAAATACTCAATATATATATATATAT
ATAATTCAACACCAAAAAGGTTGAAGGACTTTTCACGCTTTTAATATCATTTTTCATATTTTTTC
TCAACTAATTTCTAATCAAATAGAAAGAAGATTCAGATGCCCGTAAAAACAAATCCTTAAATACA
ATGTGGCTAAGACTATATTAGATGAATATAGATATCACAAGGAGTCTTAGTGCCAAAAATCATGC
AAAAATGACTCAGTTCTTTGGAACGCGTTTTTAGCCAAAAACTGTGATGATTATTACATGATTTC
GGCTAATATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGATAAAATACCCAAAA
AAAAT
Found at i:19561 original size:13 final size:13
Alignment explanation
Indices: 19524--19563 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
19514 AAATCCGCTG
*
19524 CTGCCAAGTCAAC
1 CTGCCAAGTCATC
*
19537 CTGCCATGTCATC
1 CTGCCAAGTCATC
*
19550 CTGCCACGTCATC
1 CTGCCAAGTCATC
19563 C
1 C
19564 GGTGACCGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.20, C:0.42, G:0.15, T:0.23
Consensus pattern (13 bp):
CTGCCAAGTCATC
Found at i:19619 original size:13 final size:13
Alignment explanation
Indices: 19601--19649 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
19591 ACGTCATCAA
19601 GTTGACTTTGACC
1 GTTGACTTTGACC
*
19614 GTTGACTTT-TCC
1 GTTGACTTTGACC
19626 GTGTTGACTTTGACC
1 --GTTGACTTTGACC
*
19641 ATTGACTTT
1 GTTGACTTT
19650 TTTGGTTGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 2 0.07
13 17 0.57
14 9 0.30
15 2 0.07
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (13 bp):
GTTGACTTTGACC
Found at i:28729 original size:115 final size:114
Alignment explanation
Indices: 28528--28747 Score: 395
Period size: 115 Copynumber: 1.9 Consensus size: 114
28518 ATTCTATCTT
* *
28528 AAATTACCAGGGGCATTTTGGTCATTTTCACCTCAGGGGCATTTTGGTCAAAATTACTGTTCAAT
1 AAATTAACAGGGGCATTTTGGTCATTTTCACCTCAGGGGCATTTTGGTCAAAATTACTGGTCAAT
*
28593 GTGTTCATTCTAGTCTTTGGTAGATTGCATTATAGTATGTCTCCTTAAG
66 GTGTTCATTCTAGTCTTTGGTAGATTGCATTATACTATGTCTCCTTAAG
*
28642 AAATTAACAGGGGCATTTTGGTCATTTTTCGCCTCAGGGGCATTTTGGTCAAAATTACTGGTCAA
1 AAATTAACAGGGGCATTTTGGTCA-TTTTCACCTCAGGGGCATTTTGGTCAAAATTACTGGTCAA
28707 TGTGTTCATTCTAGTCTTTGGTAGATTGCATTATACTATGT
65 TGTGTTCATTCTAGTCTTTGGTAGATTGCATTATACTATGT
28748 TCCCTTTTGC
Statistics
Matches: 101, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
114 23 0.23
115 78 0.77
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (114 bp):
AAATTAACAGGGGCATTTTGGTCATTTTCACCTCAGGGGCATTTTGGTCAAAATTACTGGTCAAT
GTGTTCATTCTAGTCTTTGGTAGATTGCATTATACTATGTCTCCTTAAG
Found at i:32379 original size:47 final size:46
Alignment explanation
Indices: 32328--32785 Score: 600
Period size: 47 Copynumber: 9.8 Consensus size: 46
32318 ACAGAGGCTG
*
32328 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAACATAGGTTA
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAA-AGAGGTTA
* *
32375 GTTTAATT-TCGGATAATTAAACTAAATAGTAAAAGAAGAAGAGTTTA
1 GTTTAATTCT-GGGTAATTAAACTAAATAGTAAAAGAA-AAGAGGTTA
* * **
32422 GTTTAATTTTGGGCAATTAAACTAAATAGTAAAAGAAGAAGCA-ACTA
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAA-AAG-AGGTTA
*
32469 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGATGTTA
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAA-AAGAGGTTA
*
32516 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAAA-AGCAATTA
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAAAGAG--GTTA
*
32563 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGGAGAGGTTA
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAA-AAGAGGTTA
*
32610 GTTTAATTCTGGGTAATTAAACTAAATAGTAAATGAAACAGAGGTTA
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAA-AGAGGTTA
* * * *
32657 GTTTAATTCCGGGTAATTAAACTAAATAGAAAAAGAAGAAGAAGTCA
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAA-AAGAGGTTA
* * * *
32704 GTTTAATTTTAGGTAATTAAACTAAATAGTAAAA-AGAAGATGTTA
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAAAGAGGTTA
* *
32749 GTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAGAA
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAA
32786 GAAGTAAACT
Statistics
Matches: 365, Mismatches: 34, Indels: 25
0.86 0.08 0.06
Matches are distributed among these distances:
45 38 0.10
46 6 0.02
47 314 0.86
48 5 0.01
49 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (46 bp):
GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAAAGAGGTTA
Found at i:32534 original size:141 final size:141
Alignment explanation
Indices: 32328--32785 Score: 669
Period size: 141 Copynumber: 3.3 Consensus size: 141
32318 ACAGAGGCTG
* *
32328 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAACATAGGTTAGTTTAATT-TCGGATAAT
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAACAGAGGTTAGTTTAATTCT-GGGTAAT
*
32392 TAAACTAAATAGTAAAAGAAGAAG-AGTTTAGTTTAATTTTGGGCAATTAAACTAAATAGTAAAA
65 TAAACTAAATAGTAAAAGAAGAAGAAG-TTAGTTTAATTTTGGGTAATTAAACTAAATAGTAAAA
**
32456 GAAGAAGCA-ACTA
129 GAAGAAG-AGGTTA
*
32469 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGA-AGATGTTAGTTTAATTCTGGGTAAT
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAA-ACAGAGGTTAGTTTAATTCTGGGTAAT
* *
32533 TAAACTAAATAGTAAAAGAAAAAGCAA-TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAA
65 TAAACTAAATAGTAAAAGAAGAAG-AAGTTAGTTTAATTTTGGGTAATTAAACTAAATAGTAAAA
*
32597 GAAGGAGAGGTTA
129 GAAGAAGAGGTTA
* *
32610 GTTTAATTCTGGGTAATTAAACTAAATAGTAAATGAAACAGAGGTTAGTTTAATTCCGGGTAATT
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAACAGAGGTTAGTTTAATTCTGGGTAATT
* * *
32675 AAACTAAATAGAAAAAGAAGAAGAAGTCAGTTTAATTTTAGGTAATTAAACTAAATAGT-AAA-A
66 AAACTAAATAGTAAAAGAAGAAGAAGTTAGTTTAATTTTGGGTAATTAAACTAAATAGTAAAAGA
*
32738 AGAAGATGTTA
131 AGAAGAGGTTA
* *
32749 GTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAGAA
1 GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAA
32786 GAAGTAAACT
Statistics
Matches: 288, Mismatches: 22, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
139 44 0.15
140 7 0.02
141 234 0.81
142 2 0.01
143 1 0.00
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (141 bp):
GTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAACAGAGGTTAGTTTAATTCTGGGTAATT
AAACTAAATAGTAAAAGAAGAAGAAGTTAGTTTAATTTTGGGTAATTAAACTAAATAGTAAAAGA
AGAAGAGGTTA
Found at i:32891 original size:54 final size:54
Alignment explanation
Indices: 32746--32889 Score: 175
Period size: 54 Copynumber: 2.7 Consensus size: 54
32736 AAAGAAGATG
* * *
32746 TTAGTTTAATTCGGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACTATAA
1 TTAGTTTAATTCCGGGTAATTAAACTAAAGAGTAAAAGAAAAAGTAAACGATAA
* * * * *
32800 CTAGTTTGATTCCGGGTAAATAAACTAAAGAGTAAAAGAAAAAGTAATCGGTAA
1 TTAGTTTAATTCCGGGTAATTAAACTAAAGAGTAAAAGAAAAAGTAAACGATAA
* *
32854 TTAG-TTAATTCTGAGTAATTAAACT-AAGAAGTAAAA
1 TTAGTTTAATTCCGGGTAATTAAACTAAAG-AGTAAAA
32890 AGCAGAAATA
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 3 0.04
53 24 0.32
54 49 0.64
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.28
Consensus pattern (54 bp):
TTAGTTTAATTCCGGGTAATTAAACTAAAGAGTAAAAGAAAAAGTAAACGATAA
Found at i:38917 original size:22 final size:21
Alignment explanation
Indices: 38865--38918 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
38855 TGCTTCTCGA
38865 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
38886 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
38905 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
38919 CATGAGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:43051 original size:23 final size:23
Alignment explanation
Indices: 43014--43064 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
43004 GACACACAAG
*
43014 CTCTCTCTCTACCAAGCTCTCAC
1 CTCTCTCTCTACCAAGCCCTCAC
43037 C-CTCTCTCCTACCAAGCCCTCAC
1 CTCTCTCT-CTACCAAGCCCTCAC
43060 CTCTC
1 CTCTC
43065 CCTTTCAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
23 16 0.64
24 3 0.12
ACGTcount: A:0.16, C:0.53, G:0.04, T:0.27
Consensus pattern (23 bp):
CTCTCTCTCTACCAAGCCCTCAC
Done.