Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012349.1 Corchorus capsularis cultivar CVL-1 contig12370, 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: 52883
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:2024 original size:142 final size:143
Alignment explanation
Indices: 1768--2045 Score: 531
Period size: 142 Copynumber: 2.0 Consensus size: 143
1758 AACGTATAAG
*
1768 CGAAACAACTAAAACCCAATAATTTTTTTGAGGGAAACTAAAACCCAATAATTAATAAGAATAGA
1 CGAAACAACTAAAACCCAATAATTTTTCTGAGGGAAACTAAAACCCAATAATTAATAAGAATAGA
1833 GACCTATATATGCAACATTCACATCAAAAGGAGAGGTAAAAAATGTAACAATATACATTTGACAT
66 GACCTATATATGCAACATTCACATCAAAAGGAGAGGTAAAAAATGTAACAATATACATTTGACAT
1898 -AGTAACAATATA
131 AAGTAACAATATA
1910 CGAAACAACTAAAACCCAATAATTTTTCTGAGGGAAACTAAAACCCAATAATTAATAAGAATAGA
1 CGAAACAACTAAAACCCAATAATTTTTCTGAGGGAAACTAAAACCCAATAATTAATAAGAATAGA
*
1975 GACCTATATATGCAACATTCACATCAAAAGGAGAGGTAAAAAATGTAACAGTATACATTTGACAT
66 GACCTATATATGCAACATTCACATCAAAAGGAGAGGTAAAAAATGTAACAATATACATTTGACAT
2040 AAGTAA
131 AAGTAA
2046 TTGTATCTTT
Statistics
Matches: 133, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
142 128 0.96
143 5 0.04
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (143 bp):
CGAAACAACTAAAACCCAATAATTTTTCTGAGGGAAACTAAAACCCAATAATTAATAAGAATAGA
GACCTATATATGCAACATTCACATCAAAAGGAGAGGTAAAAAATGTAACAATATACATTTGACAT
AAGTAACAATATA
Found at i:4561 original size:41 final size:38
Alignment explanation
Indices: 4478--4619 Score: 212
Period size: 38 Copynumber: 3.7 Consensus size: 38
4468 AGTAAAATGA
* *
4478 GATCTTTTCCTAAATTGAAAACTTTGAAAACTTGATGA
1 GATCTTTCCCTAAATTGAAAACTTTGAAAACTTGATGG
*
4516 GATCTTTCCCTAAATTGAAAAGTTTGAAAAAAACTTGATGG
1 GATCTTTCCCTAAATTGAAAACTTTG---AAAACTTGATGG
*
4557 GATCTTTCCCTAAATTGAAAACTTTGAAGACTTGATGG
1 GATCTTTCCCTAAATTGAAAACTTTGAAAACTTGATGG
*
4595 GATCTTTCCCTGAATTGAAAACTTT
1 GATCTTTCCCTAAATTGAAAACTTT
4620 TGGAAATTTC
Statistics
Matches: 95, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
38 59 0.62
41 36 0.38
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (38 bp):
GATCTTTCCCTAAATTGAAAACTTTGAAAACTTGATGG
Found at i:4680 original size:26 final size:27
Alignment explanation
Indices: 4651--4703 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
4641 TGAATTTTGG
4651 ATTTTTGAAA-ACT-TTTTTATTCCTTA
1 ATTTTTGAAATACTATTTTT-TTCCTTA
4677 ATTTTTGAAATACTCATTTTTTTCCTT
1 ATTTTTGAAATACT-ATTTTTTTCCTT
4704 TTGAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 10 0.42
27 3 0.12
28 6 0.25
29 5 0.21
ACGTcount: A:0.25, C:0.13, G:0.04, T:0.58
Consensus pattern (27 bp):
ATTTTTGAAATACTATTTTTTTCCTTA
Found at i:7082 original size:13 final size:13
Alignment explanation
Indices: 7064--7089 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7054 TTAACACGAA
7064 TAACATCCAAATT
1 TAACATCCAAATT
7077 TAACATCCAAATT
1 TAACATCCAAATT
7090 CAATGACATC
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:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
TAACATCCAAATT
Found at i:7126 original size:21 final size:22
Alignment explanation
Indices: 7078--7135 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
7068 ATCCAAATTT
* *
7078 AACATCCAAATTCAATGACATC
1 AACATCCAAATTCAATAACATA
7100 AACATCCAAATTCAATAACA-A
1 AACATCCAAATTCAATAACATA
7121 AACATCCAAATTCAA
1 AACATCCAAATTCAA
7136 ATTGACTGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 15 0.44
22 19 0.56
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.21
Consensus pattern (22 bp):
AACATCCAAATTCAATAACATA
Found at i:7796 original size:20 final size:20
Alignment explanation
Indices: 7773--7821 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
7763 AAGTAGATAT
*
7773 AAAGAGAAAAGT-GTAGCTAG
1 AAAGAGAAAAATAG-AGCTAG
*
7793 AAAGA-AAAAATAGAGCTAT
1 AAAGAGAAAAATAGAGCTAG
7812 AAAGAGAAAA
1 AAAGAGAAAA
7822 TTGACTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.61, C:0.04, G:0.22, T:0.12
Consensus pattern (20 bp):
AAAGAGAAAAATAGAGCTAG
Found at i:8391 original size:41 final size:40
Alignment explanation
Indices: 8346--8433 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 40
8336 TATCCGTGTC
* * *
8346 ACACGTCGT-TTTAATCGTGTTTTATACGATTATGACACGAA
1 ACACGTCGTCTTTAATCGTG-TTGACACGATTA-AACACGAA
**
8387 ACACGTTTTCCTTTAATCGTGTTGACACGATTAAACACGAA
1 ACACGTCGT-CTTTAATCGTGTTGACACGATTAAACACGAA
8428 ACACGT
1 ACACGT
8434 TAAGGCCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 20 0.50
42 10 0.25
43 10 0.25
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (40 bp):
ACACGTCGTCTTTAATCGTGTTGACACGATTAAACACGAA
Found at i:8434 original size:41 final size:43
Alignment explanation
Indices: 8355--8434 Score: 119
Period size: 41 Copynumber: 1.9 Consensus size: 43
8345 CACACGTCGT
* * *
8355 TTTAATCGTGTTTTATACGATTATGACACGAAACACGTTTTCC
1 TTTAATCGTGTTTGACACGATTATAACACGAAACACGTTTTCC
8398 TTTAATCGTG-TTGACACGATTA-AACACGAAACACGTT
1 TTTAATCGTGTTTGACACGATTATAACACGAAACACGTT
8435 AAGGCCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 14 0.41
42 10 0.29
43 10 0.29
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (43 bp):
TTTAATCGTGTTTGACACGATTATAACACGAAACACGTTTTCC
Found at i:10072 original size:797 final size:797
Alignment explanation
Indices: 8513--10111 Score: 2013
Period size: 797 Copynumber: 2.0 Consensus size: 797
8503 GCCAGGTCTA
* * * * *
8513 ATCAGAGCACAACGCTTAACAGCAAATTTGATCCTTTTTTTTTCTTAAAAATGTCTACTGAATCT
1 ATCAGAACACAACGCTTAACAACAAAGTTGATCCTTTTTTTTTCTTAAAAACGTCAACTGAATCT
* *
8578 TCTTAATCCACCTCTTCCACCCAGTTCTTAGCAACCGCAACACTAACTCTTCTTCTCCTTCACCT
66 TCTTAATCCACCTCTTCCACCCAGTTCTTAGCAA-CGCAACAC-AACACTACTTCTCCTTCACCT
* * *
8643 ACCTTAATCACCATCAACGCAGCTGCTTAACTACATATCAAAATTATTGCTTATAACTATCCATC
129 ACCTTAATCACCATCAACGCAGCTGCTCAACTACATATCAAAATTACTGCATATAACTATCCATC
* ** * * *
8708 GTGGAGAACACAATTTAATTTCCCTGCTCCTTGGTCTTAAACTTATTGGCAACATTGATGCCACA
194 GTGGAGAACACAATTTAATTTCACTGCTCCTTGGTCACAAACTTATTAGCAACATCGATGACACA
** *
8773 AAATCACCACCTTCGACCAAGATTCTTTCATCAGACTCACCCCTACTATGTTACAAAATCCAGAA
259 AAATCACCACCACCGACCAAGATTCTTTCATCAAACTCACCCCTACTATGTTACAAAATCCAGAA
* * *
8838 TATGATTTTTGGTACCAACAAGAACAACTATTCTGCACTTTTTCTTGCTTAACTTTCTTGAAATT
324 TATGATTTCTGGTACCAACAAGAACAACTATTCTGCACTTTTTCATGCTTAACCTTCTTGAAATT
* * *
8903 CCAAAATGGCCAAGACCAACGAACTATCAAGAATCACTAAGATAAAAAATCATTTTGAAATTCAC
389 CCAAAATGGCCAAGACCAACGAACTATCAAGAATCACTAAGATAAAAAATCACTTCGAAAATCAC
* * *
8968 TTTAAGCATCGCCCGATGACAGGCAGTATAGTGTGTCTGGTGGCATTCACTGTTGTCCAATTTCT
454 TTTAA-CA-----CGA-GACAGGCAGTATAGTGTGTCTGATGACATTCACTGTTGACCAATTTCT
* * * *
9033 GTAGGAGTTATACATTGACTCCTACTCTACGTTCAACTAGATGTCAGAAGGGGTTAAGCTTATCA
512 GTAGGAGTTATACATTGAATCCCACTCTACGTTCAACTAGATGTCAGAAAGGGTTAAGCTCATCA
* * *
9098 TTACGAAGGTCATGCCTATAAAAATCATTTGGAGCGGCCTGTGCATATTCTTCAACCTCATCAGG
577 TTACGAAGGTCATACCTATAAAAATCATTTGGAGCGGCCTGTGCATAATCTTCAACCTCAACAGG
* * * *
9163 CCGGTGGACCCAAGGAAGTGGACCATCATGAAGAAGTTCAAATGTCAGCTTAACAACATGTTGTT
642 CCGATGGACCCAAGGAAGGGGACCATCATGAAGAAGTTCAAATGCCAGCTTAACAACATGATGTT
* * * * * *
9228 TTCATCCTTTGCCATAGCAGCATATGTGATTTATACAATCCATAGAATCAGATTTGCCTTCTCAA
707 TTAATCCTTTACCATAGCAGCATACGTGATTAATACAATCCATAGAATCAGATATACCTTCTCAA
*
9293 TTATTCTGCAT-AAGCCTCTTTATGGT
772 TTATTATGC-TCAAGCCTCTTTATGGT
* *
9319 ATCAGAACACAACGCTTAACAACATAGTTGATCCGTTCTTTTTTTCCCCCTTTTAAAACGTCAAC
1 ATCAGAACACAACGCTTAACAACAAAGTTGATCC-TT-TTTTTTT----C-TTAAAAACGTCAAC
* * *
9384 TGAATCTTCTTTATCCACCTTTTCCACCCAGTTCTTAGC-A-GCTA-A-AACACTACTTCTCCTT
59 TGAATCTTCTTAATCCACCTCTTCCACCCAGTTCTTAGCAACGCAACACAACACTACTTCTCCTT
* * * *
9445 CACCTACCTTAATCACCATCAACTCAG-TCGCTCAACTACCTATCAAACTTGCTGCATATAACTA
124 CACCTACCTTAATCACCATCAACGCAGCT-GCTCAACTACATATCAAAATTACTGCATATAACTA
* * *
9509 TCCATTGTGGAGAGCACAATTTAA-TTCACTGCTCCTTGGTCACAAACTTATTAGCTACATCGAT
188 TCCATCGTGGAGAACACAATTTAATTTCACTGCTCCTTGGTCACAAACTTATTAGCAACATCGAT
* * *
9573 GATACAAAATCACCACCACCGACCAAGATTCTTTCATCAAACTCACACCTTTCTATGTTACAAAA
253 GACACAAAATCACCACCACCGACCAAGATTCTTTCATCAAACTCAC-CCCTACTATGTTACAAAA
* * * * *
9638 TCTAGAATATGATTTCTGGTACCAACAAGATCAACTCTTTTGCACTTTCTTCATGTTTAACCTTC
317 TCCAGAATATGATTTCTGGTACCAACAAGAACAACTATTCTGCACTTT-TTCATGCTTAACCTTC
* * **
9703 TTGAAATTCCAAAATGGCCAAGGCGAACGAA-TCATCAAGAATCACTAAGATCCAAAATCACTTC
381 TTGAAATTCCAAAATGGCCAAGACCAACGAACT-ATCAAGAATCACTAAGATAAAAAATCACTTC
* * *
9767 GAAAATCACTTT-A-A-GA-ACGGGTAGTATAGTGTGTCTGATGACATTCATTGTTGACCAATTT
445 GAAAATCACTTTAACACGAGACAGGCAGTATAGTGTGTCTGATGACATTCACTGTTGACCAATTT
* * *** * * *
9828 CTGTAGGGGTTATACATT-AATCCCATCTCTGCGTTCTTTTAGGTGTCGGAAAGGGTTAAGGTCA
510 CTGTAGGAGTTATACATTGAATCCCA-CTCTACGTTCAACTAGATGTCAGAAAGGGTTAAGCTCA
* * * * * *
9892 TCATTACGGAGGTCCTACCTTTAGAAATCATTTGGAGCGGCTTGTTCATAATCTTCAACCTCAAC
574 TCATTACGAAGGTCATACCTATAAAAATCATTTGGAGCGGCCTGTGCATAATCTTCAACCTCAAC
* * * *
9957 AGGCCGATGGACCCAAGGAAGGGGTCCATCGTGAAGAAGTTCAAATGCCTA-CTTGACTACATGA
639 AGGCCGATGGACCCAAGGAAGGGGACCATCATGAAGAAGTTCAAATGCC-AGCTTAACAACATGA
* * * *
10021 TGTTTTAATCTTTTACCATTGCAGCATACGTGATTAATACAA-CCTATAGAATTAGGTATACCTT
703 TGTTTTAATCCTTTACCATAGCAGCATACGTGATTAATACAATCC-ATAGAATCAGATATACCTT
*
10085 CTCAATTATTATGCTCAAGTCTCTTTA
767 CTCAATTATTATGCTCAAGCCTCTTTA
10112 CCCATATCTC
Statistics
Matches: 682, Mismatches: 96, Indels: 39
0.83 0.12 0.05
Matches are distributed among these distances:
796 8 0.01
797 269 0.39
798 1 0.00
799 2 0.00
805 1 0.00
806 106 0.16
807 154 0.23
808 87 0.13
809 1 0.00
810 3 0.00
812 2 0.00
813 48 0.07
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (797 bp):
ATCAGAACACAACGCTTAACAACAAAGTTGATCCTTTTTTTTTCTTAAAAACGTCAACTGAATCT
TCTTAATCCACCTCTTCCACCCAGTTCTTAGCAACGCAACACAACACTACTTCTCCTTCACCTAC
CTTAATCACCATCAACGCAGCTGCTCAACTACATATCAAAATTACTGCATATAACTATCCATCGT
GGAGAACACAATTTAATTTCACTGCTCCTTGGTCACAAACTTATTAGCAACATCGATGACACAAA
ATCACCACCACCGACCAAGATTCTTTCATCAAACTCACCCCTACTATGTTACAAAATCCAGAATA
TGATTTCTGGTACCAACAAGAACAACTATTCTGCACTTTTTCATGCTTAACCTTCTTGAAATTCC
AAAATGGCCAAGACCAACGAACTATCAAGAATCACTAAGATAAAAAATCACTTCGAAAATCACTT
TAACACGAGACAGGCAGTATAGTGTGTCTGATGACATTCACTGTTGACCAATTTCTGTAGGAGTT
ATACATTGAATCCCACTCTACGTTCAACTAGATGTCAGAAAGGGTTAAGCTCATCATTACGAAGG
TCATACCTATAAAAATCATTTGGAGCGGCCTGTGCATAATCTTCAACCTCAACAGGCCGATGGAC
CCAAGGAAGGGGACCATCATGAAGAAGTTCAAATGCCAGCTTAACAACATGATGTTTTAATCCTT
TACCATAGCAGCATACGTGATTAATACAATCCATAGAATCAGATATACCTTCTCAATTATTATGC
TCAAGCCTCTTTATGGT
Found at i:10404 original size:34 final size:34
Alignment explanation
Indices: 10361--10491 Score: 262
Period size: 34 Copynumber: 3.9 Consensus size: 34
10351 ACAAGGATTA
10361 AACTTTTGCAAGCTGTGGGGGCACCAAAATCTTT
1 AACTTTTGCAAGCTGTGGGGGCACCAAAATCTTT
10395 AACTTTTGCAAGCTGTGGGGGCACCAAAATCTTT
1 AACTTTTGCAAGCTGTGGGGGCACCAAAATCTTT
10429 AACTTTTGCAAGCTGTGGGGGCACCAAAATCTTT
1 AACTTTTGCAAGCTGTGGGGGCACCAAAATCTTT
10463 AACTTTTGCAAGCTGTGGGGGCACCAAAA
1 AACTTTTGCAAGCTGTGGGGGCACCAAAA
10492 GATTGGATTG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 97 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (34 bp):
AACTTTTGCAAGCTGTGGGGGCACCAAAATCTTT
Found at i:12732 original size:17 final size:16
Alignment explanation
Indices: 12687--12751 Score: 68
Period size: 17 Copynumber: 4.2 Consensus size: 16
12677 ATTTATTTTC
12687 TTATCTATTT-GTA-A
1 TTATCTATTTAGTATA
12701 TTAT-TATTTA-T-TA
1 TTATCTATTTAGTATA
12714 TTATCTATTTAGTACTA
1 TTATCTATTTAGTA-TA
*
12731 TTATCTATTTAATACTA
1 TTATCTATTTAGTA-TA
12748 TTAT
1 TTAT
12752 TTATCTATCT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
13 11 0.25
14 10 0.23
15 1 0.02
17 22 0.50
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (16 bp):
TTATCTATTTAGTATA
Found at i:12846 original size:12 final size:12
Alignment explanation
Indices: 12828--12873 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
12818 GTTTACATAC
12828 TTATTTATCTTT
1 TTATTTATCTTT
* * *
12840 TTGTTTATATAT
1 TTATTTATCTTT
*
12852 CTATTTATCTTT
1 TTATTTATCTTT
12864 TTATTTATCT
1 TTATTTATCT
12874 ATTATTTTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (12 bp):
TTATTTATCTTT
Found at i:12856 original size:24 final size:24
Alignment explanation
Indices: 12815--12889 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
12805 TATATATATA
*
12815 TTTGTTTACATA-CTTATTTATCTT
1 TTTGTTTATATATC-TATTTATCTT
12839 TTTGTTTATATATCTATTTATCTT
1 TTTGTTTATATATCTATTTATCTT
* * *
12863 TTTATTTATCTAT-TATTTTTACTT
1 TTTGTTTATATATCTATTTAT-CTT
12887 TTT
1 TTT
12890 TATAGTTATC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.13
24 38 0.84
25 1 0.02
ACGTcount: A:0.20, C:0.09, G:0.03, T:0.68
Consensus pattern (24 bp):
TTTGTTTATATATCTATTTATCTT
Found at i:13386 original size:26 final size:27
Alignment explanation
Indices: 13357--13408 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
13347 TTTTCCTGAT
**
13357 TTTTGTTTTTTGTGTTTTT-TGTTTTG
1 TTTTGTTTTTTGAATTTTTATGTTTTG
13383 TTTTGTTTTTTGAATTTTTATGTTTT
1 TTTTGTTTTTTGAATTTTTATGTTTT
13409 TTATTTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.06, C:0.00, G:0.15, T:0.79
Consensus pattern (27 bp):
TTTTGTTTTTTGAATTTTTATGTTTTG
Found at i:13394 original size:17 final size:16
Alignment explanation
Indices: 13356--13410 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
13346 TTTTTCCTGA
13356 TTTTTGTTTTTTGTGT
1 TTTTTGTTTTTTGTGT
*
13372 TTTTTGTTTTGTTTTGT
1 TTTTTGTTTT-TTGTGT
* *
13389 TTTTTGAATTTTTATGT
1 TTTTTG-TTTTTTGTGT
13406 TTTTT
1 TTTTT
13411 ATTTGATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 10 0.29
17 21 0.62
18 3 0.09
ACGTcount: A:0.05, C:0.00, G:0.15, T:0.80
Consensus pattern (16 bp):
TTTTTGTTTTTTGTGT
Found at i:13494 original size:10 final size:11
Alignment explanation
Indices: 13452--13492 Score: 61
Period size: 10 Copynumber: 4.0 Consensus size: 11
13442 ATTTTATTTC
13452 TATGA-TTATT
1 TATGATTTATT
13462 TATG-TTTATT
1 TATGATTTATT
13472 TATGATTTA-T
1 TATGATTTATT
13482 TATGATTTATT
1 TATGATTTATT
13493 ATTTAACCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 23 0.82
11 5 0.18
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (11 bp):
TATGATTTATT
Found at i:16760 original size:11 final size:11
Alignment explanation
Indices: 16731--16768 Score: 58
Period size: 11 Copynumber: 3.3 Consensus size: 11
16721 TAGTTCATCG
16731 GCATTCATACAT
1 GCATTCAT-CAT
16743 GGCATTCATCAT
1 -GCATTCATCAT
16755 GCATTCATCAT
1 GCATTCATCAT
16766 GCA
1 GCA
16769 CCTGTCGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 3 0.12
13 8 0.32
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (11 bp):
GCATTCATCAT
Found at i:24505 original size:10 final size:11
Alignment explanation
Indices: 24465--24504 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
24455 AGTAAGGTCC
24465 AAAAAAAGCAAA
1 AAAAAAAG-AAA
*
24477 AAAAAACGAAA
1 AAAAAAAGAAA
24488 AAAAAAAGAAA
1 AAAAAAAGAAA
24499 GAAAAA
1 -AAAAA
24505 GGTTTCCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 13 0.52
12 12 0.48
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:25580 original size:54 final size:54
Alignment explanation
Indices: 25512--25906 Score: 415
Period size: 54 Copynumber: 7.3 Consensus size: 54
25502 AGAGTTGATC
* *
25512 TCATTCC-AGAAGTTTTCGGTGGTTAAAGTTGATCTCCAATTGATCCGGTGCGG
1 TCATTCCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGCGG
*
25565 TCATTCCAAGAAGTTTTCGGTGGTTAGAGTTGATCTCCAATTGATCCGGTGCGG
1 TCATTCCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGCGG
*
25619 TCATTCCAAG-AGATTTTCGGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCGG
1 TCATTCCAAGAAG-TTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGCGG
* * * * *
25673 TCATTCCAAGAA-ATTTCGGGTGGTCAGAGTTTATCCCCAATTGATCTGGTGTGG
1 TCATTCCAAGAAGTTTTC-GGTGGTCAGAGTTGATCTCCAATTGATCCGGTGCGG
*** * *
25727 TCATTCCAAGAAGTTTTCAACGGTTAGAGTTGATCTCGAATTGATCCAGG-GCGG
1 TCATTCCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCC-GGTGCGG
* * * * * *
25781 TCATTCCAAGAAGTTTTTGGTTGTCAGAGTTAATCTCCAATCGAT-CTGTGTGG
1 TCATTCCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGCGG
* * ** * ** * **
25834 TC-GTCTCAAAAAGTTTTTAGCGGTCAGAGTTGATCTTGAATTAATCTAGTGCGG
1 TCATTC-CAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGCGG
* *
25888 TCATTACAAAAAGATTTTC
1 TCATTCCAAGAAG-TTTTC
25907 CAGTGTGGTT
Statistics
Matches: 285, Mismatches: 46, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
52 3 0.01
53 49 0.17
54 221 0.78
55 12 0.04
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (54 bp):
TCATTCCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGCGG
Found at i:27306 original size:17 final size:17
Alignment explanation
Indices: 27286--27322 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
27276 TATTTATTAA
*
27286 TATCTATTTAGTACTAT
1 TATCTATTTAATACTAT
27303 TATCTATTTAATACTAT
1 TATCTATTTAATACTAT
27320 TAT
1 TAT
27323 TTATCTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.54
Consensus pattern (17 bp):
TATCTATTTAATACTAT
Found at i:27380 original size:4 final size:4
Alignment explanation
Indices: 27371--27519 Score: 88
Period size: 4 Copynumber: 36.5 Consensus size: 4
27361 TATTAAGCTA
* * * * *
27371 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT ATAT TTGT TTAC ATAC
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * *
27419 TTAT TTAT CTT-T TTGT TTAT ATAT CTAT TTAT CTT-T TTAT TTAT CTAT
1 TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT
* * * * * *
27467 TATTT TTACT TTTT TTAT AGTTAT CTA- TTAC TTAA TTAT ATAT TTAT
1 T-TAT TTA-T TTAT TTAT --TTAT TTAT TTAT TTAT TTAT TTAT TTAT
27514 TTAT TT
1 TTAT TT
27520 TAATCTTAAT
Statistics
Matches: 112, Mismatches: 24, Indels: 18
0.73 0.16 0.12
Matches are distributed among these distances:
3 6 0.05
4 92 0.82
5 10 0.09
6 4 0.04
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:27407 original size:24 final size:24
Alignment explanation
Indices: 27371--27517 Score: 108
Period size: 24 Copynumber: 6.3 Consensus size: 24
27361 TATTAAGCTA
* *
27371 TTATTTATTTATTTATTTATTTAT
1 TTATTTATCTATTTATTTATATAT
* * * *
27395 TTATTTATATATTTGTTTACATAC
1 TTATTTATCTATTTATTTATATAT
* *
27419 TTATTTATCTTTTTGTTTATATAT
1 TTATTTATCTATTTATTTATATAT
* * *
27443 CTATTTATCTTTTTATTTATCTA-
1 TTATTTATCTATTTATTTATATAT
*
27466 TTATTT-T-TACTTT-TTT-TATAG
1 TTATTTATCTA-TTTATTTATATAT
* * *
27487 TTATCTAT-TACTTAATTATATAT
1 TTATTTATCTATTTATTTATATAT
27510 TTATTTAT
1 TTATTTAT
27518 TTTAATCTTA
Statistics
Matches: 98, Mismatches: 20, Indels: 11
0.76 0.16 0.09
Matches are distributed among these distances:
20 3 0.03
21 11 0.11
22 9 0.09
23 16 0.16
24 59 0.60
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (24 bp):
TTATTTATCTATTTATTTATATAT
Found at i:33268 original size:27 final size:27
Alignment explanation
Indices: 33235--33292 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
33225 CTTGTGAGGC
33235 GCCTTTTGGCAAGGGCAAATCCGTGAG
1 GCCTTTTGGCAAGGGCAAATCCGTGAG
*
33262 GCCTTTTGGCAAGGGCAAATCCGTTAG
1 GCCTTTTGGCAAGGGCAAATCCGTGAG
33289 GCCT
1 GCCT
33293 GGTCTTTACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (27 bp):
GCCTTTTGGCAAGGGCAAATCCGTGAG
Found at i:34669 original size:632 final size:633
Alignment explanation
Indices: 33435--34686 Score: 2111
Period size: 632 Copynumber: 2.0 Consensus size: 633
33425 GAGGACGTTT
*
33435 GGTAGAAGTTTGCTTGTTAACAGAATTGTTGCAATAGTAAACAAACCCACTAGGATATCTAACGT
1 GGTAGAAGTTTGCTTGTTAACAGAATTGTTGCAATAGTAAACAAACCAACTAGGATATCTAACGT
* *
33500 ACAATGTAATGAAGAGTTTGCATAATCTTTTTTGTTTTTTGAAGGCACTAAACAGGTTATTATCA
66 ACAA-GTAATGAAGAGTTTGCATAATCTTTTTTGTTTTTTGAAGACACTAAACAGGCTATTATCA
* * *
33565 AAAGCACTACAATTGCCAATAAACACTCATAAAATAGAAGGTCTATGTCCTTACCATACGTAGCT
130 AAAGCACTACAATGGCCAATAAACACTCACAAAATAGAAGGTCTATGTCCTTACCATACGTAACT
*
33630 TCCTTTTTGTGCTAGCTATCTCATGAATCTCTTCTTCTTCGGTCATCTTCAGTTTTTCTTTTGTT
195 TCCTTTTTGTGCTAGCTATCTCATGAATCTCTTCTTCTTCGGTCATATTCAGTTTTTCTTTTGTT
* * * * * *
33695 ATATAATCGTTGGGAAAATGGTTTTTTTCTATATCAAAAAAGCAACTCCTACAACCAGAGACGTT
260 ATATAATCGCTGCGAAAATGGTTTTTTTCCAGATCAAAAAAACAACTCCGACAACCAGAGACGTT
* *
33760 ATCATGCTAGACAGAAATTTTCTAAAAAACGACATTTTCAGAATTTCTTTTTTCTTAGAGAAAAC
325 ATCATGCTAGACAAAAATTTTCTAAAAAACGACATTTTCAGAATTTCTTTTTTCTTAAAGAAAAC
* *
33825 AAGGTTTGAGAAACTTTGGCAGAGAGATGAAGAATTGAAATGTTGCTGTTCCTTATTTATTATCA
390 AAGGTTTGAGAAACTTTGACAGAGAGATGAAGAATTGAAATGTTGCTGTTCCTTATTTATTACCA
* *
33890 TTTGAAGAGATAAAATTCAGGTACGGATAAAGTTGGTTCCATGCCTTGAAGTTTGTAAAGTAGTT
455 TTTGAAGAGATAAAATTCAGGTACGAATAAAGTTGGTTCCATGCCTTGAAGTTTGCAAAGTAGTT
* * *
33955 ACAAGAGGTCAAATGATTCTGTTGCATCCTTCAGCCATAATGCCACATTATGCTAAAATCACTCC
520 ACAAGAGGTCAAATAATTCTATTGCATCCTTCAGCCATAATGCCACATTATCCTAAAATCACTCC
*
34020 ACGTACGTCTTAAAATGTTGAACATTGACTTTAATAGTAAAACTCTATG
585 ACGTACGTCTTAAAATGTTGAACATCGACTTTAATAGTAAAACTCTATG
34069 GGTAGAAGTTTG-TTGTTAACAGAATTGTTGCAATAGTAAACAAACCAACTAGGATATCTAACGT
1 GGTAGAAGTTTGCTTGTTAACAGAATTGTTGCAATAGTAAACAAACCAACTAGGATATCTAACGT
34133 ACAA-T-ATGAAGAGTTTGCATAATCTTTTTTGTTTTTTGAAGACACTAAACAGGCTATTATCAA
66 ACAAGTAATGAAGAGTTTGCATAATCTTTTTTGTTTTTTGAAGACACTAAACAGGCTATTATCAA
*
34196 AAGCACTACAATGGCCACA-GAACACTCACAAAATAGAAGGTCTATGTCCTTACCCATACGTAAC
131 AAGCACTACAATGGCCA-ATAAACACTCACAAAATAGAAGGTCTATGTCCTTA-CCATACGTAAC
*
34260 TTCCTTTTTGTGCTAGCTTTCTCATGAATCTCTTCTTCTTCTTTGGTCATATTCAGTTTTTCTTT
194 TTCCTTTTTGTGCTAGCTATCTCATGAATCTCTTCTTCTTC---GGTCATATTCAGTTTTTCTTT
*
34325 TGTTATATAATCGCTGCGAAGATGG-TTTTTTCCAGATCAAAAAAACAACTCCGACAACCAGAGA
256 TGTTATATAATCGCTGCGAAAATGGTTTTTTTCCAGATCAAAAAAACAACTCCGACAACCAGAGA
34389 CGTTATCATGCTAGACAAAAATTTTCTAAAAAACGACATTTTCAGAATTTCTTTTTTCTTAAAGA
321 CGTTATCATGCTAGACAAAAATTTTCTAAAAAACGACATTTTCAGAATTTCTTTTTTCTTAAAGA
*
34454 AAACAAGGTTTGA-AAACTTTGACAGAGAGATGAAGAATTGAAATGTTGTTGTTCCTTATTTATT
386 AAACAAGGTTTGAGAAACTTTGACAGAGAGATGAAGAATTGAAATGTTGCTGTTCCTTATTTATT
* *
34518 ACCATTTGAAGAGATAGAATTCATGTACGAATAAAGTTGGTTCCATGCCTTGAAGTTTGCAAAGT
451 ACCATTTGAAGAGATAAAATTCAGGTACGAATAAAGTTGGTTCCATGCCTTGAAGTTTGCAAAGT
* *
34583 AGTTACAAGAGGTCAAATAATTCTATTGCATCCTTCAGCCATCATGCCACATTATCCTAAAGTCA
516 AGTTACAAGAGGTCAAATAATTCTATTGCATCCTTCAGCCATAATGCCACATTATCCTAAAATCA
* *
34648 CTCCATGTCCGTCTTAAAATGTTGAACATCGACTTTAAT
581 CTCCACGTACGTCTTAAAATGTTGAACATCGACTTTAAT
34687 TTTCTCATCA
Statistics
Matches: 580, Mismatches: 33, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
630 103 0.18
631 52 0.09
632 205 0.35
633 166 0.29
634 54 0.09
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (633 bp):
GGTAGAAGTTTGCTTGTTAACAGAATTGTTGCAATAGTAAACAAACCAACTAGGATATCTAACGT
ACAAGTAATGAAGAGTTTGCATAATCTTTTTTGTTTTTTGAAGACACTAAACAGGCTATTATCAA
AAGCACTACAATGGCCAATAAACACTCACAAAATAGAAGGTCTATGTCCTTACCATACGTAACTT
CCTTTTTGTGCTAGCTATCTCATGAATCTCTTCTTCTTCGGTCATATTCAGTTTTTCTTTTGTTA
TATAATCGCTGCGAAAATGGTTTTTTTCCAGATCAAAAAAACAACTCCGACAACCAGAGACGTTA
TCATGCTAGACAAAAATTTTCTAAAAAACGACATTTTCAGAATTTCTTTTTTCTTAAAGAAAACA
AGGTTTGAGAAACTTTGACAGAGAGATGAAGAATTGAAATGTTGCTGTTCCTTATTTATTACCAT
TTGAAGAGATAAAATTCAGGTACGAATAAAGTTGGTTCCATGCCTTGAAGTTTGCAAAGTAGTTA
CAAGAGGTCAAATAATTCTATTGCATCCTTCAGCCATAATGCCACATTATCCTAAAATCACTCCA
CGTACGTCTTAAAATGTTGAACATCGACTTTAATAGTAAAACTCTATG
Found at i:38205 original size:2 final size:2
Alignment explanation
Indices: 38193--38230 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
38183 AATAATGTTT
38193 TA TA GTA 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
38231 TGGCACGGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41146 original size:20 final size:19
Alignment explanation
Indices: 41108--41150 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
41098 CCATCAAATT
*
41108 AAACCAGTCAACAAAAAGA
1 AAACCAGACAACAAAAAGA
**
41127 CAAACCAGACAACAGTAAGA
1 -AAACCAGACAACAAAAAGA
41147 AAAC
1 AAAC
41151 ACCAATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.60, C:0.23, G:0.12, T:0.05
Consensus pattern (19 bp):
AAACCAGACAACAAAAAGA
Found at i:43969 original size:32 final size:34
Alignment explanation
Indices: 43933--44014 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 34
43923 GTTTAGCACA
*
43933 ATTGAGTCAATTTTTCGTT-TTTTTT-TT-CAATT
1 ATTGAGTCAATTTTT-GTTCTTTTTTATTGAAATT
*
43965 ATTGAGTCGAATTTTTTTTCTTTTTTATTGAAATT
1 ATTGAGTC-AATTTTTGTTCTTTTTTATTGAAATT
44000 ATTGAGTCATATTTT
1 ATTGAGTCA-ATTTT
44015 CTTAATTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 10 0.23
33 13 0.30
34 3 0.07
35 17 0.40
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.60
Consensus pattern (34 bp):
ATTGAGTCAATTTTTGTTCTTTTTTATTGAAATT
Found at i:51345 original size:13 final size:14
Alignment explanation
Indices: 51296--51344 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
51286 ATAAATTCTT
*
51296 TTAAGAAAATTTAG
1 TTAAGAAAATTAAG
* *
51310 TTAAG-AAATGAAA
1 TTAAGAAAATTAAG
*
51323 TTTAGAAAATTAAG
1 TTAAGAAAATTAAG
51337 TTAAGAAA
1 TTAAGAAA
51345 TGAATTTTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (14 bp):
TTAAGAAAATTAAG
Found at i:51674 original size:11 final size:11
Alignment explanation
Indices: 51660--51697 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
51650 ATTCATAACA
51660 AATTTATAATT
1 AATTTATAATT
51671 AATTTATAATT
1 AATTTATAATT
51682 -ATTTGATAATT
1 AATTT-ATAATT
*
51693 TATTT
1 AATTT
51698 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:51906 original size:2 final size:2
Alignment explanation
Indices: 51862--51888 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51852 AGTAAGTTTA
51862 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 A
51889 ATAAGTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.