Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017092.1 Corchorus olitorius cultivar O-4 contig17125, 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: 26345
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2913 original size:12 final size:13
Alignment explanation
Indices: 2895--2924 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2885 GTTTTCTTTA
2895 ATTTTCTTGATTG
1 ATTTTCTTGATTG
2908 -TTTTCTTGATTG
1 ATTTTCTTGATTG
2920 ATTTT
1 ATTTT
2925 AATTGCTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (13 bp):
ATTTTCTTGATTG
Found at i:6551 original size:16 final size:16
Alignment explanation
Indices: 6509--6552 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 16
6499 GATAACAACC
6509 AAATCATGACTCCACT
1 AAATCATGACTCCACT
* *
6525 -AA-CAAGACTCCAGT
1 AAATCATGACTCCACT
6539 AAATCATGACTCCA
1 AAATCATGACTCCA
6553 ATATCTGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.43
15 4 0.17
16 9 0.39
ACGTcount: A:0.41, C:0.30, G:0.09, T:0.20
Consensus pattern (16 bp):
AAATCATGACTCCACT
Found at i:6681 original size:15 final size:17
Alignment explanation
Indices: 6641--6685 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
6631 TTTGCTAAAC
6641 TTCATTATATGAACAAT
1 TTCATTATATGAACAAT
6658 TTCATTATATGAACAA-
1 TTCATTATATGAACAAT
6674 TT-ATTATATGAA
1 TTCATTATATGAA
6686 TAAATACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.36
16 2 0.07
17 16 0.57
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (17 bp):
TTCATTATATGAACAAT
Found at i:8447 original size:41 final size:41
Alignment explanation
Indices: 8397--8479 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
8387 ACCCGATCAA
*
8397 CCGAGAGATTAATCCGAAATTACCTGAACCGAGAGATTAAT
1 CCGAGAGATTAATCCGAAATTACCCGAACCGAGAGATTAAT
8438 CCGAGAGATTAATCCGAAATTACCCGAACCGAGAGATTAAT
1 CCGAGAGATTAATCCGAAATTACCCGAACCGAGAGATTAAT
8479 C
1 C
8480 TGAAATTACC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (41 bp):
CCGAGAGATTAATCCGAAATTACCCGAACCGAGAGATTAAT
Found at i:8459 original size:11 final size:13
Alignment explanation
Indices: 8425--8454 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
8415 ATTACCTGAA
8425 CCGAGAGATTAAT
1 CCGAGAGATTAAT
8438 CCGAGAGATTAAT
1 CCGAGAGATTAAT
8451 CCGA
1 CCGA
8455 AATTACCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (13 bp):
CCGAGAGATTAAT
Found at i:8470 original size:28 final size:28
Alignment explanation
Indices: 8438--8499 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
8428 AGAGATTAAT
8438 CCGAGAGATTAATCCGAAATTACCCGAA
1 CCGAGAGATTAATCCGAAATTACCCGAA
* *
8466 CCGAGAGATTAATCTGAAATTACCTGAA
1 CCGAGAGATTAATCCGAAATTACCCGAA
*
8494 TCGAGA
1 CCGAGA
8500 TTAATTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (28 bp):
CCGAGAGATTAATCCGAAATTACCCGAA
Found at i:12908 original size:2 final size:2
Alignment explanation
Indices: 12903--12935 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
12893 TCGTCTCTCA
12903 AT AT AT AT AT AT AT AT AT AT -T AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
12936 AAAGTACGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14197 original size:22 final size:21
Alignment explanation
Indices: 14141--14469 Score: 152
Period size: 22 Copynumber: 15.2 Consensus size: 21
14131 GTCTCTGTGT
* *
14141 GGTTAGCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* *
14162 TGGTTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
* * *
14185 GGCTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* *
14207 GGTTACCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATA-GGA
* *
14229 AGTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
* *
14251 GGTCATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
* *
14273 GGTCATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
14295 GGTTACCAAAATTTCATAGGACCA
1 GGTTATCAAAATTTCATAGG---A
* * *
14319 TGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGG-A
** *
14341 GGTTATTGAAATTTCATAGTA
1 GGTTATCAAAATTTCATAGGA
* * * *
14362 TGATTATCACAATTTTATAGAAA
1 -GGTTATCAAAATTTCATAG-GA
*
14385 AGTTATC-AAA----A-A-GA
1 GGTTATCAAAATTTCATAGGA
* * *
14399 GATTATCAAAATGTCACAGCGA
1 GGTTATCAAAATTTCATAG-GA
* *
14421 GATTAT-AAGAATTTCATAGTA
1 GGTTATCAA-AATTTCATAGGA
*
14442 TGGTTAACAAAATTTCATAAGGA
1 -GGTTATCAAAATTTCAT-AGGA
14465 GGTTA
1 GGTTA
14470 CTAATATTTC
Statistics
Matches: 233, Mismatches: 52, Indels: 44
0.71 0.16 0.13
Matches are distributed among these distances:
14 6 0.03
15 3 0.01
16 1 0.00
17 1 0.00
19 1 0.00
20 1 0.00
21 10 0.04
22 183 0.79
23 11 0.05
24 16 0.07
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:14217 original size:66 final size:66
Alignment explanation
Indices: 14137--14263 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 66
14127 TCTTGTCTCT
* ** * *
14137 GTGTGGTTAGCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGG-CTATCAAAATTCC
1 GTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATG-GGAAGGTC-ATCAAAATTCC
14200 ATA
64 ATA
*
14203 GTGTGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATGGGAAGGTCATCAAAATT
1 GTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGGGAAGGTCATCAAAATT
14264 TCATGGGAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 2 0.04
66 50 0.94
67 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGGGAAGGTCATCAAAATTCCAT
A
Found at i:14376 original size:90 final size:88
Alignment explanation
Indices: 14142--14381 Score: 230
Period size: 88 Copynumber: 2.7 Consensus size: 88
14132 TCTCTGTGTG
* * * * * * ** *
14142 GTTAGCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGCTATCAAAATTCCATAGTG
1 GTTATCAAAATTTCATAGGAAGGTCATCAAAATTTCAT-AGGAAGATTATCAAAATTTCATAGTG
*
14206 TGGTTACCAAAATTTCATATGAAA
65 TGGTTACCAAAATTTCATAGGAAA
* * * *
14230 GTTATCAAAATTTCATGGGAAGGTCATCAAAATTTCATGGGAAGGTCATCAAAATTTCATAGTGT
1 GTTATCAAAATTTCATAGGAAGGTCATCAAAATTTCATAGGAAGATTATCAAAATTTCATAGTGT
*
14295 GGTTACCAAAATTTCATAGGACCAT
66 GGTTACCAAAATTTCATAGGA--AA
* * * ** * * * *
14320 GTTATTAAAATTTCTTAGGAAGGTTATTGAAATTTCATAGTATGATTATCACAATTTTATAG
1 GTTATCAAAATTTCATAGGAAGGTCATCAAAATTTCATAGGAAGATTATCAAAATTTCATAG
14382 AAAAGTTATC
Statistics
Matches: 123, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
87 2 0.02
88 71 0.58
90 50 0.41
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35
Consensus pattern (88 bp):
GTTATCAAAATTTCATAGGAAGGTCATCAAAATTTCATAGGAAGATTATCAAAATTTCATAGTGT
GGTTACCAAAATTTCATAGGAAA
Found at i:14775 original size:41 final size:41
Alignment explanation
Indices: 14727--15032 Score: 396
Period size: 41 Copynumber: 7.4 Consensus size: 41
14717 TAAGGGTCGA
* * * *
14727 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTGTTG
1 ATGACTCGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
* * * *
14768 ACGACTTGACCTTGAATTGATAATTTAATTCAAGGGTCTTG
1 ATGACTCGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
* * *
14809 ACGACTCGATCTTCAATTGATAATAATTCGATTCAAGGGTCTCG
1 ATGACTCGATCTTGAATTGATAAT--TT-AATTCAAGGGTCTCG
* * * *
14853 ATGACTTGTTCTTGAATTAATAATTTAGTTCAAGGGTCTCG
1 ATGACTCGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
* *
14894 AAGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTCGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
*
14935 ATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTCGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
*
14976 ATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
1 ATGACTCGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
* *
15017 GTGACTCAATCTTGAA
1 ATGACTCGATCTTGAA
15033 CAAACGAAAA
Statistics
Matches: 238, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
41 202 0.85
42 2 0.01
43 2 0.01
44 32 0.13
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (41 bp):
ATGACTCGATCTTGAATTGATAATTTAATTCAAGGGTCTCG
Found at i:14953 original size:126 final size:123
Alignment explanation
Indices: 14727--15032 Score: 423
Period size: 126 Copynumber: 2.5 Consensus size: 123
14717 TAAGGGTCGA
* * * ** *
14727 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTGTTGACGACTTGACCTTGAATTGATAAT
1 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCAATCTTGAATTGATAAT
* * *
14792 TTAATTCAAGGGTCTTGACGACTCGATCTTCAATTGATAATAATTCGATTCAAGGGTCTCG
66 TTAATTCAAGGGTCTCGACGACTCAATCTTCAATTGATAAT--TT-AATTCAAGGGTCTCG
* *
14853 ATGACTTGTTCTTGAATTAATAATTTAGTTCAAGGGTCTCGAAGACTCAATCTTGAATTGATAAT
1 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCAATCTTGAATTGATAAT
* *
14918 TTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
66 TTAATTCAAGGGTCTCGACGACTCAATCTTCAATTGATAATTTAATTCAAGGGTCTCG
*** **
14976 ATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCGGTGACTCAATCTTGAA
1 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCAATCTTGAA
15033 CAAACGAAAA
Statistics
Matches: 160, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
123 64 0.40
124 2 0.01
126 94 0.59
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (123 bp):
ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGAAGACTCAATCTTGAATTGATAAT
TTAATTCAAGGGTCTCGACGACTCAATCTTCAATTGATAATTTAATTCAAGGGTCTCG
Found at i:15539 original size:22 final size:23
Alignment explanation
Indices: 15490--15796 Score: 76
Period size: 22 Copynumber: 13.8 Consensus size: 23
15480 CTTGTTCTAC
*
15490 AAGGTTATCAAAATTTTATAGTG
1 AAGGTTATCAAAATTTCATAGTG
*
15513 -TGGTTATCAAAATTTCATA-TG
1 AAGGTTATCAAAATTTCATAGTG
* *
15534 AAGGTTAT-AAAAGTCTCAATTTCA-TA
1 AAGGTTATCAAAA-TTTC-A--T-AGTG
* * **
15560 AAGAG-TACCAACATTAGATA--G
1 AAG-GTTATCAAAATTTCATAGTG
* *
15581 AAGGTTATC-AAATCTCATAGAG
1 AAGGTTATCAAAATTTCATAGTG
* * * *
15603 -TGATTATCGAAATTTCATAGCG
1 AAGGTTATCAAAATTTCATAGTG
*
15625 ATCGGATTATCAAAATTT-ATAG-G
1 A-AGG-TTATCAAAATTTCATAGTG
* *
15648 AAGATTATCAAAATTCCATAGTG
1 AAGGTTATCAAAATTTCATAGTG
** * * *
15671 -TTGTTATCAATATTTCAAAGCG
1 AAGGTTATCAAAATTTCATAGTG
* *
15693 -AGGTTATCAAAATTACATAAT-
1 AAGGTTATCAAAATTTCATAGTG
* * * *
15714 ATGATTATCAAAATTT-TTAGAG
1 AAGGTTATCAAAATTTCATAGTG
* * * **
15736 -GGGTCAACAAAAATTT-ATAAAG
1 AAGGTTATC-AAAATTTCATAGTG
**
15758 -AGGTTATCAAAATTTCATAAAG
1 AAGGTTATCAAAATTTCATAGTG
*
15780 -AGGTTATCAAATTTTCA
1 AAGGTTATCAAAATTTCA
15797 AAATGTGATG
Statistics
Matches: 207, Mismatches: 56, Indels: 43
0.68 0.18 0.14
Matches are distributed among these distances:
20 7 0.03
21 42 0.20
22 123 0.59
23 5 0.02
24 5 0.02
25 13 0.06
26 8 0.04
27 4 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (23 bp):
AAGGTTATCAAAATTTCATAGTG
Found at i:15640 original size:25 final size:22
Alignment explanation
Indices: 15604--15729 Score: 78
Period size: 22 Copynumber: 5.6 Consensus size: 22
15594 CTCATAGAGT
* *
15604 GATTATCGAAATTTCATAGCGATCG
1 GATTATCAAAATTTCATAG-GA--A
15629 GATTATCAAAATTT-ATAGGAA
1 GATTATCAAAATTTCATAGGAA
* **
15650 GATTATCAAAATTCCATAGTGTT
1 GATTATCAAAATTTCATAG-GAA
* *
15673 G-TTATCAATATTTCAAAGCG-A
1 GATTATCAAAATTTCATAG-GAA
* * ** *
15694 GGTTATCAAAATTACATAATAT
1 GATTATCAAAATTTCATAGGAA
15716 GATTATCAAAATTT
1 GATTATCAAAATTT
15730 TTAGAGGGGT
Statistics
Matches: 79, Mismatches: 18, Indels: 11
0.73 0.17 0.10
Matches are distributed among these distances:
21 14 0.18
22 44 0.56
23 4 0.05
24 4 0.05
25 13 0.16
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (22 bp):
GATTATCAAAATTTCATAGGAA
Found at i:15793 original size:21 final size:21
Alignment explanation
Indices: 15692--15790 Score: 85
Period size: 22 Copynumber: 4.6 Consensus size: 21
15682 ATTTCAAAGC
*
15692 GAGGTTATCAAAATTACATAATA
1 GAGGTTATCAAAATT-TATAA-A
* *
15715 TGA--TTATCAAAATTTTTAGA
1 -GAGGTTATCAAAATTTATAAA
* * *
15735 GGGGTCAACAAAAATTTATAAA
1 GAGGTTATC-AAAATTTATAAA
15757 GAGGTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTT-ATAAA
15779 GAGGTTATCAAA
1 GAGGTTATCAAA
15791 TTTTCAAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 12 0.20
22 44 0.73
24 2 0.03
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.31
Consensus pattern (21 bp):
GAGGTTATCAAAATTTATAAA
Found at i:15949 original size:22 final size:21
Alignment explanation
Indices: 15836--16110 Score: 122
Period size: 22 Copynumber: 13.0 Consensus size: 21
15826 ATTTCTGGGG
15836 AGGTTATCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCATAG-A
* * *
15858 TGGTTA-CCAAA-TT-A-GGA
1 AGGTTATCAAAATTTCATAGA
* * *
15875 AGGTTATTAAACTTTTATTATGA
1 AGGTTATCAAAATTTCA-TA-GA
* * *
15898 A-GTAATCAAAATTTCA-GGG
1 AGGTTATCAAAATTTCATAGA
*
15917 AGGATATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
*
15939 AGGTTATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG--A
*
15962 A-GTT-TCCAAAATTTCATAAA
1 AGGTTAT-CAAAATTTCATAGA
* * *
15982 AGGGTTATCAAGATTACATAGT
1 A-GGTTATCAAAATTTCATAGA
* * *
16004 ATGTAGATCAAAATTTCATA-T
1 AGGT-TATCAAAATTTCATAGA
* *
16025 AGGTTATCAAATTTTCATAGT
1 AGGTTATCAAAATTTCATAGA
* * *
16046 ATGTAGATCAAAATTTCATAAA
1 AGGT-TATCAAAATTTCATAGA
*
16068 GAGGTTATCAAATTTTCA-A-A
1 -AGGTTATCAAAATTTCATAGA
*
16088 ATGTGATTACCAAAATTTCATAG
1 A-G-G-TTATCAAAATTTCATAG
16111 TGGTATTTCT
Statistics
Matches: 186, Mismatches: 43, Indels: 46
0.68 0.16 0.17
Matches are distributed among these distances:
17 6 0.03
18 3 0.02
19 6 0.03
20 32 0.17
21 18 0.10
22 112 0.60
23 9 0.05
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:15951 original size:42 final size:41
Alignment explanation
Indices: 15833--16240 Score: 114
Period size: 42 Copynumber: 9.9 Consensus size: 41
15823 GGTATTTCTG
* * *
15833 GGGAGGTTATCAAAATTTCATAGTATGGTTA-CCAAA-TT-A
1 GGGAGGATATCAAAATTTCATAG-AAGGTTATCAAAATTTCA
* * * * * *
15872 GGAAGGTTATTAAACTTTTATTATGAA-GTAATCAAAATTTCA
1 GGGAGGATATCAAAATTTCA-TA-GAAGGTTATCAAAATTTCA
15914 GGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCA
1 GGGAGGATATCAAAATTTCATA-GAAGGTTATCAAAATTTCA
** *** * * * *
15956 TAGTTTAGTTTCCAAAATTTCATAAAAGGGTTATCAAGATTACA
1 GGGAGGA-TAT-CAAAATTTCATAGAA-GGTTATCAAAATTTCA
* * * * * *
16000 TAGTATGTAGATCAAAATTTCATA-TAGGTTATCAAATTTTCA
1 -GGGA-GGATATCAAAATTTCATAGAAGGTTATCAAAATTTCA
* * * * * *
16042 TAGTATGTAGATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 -GGGA-GGATATCAAAATTTCATAGA-AGGTTATCAAAATTTCA
** * * *
16086 -AAATGTGATTACCAAAATTTCATAG-TGG---T----ATTTCT
1 GGGA-G-GA-TATCAAAATTTCATAGAAGGTTATCAAAATTTCA
* * *
16121 GGGAGGTTATCAAAATTTCATAGTATGGTTA-CCAAA-TT-A
1 GGGAGGATATCAAAATTTCATAG-AAGGTTATCAAAATTTCA
* * * * * * *
16160 GGAAGGTTATTAAACTTTTATTATGGA-GTAATCAAAATTTCA
1 GGGAGGATATCAAAATTTCA-TA-GAAGGTTATCAAAATTTCA
16202 GGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATT
1 GGGAGGATATCAAAATTTCATA-GAAGGTTATCAAAATT
16241 CCATAGTTTA
Statistics
Matches: 275, Mismatches: 63, Indels: 59
0.69 0.16 0.15
Matches are distributed among these distances:
33 15 0.05
34 1 0.00
35 8 0.03
36 1 0.00
39 39 0.14
40 15 0.05
41 18 0.07
42 101 0.37
43 6 0.02
44 68 0.25
45 1 0.00
46 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (41 bp):
GGGAGGATATCAAAATTTCATAGAAGGTTATCAAAATTTCA
Found at i:15979 original size:44 final size:43
Alignment explanation
Indices: 15922--16085 Score: 199
Period size: 44 Copynumber: 3.8 Consensus size: 43
15912 CAGGGAGGAT
*
15922 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGT-T-TAG
1 ATCAAAATTTCATA-AAAGGTTATCAAAATTTCATAGTATGTAG
* * *
15964 TTTCCAAAATTTCATAAAAGGGTTATCAAGATTACATAGTATGTAG
1 -AT-CAAAATTTCATAAAA-GGTTATCAAAATTTCATAGTATGTAG
* *
16010 ATCAAAATTTCAT-ATAGGTTATCAAATTTTCATAGTATGTAG
1 ATCAAAATTTCATAAAAGGTTATCAAAATTTCATAGTATGTAG
*
16052 ATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 ATCAAAATTTCATAAA-AGGTTATCAAAATTTCA
16086 AAATGTGATT
Statistics
Matches: 105, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
42 36 0.34
43 6 0.06
44 58 0.55
45 2 0.02
46 3 0.03
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.37
Consensus pattern (43 bp):
ATCAAAATTTCATAAAAGGTTATCAAAATTTCATAGTATGTAG
Found at i:16102 original size:44 final size:43
Alignment explanation
Indices: 15922--16109 Score: 165
Period size: 44 Copynumber: 4.3 Consensus size: 43
15912 CAGGGAGGAT
* * *
15922 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAG--TTTAG
1 ATCAAAATTTCATAAG-AGGTTATCAAATTTTCATAGAATGTAG
* * * *
15964 TTTCCAAAATTTCATAAAAGGGTTATCAAGA-TTACATAGTATGTAG
1 -AT-CAAAATTTCATAAGA-GGTTATCAA-ATTTTCATAGAATGTAG
* *
16010 ATCAAAATTTCAT-ATAGGTTATCAAATTTTCATAGTATGTAG
1 ATCAAAATTTCATAAGAGGTTATCAAATTTTCATAGAATGTAG
16052 ATCAAAATTTCATAAAGAGGTTATCAAATTTTCA-A-AATGT-G
1 ATCAAAATTTCAT-AAGAGGTTATCAAATTTTCATAGAATGTAG
16093 ATTACCAAAATTTCATA
1 A-T--CAAAATTTCATA
16110 GTGGTATTTC
Statistics
Matches: 124, Mismatches: 10, Indels: 22
0.79 0.06 0.14
Matches are distributed among these distances:
41 3 0.02
42 41 0.33
43 6 0.05
44 68 0.55
45 2 0.02
46 4 0.03
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (43 bp):
ATCAAAATTTCATAAGAGGTTATCAAATTTTCATAGAATGTAG
Found at i:16203 original size:288 final size:289
Alignment explanation
Indices: 15763--16311 Score: 1019
Period size: 288 Copynumber: 1.9 Consensus size: 289
15753 TAAAGAGGTT
15763 ATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATGACCAAAATTTCATAGTGGTAT
1 ATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATGACCAAAATTTCATAGTGGTAT
15828 TTCTGGGGAGGTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTTAT
66 TTCTGGGGAGGTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTTAT
*
15893 TATGAAGTAATCAAAATTTCAGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATA
131 TATGAAGTAATCAAAATTTCAGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTCCATA
* *
15958 GTTTAGTTTCCAAAATTTCATAAAAGGGTTATCAAGATTACATAGTATGTAGATCAAAATTTCAT
196 GTTTAGTTTCCAAAATTTCATAAAAGGGTTATCAAAATTACATAGTATGTACATCAAAATTTCAT
16023 ATAGGTTATCAAATTTTCATAGTATGTAG
261 ATAGGTTATCAAATTTTCATAGTATGTAG
*
16052 ATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTACCAAAATTTCATAGTGGTAT
1 ATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATGACCAAAATTTCATAGTGGTAT
16117 TTCT-GGGAGGTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTTAT
66 TTCTGGGGAGGTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTTAT
*
16181 TATGGAGTAATCAAAATTTCAGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTCCATA
131 TATGAAGTAATCAAAATTTCAGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTCCATA
* * *
16246 GTTTAGTTTTCAAAATTTCATAAAAGGGTTATCAAAATTTCATAGTTTGTACATCAAAATTTCAT
196 GTTTAGTTTCCAAAATTTCATAAAAGGGTTATCAAAATTACATAGTATGTACATCAAAATTTCAT
16311 A
261 A
16312 GGGAGATTAA
Statistics
Matches: 252, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
288 184 0.73
289 68 0.27
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (289 bp):
ATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATGACCAAAATTTCATAGTGGTAT
TTCTGGGGAGGTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTATTAAACTTTTAT
TATGAAGTAATCAAAATTTCAGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTCCATA
GTTTAGTTTCCAAAATTTCATAAAAGGGTTATCAAAATTACATAGTATGTACATCAAAATTTCAT
ATAGGTTATCAAATTTTCATAGTATGTAG
Found at i:16237 original size:22 final size:22
Alignment explanation
Indices: 16124--16503 Score: 147
Period size: 22 Copynumber: 17.8 Consensus size: 22
16114 TATTTCTGGG
*
16124 AGGTTATCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCATAGGA
* *
16146 TGGTTA-CCAAA--T--TAGGA
1 AGGTTATCAAAATTTCATAGGA
* * *
16163 AGGTTATTAAACTTTTATTATGG-
1 AGGTTATCAAAATTTCA-TA-GGA
* *
16186 A-GTAATCAAAATTTC--AGGG
1 AGGTTATCAAAATTTCATAGGA
* *
16205 AGGATATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATAGGA
* **
16227 AGGTTATCAAAATTCCATAGTTT
1 AGGTTATCAAAATTTCATAG-GA
* *
16250 A-GTTTTCAAAATTTCATA-AA
1 AGGTTATCAAAATTTCATAGGA
*
16270 AGGGTTATCAAAATTTCATA-GT
1 A-GGTTATCAAAATTTCATAGGA
** * *
16292 TTGTACATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATAGGA
* * *
16315 AGATTAACAAAATTTCATAATG-
1 AGGTTATCAAAATTTCAT-AGGA
* ***
16337 AGGTTATAAAAAAAACATAGGA
1 AGGTTATCAAAATTTCATAGGA
* *
16359 AGATTATCAAAA-TT--T--GT
1 AGGTTATCAAAATTTCATAGGA
* *
16376 A-GTTATCAAGATTCCATAAGG-
1 AGGTTATCAAAATTTCAT-AGGA
* * *
16397 AGGTTATCAAAGTTTTATAGGG
1 AGGTTATCAAAATTTCATAGGA
*
16419 AGGTTTATCAAAATTTTATAGGA
1 AGG-TTATCAAAATTTCATAGGA
*
16442 AGGTTTATCAAAATTTCAT-GGCG
1 AGG-TTATCAAAATTTCATAGG-A
* *
16465 AGGTTATCACAATTTTATAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* *
16487 TGATTATCAAAATTTCA
1 AGGTTATCAAAATTTCA
16504 GAGTGCGAGT
Statistics
Matches: 262, Mismatches: 66, Indels: 60
0.68 0.17 0.15
Matches are distributed among these distances:
16 8 0.03
17 12 0.05
18 4 0.02
19 5 0.02
20 14 0.05
21 12 0.05
22 157 0.60
23 47 0.18
24 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:16615 original size:23 final size:23
Alignment explanation
Indices: 16567--16641 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 23
16557 TATTAATATA
* * *
16567 TCATA-TGGAGGTTATCAATATC
1 TCATAGTGGAAGTTATCAAAATT
** *
16589 TCATAGTGTTAGTTATCAAATTT
1 TCATAGTGGAAGTTATCAAAATT
*
16612 TCATTG-GGAAGTTATCAAAATT
1 TCATAGTGGAAGTTATCAAAATT
16634 TCATAGTG
1 TCATAGTG
16642 AGGTTTTTAA
Statistics
Matches: 40, Mismatches: 11, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
22 23 0.57
23 17 0.43
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (23 bp):
TCATAGTGGAAGTTATCAAAATT
Found at i:20763 original size:27 final size:26
Alignment explanation
Indices: 20720--20778 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
20710 GAGTGTTATT
*
20720 AAAATAAAAAAGGGTTTT-ATTAAAA
1 AAAAAAAAAAAGGGTTTTAATTAAAA
*
20745 CAAAAAAAAAGAAGTGTTTTAAATTAAAA
1 -AAAAAAAAA-AAGGGTTTT-AATTAAAA
20774 AAAAA
1 AAAAA
20779 TTAATTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.29
27 8 0.29
28 5 0.18
29 7 0.25
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (26 bp):
AAAAAAAAAAAGGGTTTTAATTAAAA
Found at i:20865 original size:32 final size:32
Alignment explanation
Indices: 20829--20916 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 32
20819 TTTGAGGTTT
20829 TGCAATTTTCTTCTTCTTCTTCCTTGAAATCC
1 TGCAATTTTCTTCTTCTTCTTCCTTGAAATCC
*
20861 TGCAA--TT-TTCTTATTCTTCCTTGAAATCC
1 TGCAATTTTCTTCTTCTTCTTCCTTGAAATCC
*
20890 TGCAATTTTCTTATTCTTCTTCCTTGA
1 TGCAATTTTCTTCTTCTTCTTCCTTGA
20917 GGAAATTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
29 26 0.52
30 2 0.04
31 2 0.04
32 20 0.40
ACGTcount: A:0.17, C:0.25, G:0.07, T:0.51
Consensus pattern (32 bp):
TGCAATTTTCTTCTTCTTCTTCCTTGAAATCC
Found at i:22465 original size:33 final size:33
Alignment explanation
Indices: 22423--22493 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
22413 AAGCATCTGA
* * *
22423 TCAGCAAAAGGTCAGTGAGCTGATTAATCCAAG
1 TCAGCAAAAGGTCAATGAGATGATCAATCCAAG
22456 TCAGCAAAAGGTCAATGAGATGATCAATCCAAG
1 TCAGCAAAAGGTCAATGAGATGATCAATCCAAG
*
22489 CCAGC
1 TCAGC
22494 TGAAGGAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (33 bp):
TCAGCAAAAGGTCAATGAGATGATCAATCCAAG
Found at i:23169 original size:14 final size:16
Alignment explanation
Indices: 23140--23180 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
23130 CCTCTACACA
23140 GAGAAGAAATATATAT
1 GAGAAGAAATATATAT
23156 GAGAAGAAATATATAT
1 GAGAAGAAATATATAT
23172 G-G-AGAAATA
1 GAGAAGAAATA
23181 GGATCGCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.28
15 1 0.04
16 17 0.68
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (16 bp):
GAGAAGAAATATATAT
Done.