Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013514.1 Corchorus olitorius cultivar O-4 contig13547, 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: 58250
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3715 original size:22 final size:22
Alignment explanation
Indices: 3672--3713 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
3662 TTTCCCTGTT
3672 TCGACCTTCATCAGGGTCAAAC
1 TCGACCTTCATCAGGGTCAAAC
*
3694 TCGACCTTC-TCTGGGTCAAA
1 TCGACCTTCATCAGGGTCAAA
3714 ACAGGGCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (22 bp):
TCGACCTTCATCAGGGTCAAAC
Found at i:16723 original size:46 final size:45
Alignment explanation
Indices: 16603--16786 Score: 241
Period size: 45 Copynumber: 4.1 Consensus size: 45
16593 TTTCAAAAAA
* *
16603 AAAAAAGAATATTTTCTATTTTAGTAATTCCAAAAGAAGATTTTGG
1 AAAAAA-AATGTTTTCTATTTAAGTAATTCCAAAAGAAGATTTTGG
*
16649 AAAAACAAATGTTTTCT-TTTAAGTAATTCCAAAATAAGATTTTGG
1 AAAAA-AAATGTTTTCTATTTAAGTAATTCCAAAAGAAGATTTTGG
*
16694 AAAAAAGAATGTTTTCTATTTTAGTAATTCCAAAAG-AGAATTTTGG
1 AAAAAA-AATGTTTTCTATTTAAGTAATTCCAAAAGAAG-ATTTTGG
* *
16740 AAAATAAAA-GTTTTTTCTTTAAG-AATTCCAAAAGAAGATTTTGG
1 AAAA-AAAATGTTTTCTATTTAAGTAATTCCAAAAGAAGATTTTGG
16784 AAA
1 AAA
16787 TCAAGAAAAT
Statistics
Matches: 124, Mismatches: 8, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
44 22 0.18
45 56 0.45
46 43 0.35
47 3 0.02
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.36
Consensus pattern (45 bp):
AAAAAAAATGTTTTCTATTTAAGTAATTCCAAAAGAAGATTTTGG
Found at i:16793 original size:91 final size:91
Alignment explanation
Indices: 16603--16786 Score: 286
Period size: 91 Copynumber: 2.0 Consensus size: 91
16593 TTTCAAAAAA
16603 AAAAAAGAATATTTTCTATTTTAGTAATTCCAAAAGAAGATTTTGGAAAAACAAATGTTTTCTTT
1 AAAAAAGAATATTTTCTATTTTAGTAATTCCAAAAGAAGATTTTGGAAAAACAAATGTTTTCTTT
*
16668 TAAGTAATTCCAAAATAAGATTTTGG
66 TAAGTAATTCCAAAAGAAGATTTTGG
* *
16694 AAAAAAGAATGTTTTCTATTTTAGTAATTCCAAAAG-AGAATTTTGGAAAATA-AAA-GTTTTTT
1 AAAAAAGAATATTTTCTATTTTAGTAATTCCAAAAGAAG-ATTTTGGAAAA-ACAAATGTTTTCT
16756 CTTTAAG-AATTCCAAAAGAAGATTTTGG
64 -TTTAAGTAATTCCAAAAGAAGATTTTGG
16784 AAA
1 AAA
16787 TCAAGAAAAT
Statistics
Matches: 87, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
90 31 0.36
91 55 0.63
92 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.36
Consensus pattern (91 bp):
AAAAAAGAATATTTTCTATTTTAGTAATTCCAAAAGAAGATTTTGGAAAAACAAATGTTTTCTTT
TAAGTAATTCCAAAAGAAGATTTTGG
Found at i:17369 original size:8 final size:8
Alignment explanation
Indices: 17358--17397 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
17348 AAATAGATGA
*
17358 ATAAAAAG
1 ATAAATAG
17366 ATAAATAG
1 ATAAATAG
*
17374 GTAAATAG
1 ATAAATAG
*
17382 ATAATTAG
1 ATAAATAG
17390 ATAAATAG
1 ATAAATAG
17398 GTAGGTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (8 bp):
ATAAATAG
Found at i:18959 original size:54 final size:53
Alignment explanation
Indices: 18854--19657 Score: 714
Period size: 54 Copynumber: 15.0 Consensus size: 53
18844 AAACCTTTCA
* * * * * * *
18854 TGGAATGACCGCACTGGATCAACTTGAAGATCAATTATGATCATCGAAAACTTTT
1 TGGAATGACCGCACTAGATCATC-TG-GGATCAACTCTGATCATTGAAAACTTCT
* * * *
18909 TAGAATGACTGCACTATATCAAT-TGGAGATCAACTCTGATCATTGCAAACTTCT
1 TGGAATGACCGCACTAGATC-ATCTGG-GATCAACTCTGATCATTGAAAACTTCT
*
18963 TGGAATGACCGCACTAGATCATCTGGGATCAACTCTGATC-TCTAAAAACTTCT
1 TGGAATGACCGCACTAGATCATCTGGGATCAACTCTGATCAT-TGAAAACTTCT
*
19016 TGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCATTGAAAACTTCT
1 TGGAATGACCGCACTAGATCATCT-GGGATCAACTCTGATCATTGAAAACTTCT
* * * * * *
19070 TGGAATGACCGCACTGGATCATCTAGGAATCAACTCTAATTACTAAAAACTTCT
1 TGGAATGACCGCACTAGATCATCT-GGGATCAACTCTGATCATTGAAAACTTCT
* * *
19124 TGGCATGA-CGACACTGGATCATCTGGAGATCAACTCTGATC-TCTAAAAACTTCT
1 TGGAATGACCG-CACTAGATCATCTGG-GATCAACTCTGATCAT-TGAAAACTTCT
* ** * *
19178 TGGAATGACCGCACTGGATC-T-AAGGATCAACTATGATC-TCTAAAAACTTCT
1 TGGAATGACCGCACTAGATCATCTGGGATCAACTCTGATCAT-TGAAAACTTCT
* *
19229 CGGAATGACCGAAC-AGGATCATCTAGGGATCAACTCTGATCATTGAAAACTTCT
1 TGGAATGACCGCACTA-GATCATCT-GGGATCAACTCTGATCATTGAAAACTTCT
* * *
19283 TTGAAAGACCGCAC-AGGATCAAT-TGGAGATCAACTCTGATCATCGAAAACTTCT
1 TGGAATGACCGCACTA-GATC-ATCTGG-GATCAACTCTGATCATTGAAAACTTCT
* * ** * * **
19337 TGGAATGGCCACACCGGATAATCTGGGGATCAACTTTGATCATTGATTACTTCT
1 TGGAATGACCGCACTAGATCATCT-GGGATCAACTCTGATCATTGAAAACTTCT
* * * *
19391 TGGAATGACCGCACTGGATCATCTGGGATCAACTATAATCATCGAAAACTTCT
1 TGGAATGACCGCACTAGATCATCTGGGATCAACTCTGATCATTGAAAACTTCT
* * * * * **
19444 TGAAATGACCACACTGGATCAAT-TGGAGATTAACTTTGATCATCAAAAACTTCT
1 TGGAATGACCGCACTAGATC-ATCTGG-GATCAACTCTGATCATTGAAAACTTCT
* * **
19498 TGGGATGACCACACCGGATCATCTGGGGATCAACTCTGATCATTGAAAACTTCT
1 TGGAATGACCGCACTAGATCATCT-GGGATCAACTCTGATCATTGAAAACTTCT
* * * *
19552 TGGAATAACCGCACTAGGTCATCTAGGGATCAACTCTGATCATCGAAATCTTCT
1 TGGAATGACCGCACTAGATCATCT-GGGATCAACTCTGATCATTGAAAACTTCT
** * ** * * *
19606 TCAAACGACCAAACTTGATCAAT-TGGAGATAAACTCTGATCATCGAAAACTT
1 TGGAATGACCGCACTAGATC-ATCTGG-GATCAACTCTGATCATTGAAAACTT
19658 TTATGAAAGA
Statistics
Matches: 628, Mismatches: 95, Indels: 53
0.81 0.12 0.07
Matches are distributed among these distances:
51 42 0.07
52 3 0.00
53 106 0.17
54 448 0.71
55 28 0.04
56 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (53 bp):
TGGAATGACCGCACTAGATCATCTGGGATCAACTCTGATCATTGAAAACTTCT
Found at i:21920 original size:42 final size:42
Alignment explanation
Indices: 21855--21988 Score: 189
Period size: 42 Copynumber: 3.2 Consensus size: 42
21845 CTTAGGCAAT
* * * *
21855 TCCAATAAGCTTGAAACCATCTCCAATGAGTTTGGAACTTTC
1 TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAACTTTC
**
21897 TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAACCATC
1 TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAACTTTC
*
21939 TCCAATGAGCTTGGAA-CTTGCTCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACCTT-CTCCAATGAGCTTGGAACTTTC
21981 TCCAATGA
1 TCCAATGA
21989 ACTCCTAGCA
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 3 0.04
42 79 0.96
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (42 bp):
TCCAATGAGCTTGGAACCTTCTCCAATGAGCTTGGAACTTTC
Found at i:21954 original size:63 final size:63
Alignment explanation
Indices: 21855--21988 Score: 216
Period size: 63 Copynumber: 2.1 Consensus size: 63
21845 CTTAGGCAAT
* * *
21855 TCCAATAAGCTTGAAACCATCTCCAATGAGTTTGGAACTTTCTCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGAAACCATCTCCAATGAGCTTGGAACTTGCTCCAATGAGCTTGGAA-CTTGC
*
21918 TCCAATGAGCTTGGAACCATCTCCAATGAGCTTGGAACTTGCTCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGAAACCATCTCCAATGAGCTTGGAACTTGCTCCAATGAGCTTGGAACTTGC
21981 TCCAATGA
1 TCCAATGA
21989 ACTCCTAGCA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
62 3 0.05
63 63 0.95
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (63 bp):
TCCAATGAGCTTGAAACCATCTCCAATGAGCTTGGAACTTGCTCCAATGAGCTTGGAACTTGC
Found at i:21977 original size:21 final size:20
Alignment explanation
Indices: 21855--21988 Score: 169
Period size: 21 Copynumber: 6.4 Consensus size: 20
21845 CTTAGGCAAT
* * *
21855 TCCAATAAGCTTGAAACCATC
1 TCCAATGAGCTTGGAA-CTTC
*
21876 TCCAATGAGTTTGGAACTTTC
1 TCCAATGAGCTTGGAAC-TTC
21897 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAA-CTTC
*
21918 TCCAATGAGCTTGGAACCATC
1 TCCAATGAGCTTGGAA-CTTC
21939 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTT-C
21960 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTT-C
21981 TCCAATGA
1 TCCAATGA
21989 ACTCCTAGCA
Statistics
Matches: 103, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
20 3 0.03
21 99 0.96
22 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (20 bp):
TCCAATGAGCTTGGAACTTC
Found at i:24075 original size:15 final size:15
Alignment explanation
Indices: 24055--24083 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24045 AAACTAAGTG
24055 GAGCTTGTTGATTTT
1 GAGCTTGTTGATTTT
24070 GAGCTTGTTGATTT
1 GAGCTTGTTGATTT
24084 CGAACATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.28, T:0.52
Consensus pattern (15 bp):
GAGCTTGTTGATTTT
Found at i:25050 original size:25 final size:24
Alignment explanation
Indices: 25013--25059 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
25003 CTAGAAAATT
25013 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
25039 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
25060 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:25951 original size:21 final size:21
Alignment explanation
Indices: 25927--26039 Score: 183
Period size: 21 Copynumber: 5.4 Consensus size: 21
25917 CTTAGGCAAT
*
25927 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* *
25948 TCCAATGAGTTTGGAACTTTC
1 TCCAATGAGCTTGGAACCTTC
25969 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
25990 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
26011 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
26032 TCCAATGA
1 TCCAATGA
26040 ACTCCTAGCA
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
20 3 0.03
21 83 0.97
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:26305 original size:25 final size:27
Alignment explanation
Indices: 26261--26316 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 27
26251 TTTTCCTCCA
*
26261 TTTTTACTTTTTCAGCTTCTTT-CTTTC
1 TTTTTACTTTTTCAGATTCTTTAC-TTC
26288 TTTTT-CTTTTTCA-ATTCTTTACTTC
1 TTTTTACTTTTTCAGATTCTTTACTTC
26313 TTTT
1 TTTT
26317 CTTCTCTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 13 0.48
26 9 0.33
27 5 0.19
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (27 bp):
TTTTTACTTTTTCAGATTCTTTACTTC
Found at i:26828 original size:23 final size:22
Alignment explanation
Indices: 26774--26829 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
26764 AATCAGTCCA
* *
26774 TTTCTTTCGCATTTTCTTTTTT
1 TTTCTTTTGCTTTTTCTTTTTT
**
26796 TTTCACTTGCTTTTTCTTTTTTT
1 TTTCTTTTGCTTTTTC-TTTTTT
26819 TTTCTTTTGCT
1 TTTCTTTTGCT
26830 GATGGGAATC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.73
Consensus pattern (22 bp):
TTTCTTTTGCTTTTTCTTTTTT
Found at i:30607 original size:41 final size:41
Alignment explanation
Indices: 30527--30713 Score: 207
Period size: 41 Copynumber: 4.5 Consensus size: 41
30517 CCAATAACCA
* *
30527 AAAGTCCCCAAACACATATATAACACAACAGCACCTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACAC-AGAG-GCCTCTATAT-C
* * *
30570 AAAGTCCTCAAACACATATATAACACAGAGGCGTCTATATG
1 AAAGTCCCCAAACACATATATAACACAGAGGCCTCTATATC
*
30611 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTAT-TAC
1 AAAGTCCCCAAACACATATATAACACAGAGGC--CTCTATAT-C
* * * * *
30654 GAAGTCCTCAAACACATATAAAACATAGAGGCATCTATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCCTCTATATC
30695 AAAGTCCCCAAACACATAT
1 AAAGTCCCCAAACACATAT
30714 TACAAAGTCC
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
41 59 0.48
42 6 0.05
43 57 0.47
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (41 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCCTCTATATC
Found at i:30621 original size:84 final size:84
Alignment explanation
Indices: 30527--30713 Score: 293
Period size: 84 Copynumber: 2.2 Consensus size: 84
30517 CCAATAACCA
* *
30527 AAAGTCCCCAAACACATATATAACACAACAGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAACAGCAACTCTATTACAAAGTCCTCAAACACATATAAA
* *
30592 ACACAGAGGCGTCTATATG
66 ACACAGAGGCATCTATATC
*** *
30611 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACGAAGTCCTCAAACACATATAAA
1 AAAGTCCCCAAACACATATATAACACAACAGCAACTCTATTACAAAGTCCTCAAACACATATAAA
*
30676 ACATAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
30695 AAAGTCCCCAAACACATAT
1 AAAGTCCCCAAACACATAT
30714 TACAAAGTCC
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 94 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAACAGCAACTCTATTACAAAGTCCTCAAACACATATAAA
ACACAGAGGCATCTATATC
Found at i:30719 original size:22 final size:22
Alignment explanation
Indices: 30694--30735 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
30684 GCATCTATAT
30694 CAAAGTCCCCAAACACATATTA
1 CAAAGTCCCCAAACACATATTA
*
30716 CAAAGTCCTCAAACACATAT
1 CAAAGTCCCCAAACACATAT
30736 ATAACACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.31, G:0.05, T:0.19
Consensus pattern (22 bp):
CAAAGTCCCCAAACACATATTA
Found at i:37041 original size:35 final size:33
Alignment explanation
Indices: 36945--37042 Score: 88
Period size: 35 Copynumber: 2.8 Consensus size: 33
36935 AAGATTAATG
* *
36945 CTCCTTCCTCATTCAACACTTGGGGGCTCCGGAAA
1 CTCCTTCATCATTC-A-ACTTGGGGGCTCCAGAAA
* * *
36980 CCCCTTTCATCATTCAACATTCGGGGCTCCAGCAA
1 CTCC-TTCATCATTCAAC-TTGGGGGCTCCAGAAA
*
37015 TTCCTTCATCATTCAATGCTTGGGGGCT
1 CTCCTTCATCATTCAA--CTTGGGGGCT
37043 ATGTCATACT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
34 14 0.27
35 27 0.53
36 10 0.20
ACGTcount: A:0.19, C:0.33, G:0.18, T:0.30
Consensus pattern (33 bp):
CTCCTTCATCATTCAACTTGGGGGCTCCAGAAA
Found at i:37404 original size:72 final size:72
Alignment explanation
Indices: 37318--37659 Score: 519
Period size: 72 Copynumber: 4.8 Consensus size: 72
37308 CCTCTTCTTC
* *
37318 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATACTTACGGGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGGGATAAT
37383 CTTCCAT
66 CTTCCAT
* * *
37390 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGGGATAAT
**
37455 CTTCTGT
66 CTTCCAT
* * * **
37462 ATTGTGGTTGTAGCCGAGGCAATTCCAACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGGGATAAT
37527 CTTCCAT
66 CTTCCAT
*
37534 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA-GGTGATTA
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGG-GATAA
37598 TCTTCC-T
65 TCTTCCAT
*
37605 CATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCTT
1 -ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
37660 GCTACTAATC
Statistics
Matches: 246, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
71 25 0.10
72 221 0.90
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (72 bp):
ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACGGGATAAT
CTTCCAT
Found at i:37570 original size:144 final size:144
Alignment explanation
Indices: 37310--37659 Score: 587
Period size: 144 Copynumber: 2.4 Consensus size: 144
37300 CACATGGTCC
* *
37310 TCTTCTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATACTTAC
1 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
*
37375 GGGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
66 AGGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
*
37440 TCCTTATGTGATTA
131 TCCTTAGGTGATTA
* * * * *
37454 TCTT-CTGTATTGTGGTTGTAGCCGAGGCAATTCCAACATTTGGCAGTCCTTCGCACAATCCTTA
1 TCTTCCT-CATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
*
37518 CATGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACA
65 CAGGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACA
37583 ATCCTTAGGTGATTA
130 ATCCTTAGGTGATTA
37598 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCTT
1 TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
37660 GCTACTAATC
Statistics
Matches: 189, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
143 25 0.13
144 162 0.86
145 2 0.01
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.32
Consensus pattern (144 bp):
TCTTCCTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
AGGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
TCCTTAGGTGATTA
Found at i:39110 original size:43 final size:43
Alignment explanation
Indices: 38866--39110 Score: 345
Period size: 43 Copynumber: 5.8 Consensus size: 43
38856 CCAATAACCA
* *
38866 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
38909 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-G
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
38950 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
38993 GAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
*
39034 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
39077 AAAGTCCTCAAACACATATATAATACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
39111 TTCTCCTTAT
Statistics
Matches: 176, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
41 71 0.40
42 4 0.02
43 101 0.57
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:39139 original size:84 final size:84
Alignment explanation
Indices: 38866--39110 Score: 445
Period size: 84 Copynumber: 2.9 Consensus size: 84
38856 CCAATAACCA
*
38866 AAAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
38931 ACACAGAGGCATCTATATG
66 ACACAGAGGCATCTATATC
*
38950 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACGAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
39015 ACACAGAGGCATCTATATC
66 ACACAGAGGCATCTATATC
*
39034 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAGTCCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
*
39099 ATACAGAGGCAT
66 ACACAGAGGCAT
39111 TTCTCCTTAT
Statistics
Matches: 155, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 155 1.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (84 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAGTCCTCAAACACATATATA
ACACAGAGGCATCTATATC
Found at i:42201 original size:16 final size:18
Alignment explanation
Indices: 42159--42217 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
42149 TAAGAAAATT
* *
42159 AAAATAGATAAATAATTA
1 AAAATAGAAAAATAAGTA
* *
42177 AGTAATAGATAAAT-AG-A
1 A-AAATAGAAAAATAAGTA
42194 AAAATAGAAAAATAAGTA
1 AAAATAGAAAAATAAGTA
42212 AAAATA
1 AAAATA
42218 ATAGTGTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.29
17 4 0.12
18 9 0.26
19 11 0.32
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (18 bp):
AAAATAGAAAAATAAGTA
Found at i:43553 original size:55 final size:55
Alignment explanation
Indices: 43450--43568 Score: 145
Period size: 55 Copynumber: 2.2 Consensus size: 55
43440 TTCTTAATTA
* * * *
43450 ACCGCACTGGATCATTTAAGATTCAACCTTGATCATGGAAACCTTTCTTGGAATG
1 ACCGCACTGGATCATTGAAGATTCAACCTTAATCATCGAAAACTTTCTTGGAATG
43505 ACCGCACTGGATCAAATTGAAGA-TCAA-CTCTAATCATCGAAAAC-TTCTTGGAATG
1 ACCGCACTGGATC--ATTGAAGATTCAACCT-TAATCATCGAAAACTTTCTTGGAATG
*
43560 ACTGCACTG
1 ACCGCACTG
43569 TATCTGTTGC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
55 34 0.61
56 15 0.27
57 7 0.12
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (55 bp):
ACCGCACTGGATCATTGAAGATTCAACCTTAATCATCGAAAACTTTCTTGGAATG
Found at i:45726 original size:54 final size:54
Alignment explanation
Indices: 45592--46384 Score: 829
Period size: 54 Copynumber: 14.8 Consensus size: 54
45582 ATCAATTGGA
*
45592 GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTAGATCATCT-GG
1 GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* *
45645 GATCAACTCTGATC-TCTAAAAACTTCTTGGAATGACCGCACTTGATCATCTGGG
1 GATCAACTCTGATCAT-TGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* *
45699 GATCAACTCTGATCATTGAAAAATTCTTGGAATGACCGCACTGGATCAT-TCAGG
1 GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCT-GGG
* * * *
45753 GATCAACTCTAATCACT-AGAAACTTCTTGGAATGACGGCACTGGATCATCTGGA
1 GATCAACTCTGATCATTGA-AAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* ** * *
45807 GATCAACTCTGATC-TCTAAAAACTTCTTGGAATGATTGCACTAGATCATCTAGG
1 GATCAACTCTGATCAT-TGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * **
45861 GATCAACTCTGATC-TCTAAAAACTTCTCGGAATGACCGCACTAGATTTTCTGGG
1 GATCAACTCTGATCAT-TGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * ** * *
45915 GATCAACTCTGATCATTGAAAACTTCTTTGAAAGACTACACAGGATCAAT-TGGA
1 GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATC-ATCTGGG
* * ** *
45969 GATCAACTCTGATCATCGAAAACTTCTTGAAATGGTCACACTGGATCATCTGGG
1 GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* *
46023 GATCAACTCTGATCATTGAAAACTTCTTGGAATGGCCGCACTGGATCATTTGGG
1 GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * ** * *
46077 GATCAACTCTGATCATCGAAAGCTTCTTGAAACAACCACACTGGA--AT-TGGA
1 GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * * *
46128 GATTAACTTTGATCATCGAAAACTTCTTGGAATGACCGCACCGGATCATCTAGG
1 GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * *
46182 GATAAACTTTGATCATTGAAAACTTCTTCGAATGACCGCACTGGATCAT-TTGG
1 GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * * *
46235 GATCAACTGTAATCATTGAAAACTTCTTAGAATGATCGCACTGGATCATCTGAG
1 GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * ** * ** * *
46289 GATCAACTCTGATCATCGAAAATTTCTTTCAAACGACAACACTAGATCAAT-TGGA
1 GATCAACTCTGATCATTGAAAACTTC-TTGGAATGACCGCACTGGATC-ATCTGGG
* * *
46344 GATTAACTCTGATCATCGAAAACTTCTAT-GAAAGACCGCAC
1 GATCAACTCTGATCATTGAAAACTTCT-TGGAATGACCGCAC
46385 AGAGTCATTT
Statistics
Matches: 623, Mismatches: 99, Indels: 35
0.82 0.13 0.05
Matches are distributed among these distances:
51 40 0.06
52 3 0.00
53 100 0.16
54 432 0.69
55 46 0.07
56 2 0.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (54 bp):
GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
Found at i:47317 original size:2 final size:2
Alignment explanation
Indices: 47310--47344 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
47300 TCTTTTAGAA
*
47310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47345 AAATTCAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:50329 original size:1 final size:1
Alignment explanation
Indices: 50323--50349 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
50313 CTCAAAACAG
50323 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
50350 GAAGCTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:51356 original size:20 final size:18
Alignment explanation
Indices: 51321--51358 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
51311 CTAAAGGTAA
51321 AAGAAAGAAAAAGCAAAC
1 AAGAAAGAAAAAGCAAAC
51339 AAGAAGAGAAAGAAGCAAAC
1 AAGAA-AGAAA-AAGCAAAC
51359 CTCCATTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.68, C:0.11, G:0.21, T:0.00
Consensus pattern (18 bp):
AAGAAAGAAAAAGCAAAC
Found at i:51754 original size:2 final size:2
Alignment explanation
Indices: 51747--51773 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51737 TCCCAAAAGA
51747 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
51774 CTTTTAAAAC
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
Found at i:53760 original size:74 final size:74
Alignment explanation
Indices: 53639--53790 Score: 304
Period size: 74 Copynumber: 2.1 Consensus size: 74
53629 TGTGAGTTTC
53639 TTTGTAATTTGTTTGTTTATTTGGTAGATAGATAGTTTATTTATGGTATAGTTTGTTGAATTCTC
1 TTTGTAATTTGTTTGTTTATTTGGTAGATAGATAGTTTATTTATGGTATAGTTTGTTGAATTCTC
53704 ATTTAGATG
66 ATTTAGATG
53713 TTTGTAATTTGTTTGTTTATTTGGTAGATAGATAGTTTATTTATGGTATAGTTTGTTGAATTCTC
1 TTTGTAATTTGTTTGTTTATTTGGTAGATAGATAGTTTATTTATGGTATAGTTTGTTGAATTCTC
53778 ATTTAGATG
66 ATTTAGATG
53787 TTTG
1 TTTG
53791 GCCATAGAGA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.22, C:0.03, G:0.20, T:0.55
Consensus pattern (74 bp):
TTTGTAATTTGTTTGTTTATTTGGTAGATAGATAGTTTATTTATGGTATAGTTTGTTGAATTCTC
ATTTAGATG
Found at i:54836 original size:41 final size:39
Alignment explanation
Indices: 54754--54843 Score: 94
Period size: 43 Copynumber: 2.2 Consensus size: 39
54744 TTGTCCCTCA
*
54754 TAATAATAAGGTAATAAATTAAATCCAGATTTAGCTTCCC
1 TAATAATAAGGTAATAAATTAAATCCAGATTTAAC-TCCC
*
54794 TAATAATTAAGGTATAATAAATTAAATCTATG-TTTAAC-CCC
1 TAATAA-TAAGG--TAATAAATTAAATCCA-GATTTAACTCCC
*
54835 TAATTATAA
1 TAATAATAA
54844 ATACGGAGAG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
40 9 0.21
41 13 0.30
43 20 0.47
44 1 0.02
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (39 bp):
TAATAATAAGGTAATAAATTAAATCCAGATTTAACTCCC
Found at i:56665 original size:2 final size:2
Alignment explanation
Indices: 56658--56689 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
56648 TACATATACA
56658 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56690 AGTCTAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56947 original size:39 final size:40
Alignment explanation
Indices: 56891--56971 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
56881 TTTAATTCCT
56891 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
56931 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
56970 AT
1 AT
56972 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:57009 original size:24 final size:24
Alignment explanation
Indices: 56962--57011 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 24
56952 AATACTTACA
56962 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
56986 TTAATTCAAATTCTTAGGTATTTTT
1 TTAATT-AAATTCTTAGGTATTTTT
57011 T
1 T
57012 GTTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:57889 original size:36 final size:36
Alignment explanation
Indices: 57842--57911 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
57832 GAGATTTTGG
* *
57842 AGAAACATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAACATGATAACCAAAATCACAAAAAATGTAATA
* *
57878 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAACATGATAACCAAAATCACAAAAAATGTAA
57912 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (36 bp):
AGAAACATGATAACCAAAATCACAAAAAATGTAATA
Done.