Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012716.1 Corchorus olitorius cultivar O-4 contig12749, 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: 34098
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1557 original size:2 final size:2
Alignment explanation
Indices: 1550--1602 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
1540 AAATCTGAGA
1550 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1591 AT ACT AT AT AT A
1 AT A-T AT AT AT A
1603 AAAGTACGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 46 0.94
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3679 original size:17 final size:17
Alignment explanation
Indices: 3657--3690 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3647 TCTTTTTTTT
*
3657 AAAAAAA-AAAAACAGG
1 AAAAAAAGAAAAAAAGG
3673 AAAAAAAGAAAAAAAGG
1 AAAAAAAGAAAAAAAGG
3690 A
1 A
3691 CATCAACTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAGG
Found at i:6531 original size:35 final size:35
Alignment explanation
Indices: 6486--7612 Score: 1431
Period size: 35 Copynumber: 31.8 Consensus size: 35
6476 ATCAATGTGA
* *
6486 AGATCAACTCTGATCATCGAAAACTTCTTGAAATA
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
6521 AGATCAACTCTGATCATAAAAAAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCAT-----CAAAAACTTCTTGAAATG
*
6561 AGATCAACTCTGATCATAAAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAATG
* * * *
6597 AGATCAACTCTTATCGA-CGAAAACTTCTTAAAAGG
1 AGATCAACTCTGATC-ATCAAAAACTTCTTGAAATG
*
6632 AAATCAACTCTGATCAT-AAAAACCTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAA-CTTCTTGAAATG
* * * *
6667 AGATCAACTATAATCATCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
6702 AGATCAACTCTGATAATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
6737 AGATCAACTTTGATCATCGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
6772 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
6807 TGATCAACTCTGATCATCAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
6842 AGATCAACTCTGATCACCGAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
6877 AGATCAACTCTGATCATCGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
6912 AGATCAACTCTGATCAT-AAAAGCTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
6946 AGATCAACTTTGATCAT-AAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* **
6980 AGATCAACTCTGATAAAAAAAAAAGACTTCTTGAAATG
1 AGATCAACTCTGAT--CATCAAAA-ACTTCTTGAAATG
* * *
7018 AGATCAACTCTGATCAACCAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
7053 AGATCAACTCTGATAATCGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
7088 AGATCAACTCTGATCAT-AAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
7122 AGATCAACTCTGATCAACAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
7157 AGATCAACTCTAATCATAAGAAAAACTTCTTGAAATG
1 AGATCAACTCTGATCAT--CAAAAACTTCTTGAAATG
* *
7194 AGATCAACTCTGATCAACGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
7229 AGATCAACTCTGATCAACGAAAACTTCTTGAAATG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* *
7264 AGATCAACTCTGATCAACAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATC-AAAAACTTCTTGAAATG
* *
7300 AGATCAACTCTGATCATAAAAAACTTCTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
7335 AGATCAACTCTGATCATAAAAAACTTCTTTG-AATG
1 AGATCAACTCTGATCATCAAAAACTTC-TTGAAATG
* *
7370 AGATCAACTCTGATCATAAAAAAATTTCTTGAAATG
1 AGATCAACTCTGATCAT-CAAAAACTTCTTGAAATG
* * *
7406 AGATCAACTCTGATCAACGAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
* * *
7441 AGATCAACTCTTATCATAAAAAACTTCTTTGAAACG
1 AGATCAACTCTGATCATCAAAAACTTC-TTGAAATG
* * * *
7477 AGATCAACTCTGATCAACGAAAATTTCTTGAAAGG
1 AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
*
7512 AGATCAACTCTGATCATAAAAAACTTCTTTG-AATG
1 AGATCAACTCTGATCATCAAAAACTTC-TTGAAATG
* *
7547 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAAGG
1 AGATCAACTCTGATCAT--CAAAAACTTCTTGAAATG
*
7584 AGATCAACTCTGATCATAAAAAACTTCTT
1 AGATCAACTCTGATCATCAAAAACTTCTT
7613 TGAATGACCA
Statistics
Matches: 973, Mismatches: 94, Indels: 50
0.87 0.08 0.04
Matches are distributed among these distances:
34 95 0.10
35 614 0.63
36 140 0.14
37 66 0.07
38 27 0.03
40 31 0.03
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.27
Consensus pattern (35 bp):
AGATCAACTCTGATCATCAAAAACTTCTTGAAATG
Found at i:7109 original size:106 final size:105
Alignment explanation
Indices: 6486--7612 Score: 1412
Period size: 106 Copynumber: 10.6 Consensus size: 105
6476 ATCAATGTGA
* * * *
6486 AGATCAACTCTGATCATCGAAAACTTCTTGAAATAAGATCAACTCTGATCATAAAAAAAAAAACT
1 AGATCAACTCTGATCAACAAAAACTTCTTGAAATGAGATCAACTCTGATCAT-----CAAAAACT
*
6551 TCTTGAAAGGAGATCAACTCTGATCATAAAAAAACTTCTTGAAATG
61 TCTTGAAATGAGATCAACTCTGATCAT-AAAAAACTTCTTGAAATG
* * * * * *
6597 AGATCAACTCTTATCGACGAAAACTTCTTAAAAGGAAATCAACTCTGATCAT-AAAAACCTTCTT
1 AGATCAACTCTGATCAACAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAA-CTTCTT
* * ** *
6661 GAAATGAGATCAACTATAATCATCGAAAACTTCTTGAAACG
65 GAAATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATG
* * *
6702 AGATCAACTCTGAT-AATCGAAAACTTCTTGAAATGAGATCAACTTTGATCATCGAAAACTTCTT
1 AGATCAACTCTGATCAA-CAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAACTTCTT
*
6766 GAAATGAGATCAACTCTGATCATCAAAAACTTCTTGAAATG
65 GAAATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATG
* * * * *
6807 TGATCAACTCTGATCATCAAAAACTTCTTGAAAGGAGATCAACTCTGATCACCGAAAACTTCTTG
1 AGATCAACTCTGATCAACAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAACTTCTTG
* ** *
6872 AAACGAGATCAACTCTGATCATCGAAAACTTCTTGAAAGG
66 AAATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATG
* * *
6912 AGATCAACTCTGATC-ATAAAAGCTTCTTGAAATGAGATCAACTTTGATCAT-AAAAACTTCTTG
1 AGATCAACTCTGATCAACAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAACTTCTTG
* *
6975 AAATGAGATCAACTCTGATAAAAAAAAAAGACTTCTTGAAATG
66 AAATGAGATCAACTCTGAT--CATAAAAA-ACTTCTTGAAATG
* * * *
7018 AGATCAACTCTGATCAACCAAAACTTCTTGAAACGAGATCAACTCTGATAATCGAAAACTTCTTG
1 AGATCAACTCTGATCAACAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAACTTCTTG
* *
7083 AAAGGAGATCAACTCTGATCAT-AAAAACTTCTTGAAACG
66 AAATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATG
* * *
7122 AGATCAACTCTGATCAACAAAAACTTCTTGAAAGGAGATCAACTCTAATCATAAGAAAAACTTCT
1 AGATCAACTCTGATCAACAAAAACTTCTTGAAATGAGATCAACTCTGATCAT--CAAAAACTTCT
*
7187 TGAAATGAGATCAACTCTGATCA-ACGAAAACTTCTTGAAATG
64 TGAAATGAGATCAACTCTGATCATA-AAAAACTTCTTGAAATG
* *
7229 AGATCAACTCTGATCAACGAAAACTTCTTGAAATGAGATCAACTCTGATCAACAAAAAACTTCTT
1 AGATCAACTCTGATCAACAAAAACTTCTTGAAATGAGATCAACTCTGATCATC-AAAAACTTCTT
* *
7294 GAAAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACG
65 GAAATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATG
* *
7335 AGATCAACTCTGATCATA-AAAAACTTCTTTG-AATGAGATCAACTCTGATCATAAAAAAATTTC
1 AGATCAACTCTGATCA-ACAAAAACTTC-TTGAAATGAGATCAACTCTGATCAT-CAAAAACTTC
* *
7398 TTGAAATGAGATCAACTCTGATCA-ACGAAAACTTCTTGAAAGG
63 TTGAAATGAGATCAACTCTGATCATA-AAAAACTTCTTGAAATG
* * * * *
7441 AGATCAACTCTTATCATA-AAAAACTTCTTTGAAACGAGATCAACTCTGATCAACGAAAATTTCT
1 AGATCAACTCTGATCA-ACAAAAACTTC-TTGAAATGAGATCAACTCTGATCATCAAAAACTTCT
*
7505 TGAAAGGAGATCAACTCTGATCATAAAAAACTTCTTTG-AATG
64 TGAAATGAGATCAACTCTGATCATAAAAAACTTC-TTGAAATG
* * *
7547 AGATCAACTCTGATCATAAAAAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAACTTCT
1 AGATCAACTCTGATC--AACAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAACTTCT
7612 T
64 T
7613 TGAATGACCA
Statistics
Matches: 895, Mismatches: 96, Indels: 54
0.86 0.09 0.05
Matches are distributed among these distances:
103 29 0.03
104 91 0.10
105 224 0.25
106 313 0.35
107 154 0.17
108 39 0.04
111 45 0.05
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.27
Consensus pattern (105 bp):
AGATCAACTCTGATCAACAAAAACTTCTTGAAATGAGATCAACTCTGATCATCAAAAACTTCTTG
AAATGAGATCAACTCTGATCATAAAAAACTTCTTGAAATG
Found at i:9559 original size:16 final size:15
Alignment explanation
Indices: 9538--9569 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
9528 TTCTTTCACA
9538 TTTTCTTTTTTCTTTT
1 TTTTCTTTTTT-TTTT
9554 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
9569 T
1 T
9570 GCTTTCGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:18281 original size:30 final size:31
Alignment explanation
Indices: 18241--18314 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 31
18231 TTTGGCGCCG
18241 TTGCC-GGGGAAGGGTAACTTTTTCTGGTAT
1 TTGCCAGGGGAAGGGTAACTTTTTCTGGTAT
* *
18271 TTGTCA-GGGAAGGGTAACTTTTTCTGGTTT
1 TTGCCAGGGGAAGGGTAACTTTTTCTGGTAT
18301 TTGCCAGGGGAAGG
1 TTGCCAGGGGAAGG
18315 AAAATAGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 32 0.82
31 7 0.18
ACGTcount: A:0.18, C:0.12, G:0.35, T:0.35
Consensus pattern (31 bp):
TTGCCAGGGGAAGGGTAACTTTTTCTGGTAT
Found at i:20878 original size:22 final size:22
Alignment explanation
Indices: 20853--20894 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
20843 TCGCGCCACT
**
20853 ACCAAGCCATTACCGGCCATAC
1 ACCAAGCCACCACCGGCCATAC
*
20875 ACCATGCCACCACCGGCCAT
1 ACCAAGCCACCACCGGCCAT
20895 GCTCGTGCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.45, G:0.14, T:0.12
Consensus pattern (22 bp):
ACCAAGCCACCACCGGCCATAC
Found at i:27786 original size:27 final size:28
Alignment explanation
Indices: 27755--27828 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
27745 AAGTTAACCT
*
27755 AAAATGACCAAAATGCCCTTAGA-CGTG
1 AAAATGACCAAAATGCCCCTAGATCGTG
* * * * *
27782 CAAATGACTAAAATTCCCCTGGATCTTG
1 AAAATGACCAAAATGCCCCTAGATCGTG
27810 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
27829 CTAGTTGATC
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 18 0.49
28 19 0.51
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTAGATCGTG
Found at i:29188 original size:47 final size:45
Alignment explanation
Indices: 29137--29914 Score: 191
Period size: 47 Copynumber: 16.1 Consensus size: 45
29127 AACTAAAGAG
**
29137 TAAAAGAAGAAGTAAACAGAGGCTAGTTTAATTCAGAGTAATTAAAC
1 TAAAAGAAGAAGTAAA-AGAAAC-AGTTTAATTCAGAGTAATTAAAC
*
29184 TAAAAAGCAAG-AG-AAGAAGAAAAGAGTTTAATTCAGAGTAATTAAAC
1 T-AAAAG-AAGAAGTAA-AAG-AAACAGTTTAATTCAGAGTAATTAAAC
29231 -AAAAG-AGCAA-TAGAAGAAGAAAACAGTTTAATTCAGAGTAATTAAAC
1 TAAAAGAAG-AAGT--AA-AAG-AAACAGTTTAATTCAGAGTAATTAAAC
* *
29278 TAAAAAGCAAG-AG-AAGAAGAAAAGAGTTTAATTCGGAGTAATTAAAC
1 T-AAAAG-AAGAAGTAA-AAG-AAACAGTTTAATTCAGAGTAATTAAAC
* *
29325 TAAAGAGCAAG-AG-AAGAAGAAAAGAGTTTAATTCTTG-GTAATTAAAC
1 TAAA-AG-AAGAAGTAA-AAG-AAACAGTTTAATTC-AGAGTAATTAAAC
* * * * *
29372 TAAAGAGTAAAAGAAGAAGTAAACAAAGGTTAGTTTAATTCTGGGTAATTAAAC
1 TAAA-AG---AAGAAGTA--AAAGAAA---CAGTTTAATTCAGAGTAATTAAAC
* *
29426 TAAAAAGTAAGAGGAG-AAAA-AAAGGAGTTTAATT-ATGGGTAATTAAAC
1 T-AAAAG-AAGA--AGTAAAAGAAA-CAGTTTAATTCA-GAGTAATTAAAC
*
29474 TAAAGAGTAAGAA--AAGAAGAAAACAGTTTAATTCTTG-GTAATTAAAC
1 TAAA-AG-AAGAAGTAA-AAG-AAACAGTTTAATTC-AGAGTAATTAAAC
* * * * * *
29521 TAAAGAGTAAAAGAAGAAGTGAACAGAGACTAGTTTAGTTCTGGGTAATTAAAA
1 -------TAAAAGAAGAAGT-AAAAGAAAC-AGTTTAATTCAGAGTAATTAAAC
* * *
29575 TAAAAAGTAAGAAG-AAAAG----AGTTTAATTCCGGGTAATTAAAT
1 T-AAAAG-AAGAAGTAAAAGAAACAGTTTAATTCAGAGTAATTAAAC
* * *
29617 TAGAAAGTAAG-AG-AAGAAGGAAAGAGTTTAATTCTGGGTAATTAAAC
1 TA-AAAG-AAGAAGTAA-AA-GAAACAGTTTAATTCAGAGTAATTAAAC
* *
29664 TAAAAAGCAAG-AG-AAGAAGAAAACAGTGTTAAACAATTCTGGGTAATTAAAC
1 T-AAAAG-AAGAAGTAA-AAG-AAACAGT-TT----AATTCAGAGTAATTAAAC
** * *
29716 TAAAGAGTAAAAGAAGAAGTAAACAGAGGCTAGTTTAATTCCGGGTAATTAAAC
1 -------TAAAAGAAGAAGTAAA-AGAAAC-AGTTTAATTCAGAGTAATTAAAC
29770 TAATAAGTAAG-AG-AAGAAGGAAACAGTTTAATTCTAG-GTAATTAAAC
1 TAA-AAG-AAGAAGTAA-AA-GAAACAGTTTAATTC-AGAGTAATTAAAC
* * * *
29817 TAGAAAGTAAG-AG-AAGAAGAAAAGAGTTTAACTCTGGGTAATTAAAC
1 TA-AAAG-AAGAAGTAA-AAG-AAACAGTTTAATTCAGAGTAATTAAAC
* *
29864 TAAAGAGCAAG-AG-AAGAGGAAAACAGTTTAATTCTTG-GTAATTAAAC
1 TAAA-AG-AAGAAGTAA-AAG-AAACAGTTTAATTC-AGAGTAATTAAAC
29911 TAAA
1 TAAA
29915 GAGTAAAAGA
Statistics
Matches: 605, Mismatches: 41, Indels: 170
0.74 0.05 0.21
Matches are distributed among these distances:
41 5 0.01
42 31 0.05
43 3 0.00
45 8 0.01
46 11 0.02
47 314 0.52
48 64 0.11
49 21 0.03
50 5 0.01
51 9 0.01
52 29 0.05
53 11 0.02
54 66 0.11
55 5 0.01
57 3 0.00
58 12 0.02
59 8 0.01
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.23
Consensus pattern (45 bp):
TAAAAGAAGAAGTAAAAGAAACAGTTTAATTCAGAGTAATTAAAC
Found at i:29409 original size:195 final size:190
Alignment explanation
Indices: 29091--30061 Score: 1120
Period size: 195 Copynumber: 5.0 Consensus size: 190
29081 TAAAAAAATT
29091 AAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG
1 AAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGT-AACAG
* * * * *
29156 AGGCTAGTTTAATTCAGAGTAATTAAACTAAAAAGCAAGAGAAGAAGAAAAGAGTTTAATTCAGA
65 A-GC-AGTTTAATTCTGGGTAATTAAACT-AAAAGTAAAAGAAGAAGAAAAGAGTTTAATTCAGG
* * * * *
29221 GTAATTAAACAAAAGAGCAATAGAAGAAGAAAACAGTTTAATTCAGAGTAATTAAACTAAAAAGC
127 GTAATTAAACAAAA-AGTAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAAAGC
* * * *
29286 AAGAGAAGAAGAAAAGAGTTTAATTC-GGAGTAATTAAACTAAAGAGCAAGAGAAGAAG-AA-A-
1 AAGAGAAGAAGAAAACAGTTTAATTCTTG-GTAATTAAACTAAAGAGTAAAAGAAGAAGTAACAG
*
29347 AG-AGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGGTTAGTTTAAT
65 AGCAGTTTAATTCTGGGTAATTAAACTAAA-AGTAAAAGAAGAAG---A-AAA-G--AGTTTAAT
* * * *
29411 TCTGGGTAATTAAACTAAAAAGTAAGAGGAGAAAAAAAGGAGTTTAATTATGGGTAATTAAACTA
122 TCAGGGTAATTAAAC-AAAAAGTAAGAGAAGAAGAAAA-GAGTTTAATTCTGGGTAATTAAACTA
* *
29476 AAGAGT
185 AAAAGC
*
29482 AAGAAAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTGAACAG
1 AAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGT-AACAG
* * *
29547 AGACTAGTTTAGTTCTGGGTAATT-AA--AATA--AAAAGTAAGAAGAAAAGAGTTTAATTCCGG
65 AG-C-AGTTTAATTCTGGGTAATTAAACTAAAAGTAAAAG-AAGAAGAAAAGAGTTTAATTCAGG
* * *
29607 GTAATTAAATTAGAAAGTAAGAGAAGAAGGAAAGAGTTTAATTCTGGGTAATTAAACTAAAAAGC
127 GTAATTAAA-CAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAAAGC
*
29672 AAGAGAAGAAGAAAACAGTGTTAAACAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTA
1 AAGAGAAGAAGAAAACAGT-TT----AATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGT-
* * * *
29737 AACAGAGGCTAGTTTAATTCCGGGTAATTAAACTAATAAGTAAGAGAAGAAGGAAACAGTTTAAT
60 AACAGA-GC-AGTTTAATTCTGGGTAATTAAACTAA-AAGTAAAAGAAGAAGAAAAGAGTTTAAT
* *
29802 TCTA-GGTAATTAAACTAGAAAGTAAGAGAAGAAGAAAAGAGTTTAACTCTGGGTAATTAAACTA
122 TC-AGGGTAATTAAAC-AAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTA
*
29866 AAGAGC
185 AAAAGC
*
29872 AAGAGAAGAGGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTACACAG
1 AAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTA-ACAG
*
29937 AGCCTAGTTTAATTCTGGGTAATTAAACTATAAAGTAAAAGTAGAAGAAAAGAGTTTAATT-ATG
65 AG-C-AGTTTAATTCTGGGTAATTAAACTA-AAAGTAAAAGAAGAAGAAAAGAGTTTAATTCA-G
* * * * * *
30001 GGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAATTTGATTCTGGGTAATTAAGCTAA
126 GGTAATTAAAC-AAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAA
30062 GAAGTAAAAG
Statistics
Matches: 669, Mismatches: 67, Indels: 80
0.82 0.08 0.10
Matches are distributed among these distances:
187 3 0.00
188 33 0.05
190 48 0.07
191 43 0.06
192 4 0.01
193 5 0.01
194 6 0.01
195 296 0.44
196 85 0.13
197 6 0.01
198 10 0.01
199 5 0.01
200 102 0.15
201 4 0.01
202 2 0.00
203 17 0.03
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.23
Consensus pattern (190 bp):
AAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAACAGA
GCAGTTTAATTCTGGGTAATTAAACTAAAAGTAAAAGAAGAAGAAAAGAGTTTAATTCAGGGTAA
TTAAACAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAAAGC
Found at i:29599 original size:42 final size:42
Alignment explanation
Indices: 29552--29683 Score: 149
Period size: 42 Copynumber: 3.0 Consensus size: 42
29542 AACAGAGACT
*
29552 AGTTTAGTTCTGGGTAATTAAAATAAAAAGTAAGAAGAAAAG
1 AGTTTAATTCTGGGTAATTAAAATAAAAAGTAAGAAGAAAAG
* * *
29594 AGTTTAATTCCGGGTAATTAAATTAGAAAGTAAGAGAAGAAGGAAAG
1 AGTTTAATTCTGGGTAATTAAAATAAAAAGT-A-AGAAG-A--AAAG
* *
29641 AGTTTAATTCTGGGTAATTAAACTAAAAAGCAAG-AGAAGAAG
1 AGTTTAATTCTGGGTAATTAAAATAAAAAGTAAGAAGAA-AAG
29683 A
1 A
29684 AAACAGTGTT
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
41 1 0.01
42 31 0.41
43 2 0.03
44 7 0.09
45 3 0.04
46 1 0.01
47 31 0.41
ACGTcount: A:0.48, C:0.05, G:0.23, T:0.24
Consensus pattern (42 bp):
AGTTTAATTCTGGGTAATTAAAATAAAAAGTAAGAAGAAAAG
Found at i:29915 original size:47 final size:46
Alignment explanation
Indices: 29747--30073 Score: 366
Period size: 47 Copynumber: 6.8 Consensus size: 46
29737 AACAGAGGCT
* *
29747 AGTTTAATTCCGGGTAATTAAACTAATAAGTAAGAGAAGAAGGAAAC
1 AGTTTAATTCTGGGTAATTAAACTAA-AAGTAAGAGAAGAAGAAAAC
* *
29794 AGTTTAATTCTAGGTAATTAAACTAGAAAGTAAGAGAAGAAGAAAAG
1 AGTTTAATTCTGGGTAATTAAACTA-AAAGTAAGAGAAGAAGAAAAC
* * *
29841 AGTTTAACTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAGGAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAA-AGTAAGAGAAGAAGAAAAC
* *
29888 AGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTACACAGAGCC
1 AGTTTAATTCTGGGTAATTAAACTAAA-AGTAAGAGAAGAAG-A-A-A-A--C
* * *
29941 TAGTTTAATTCTGGGTAATTAAACTATAAAGTAAAAGTAGAAGAAAAG
1 -AGTTTAATTCTGGGTAATTAAACTA-AAAGTAAGAGAAGAAGAAAAC
* *
29989 AGTTTAATTATGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
1 AGTTTAATTCTGGGTAATTAAACTAAA-AGTAAGAGAAGAAGAAAAC
* * * *
30036 AATTTGATTCTGGGTAATTAAGCTAAGAAGTAAAAGAA
1 AGTTTAATTCTGGGTAATTAAACTAA-AAGTAAGAGAA
30074 AGAGTAATCA
Statistics
Matches: 240, Mismatches: 28, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
46 4 0.02
47 186 0.77
48 3 0.01
49 1 0.00
50 2 0.01
51 2 0.01
52 1 0.00
53 2 0.01
54 37 0.15
55 2 0.01
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (46 bp):
AGTTTAATTCTGGGTAATTAAACTAAAAGTAAGAGAAGAAGAAAAC
Found at i:30092 original size:22 final size:22
Alignment explanation
Indices: 30061--30218 Score: 192
Period size: 22 Copynumber: 7.2 Consensus size: 22
30051 AATTAAGCTA
30061 AGAAGTAAAAGAAAGAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
* *
30083 AGGAGTAAAAGGAAGAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
* * *
30105 AAAAGCAGAAGAAAGAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
* *
30127 AG-AGTAAAAGGAAGAATAATC
1 AGAAGTAAAAGAAAGAGTAATC
* * *
30148 AAAAGCAAAAGAAAGAGTGATC
1 AGAAGTAAAAGAAAGAGTAATC
* * *
30170 AGAAGCATAAGAAAGAATAATC
1 AGAAGTAAAAGAAAGAGTAATC
30192 AGAAGTAAAAGAAAGAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
30214 AGAAG
1 AGAAG
30219 ATTAGAGTGA
Statistics
Matches: 111, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
21 16 0.14
22 95 0.86
ACGTcount: A:0.58, C:0.06, G:0.24, T:0.12
Consensus pattern (22 bp):
AGAAGTAAAAGAAAGAGTAATC
Found at i:30147 original size:65 final size:66
Alignment explanation
Indices: 30061--30218 Score: 219
Period size: 65 Copynumber: 2.4 Consensus size: 66
30051 AATTAAGCTA
* * * *
30061 AGAAGTAAAAGAAAGAGTAATCAGGAGTAAAAGGAAGAGTAATCAAAAGCAGAAGAAAGAGTAAT
1 AGAAGTAAAAGAAAGAGTAATCAGAAGCAAAAGAAAGAGTAATCAAAAGCAGAAGAAAGAATAAT
30126 C
66 C
* * * * * *
30127 AG-AGTAAAAGGAAGAATAATCAAAAGCAAAAGAAAGAGTGATCAGAAGCATAAGAAAGAATAAT
1 AGAAGTAAAAGAAAGAGTAATCAGAAGCAAAAGAAAGAGTAATCAAAAGCAGAAGAAAGAATAAT
30191 C
66 C
30192 AGAAGTAAAAGAAAGAGTAATCAGAAG
1 AGAAGTAAAAGAAAGAGTAATCAGAAG
30219 ATTAGAGTGA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
65 55 0.71
66 23 0.29
ACGTcount: A:0.58, C:0.06, G:0.24, T:0.12
Consensus pattern (66 bp):
AGAAGTAAAAGAAAGAGTAATCAGAAGCAAAAGAAAGAGTAATCAAAAGCAGAAGAAAGAATAAT
C
Found at i:30202 original size:44 final size:44
Alignment explanation
Indices: 30067--30218 Score: 216
Period size: 44 Copynumber: 3.5 Consensus size: 44
30057 GCTAAGAAGT
* *
30067 AAAAGAAAGAGTAATCAGGAGTAAAAGGAAGAGTAATCAAAAGC
1 AAAAGAAAGAGTAATCAGAAGTAAAAGGAAGAATAATCAAAAGC
*
30111 AGAAGAAAGAGTAATCAG-AGTAAAAGGAAGAATAATCAAAAGC
1 AAAAGAAAGAGTAATCAGAAGTAAAAGGAAGAATAATCAAAAGC
* * * * * *
30154 AAAAGAAAGAGTGATCAGAAGCATAAGAAAGAATAATCAGAAGT
1 AAAAGAAAGAGTAATCAGAAGTAAAAGGAAGAATAATCAAAAGC
30198 AAAAGAAAGAGTAATCAGAAG
1 AAAAGAAAGAGTAATCAGAAG
30219 ATTAGAGTGA
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 40 0.41
44 57 0.59
ACGTcount: A:0.58, C:0.07, G:0.24, T:0.12
Consensus pattern (44 bp):
AAAAGAAAGAGTAATCAGAAGTAAAAGGAAGAATAATCAAAAGC
Found at i:30287 original size:47 final size:47
Alignment explanation
Indices: 30192--30292 Score: 129
Period size: 47 Copynumber: 2.2 Consensus size: 47
30182 AAGAATAATC
* *
30192 AGAAGTAAAAGAAAGAGTAATCAGAAGATTAGAGTGATTAAGCTAAA
1 AGAAGTAAAAGAAAGAGTAATCAGAAGATAAGAGTAATTAAGCTAAA
* *
30239 AGAAGTAAAAGCAAGAGTAATCAGTAG-TAAG-GTTAATTAAGCT-AA
1 AGAAGTAAAAGAAAGAGTAATCAGAAGATAAGAG-TAATTAAGCTAAA
30284 A-AAGTAAAA
1 AGAAGTAAAA
30293 AGTAATAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
44 8 0.16
45 4 0.08
46 12 0.24
47 25 0.51
ACGTcount: A:0.53, C:0.05, G:0.22, T:0.20
Consensus pattern (47 bp):
AGAAGTAAAAGAAAGAGTAATCAGAAGATAAGAGTAATTAAGCTAAA
Done.