Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012042.1 Corchorus olitorius cultivar O-4 contig12075, 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: 20737
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:634 original size:54 final size:54
Alignment explanation
Indices: 569--1683 Score: 809
Period size: 54 Copynumber: 20.8 Consensus size: 54
559 TGGATCAAAT
* *
569 TGGAGATCAACTCTGATCATCGAAAACTTCTTAAAATGACCGCACCGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * *
623 CGGAGATCAACTCTGATCTTCGAAAACTTCTTAAAACGACTGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
677 TGGAGATCAACTCTGATCATCGAAGACTTCTTAAAATGACTGCACCGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
731 TGGAGATCAACTCTGATCTTTGAAAACTTCTTGAAACGATCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
785 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGGAAGGACTGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
839 TGGATATCAACTCTGATCTTCGAAAACTTCTTGGAAGGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * * *
893 TGGATATCAACTCTGATCATTGAAAACTTTTTTG-AATGACCACACTGGATAATC
1 TGGAGATCAACTCTGATCATCGAAAAC-TTCTTGAAATGACCGCACTGGATCATC
* * *
947 TGG-GATCAACTCTGATCA-CTGGAAACTTCTTCAAATGACAGCACTGGATCATC
1 TGGAGATCAACTCTGATCATC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * * *
1000 T-GAGGATCAACTCTAATCATTGAAAACTTCTTTGGAATGACCGCACTGGATCATG
1 TGGA-GATCAACTCTGATCATCGAAAACTTC-TTGAAATGACCGCACTGGATCATC
* * * *
1055 TAGG-GATCAACCCTGATC-TCTAAAAACTTCTT-AGAATGACCGCATTGGGTCATC
1 T-GGAGATCAACTCTGATCATC-GAAAACTTCTTGA-AATGACCGCACTGGATCATC
* * * *
1109 TAG-GATCGACTCTG---ATC--AAACTTATTGGAATGACCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
* ** * *
1157 TGGGGATCAACTCTGATCA-CTGAAAACTTCTTGAAATGATTGCACTAGATCATT
1 TGGAGATCAACTCTGATCATC-GAAAACTTCTTGAAATGACCGCACTGGATCATC
* * *
1211 TGGGGATCAACTCTGATCAT-TAAACACTTCTTGAAATGATCGCACTGGATCATC
1 TGGAGATCAACTCTGATCATCGAAA-ACTTCTTGAAATGACCGCACTGGATCATC
* * * * *
1265 TAGG-GATCAACTCTGATC-TCTAAAAACTTCTACGAAAGGTA--ACACCGGATCATC
1 T-GGAGATCAACTCTGATCATC-GAAAACTTCT-TGAAATG-ACCGCACTGGATCATC
* * * *
1319 TGAAGATCAACT-TAGAT-TTCTGAAAGCTT-TATGAAA-GACCGCA-TAGGGTCATC
1 TGGAGATCAACTCT-GATCATC-GAAAACTTCT-TGAAATGACCGCACT-GGATCATC
* * * * *
1372 AT-AAAATCAACT-TAAATC-TCTGAAAACTTCTATGAAA-GACCGCACAGGGTCATC
1 -TGGAGATCAACTCT-GATCATC-GAAAACTTCT-TGAAATGACCGCACTGGATCATC
* * * * * * *
1426 TGAAGATCAACT-TAAACCTAT-GAAAACTTCTATGAAA-GACCGAACAGGGTTATC
1 TGGAGATCAACTCT-GATC-ATCGAAAACTTCT-TGAAATGACCGCACTGGATCATC
* * * * * * *
1480 TGAAGATCAACT-TAAACCTCTGAAAACTTCTATGAAA-GACCGCACAGGGTCATT
1 TGGAGATCAACTCTGATCATC-GAAAACTTCT-TGAAATGACCGCACTGGATCATC
* * * * * * *
1534 TGAAGATCAACT-TAAACCTCTGAAAGCTTCTATGAAAT-ACCGCACAGGGTCATC
1 TGGAGATCAACTCTGATCATC-GAAAACTTCT-TGAAATGACCGCACTGGATCATC
* * * *
1588 TGAAGATCAACT-TAAATC-TCTGAAAACTTCTATGAAAT-ACCGCACAGGGTCATC
1 TGGAGATCAACTCT-GATCATC-GAAAACTTCT-TGAAATGACCGCACTGGATCATC
* *
1642 TGAAGATCAACT-TAAATC-TCTGAAAACTTCTATGAAA-GACCG
1 TGGAGATCAACTCT-GATCATC-GAAAACTTCT-TGAAATGACCG
1684 TGCAGGGTTA
Statistics
Matches: 914, Mismatches: 102, Indels: 90
0.83 0.09 0.08
Matches are distributed among these distances:
48 28 0.03
49 10 0.01
51 4 0.00
52 8 0.01
53 95 0.10
54 707 0.77
55 59 0.06
56 2 0.00
57 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (54 bp):
TGGAGATCAACTCTGATCATCGAAAACTTCTTGAAATGACCGCACTGGATCATC
Found at i:1690 original size:54 final size:54
Alignment explanation
Indices: 1314--1776 Score: 648
Period size: 54 Copynumber: 8.6 Consensus size: 54
1304 TAACACCGGA
* * * *
1314 TCATCTGAAGATCAACTTAGATTTCTGAAAGCTT-TATGAAAGACCGCATAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
*
1367 TCATCAT-AAAATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
1 TCATC-TGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * *
1421 TCATCTGAAGATCAACTTAAACCTATGAAAACTTCTATGAAAGACCGAACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* *
1475 TTATCTGAAGATCAACTTAAACCTCTGAAAACTTCTATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * * *
1529 TCATTTGAAGATCAACTTAAACCTCTGAAAGCTTCTATGAAATACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
*
1583 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAATACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
**
1637 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGTGCAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * * * *
1691 TTATTTGAAGATCAACTTAAACCTCTTAAAACTTATATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* * *
1745 CCA--TGAACG-TTAACTTAGATCTCTGAAAACTT
1 TCATCTGAA-GATCAACTTAAATCTCTGAAAACTT
1777 TAGAAGATCA
Statistics
Matches: 371, Mismatches: 35, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
52 23 0.06
53 30 0.08
54 318 0.86
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (54 bp):
TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
Found at i:7092 original size:38 final size:39
Alignment explanation
Indices: 7015--7094 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 39
7005 ATCTTTTTGA
** * *
7015 AAAACATTTTTTCTCTTTTGAAAAGATTGCACTTTGAGG
1 AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
7054 AAAACATTTTTT-TCTTTTGAAAAGATCACACCTAGAGG
1 AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
7092 AAA
1 AAA
7095 GTTTCATTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 25 0.68
39 12 0.32
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (39 bp):
AAAACATTTTTTCTCTTTTGAAAAGATCACACCTAGAGG
Found at i:7298 original size:21 final size:21
Alignment explanation
Indices: 7274--7319 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
7264 CTTTCCTCCG
7274 TCTTTTGCTTTTTCAACT-TTT
1 TCTTTT-CTTTTTCAACTCTTT
*
7295 TCTTTTCTTTTTCAATTCTTT
1 TCTTTTCTTTTTCAACTCTTT
7316 TCTT
1 TCTT
7320 CTTTCTTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (21 bp):
TCTTTTCTTTTTCAACTCTTT
Found at i:7306 original size:20 final size:19
Alignment explanation
Indices: 7274--7339 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 19
7264 CTTTCCTCCG
7274 TCTTTTGCTTTTTCAACTTTT
1 TCTTTT-CTTTTTCAA-TTTT
7295 TCTTTTCTTTTTCAATTCTT
1 TCTTTTCTTTTTCAATT-TT
*
7315 T-TCTTCTTTCTTC-ATTTT
1 TCTTTTCTTT-TTCAATTTT
7333 TCTTTTC
1 TCTTTTC
7340 CTCTCCTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 3 0.08
19 16 0.40
20 15 0.38
21 6 0.15
ACGTcount: A:0.08, C:0.21, G:0.02, T:0.70
Consensus pattern (19 bp):
TCTTTTCTTTTTCAATTTT
Found at i:9581 original size:41 final size:41
Alignment explanation
Indices: 9536--9662 Score: 245
Period size: 41 Copynumber: 3.1 Consensus size: 41
9526 ATCTTTCTAC
*
9536 TGTTAGGAGCCCCTTTCTTTTACCAAGCCCATTACCTAGTT
1 TGTTAGGAGCCCATTTCTTTTACCAAGCCCATTACCTAGTT
9577 TGTTAGGAGCCCATTTCTTTTACCAAGCCCATTACCTAGTT
1 TGTTAGGAGCCCATTTCTTTTACCAAGCCCATTACCTAGTT
9618 TGTTAGGAGCCCATTTCTTTTACCAAGCCCATTACCTAGTT
1 TGTTAGGAGCCCATTTCTTTTACCAAGCCCATTACCTAGTT
9659 TGTT
1 TGTT
9663 GGGCTAAGCA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 85 1.00
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.38
Consensus pattern (41 bp):
TGTTAGGAGCCCATTTCTTTTACCAAGCCCATTACCTAGTT
Found at i:9591 original size:23 final size:23
Alignment explanation
Indices: 9561--9632 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
9551 TCTTTTACCA
9561 AGCCCATTACCTAGTTTGTTAGG
1 AGCCCATTACCTAGTTTGTTAGG
* ***
9584 AGCCCATT-TCT--TTTACCA--
1 AGCCCATTACCTAGTTTGTTAGG
9602 AGCCCATTACCTAGTTTGTTAGG
1 AGCCCATTACCTAGTTTGTTAGG
9625 AGCCCATT
1 AGCCCATT
9633 TCTTTTACCA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
18 8 0.22
19 2 0.06
20 4 0.11
21 4 0.11
22 2 0.06
23 16 0.44
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (23 bp):
AGCCCATTACCTAGTTTGTTAGG
Found at i:9607 original size:18 final size:18
Alignment explanation
Indices: 9584--9650 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 18
9574 GTTTGTTAGG
9584 AGCCCATTTCTTTTACCA
1 AGCCCATTTCTTTTACCA
* ***
9602 AGCCCATTACCTAGTTTGTTA
1 AGCCCATT-TCT--TTTACCA
9623 GGAGCCCATTTCTTTTACCA
1 --AGCCCATTTCTTTTACCA
9643 AGCCCATT
1 AGCCCATT
9651 ACCTAGTTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
18 16 0.44
19 2 0.06
20 4 0.11
21 4 0.11
22 2 0.06
23 8 0.22
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.36
Consensus pattern (18 bp):
AGCCCATTTCTTTTACCA
Found at i:9993 original size:95 final size:94
Alignment explanation
Indices: 9826--10015 Score: 371
Period size: 95 Copynumber: 2.0 Consensus size: 94
9816 TAACTTACAA
9826 GTCCAATACAAAAATAACCATAATTACATGCCAAAAAAAAAGAGAGAATACATAGAGGATTATTT
1 GTCCAATACAAAAATAACCATAATTACATGCCAAAAAAAAAGAGAGAATACATAGAGGATTATTT
9891 ACTACAATGCTAAATAAAGAGTACAGGAG
66 ACTACAATGCTAAATAAAGAGTACAGGAG
9920 GTCCAATACAAAAATAACCATAATTACATGCCAAAAAAAAGAGAGAGAATACATAGAGGATTATT
1 GTCCAATACAAAAATAACCATAATTACATGCCAAAAAAAA-AGAGAGAATACATAGAGGATTATT
9985 TACTACAATGCTAAATAAAGAGTACAGGAG
65 TACTACAATGCTAAATAAAGAGTACAGGAG
10015 G
1 G
10016 ATCACGTGAC
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 40 0.42
95 55 0.58
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.20
Consensus pattern (94 bp):
GTCCAATACAAAAATAACCATAATTACATGCCAAAAAAAAAGAGAGAATACATAGAGGATTATTT
ACTACAATGCTAAATAAAGAGTACAGGAG
Found at i:13223 original size:33 final size:33
Alignment explanation
Indices: 13181--13270 Score: 171
Period size: 33 Copynumber: 2.7 Consensus size: 33
13171 GAATTTCATC
*
13181 AAGTTTTAAATTGGGACAGTTCCCACCAGTTTT
1 AAGTTTTAAATTGGGAAAGTTCCCACCAGTTTT
13214 AAGTTTTAAATTGGGAAAGTTCCCACCAGTTTT
1 AAGTTTTAAATTGGGAAAGTTCCCACCAGTTTT
13247 AAGTTTTAAATTGGGAAAGTTCCC
1 AAGTTTTAAATTGGGAAAGTTCCC
13271 CGTTCAGTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (33 bp):
AAGTTTTAAATTGGGAAAGTTCCCACCAGTTTT
Found at i:18151 original size:54 final size:53
Alignment explanation
Indices: 18104--19275 Score: 806
Period size: 54 Copynumber: 21.8 Consensus size: 53
18094 TGGATCAAAT
* * *
18104 TGGAGATCAACTCTGATCATCGAAAACTTCTTGAACGACCACACTGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAATGACCGCACTGGATCATC
* * **
18157 TGGAGATCAACTCTGATCTTTGAAAACTTCTTGAAACGACCAG-AGCCAGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTG-AATGACC-GCA-CTGGATCATC
* * * * *
18212 TGAAGATCAATTCTCATCTTCGAAAACTTCTTGAAACGACCGCACCGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTG-AATGACCGCACTGGATCATC
* * *
18266 TAGAGATCAACTCTGATCTTCGAAAACTTCTCGGAA-GAACCGCACCGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCT-TGAATG-ACCGCACTGGATCATC
* * * * * * *
18320 TGGACATCTACTCTGAACTTCGAAAATTTCTCGGAAGGACCGCACTAGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCT-TGAATGACCGCACTGGATCATC
* * * *
18374 TAGAGATCAACTCTGATCATT-AAAAACTTCTCGAAATGACCGCACTGGATCATT
1 TGGAGATCAACTCTGATC-TTCGAAAACTTCTTG-AATGACCGCACTGGATCATC
* * * *
18428 TGGAGATCAATTCTGATCATT-GAAAACTTTTTGGAATGA-C-CACCGGATCACC
1 TGGAGATCAACTCTGATC-TTCGAAAACTTCTT-GAATGACCGCACTGGATCATC
* * *
18480 TGGAGATCAACTCTGGTCTTCGAAAACTTCTTGAAAAGACCGCACCGGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTG-AATGACCGCACTGGATCATC
* * *
18534 TGGAGATCAACTCTGATCTTCCAAAACTTCTTGGAA-GAACCGCATTGGATCATT
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTT-GAATG-ACCGCACTGGATCATC
* *
18588 TAGG-GATCAACTCTGATC-TCTACAAACTTCTTGGAATGACCGCACTGGGTCATC
1 T-GGAGATCAACTCTGATCTTCGA-AAACTTCTT-GAATGACCGCACTGGATCATC
* *** * * * *
18642 TGG-GATCAACTCCGATCAAAGAGAACTACTTGGAATGATCGCACTAGATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTT-GAATGACCGCACTGGATCATC
* * * *
18695 TGGGGATCAATTCTGATCATT-GAAAACTTTTTGGAATGA-C-CACCGGATCA-C
1 TGGAGATCAACTCTGATC-TTCGAAAACTTCTT-GAATGACCGCACTGGATCATC
** *
18746 TTGGAGATCAACTCT-AGTCTTCGAAAACTTCTTGAAAAAACCGCACCGGATCATC
1 -TGGAGATCAACTCTGA-TCTTCGAAAACTTCTTG-AATGACCGCACTGGATCATC
* * *
18801 TGGAGATCAACTCTGACCTTCGAAAACTTCTTGGAAGGACTGCACT-GATCATC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTT-GAATGACCGCACTGGATCATC
* * *
18854 TAGG-GATCAACTCTGATC-TCTAAAAACTTCTTGGAATGACTGCACTGGATCATT
1 T-GGAGATCAACTCTGATCTTC-GAAAACTTCTT-GAATGACCGCACTGGATCATC
* * * *
18908 TGGGGATCAACTCTGATCATT-AAAAACTTCTTGAAATGATCGCACTGGATCATT
1 TGGAGATCAACTCTGATC-TTCGAAAACTTCTTG-AATGACCGCACTGGATCATC
* * * *** **
18962 TAGG-GATCAACTCTGATC-TCTAAAAACTTCTACGAAAGATAACACCAGATCATC
1 T-GGAGATCAACTCTGATCTTC-GAAAACTTCT-TGAATGACCGCACTGGATCATC
* * * * *
19016 TGAAGATCAACT-TAGAT-TTCTGAAAGCTT-TATGAAAGACCGCACAGGGTCATC
1 TGGAGATCAACTCT-GATCTTC-GAAAACTTCT-TGAATGACCGCACTGGATCATC
* * * * * *
19069 AT-AAAATCAACT-TAAATC-TCTGAAAACTTCTATGAAAGACCGCACAGGGTCATC
1 -TGGAGATCAACTCT-GATCTTC-GAAAACTTCT-TGAATGACCGCACTGGATCATC
* * * * * * *
19123 TGAAGATCAACT-TAAACCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATC
1 TGGAGATCAACTCTGATCTTC-GAAAACTTCT-TGAATGACCGCACTGGATCATC
* * * * *
19177 TGAAGATCAACT-TAAATC-TCTGAAAACTTCTATGAAAGACCGCACAAGG-TTATC
1 TGGAGATCAACTCT-GATCTTC-GAAAACTTCT-TGAATGACCGCAC-TGGATCATC
* * * * *
19231 TGAAGATCAACT-TAAACCTCTGAAAACTTCTATGAAAGACCGCAC
1 TGGAGATCAACTCTGATCTTC-GAAAACTTCT-TGAATGACCGCAC
19276 AGGGCCATGA
Statistics
Matches: 953, Mismatches: 113, Indels: 105
0.81 0.10 0.09
Matches are distributed among these distances:
51 8 0.01
52 77 0.08
53 181 0.19
54 619 0.65
55 67 0.07
56 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (53 bp):
TGGAGATCAACTCTGATCTTCGAAAACTTCTTGAATGACCGCACTGGATCATC
Found at i:18775 original size:213 final size:213
Alignment explanation
Indices: 18104--18980 Score: 820
Period size: 213 Copynumber: 4.1 Consensus size: 213
18094 TGGATCAAAT
* *
18104 TGGAGATCAACTCTGATCATCGAAAACTTCTT-GAACG-ACCACACTGGATCATCT-GGAGATCA
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGGAA-GAACCGCACTGGATCATCTAGG-GATCA
* * * ** * * *
18166 ACTCTGATC-TTTGAAAACTTCTTGAAACGACCAG-AGCCAGATCATCTGAAGATCAATTCTCAT
64 ACTCTGATCATCT-AAAACTTCTTGGAATGACC-GCA-CTGGATCATCTG-GGATCAACTCTGAT
*** * * * *
18229 CTTCGAAAACTTCTTGAAACGACCGCACCGGATCATCTAGAGATCAACTCTGATCTTCGAAAACT
125 CAAAG-AAACTTCTTGGAATGA-CGCACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAACT
* *
18294 TCTCGGAA-GAACCGCACCGGATCATC
188 TCTTGAAATG-ACCGCACCGGATCATC
* * * * * * * *
18320 TGGACATCTACTCTGAACTTCGAAAATTTCTCGGAAGGACCGCACTAGATCATCTAGAGATCAAC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGGAAGAACCGCACTGGATCATCTAGGGATCAAC
* * * * **
18385 TCTGATCAT-TAAAAACTTCTCGAAATGACCGCACTGGATCATTTGGAGATCAATTCTGATCATT
66 TCTGATCATCT-AAAACTTCTTGGAATGACCGCACTGGATCATCTGG-GATCAACTCTGATCAAA
* * * *
18449 GAAAACTTTTTGGAATGAC-CACCGGATCACCTGGAGATCAACTCTGGTCTTCGAAAACTTCTTG
129 G-AAACTTCTTGGAATGACGCACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAACTTCTTG
*
18513 AAAAGACCGCACCGGATCATC
193 AAATGACCGCACCGGATCATC
* * *
18534 TGGAGATCAACTCTGATCTTCCAAAACTTCTTGGAAGAACCGCATTGGATCATTTAGGGATCAAC
1 TGGAGATCAACTCTGATCTTCGAAAACTTCTTGGAAGAACCGCACTGGATCATCTAGGGATCAAC
* *
18599 TCTGATC-TCTACAAACTTCTTGGAATGACCGCACTGGGTCATCTGGGATCAACTCCGATCAAAG
66 TCTGATCATCTA-AAACTTCTTGGAATGACCGCACTGGATCATCTGGGATCAACTCTGATCAAAG
* * * * *
18663 AGAACTACTTGGAATGATCGCACTAGATCATCTGGGGATCAATTCTGATCATT-GAAAACTTTTT
130 A-AACTTCTTGGAATGA-CGCACTGGATCATCTGGAGATCAACTCTGATC-TTCGAAAACTTCTT
*
18727 GGAATGA-C-CACCGGATCA-C
192 GAAATGACCGCACCGGATCATC
* * *
18746 TTGGAGATCAACTCT-AGTCTTCGAAAACTTCTTGAAAAAACCGCACCGGATCATCT-GGAGATC
1 -TGGAGATCAACTCTGA-TCTTCGAAAACTTCTTGGAAGAACCGCACTGGATCATCTAGG-GATC
* * * * *
18809 AACTCTGACCTTCGAAAACTTCTTGGAAGGACTGCACT-GATCATCTAGGGATCAACTCTGATCT
63 AACTCTGATCATCTAAAACTTCTTGGAATGACCGCACTGGATCATCT-GGGATCAACTCTGA--T
* * * *
18873 CTAA-AAACTTCTTGGAATGACTGCACTGGATCATTTGGGGATCAACTCTGATCATT-AAAAACT
125 CAAAGAAACTTCTTGGAATGAC-GCACTGGATCATCTGGAGATCAACTCTGATC-TTCGAAAACT
* * *
18936 TCTTGAAATGATCGCACTGGATCATT
188 TCTTGAAATGACCGCACCGGATCATC
18962 TAGG-GATCAACTCTGATCT
1 T-GGAGATCAACTCTGATCT
18981 CTAAAAACTT
Statistics
Matches: 556, Mismatches: 79, Indels: 53
0.81 0.11 0.08
Matches are distributed among these distances:
212 13 0.02
213 193 0.35
214 158 0.28
215 68 0.12
216 71 0.13
217 51 0.09
218 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (213 bp):
TGGAGATCAACTCTGATCTTCGAAAACTTCTTGGAAGAACCGCACTGGATCATCTAGGGATCAAC
TCTGATCATCTAAAACTTCTTGGAATGACCGCACTGGATCATCTGGGATCAACTCTGATCAAAGA
AACTTCTTGGAATGACGCACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAACTTCTTGAAA
TGACCGCACCGGATCATC
Found at i:18990 original size:267 final size:267
Alignment explanation
Indices: 18076--18979 Score: 1135
Period size: 267 Copynumber: 3.4 Consensus size: 267
18066 ACGGAAACTT
* ** **
18076 TTCTTGGAGTGACCATACTGGATCAAAT-TGGAGATCAACTCTGATCATCGAAAACTTCTTG-AA
1 TTCTTGGAATGACCGCACTGGATC--ATCTGGAGATCAACTCTGATCATTAAAAACTTCTTGAAA
* * * * * *
18139 CGACCACACTGGATCATCTGGAGATCAACTCTGATCTTTGAAAACTTCTTGAAACGACCAGAGCC
64 TGACCGCACTGGATCATCTGGAGATCAACTCTGATCATTGAAAACTTTTTGGAATGACC--A-CC
* * * *
18204 AGATCA-TCTGAAGATCAATTCTCA-TCTTCGAAAACTTCTTGAAACGACCGCACCGGATCATCT
126 GGATCACT-TGGAGATCAACTCT-AGTCTTCGAAAACTTCTTGAAAAGACCGCACCGGATCATCT
* * * * *
18267 AGAGATCAACTCTGATCTTCGAAAACTTCTCGGAAGAACCGCACCGGATCATCT-GGACATCTAC
189 GGAGATCAACTCTGATCTTCGAAAACTTCTTGGAAGAACCGCA-CTGATCATCTAGG-GATCAAC
* * *
18331 TCTGAACT-TCGAAAAT
252 TCTGATCTCT-AAAAAC
* * * * *
18347 TTCTCGGAAGGACCGCACTAGATCATCTAGAGATCAACTCTGATCATTAAAAACTTCTCGAAATG
1 TTCTTGGAATGACCGCACTGGATCATCTGGAGATCAACTCTGATCATTAAAAACTTCTTGAAATG
* *
18412 ACCGCACTGGATCATTTGGAGATCAATTCTGATCATTGAAAACTTTTTGGAATGACCACCGGATC
66 ACCGCACTGGATCATCTGGAGATCAACTCTGATCATTGAAAACTTTTTGGAATGACCACCGGATC
* *
18477 ACCTGGAGATCAACTCTGGTCTTCGAAAACTTCTTGAAAAGACCGCACCGGATCATCTGGAGATC
131 ACTTGGAGATCAACTCTAGTCTTCGAAAACTTCTTGAAAAGACCGCACCGGATCATCTGGAGATC
* * *
18542 AACTCTGATCTTCCAAAACTTCTTGGAAGAACCGCATTGGATCATTTAGGGATCAACTCTGATCT
196 AACTCTGATCTTCGAAAACTTCTTGGAAGAACCGCACT-GATCATCTAGGGATCAACTCTGATCT
*
18607 CTACAAAC
260 CTAAAAAC
* * * *
18615 TTCTTGGAATGACCGCACTGGGTCATCTGG-GATCAACTCCGATCA--AAGAGAACTACTTGGAA
1 TTCTTGGAATGACCGCACTGGATCATCTGGAGATCAACTCTGATCATTAA-A-AACTTCTTGAAA
* * * *
18677 TGATCGCACTAGATCATCTGGGGATCAATTCTGATCATTGAAAACTTTTTGGAATGACCACCGGA
64 TGACCGCACTGGATCATCTGGAGATCAACTCTGATCATTGAAAACTTTTTGGAATGACCACCGGA
*
18742 TCACTTGGAGATCAACTCTAGTCTTCGAAAACTTCTTGAAAAAACCGCACCGGATCATCTGGAGA
129 TCACTTGGAGATCAACTCTAGTCTTCGAAAACTTCTTGAAAAGACCGCACCGGATCATCTGGAGA
* * *
18807 TCAACTCTGACCTTCGAAAACTTCTTGGAAGGACTGCACTGATCATCTAGGGATCAACTCTGATC
194 TCAACTCTGATCTTCGAAAACTTCTTGGAAGAACCGCACTGATCATCTAGGGATCAACTCTGATC
18872 TCTAAAAAC
259 TCTAAAAAC
* * *
18881 TTCTTGGAATGACTGCACTGGATCATTTGGGGATCAACTCTGATCATTAAAAACTTCTTGAAATG
1 TTCTTGGAATGACCGCACTGGATCATCTGGAGATCAACTCTGATCATTAAAAACTTCTTGAAATG
* *
18946 ATCGCACTGGATCATTTAGG-GATCAACTCTGATC
66 ACCGCACTGGATCATCT-GGAGATCAACTCTGATC
18980 TCTAAAAACT
Statistics
Matches: 552, Mismatches: 68, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
265 2 0.00
266 60 0.11
267 235 0.43
268 147 0.27
269 8 0.01
270 29 0.05
271 71 0.13
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (267 bp):
TTCTTGGAATGACCGCACTGGATCATCTGGAGATCAACTCTGATCATTAAAAACTTCTTGAAATG
ACCGCACTGGATCATCTGGAGATCAACTCTGATCATTGAAAACTTTTTGGAATGACCACCGGATC
ACTTGGAGATCAACTCTAGTCTTCGAAAACTTCTTGAAAAGACCGCACCGGATCATCTGGAGATC
AACTCTGATCTTCGAAAACTTCTTGGAAGAACCGCACTGATCATCTAGGGATCAACTCTGATCTC
TAAAAAC
Found at i:19080 original size:161 final size:162
Alignment explanation
Indices: 18928--19278 Score: 417
Period size: 161 Copynumber: 2.2 Consensus size: 162
18918 CTCTGATCAT
* * * * * *
18928 TAAAAACTTCT-TGAAATGATCGCACTGGATCAT-TTAGGGATCAACTCT-GATCTCTAAAAACT
1 TAAAAACTTCTATGAAA-GACCGCACAGGATCATCTGA-AGATCAACT-TAAACCTCTAAAAACT
* * * *
18990 TCTACGAAAGATAACACCA-GATCATCTGAAGATCAACTTAGATTTCTGAAAGCTT-TATGAAAG
63 TCTACGAAAGACAACA-CAGGATCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAG
19053 ACCGCACAGGGTCATCATAAAATCAACTTAAATCTC
127 ACCGCACAGGGTCATCATAAAATCAACTTAAATCTC
* * *
19089 TGAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAAACCTCTGAAAACTTCT
1 TAAAAACTTCTATGAAAGACCGCACAGGATCATCTGAAGATCAACTTAAACCTCTAAAAACTTCT
* ** *
19154 ATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCG
66 ACGAAAGACAACACAGGATCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCG
* * * *
19219 CACAAGGTTATC-TGAAGATCAACTTAAACCTC
131 CACAGGGTCATCAT-AAAATCAACTTAAATCTC
*
19251 TGAAAACTTCTATGAAAGACCGCACAGG
1 TAAAAACTTCTATGAAAGACCGCACAGG
19279 GCCATGAACG
Statistics
Matches: 163, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
160 3 0.02
161 87 0.53
162 73 0.45
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (162 bp):
TAAAAACTTCTATGAAAGACCGCACAGGATCATCTGAAGATCAACTTAAACCTCTAAAAACTTCT
ACGAAAGACAACACAGGATCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCG
CACAGGGTCATCATAAAATCAACTTAAATCTC
Found at i:19080 original size:215 final size:216
Alignment explanation
Indices: 18869--19279 Score: 465
Period size: 215 Copynumber: 1.9 Consensus size: 216
18859 ATCAACTCTG
* * * * ** * *
18869 ATCTCTAAAAACTTCT-TGGAATGACTGCACTGGATCATTTGGGGATCAACTCTGATCAT-TAAA
1 ATCTCTAAAAACTTCTAT-GAAAGACCGCACAGGATCATCTGAAGATCAACT-TAAACATCTAAA
* * * * *
18932 AACTTCT-TGAAATGATCGCACTGGATCAT-TTAGGGATCAACTCT-GATCTCTAAAAACTTCTA
64 AACTTCTATGAAA-GACCGCACAGGATCATCTGA-AGATCAACT-TAAATCTCTAAAAACTTCTA
* * * ** *
18994 CGAAAGATAACACCAGATCATCTGAAGATCAACTTAGATTTCTGAAAGCTT-TATGAAAGACCGC
126 CGAAAGACAACACAAGATCATCTGAAGATCAACTTAAACCTCTGAAAACTTCTATGAAAGACCGC
19058 ACAGGGTCATCATAAAATCAACTTAA
191 ACAGGGTCATCATAAAATCAACTTAA
* * * *
19084 ATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAAACCTCTGAAAA
1 ATCTCTAAAAACTTCTATGAAAGACCGCACAGGATCATCTGAAGATCAACTTAAACATCTAAAAA
* * *
19149 CTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAA
66 CTTCTATGAAAGACCGCACAGGATCATCTGAAGATCAACTTAAATCTCTAAAAACTTCTACGAAA
** * *
19214 GACCGCACAAGGTTATCTGAAGATCAACTTAAACCTCTGAAAACTTCTATGAAAGACCGCACAGG
131 GACAACACAAGATCATCTGAAGATCAACTTAAACCTCTGAAAACTTCTATGAAAGACCGCACAGG
19279 G
196 G
19280 CCATGAACGT
Statistics
Matches: 160, Mismatches: 30, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
214 5 0.03
215 128 0.80
216 27 0.17
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (216 bp):
ATCTCTAAAAACTTCTATGAAAGACCGCACAGGATCATCTGAAGATCAACTTAAACATCTAAAAA
CTTCTATGAAAGACCGCACAGGATCATCTGAAGATCAACTTAAATCTCTAAAAACTTCTACGAAA
GACAACACAAGATCATCTGAAGATCAACTTAAACCTCTGAAAACTTCTATGAAAGACCGCACAGG
GTCATCATAAAATCAACTTAA
Found at i:19276 original size:54 final size:54
Alignment explanation
Indices: 19011--19311 Score: 459
Period size: 54 Copynumber: 5.6 Consensus size: 54
19001 TAACACCAGA
* * *
19011 TCATCTGAAGATCAACTTAGATTTCTGAAAGCTT-TATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
*
19064 TCATCAT-AAAATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
1 TCATC-TGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
*
19118 TCATCTGAAGATCAACTTAAACCTCTGAAAACTTCTATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
*
19172 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAAGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* *
19226 TTATCTGAAGATCAACTTAAACCTCTGAAAACTTCTATGAAAGACCGCACAGGG
1 TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
* *
19280 CCA--TGAACG-TCAACTTAGATCTCTGAAAACTT
1 TCATCTGAA-GATCAACTTAAATCTCTGAAAACTT
19312 TAAAAGATCG
Statistics
Matches: 229, Mismatches: 15, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
52 25 0.11
53 30 0.13
54 174 0.76
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (54 bp):
TCATCTGAAGATCAACTTAAATCTCTGAAAACTTCTATGAAAGACCGCACAGGG
Found at i:19276 original size:108 final size:108
Alignment explanation
Indices: 18977--19311 Score: 473
Period size: 108 Copynumber: 3.1 Consensus size: 108
18967 ATCAACTCTG
* * *** * * * ** *
18977 ATCTCTAAAAACTTCTACGAAAGATAACACCAGATCATCTGAAGATCAACTTAGATTTCTGAAAG
1 ATCTCTGAAAACTTCTATGAAAGACCGCACAAGGTCATCTGAAGATCAACTTAAACCTCTGAAAA
*
19042 CTT-TATGAAAGACCGCACAGGGTCATCAT-AAAATCAACTTAA
66 CTTCTATGAAAGACCGCACAGGGTCATC-TGAAGATCAACTTAA
*
19084 ATCTCTGAAAACTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAAACCTCTGAAAA
1 ATCTCTGAAAACTTCTATGAAAGACCGCACAAGGTCATCTGAAGATCAACTTAAACCTCTGAAAA
19149 CTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAA
66 CTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAA
*
19192 ATCTCTGAAAACTTCTATGAAAGACCGCACAAGGTTATCTGAAGATCAACTTAAACCTCTGAAAA
1 ATCTCTGAAAACTTCTATGAAAGACCGCACAAGGTCATCTGAAGATCAACTTAAACCTCTGAAAA
* *
19257 CTTCTATGAAAGACCGCACAGGGCCA--TGAACG-TCAACTTAG
66 CTTCTATGAAAGACCGCACAGGGTCATCTGAA-GATCAACTTAA
19298 ATCTCTGAAAACTT
1 ATCTCTGAAAACTT
19312 TAAAAGATCG
Statistics
Matches: 208, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
106 26 0.12
107 58 0.28
108 124 0.60
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.24
Consensus pattern (108 bp):
ATCTCTGAAAACTTCTATGAAAGACCGCACAAGGTCATCTGAAGATCAACTTAAACCTCTGAAAA
CTTCTATGAAAGACCGCACAGGGTCATCTGAAGATCAACTTAA
Done.