Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022050.1 Corchorus olitorius cultivar O-4 contig22083, 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: 59556
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2878 original size:137 final size:136
Alignment explanation
Indices: 2726--2986 Score: 477
Period size: 137 Copynumber: 1.9 Consensus size: 136
2716 AAGTTAAAAC
2726 TTAAAATTAAATAAAAAGTTTAAGAAGATATTTTAGATATGTTCTTTTGATGAAATAAAAAAACA
1 TTAAAATTAAATAAAAAGTTTAAGAAGATATTTTAGATATGTTCTTTTGATGAAATAAAAAAACA
*
2791 TGTTTACCCTTTAAAGGGATACTAAAATTTTAAAATTAAAAAGGATATTTTAGATATTTCGGAAA
66 TGTTTACCCTTTAAA-GGATACTAAAAATTTAAAATTAAAAAGGATATTTTAGATATTTCGGAAA
2856 TTTAAAG
130 TTTAAAG
* **
2863 TTAAAATTAAATAAAAAGTTTAAGAAGATGTTTTAGATATGTTCTTTTGATGAAATAAAAATGCA
1 TTAAAATTAAATAAAAAGTTTAAGAAGATATTTTAGATATGTTCTTTTGATGAAATAAAAAAACA
2928 TGTTTACCCTTTAAAGGATACTAAAAATTTAAAATTAAAAAGGATATTTTAGATATTTC
66 TGTTTACCCTTTAAAGGATACTAAAAATTTAAAATTAAAAAGGATATTTTAGATATTTC
2987 AGATAAAGGT
Statistics
Matches: 120, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
136 43 0.36
137 77 0.64
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.37
Consensus pattern (136 bp):
TTAAAATTAAATAAAAAGTTTAAGAAGATATTTTAGATATGTTCTTTTGATGAAATAAAAAAACA
TGTTTACCCTTTAAAGGATACTAAAAATTTAAAATTAAAAAGGATATTTTAGATATTTCGGAAAT
TTAAAG
Found at i:3040 original size:2 final size:2
Alignment explanation
Indices: 3033--3066 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
3023 AAAGATAAAG
*
3033 AT AT AT AT AT AT AT AT AT AT TT 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
3067 AAAGTACGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6018 original size:22 final size:21
Alignment explanation
Indices: 5882--6049 Score: 106
Period size: 22 Copynumber: 7.8 Consensus size: 21
5872 GACAGAAAGA
* *
5882 TTATCAAAAATT-ATAGGAAGG
1 TTATCAAAATTTCATAGG-TGG
* *
5903 TTA-CAAAATTTCATAGGAAAGT
1 TTATCAAAATTTCATAGG--TGG
* *
5925 TTATTAAAATTTCATAGTTAGG
1 TTATCAAAATTTCATAGGT-GG
* * * *
5947 TTATCAAAGTTTCTTATGGAGT
1 TTATCAAAATTTCATA-GGTGG
* * **
5969 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTCATAGGTGG
5990 TTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTCATA-GGTGG
* *
6012 TTATCAAAATTTAATAGGGTAG
1 TTATCAAAATTTCATA-GGTGG
*
6034 CTATCAAAATTTCATA
1 TTATCAAAATTTCATA
6050 AAAATATCCA
Statistics
Matches: 113, Mismatches: 28, Indels: 11
0.74 0.18 0.07
Matches are distributed among these distances:
20 7 0.06
21 24 0.21
22 69 0.61
23 13 0.12
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGTGG
Found at i:6115 original size:2 final size:2
Alignment explanation
Indices: 6108--6132 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6098 CTAAAACTAG
6108 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6133 TATGCTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6878 original size:12 final size:12
Alignment explanation
Indices: 6861--6887 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6851 ATAAGAGGCC
6861 CAAGTAACCCAT
1 CAAGTAACCCAT
6873 CAAGTAACCCAT
1 CAAGTAACCCAT
6885 CAA
1 CAA
6888 AGACTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.33, G:0.07, T:0.15
Consensus pattern (12 bp):
CAAGTAACCCAT
Found at i:8052 original size:6 final size:6
Alignment explanation
Indices: 8037--8068 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
8027 TAAGTACGAC
8037 TAAA-T TAAAGT TAAAGT TAAA-T TAAAGT TAAA
1 TAAAGT TAAAGT TAAAGT TAAAGT TAAAGT TAAA
8069 CTTATTATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 9 0.36
6 16 0.64
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (6 bp):
TAAAGT
Found at i:8061 original size:11 final size:12
Alignment explanation
Indices: 8037--8068 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
8027 TAAGTACGAC
8037 TAAA-TTAAAGT
1 TAAAGTTAAAGT
8048 TAAAGTTAAA-T
1 TAAAGTTAAAGT
8059 TAAAGTTAAA
1 TAAAGTTAAA
8069 CTTATTATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (12 bp):
TAAAGTTAAAGT
Found at i:23682 original size:44 final size:43
Alignment explanation
Indices: 23619--23913 Score: 230
Period size: 41 Copynumber: 7.0 Consensus size: 43
23609 TACCCAATAA
23619 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTTT
1 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAA-TCTCTTT
** * * * * *
23663 CTAAAGTCCTTAAGCACATTTATAACATAGAGGC-A-CCCATAT
1 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATCTC-TTT
* * *
23705 C-GAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTG
1 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAA-TCTCTTT
* * * * * *
23748 CTAAAGTCCTCAAACACATTTATAACACAGAGG-TATATATAT
1 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATCTCTTT
* *
23790 C-AAAGTCCCCAAACACAATTATAACACATGGGCAAT-TCTTT
1 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATCTCTTT
* * ** *
23831 CTAAAAGTCCTCAGACACATTTATAACACATAGGC-ATC-CATAT
1 CT-AAAGTCCCCAAACACATTTATAACACAGGGGCAATCTC-TTT
* * * * *
23874 -TAAAGTCCCTAAATACAATTATAGCACAAGGGCAATCTCT
1 CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATCTCT
23914 ATGTGGCAAA
Statistics
Matches: 193, Mismatches: 46, Indels: 26
0.73 0.17 0.10
Matches are distributed among these distances:
41 82 0.42
42 18 0.09
43 35 0.18
44 58 0.30
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (43 bp):
CTAAAGTCCCCAAACACATTTATAACACAGGGGCAATCTCTTT
Found at i:23717 original size:85 final size:84
Alignment explanation
Indices: 23621--23913 Score: 374
Period size: 85 Copynumber: 3.5 Consensus size: 84
23611 CCCAATAACT
*
23621 AAAGTCCCCAAACACATTTATAACACAGGGGCAATTCTCTTTCTAAAGTCCTTAAGCACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAA-TCTCTTTCTAAAGTCCTTAAGCACATTTAT
* *
23686 AACATAGAGGCACCCATATC
65 AACACAGAGGCATCCATATC
* * * *
23706 GAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTTGCTAAAGTCCTCAAACACATTTAT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAA-TCTCTTTCTAAAGTCCTTAAGCACATTTAT
* **
23771 AACACAGAGGTATATATATC
65 AACACAGAGGCATCCATATC
* *
23791 AAAGTCCCCAAACACAATTATAACACATGGGCAAT-TCTTTCTAAAAGTCC-TCAGACACATTTA
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTTTCT-AAAGTCCTTAAG-CACATTTA
* *
23854 TAACACATAGGCATCCATATT
64 TAACACAGAGGCATCCATATC
* * * *
23875 AAAGTCCCTAAATACAATTATAGCACAAGGGCAATCTCT
1 AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCT
23914 ATGTGGCAAA
Statistics
Matches: 180, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
83 7 0.04
84 63 0.35
85 110 0.61
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.25
Consensus pattern (84 bp):
AAAGTCCCCAAACACAATTATAACACAGGGGCAATCTCTTTCTAAAGTCCTTAAGCACATTTATA
ACACAGAGGCATCCATATC
Found at i:26967 original size:26 final size:26
Alignment explanation
Indices: 26938--27007 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
26928 TAATTTTAAT
26938 TTTTTAGTTTATAATTTATAT-ATAA
1 TTTTTAGTTTATAATTTATATAATAA
* *
26963 GTTTTTA-TTTTTAATGTTTTATAATAA
1 -TTTTTAGTTTATAAT-TTATATAATAA
* *
26990 TTTATAGTTTATATTTTA
1 TTTTTAGTTTATAATTTA
27008 ACATTTAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
25 7 0.20
26 18 0.51
27 10 0.29
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (26 bp):
TTTTTAGTTTATAATTTATATAATAA
Found at i:33440 original size:28 final size:28
Alignment explanation
Indices: 33400--33456 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
33390 TGTTAATCTT
33400 GTTGGAGCTCGGGTCGGCTCACTGTGGG
1 GTTGGAGCTCGGGTCGGCTCACTGTGGG
*
33428 GTTGGAGTTCGGGTCGGCTCACTGTGGG
1 GTTGGAGCTCGGGTCGGCTCACTGTGGG
33456 G
1 G
33457 GTAAAGGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.07, C:0.19, G:0.47, T:0.26
Consensus pattern (28 bp):
GTTGGAGCTCGGGTCGGCTCACTGTGGG
Found at i:40312 original size:11 final size:11
Alignment explanation
Indices: 40296--40334 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
40286 CGCTATATAT
40296 ATATATACTAA
1 ATATATACTAA
40307 ATATATACTATA
1 ATATATACTA-A
40319 TATATATACT-A
1 -ATATATACTAA
40330 ATATA
1 ATATA
40335 CTAAATTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.19
11 11 0.42
12 1 0.04
13 9 0.35
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATATACTAA
Found at i:40312 original size:13 final size:13
Alignment explanation
Indices: 40294--40350 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
40284 AGCGCTATAT
40294 ATATATATACT-A
1 ATATATATACTAA
*
40306 A-ATATATACTAT
1 ATATATATACTAA
40318 ATATATATACTAA
1 ATATATATACTAA
*
40331 TATACTAAATTACTAA
1 -ATA-TATA-TACTAA
40347 ATAT
1 ATAT
40351 TATTTGAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 9 0.24
12 2 0.05
13 10 0.27
14 4 0.11
15 6 0.16
16 6 0.16
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATATACTAA
Found at i:42639 original size:11 final size:11
Alignment explanation
Indices: 42616--42668 Score: 58
Period size: 11 Copynumber: 4.8 Consensus size: 11
42606 CCGGTCTGAC
42616 AAAA-AAAACAT
1 AAAATAAAA-AT
42627 AAAATAAAAAT
1 AAAATAAAAAT
42638 AAAATAAAAAT
1 AAAATAAAAAT
42649 -AAATAAATAA-
1 AAAATAAA-AAT
42659 ATAAATAAAA
1 A-AAATAAAA
42669 TACCCCTAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.18
11 20 0.53
12 11 0.29
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:46012 original size:22 final size:22
Alignment explanation
Indices: 45987--46107 Score: 70
Period size: 22 Copynumber: 5.5 Consensus size: 22
45977 ATTAAATTAT
*
45987 TTTTGATGA-CTTGCTTATGAAA
1 TTTTGATAACCTT-CTTATGAAA
*
46009 TTTT-TTAACCTTCTTATGAAA
1 TTTTGATAACCTTCTTATGAAA
* * * * *
46030 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCTTCTTATGAAA
* * *
46052 TTTTTAAAACC-TCATTATAAAA
1 TTTTGATAACCTTC-TTATGAAA
**
46074 TTTTTGATAA-CTTCCCAATGAAA
1 -TTTTGATAACCTT-CTTATGAAA
46097 TTTTGATAACC
1 TTTTGATAACC
46108 GACACTGAGA
Statistics
Matches: 73, Mismatches: 19, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
21 16 0.22
22 42 0.58
23 14 0.19
24 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTTGATAACCTTCTTATGAAA
Found at i:46026 original size:21 final size:22
Alignment explanation
Indices: 46000--46041 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
45990 TGATGACTTG
46000 CTTATGAAATTTT-TTAACCTT
1 CTTATGAAATTTTGTTAACCTT
46021 CTTATGAAATTTTGTTAACCT
1 CTTATGAAATTTTGTTAACCT
46042 CCCTAAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (22 bp):
CTTATGAAATTTTGTTAACCTT
Found at i:46215 original size:22 final size:22
Alignment explanation
Indices: 46190--46258 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
46180 GAATTGTTAG
46190 TAATCACACTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
46212 TAATCATACTAT-AAATTTGTGA
1 TAATCACACTATGAAATTT-TGA
* * * *
46234 TAACCTCGCTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
46256 TAA
1 TAA
46259 ACCTTCTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 6 0.15
22 27 0.69
23 6 0.15
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:46261 original size:23 final size:23
Alignment explanation
Indices: 46247--46326 Score: 126
Period size: 23 Copynumber: 3.5 Consensus size: 23
46237 CCTCGCTCTG
*
46247 AAATTTTGATAAACCTTCTTATA
1 AAATTTTGATAAACCTCCTTATA
46270 AAATTTTGATAAACCTCCTTATA
1 AAATTTTGATAAACCTCCTTATA
*
46293 AAATTTTGAT-AACCTCCTTATG
1 AAATTTTGATAAACCTCCTTATA
*
46315 AAATCTTGATAA
1 AAATTTTGATAA
46327 CTACAACTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
22 20 0.38
23 33 0.62
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCTTATA
Found at i:46309 original size:22 final size:22
Alignment explanation
Indices: 46203--46327 Score: 121
Period size: 23 Copynumber: 5.6 Consensus size: 22
46193 TCACACTATG
* *
46203 AAATTTTGATAATCATAC-TAT-
1 AAATTTTGATAA-CCTCCTTATA
* *
46224 AAATTTGTGATAACCTCGC-TCTG
1 AAATTT-TGATAACCTC-CTTATA
*
46247 AAATTTTGATAAACCTTCTTATA
1 AAATTTTGAT-AACCTCCTTATA
46270 AAATTTTGATAAACCTCCTTATA
1 AAATTTTGAT-AACCTCCTTATA
*
46293 AAATTTTGATAACCTCCTTATG
1 AAATTTTGATAACCTCCTTATA
*
46315 AAATCTTGATAAC
1 AAATTTTGATAAC
46328 TACAACTTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.09
22 37 0.41
23 45 0.50
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAACCTCCTTATA
Found at i:46435 original size:22 final size:20
Alignment explanation
Indices: 46355--46487 Score: 79
Period size: 22 Copynumber: 6.2 Consensus size: 20
46345 CTCCCTATGA
46355 GATAACCTCATTATGAAATTTT
1 GATAACCTC--TATGAAATTTT
* *
46377 GTTAATCTCCCTATGAAATTTT
1 GATAA-C-CTCTATGAAATTTT
* *
46399 GATCTACATACTATGAAATTTT
1 GAT-AACCT-CTATGAAATTTT
46421 GATAACCCTCTTATGAAATTTT
1 GATAA-CCTC-TATGAAATTTT
* *
46443 GA-AAACTAAACTATGAAATTTC
1 GATAACCT---CTATGAAATTTT
* **
46465 GATATCCTCCCTGAAATTTT
1 GATAACCTCTATGAAATTTT
46485 GAT
1 GAT
46488 TACTCCATAA
Statistics
Matches: 86, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
20 14 0.16
21 4 0.05
22 60 0.70
23 6 0.07
24 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (20 bp):
GATAACCTCTATGAAATTTT
Found at i:46456 original size:44 final size:44
Alignment explanation
Indices: 46366--46486 Score: 121
Period size: 44 Copynumber: 2.8 Consensus size: 44
46356 ATAACCTCAT
* *
46366 TATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATAC
1 TATGAAATTTTGATAATCTCCCTATGAAATTTTGAACTACATAC
46410 TATGAAATTTTGATAA-C-CCTCTTATGAAATTTTGAAAACTA-A-AC
1 TATGAAATTTTGATAATCTCC-C-TATGAAATTTTG--AACTACATAC
*
46454 TATGAAATTTCGAT-ATCCTCCC--TGAAATTTTGA
1 TATGAAATTTTGATAAT-CTCCCTATGAAATTTTGA
46487 TTACTCCATA
Statistics
Matches: 67, Mismatches: 3, Indels: 18
0.76 0.03 0.20
Matches are distributed among these distances:
40 1 0.01
42 12 0.18
43 3 0.04
44 42 0.63
45 3 0.04
46 6 0.09
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (44 bp):
TATGAAATTTTGATAATCTCCCTATGAAATTTTGAACTACATAC
Found at i:46618 original size:22 final size:22
Alignment explanation
Indices: 46569--46839 Score: 139
Period size: 22 Copynumber: 12.4 Consensus size: 22
46559 GAAATACCAC
* * *
46569 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCTC-TT
*
46592 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
* *
46613 TATGAAATTTTTATAGCCTCTT
1 TATGAAATTTTGATAACCTCTT
* * * * *
46635 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCTCTT
* * *
46657 TATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAACCTCTT
*
46679 TATGTAATTTTGATAACCTCGCTT
1 TATGAAATTTTGATAACCT--CTT
** **
46703 TA--AAATTTTGATAACAACAG
1 TATGAAATTTTGATAACCTCTT
46723 TATGAAATTTTGATAA--TCTT
1 TATGAAATTTTGATAACCTCTT
* *
46743 CCCAT-AAATTTTGATAATCCGATCTC
1 --TATGAAATTTTGATAA-CC--TCTT
* * * *
46769 TATGAAATTTCGATAATCACTC
1 TATGAAATTTTGATAACCTCTT
* *
46791 TATGAGA-TTTGATAACCT-TC
1 TATGAAATTTTGATAACCTCTT
* *
46811 TATCAAATTTTGAT-A-CTCCT
1 TATGAAATTTTGATAACCTCTT
46831 TATGAAATT
1 TATGAAATT
46840 GAGACTTTTA
Statistics
Matches: 185, Mismatches: 48, Indels: 33
0.70 0.18 0.12
Matches are distributed among these distances:
19 2 0.01
20 20 0.11
21 29 0.16
22 112 0.61
23 1 0.01
24 7 0.04
25 11 0.06
26 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:46682 original size:66 final size:66
Alignment explanation
Indices: 46593--46740 Score: 154
Period size: 66 Copynumber: 2.2 Consensus size: 66
46583 AATCACATTT
* * * * * * * * * ** *
46593 TGAAAATTTGATAACCTCTTTATGAAATTTTTATAGCCTC-TTTATAAAATTTTGTTGACCCCTC
1 TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCGCTT-TAAAATTTTGATAACAACAC
46657 TA
65 TA
* *
46659 TGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTTTAAAATTTTGATAACAACAGT
1 TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCGCTTTAAAATTTTGATAACAACACT
46724 A
66 A
46725 TGAAATTTTGATAATC
1 TGAAATTTTGATAATC
46741 TTCCCATAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
66 65 0.97
67 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (66 bp):
TGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCGCTTTAAAATTTTGATAACAACACT
A
Found at i:46874 original size:22 final size:22
Alignment explanation
Indices: 46657--46977 Score: 114
Period size: 22 Copynumber: 14.4 Consensus size: 22
46647 TTGACCCCTC
* *
46657 TATGAAATTTTGATAATC-ACA
1 TATGAAATTTTGATAACCTTCA
* *
46678 TTATGTAATTTTGATAACC-TCGC
1 -TATGAAATTTTGATAACCTTC-A
* * **
46701 TTTAAAATTTTGATAA-CAACA
1 TATGAAATTTTGATAACCTTCA
* *
46722 GTATGAAATTTTGATAATCTTCC
1 -TATGAAATTTTGATAACCTTCA
*
46745 CAT-AAATTTTGATAATCCGATCTC-
1 TATGAAATTTTGATAA-CC--T-TCA
*
46769 TATGAAATTTCGATAATCAC-TC-
1 TATGAAATTTTGATAA-C-CTTCA
*
46791 TATGAGA-TTTGATAACCTTC-
1 TATGAAATTTTGATAACCTTCA
* *
46811 TATCAAATTTTGATACTCCTT-A
1 TATGAAATTTTGATA-ACCTTCA
*
46833 TGAAATTGAGACTTTT-ATAACCTTCA
1 T---A-TGA-AATTTTGATAACCTTCA
*
46859 TATGAAATTTTGATAACC-ACA
1 TATGAAATTTTGATAACCTTCA
** *
46880 CTAAAAAATTTTGATAACC-ACA
1 -TATGAAATTTTGATAACCTTCA
* *
46902 TTATGAAATTTTGATAACCTCCC
1 -TATGAAATTTTGATAACCTTCA
* * * *
46925 CATGAAATATT-AGTAACCTCCT
1 TATGAAATTTTGA-TAACCTTCA
* *
46947 TATGAAATTTTGTTAACC-ACA
1 TATGAAATTTTGATAACCTTCA
46968 CTATGAAATT
1 -TATGAAATT
46978 CTTACAACCT
Statistics
Matches: 230, Mismatches: 43, Indels: 52
0.71 0.13 0.16
Matches are distributed among these distances:
19 1 0.00
20 8 0.03
21 36 0.16
22 145 0.63
23 4 0.02
24 3 0.01
25 20 0.09
26 8 0.03
27 5 0.02
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCA
Found at i:46930 original size:66 final size:65
Alignment explanation
Indices: 46860--47243 Score: 243
Period size: 66 Copynumber: 5.6 Consensus size: 65
46850 TAACCTTCAT
** *
46860 ATGAAATTTTGATAACCACACTAAAAAATTTTGATAACCACATTATGAAATTTTGATAACCTCCC
1 ATGAAATTTTGATAACCAC-CTATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCC
46925 C
65 C
* * * *
46926 ATGAAATATT-AGTAACCTCCTTATGAAATTTTGTTAACCACACTATGAAATTCTT-ACAACCTC
1 ATGAAATTTTGA-TAACCACC-TATGAAATTTTGATAACCACACTATGAAATT-TTGATAACCTC
* *
46989 GCT
63 CCC
* * * * *
46992 ATGACATTTTGATAATCTCTTTGATAACTTTTCTATAAAATTGTGATAACCACACTATAAAATTT
1 ATGAAATTTTGATAA-C-C-------AC---C-TATGAAATTTTGATAACCACACTATGAAATTT
** *
47057 CAATAACCAT-CCT
53 TGATAACC-TCCCC
** * * * *
47070 AAAAAATTTTAATAACCTGATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAATCTT
1 ATGAAATTTTGATAACC--A-CCTATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTC
47135 CCC
63 CCC
** * * * *
47138 ATGAAATTTTGATAACTTCCATATGAAATTTTGGTAACTACACTATGGAATTTTGATAACCTCCT
1 ATGAAATTTTGATAACCACC-TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCC
47203 C
65 C
* * * *
47204 ATGAAATTATAATAACAATCTTATGAAATTTTGATAACCA
1 ATGAAATTTTGATAACCA-CCTATGAAATTTTGATAACCA
47244 TACAGAGATA
Statistics
Matches: 244, Mismatches: 52, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
65 4 0.02
66 132 0.54
67 6 0.02
68 49 0.20
71 2 0.01
72 1 0.00
75 1 0.00
76 1 0.00
77 2 0.01
78 45 0.18
79 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (65 bp):
ATGAAATTTTGATAACCACCTATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCCCC
Found at i:46974 original size:44 final size:44
Alignment explanation
Indices: 46849--47242 Score: 155
Period size: 44 Copynumber: 9.1 Consensus size: 44
46839 TGAGACTTTT
* * ** *
46849 ATAACCTTCATATGAAATTTTGATAACCACACTAAAAAATTTTG
1 ATAACCTCCTTATGAAATTTTGATAACCACACTATGAAATTTAG
* * * * *
46893 ATAACCACATTATGAAATTTTGATAACCTCCCCATGAAATATTAG
1 ATAACCTCCTTATGAAATTTTGATAACCACACTATGAAAT-TTAG
* *
46938 -TAACCTCCTTATGAAATTTTGTTAACCACACTATGAAATTCT-T
1 ATAACCTCCTTATGAAATTTTGATAACCACACTATGAAATT-TAG
* * * *
46981 ACAACCTCGC-TATGACATTTTGAT----A-A-TCT---CTTT-G
1 ATAACCTC-CTTATGAAATTTTGATAACCACACTATGAAATTTAG
** * * *
47015 ATAA-CTTTTCTATAAAATTGTGATAACCACACTATAAAATTTCA-
1 ATAACCTCCT-TATGAAATTTTGATAACCACACTATGAAATTT-AG
** * *
47059 ATAACCATCC-TAAAAAATTTTAATAACCTGATC-CTATGAAATTTTG
1 ATAACC-TCCTTATGAAATTTTGATAACC--A-CACTATGAAATTTAG
* * ** * *
47105 GTAACCACAC-TATGAAATTTTGATAATCTTC-CCATGAAATTTTG
1 ATAACCTC-CTTATGAAATTTTGATAA-CCACACTATGAAATTTAG
* * * * * *
47149 ATAACTTCCATATGAAATTTTGGTAACTACACTATGGAATTTTG
1 ATAACCTCCTTATGAAATTTTGATAACCACACTATGAAATTTAG
* * * *
47193 ATAACCTCCTCATGAAATTATAATAA-CA-ATCTTATGAAATTTTG
1 ATAACCTCCTTATGAAATTTTGATAACCACA-C-TATGAAATTTAG
47237 ATAACC
1 ATAACC
47243 ATACAGAGAT
Statistics
Matches: 260, Mismatches: 61, Indels: 58
0.69 0.16 0.15
Matches are distributed among these distances:
33 2 0.01
34 15 0.06
35 2 0.01
38 3 0.01
39 2 0.01
40 3 0.01
42 1 0.00
43 10 0.04
44 183 0.70
45 6 0.02
46 31 0.12
47 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (44 bp):
ATAACCTCCTTATGAAATTTTGATAACCACACTATGAAATTTAG
Found at i:47003 original size:180 final size:179
Alignment explanation
Indices: 46679--47005 Score: 392
Period size: 180 Copynumber: 1.8 Consensus size: 179
46669 ATAATCACAT
* * * ** * *
46679 TATGTAATTTTGATAACCTCGCTTTAAAATTTTGATAACAACAGTATGAAATTTTGATAATCTTC
1 TATGAAATTTTGATAACCACACTAAAAAATTTTGATAACAACAGTATGAAATTTTGATAACCTCC
* * * * *
46744 CCATAAATTTTGATAATCCGATCTCTATGAAATTTCGATAATCACTCTATGAGATTTGATAACCT
66 CCATAAATTTAGATAATCC-ATCTCTATGAAATTTCGATAACCACACTATGAAATTTGACAACCT
*
46809 TCTATCAAATTTTGATACTCCTTATGAAATTGAGACTTTTATAACCTTCA
130 GCTATCAAATTTTGATACTCCTTATGAAATTGAGACTTTTATAACCTTCA
* *
46859 TATGAAATTTTGATAACCACACTAAAAAATTTTGATAACCACATTATGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCACACTAAAAAATTTTGATAACAACAGTATGAAATTTTGATAACCTCC
* * *
46924 CCATGAAATATTAG-TAA-CC-TC-CTTATGAAATTTTGTTAACCACACTATGAAATTCTTACAA
66 CCAT-AAAT-TTAGATAATCCATCTC-TATGAAATTTCGATAACCACACTATGAAATT-TGACAA
* *
46985 CCTCGCTATGACATTTTGATA
127 CCT-GCTATCAAATTTTGATA
47006 ATCTCTTTGA
Statistics
Matches: 122, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
177 1 0.01
178 28 0.23
179 7 0.06
180 76 0.62
181 7 0.06
182 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.38
Consensus pattern (179 bp):
TATGAAATTTTGATAACCACACTAAAAAATTTTGATAACAACAGTATGAAATTTTGATAACCTCC
CCATAAATTTAGATAATCCATCTCTATGAAATTTCGATAACCACACTATGAAATTTGACAACCTG
CTATCAAATTTTGATACTCCTTATGAAATTGAGACTTTTATAACCTTCA
Found at i:47049 original size:22 final size:22
Alignment explanation
Indices: 47024--47244 Score: 128
Period size: 22 Copynumber: 10.0 Consensus size: 22
47014 GATAACTTTT
*
47024 CTATAAAATTGTGATAACCA-C
1 CTATAAAATTTTGATAACCATC
**
47045 ACTATAAAATTTCAATAACCATC
1 -CTATAAAATTTTGATAACCATC
* *
47068 CTAAAAAATTTTAATAACCTGATC
1 CTATAAAATTTTGATAACC--ATC
* *
47092 CTATGAAATTTTGGTAACCA-C
1 CTATAAAATTTTGATAACCATC
* * *
47113 ACTATGAAATTTTGATAATCTTC
1 -CTATAAAATTTTGATAACCATC
* * *
47136 CCATGAAATTTTGATAA-CTTC
1 CTATAAAATTTTGATAACCATC
* * *
47157 CATATGAAATTTTGGTAACTA-C
1 C-TATAAAATTTTGATAACCATC
**
47179 ACTATGGAATTTTGATAACC-TC
1 -CTATAAAATTTTGATAACCATC
* * * *
47201 CTCATGAAATTATAATAACAATC
1 CT-ATAAAATTTTGATAACCATC
* *
47224 TTATGAAATTTTGATAACCAT
1 CTATAAAATTTTGATAACCAT
47245 ACAGAGATAA
Statistics
Matches: 160, Mismatches: 28, Indels: 22
0.76 0.13 0.10
Matches are distributed among these distances:
21 8 0.05
22 128 0.80
23 6 0.04
24 18 0.11
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (22 bp):
CTATAAAATTTTGATAACCATC
Found at i:47111 original size:46 final size:44
Alignment explanation
Indices: 47059--47153 Score: 102
Period size: 46 Copynumber: 2.1 Consensus size: 44
47049 TAAAATTTCA
*
47059 ATAACCATC-CTAAAAAATTTTAATAACCTGATCCTATGAAATTTTG
1 ATAACCA-CACTAAAAAATTTTAATAACCT--TCCCATGAAATTTTG
* ** * *
47105 GTAACCACACTATGAAATTTTGATAATCTTCCCATGAAATTTTG
1 ATAACCACACTAAAAAATTTTAATAACCTTCCCATGAAATTTTG
47149 ATAAC
1 ATAAC
47154 TTCCATATGA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
44 18 0.44
45 1 0.02
46 22 0.54
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (44 bp):
ATAACCACACTAAAAAATTTTAATAACCTTCCCATGAAATTTTG
Found at i:48447 original size:31 final size:31
Alignment explanation
Indices: 48394--48453 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
48384 AGTTTAGAGG
*
48394 CTAAAAGCTCAATTTAACACTAAATTTTTTA
1 CTAAAAGCTCAATTTAACACTAAACTTTTTA
* **
48425 CTAAATGCTCAATTTAGTACTAAACTTTT
1 CTAAAAGCTCAATTTAACACTAAACTTTT
48454 AAAGTTGCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (31 bp):
CTAAAAGCTCAATTTAACACTAAACTTTTTA
Found at i:56011 original size:10 final size:10
Alignment explanation
Indices: 55990--56018 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
55980 TTAAAAAAGG
55990 AAATAAAA-T
1 AAATAAAATT
55999 AAATAAAATT
1 AAATAAAATT
56009 AAATAAAATT
1 AAATAAAATT
56019 GTTAATATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.42
10 11 0.58
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATAAAATT
Done.