Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010210.1 Corchorus capsularis cultivar CVL-1 contig10231, 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: 105976
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:877 original size:197 final size:195
Alignment explanation
Indices: 454--1148 Score: 811
Period size: 197 Copynumber: 3.5 Consensus size: 195
444 GGGGCGTGAC
*
454 AATATGTATTAATATTAAATATTTAATTATGAAATAGGG-TATGTGTTAACTTCTTAACCCGCTT
1 AATATGTATTAATATTAAATATTTAATTATGAAAT-GGGATATGTGTCAACTTCTTAACCCGCTT
* * *
518 ATGGAGTCCAAAATTTATACTGATAGTGTATTGTATAATAATCCTATAAGAAAATTTATATAATA
65 ATGGAGTCCAAAA-TTACACTGACAGTGTATTG-----TAATCCTATAAGAAAATTTATACAATA
* * *
583 CACCTTTAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGGGTTGACATGTGTACC
124 CACCGTCAGTGGAATTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGGGTTGACATGTGTACC
648 CTTAGGG
189 CTTAGGG
*
655 AATATGTATTAATATTAAATATTTAATTATGAAATGGGATATGTGTCAACTTCTTAACCCGTTTA
1 AATATGTATTAATATTAAATATTTAATTATGAAATGGGATATGTGTCAACTTCTTAACCCGCTTA
*
720 TGGAGTCCAAAATTCACACTGGCAGTGTATTGTAATCCTATAAGAAAATTTATACAATACACCGT
66 TGGAGTCCAAAATT-ACACTGACAGTGTATTGTAATCCTATAAGAAAATTTATACAATACACCGT
785 CAGTGGAAATTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGGGTTGACATGTGTACCCTTAG
130 CAGTGG-AATTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGGGTTGACATGTGTACCCTTAG
850 GG
194 GG
* * *
852 AATATGTATTAATATTAAATATTTAATTATGAAATGGGGTATTTGTTAA---CTTAACCCGCTTA
1 AATATGTATTAATATTAAATATTTAATTATGAAATGGGATATGTGTCAACTTCTTAACCCGCTTA
* * * * * *
914 TGGAGTCCAAAACTTACACTGACAATATATTATATAATAATTCTATAAGAAAAATTATACTATAC
66 TGGAGTCCAAAA-TTACACTGAC-A-GT-GTAT-T-GTAATCCTATAAGAAAATTTATACAATAC
* * * ** * * *
979 -CCGTCAATGGATTTTAGCAGGCTGCACGTG-TAGG----A-TTTATGAGTTGACATGTGACGTC
125 ACCGTCAGTGGAATTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGGGTTGACATGT---GTA
1037 CCCTTAGGG
187 CCCTTAGGG
*
1046 AATATGTATTAATATTAAATATTTAATTAATTATGAAAT-AGAGTATGTGTCAACTTCTTAACCC
1 AATATGTATTAATATTAAATA--T--TTAATTATGAAATGGGA-TATGTGTCAACTTCTTAACCC
* * * *
1110 GCTTATGGAGTCAAAAATTTACATTGACATTATATTGTA
61 GCTTATGGAGTCCAAAA-TTACACTGACAGTGTATTGTA
1149 TAATAATCCT
Statistics
Matches: 436, Mismatches: 38, Indels: 45
0.84 0.07 0.09
Matches are distributed among these distances:
191 15 0.03
192 1 0.00
194 63 0.14
195 3 0.01
196 42 0.10
197 128 0.29
198 34 0.08
199 26 0.06
200 6 0.01
201 118 0.27
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (195 bp):
AATATGTATTAATATTAAATATTTAATTATGAAATGGGATATGTGTCAACTTCTTAACCCGCTTA
TGGAGTCCAAAATTACACTGACAGTGTATTGTAATCCTATAAGAAAATTTATACAATACACCGTC
AGTGGAATTTAGCAGACTGCACGTGCGGGGTTTAACTTTAAGGGTTGACATGTGTACCCTTAGGG
Found at i:6614 original size:31 final size:31
Alignment explanation
Indices: 6579--6638 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
6569 ATGTTTTTCG
* *
6579 ATTGTACCCTTATTTT-TAAAACATATTTCCA
1 ATTGTACCATT-TTTTAAAAAACATATTTCCA
6610 ATTGTACCATTTTTTAAAAAACATATTTC
1 ATTGTACCATTTTTTAAAAAACATATTTC
6639 TAAATTGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (31 bp):
ATTGTACCATTTTTTAAAAAACATATTTCCA
Found at i:6840 original size:19 final size:20
Alignment explanation
Indices: 6813--6850 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
6803 TACTATTAGT
6813 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
6833 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
6851 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:7084 original size:44 final size:42
Alignment explanation
Indices: 7015--7190 Score: 172
Period size: 44 Copynumber: 4.0 Consensus size: 42
7005 GTCTCTATGT
* * * *
7015 GGTTATCAAAATTACATAAGATGGTTACTATAATTTCATGAGGA
1 GGTTATCAAAATTTCAT-AGTTGGTTACCAAAATTTCAT-AGGA
* *
7059 GGTTATCAAAATTCCATAGCTTGGTTACCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAG-TTGGTTACCAAAATTTCATA-GGA
*
7103 AGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGT-TGGTTACCAAAATTTCATAGG---A
* * **
7149 GGTTATTAAAATTTCTTAGGTTGGTTATTAAAATTTCATAGG
1 GGTTATCAAAATTTCATA-GTTGGTTACCAAAATTTCATAGG
7191 GTGGTTAATT
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
43 5 0.04
44 70 0.62
46 35 0.31
47 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (42 bp):
GGTTATCAAAATTTCATAGTTGGTTACCAAAATTTCATAGGA
Found at i:7195 original size:22 final size:22
Alignment explanation
Indices: 7013--7197 Score: 140
Period size: 22 Copynumber: 8.3 Consensus size: 22
7003 TTGTCTCTAT
* *
7013 GTGGTTATCAAAATTACATAAG
1 GTGGTTATCAAAATTTCATAGG
* *
7035 ATGGTTA-CTATAATTTCAT-GAG
1 GTGGTTATC-AAAATTTCATAG-G
* * *
7057 GAGGTTATCAAAATTCCATAGC
1 GTGGTTATCAAAATTTCATAGG
* * *
7079 TTGGTTACCAAAATTTCATATG
1 GTGGTTATCAAAATTTCATAGG
*** *
7101 AAAGTTATCAAAATTTCATAGT
1 GTGGTTATCAAAATTTCATAGG
*
7123 GTGGTTACCAAAATTTCATAGG
1 GTGGTTATCAAAATTTCATAGG
* * *
7145 ATCAGGTTATTAAAATTTCTTAGG
1 GT--GGTTATCAAAATTTCATAGG
* *
7169 TTGGTTATTAAAATTTCATAGG
1 GTGGTTATCAAAATTTCATAGG
7191 GTGGTTA
1 GTGGTTA
7198 ATTTTCACAA
Statistics
Matches: 124, Mismatches: 33, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
21 1 0.01
22 103 0.83
23 2 0.02
24 18 0.15
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
GTGGTTATCAAAATTTCATAGG
Found at i:7258 original size:22 final size:21
Alignment explanation
Indices: 7233--7372 Score: 88
Period size: 22 Copynumber: 6.4 Consensus size: 21
7223 ATCAAAGAGA
*
7233 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
7255 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
7277 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
7299 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* * *
7321 TTATCAAAATTTTATAACGTGG
1 TTATCAAAATTTCAT-AGGAGG
* * *
7343 TAATCAAAATTCCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
7365 TTAT-AAAA
1 TTATCAAAA
7373 GTCTCAATTT
Statistics
Matches: 91, Mismatches: 20, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
21 9 0.10
22 76 0.84
23 6 0.07
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:7299 original size:44 final size:44
Alignment explanation
Indices: 7237--7332 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
7227 AAGAGATTAT
* * *
7237 CAAAATGTCATAGCGAGGTTA-TAAGAATTTCATAGTGTGGTTAA
1 CAAAATTTCATAGCGAGGTTACTAA-AATTTCATAGGGAGGTTAA
* * *
7281 CAAAATTTCATTAG-GAGGTTACTAATATTTCATGGGGAGGTTAT
1 CAAAATTTCA-TAGCGAGGTTACTAAAATTTCATAGGGAGGTTAA
7325 CAAAATTT
1 CAAAATTT
7333 TATAACGTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 38 0.86
45 6 0.14
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.34
Consensus pattern (44 bp):
CAAAATTTCATAGCGAGGTTACTAAAATTTCATAGGGAGGTTAA
Found at i:7448 original size:22 final size:24
Alignment explanation
Indices: 7423--7473 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
7413 TATCAAATCT
*
7423 CATAGA-AT-GATTATCGAAATTC
1 CATAGATATAGATTATCAAAATTC
*
7445 CATAGATATCAGATTATCAAAATTT
1 CATAGATAT-AGATTATCAAAATTC
7470 CATA
1 CATA
7474 ATGTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.25
23 2 0.08
25 16 0.67
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (24 bp):
CATAGATATAGATTATCAAAATTC
Found at i:7486 original size:22 final size:22
Alignment explanation
Indices: 7456--7627 Score: 89
Period size: 22 Copynumber: 7.8 Consensus size: 22
7446 ATAGATATCA
7456 GATTATCAAAATTTCATAATGT
1 GATTATCAAAATTTCATAATGT
** * * *
7478 TTTTATCAAAATTCCA-AACCGA
1 GATTATCAAAATTTCATAA-TGT
* *
7500 GGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCATAATGT
* *
7522 GATTATCAGAATTTCATAGA-GG
1 GATTATCAAAATTTCATA-ATGT
* * * * ***
7544 GGTCAACAAAATTTTATAAAAA
1 GATTATCAAAATTTCATAATGT
* * * *
7566 GGTTATCAAAATTTCAGAAAGA
1 GATTATCAAAATTTCATAATGT
* * *
7588 GGTTATCAAATTTTCAGAATGT
1 GATTATCAAAATTTCATAATGT
7610 GATTA-CAAAAATTTCATA
1 GATTATC-AAAATTTCATA
7628 GTGGTATTTC
Statistics
Matches: 113, Mismatches: 32, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
21 4 0.04
22 106 0.94
23 3 0.03
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (22 bp):
GATTATCAAAATTTCATAATGT
Found at i:7728 original size:20 final size:20
Alignment explanation
Indices: 7703--7761 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
7693 CTTTTATTAT
7703 GGAGGATATCAAAATTTCAG
1 GGAGGATATCAAAATTTCAG
*
7723 GGAGGATATCAAAATTTCAT
1 GGAGGATATCAAAATTTCAG
7743 GGAGGATATCAAAATTTCA
1 GGAGGATATCAAAATTTCA
7762 TAGTTTAGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (20 bp):
GGAGGATATCAAAATTTCAG
Found at i:7798 original size:22 final size:21
Alignment explanation
Indices: 7709--8021 Score: 137
Period size: 22 Copynumber: 14.6 Consensus size: 21
7699 TTATGGAGGA
** *
7709 TATCAAAATTTCAGGGA-GGA
1 TATCAAAATTTCATAGAGGGT
* *
7729 TATCAAAATTTCATGGA-GGA
1 TATCAAAATTTCATAGAGGGT
*
7749 TATCAAAATTTCATAGTTTA-GAT
1 TATCAAAATTTCATAG---AGGGT
7772 T-TCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCAT-AGAGGGT
* **
7793 TATCAAAATTTCATAGTATGCA
1 TATCAAAATTTCATAG-AGGGT
*
7815 GATCAAAATTTCATAG-GGAGAT
1 TATCAAAATTTCATAGAGG-G-T
*
7837 TAACAAAATTTCATA-ATGAGGT
1 TATCAAAATTTCATAGA-G-GGT
** *
7859 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGAG-GGT
*
7881 TATCAAAATTT--T-TA--GT
1 TATCAAAATTTCATAGAGGGT
* **
7897 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCAT-AGAGGGT
* * *
7919 TATCAAAATTTTATGGGGAGGTT
1 TATCAAAATTTCAT--AGAGGGT
* **
7942 TATCAAAAATTT-TTAGGAAGATT
1 TATC-AAAATTTCATA-G-AGGGT
*
7965 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAGAG-GGT
* *
7987 TATCAAAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGAG-GGT
8009 TATCAAAATTTCA
1 TATCAAAATTTCA
8022 GAGTATGATT
Statistics
Matches: 227, Mismatches: 41, Indels: 48
0.72 0.13 0.15
Matches are distributed among these distances:
16 12 0.05
18 1 0.00
20 38 0.17
21 6 0.03
22 137 0.60
23 25 0.11
24 8 0.04
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
TATCAAAATTTCATAGAGGGT
Found at i:7829 original size:66 final size:64
Alignment explanation
Indices: 7724--7866 Score: 173
Period size: 66 Copynumber: 2.2 Consensus size: 64
7714 AAATTTCAGG
* * * ** *
7724 GAGGATATCAAAATTTCATGGAGGATATCAAAATTTCATAGTTTAGATT-TCAAAATTTCATAA-
1 GAGGTTATCAAAATTTCATGGAGCAGATCAAAATTTCATAG-GGAGATTAACAAAATTTCATAAT
*
7787 GAGGGTTATCAAAATTTCATAGTATGCAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATA
1 GA-GGTTATCAAAATTTCAT-GGA-GCAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATA
7852 AT
63 AT
7854 GAGGTTATCAAAA
1 GAGGTTATCAAAA
7867 AATCATAGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
63 2 0.03
64 16 0.24
65 7 0.10
66 41 0.60
67 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (64 bp):
GAGGTTATCAAAATTTCATGGAGCAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAT
Found at i:7864 original size:44 final size:44
Alignment explanation
Indices: 7724--8210 Score: 223
Period size: 44 Copynumber: 11.2 Consensus size: 44
7714 AAATTTCAGG
* *
7724 GAGGATATCAAAATTTCAT--GGAGGA-TATCAAAATTTCATAGTT
1 GAGGTTATCAAAATTTCATAGGGA-GATTATCAAAATTTCATA-AT
* *
7767 TAGATT-TCAAAATTTCATAAGAGG-G-TTATCAAAATTTCATAGTAT
1 GAGGTTATCAAAATTTCAT-AG-GGAGATTATCAAAATTTCATA--AT
*
7812 GCA-G--ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAT
1 G-AGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT
** *
7854 GAGGTTATCAAAAAATCATAGGGAGGTTATCAAAATTT--T--T
1 GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT
* * * * ***
7894 -A-GTTATCAAGATTTCATA-AGAAAGTTATCAAAATTTTATGGG
1 GAGGTTATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAAT
* * **
7936 GAGGTTTATCAAAAATTT-TTAGGAAGATTTATCAAAATTTCATAGC
1 GAGG-TTATC-AAAATTTCATAGGGAGA-TTATCAAAATTTCATAAT
* * *
7982 GAGGTTATCAAAATTTCATAGTGTGATTATCAAAATTTCAGAGTAT
1 GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATA--AT
* * * * * *
8028 GA--TTA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAAC
1 GAGGTTATC-AA-AATTTCATAGGGAGATTATCAAAATTTCATAAT
* * * * * * *
8070 GTA-GTTATCAATATATCATATGGAAGGTTATCAACATCTCATAGT
1 G-AGGTTATCAAAATTTCATA-GGGAGATTATCAAAATTTCATAAT
* * *
8115 GTTGGTTATCAAAATTTCATTGGGA-AGTTATCAAAATTTCATACT
1 G-AGGTTATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAAT
* * * * *
8160 GAGGTCT-TCAAAATTCCTTAGGGAGGTTAACAAATTTTCATAA-
1 GAGGT-TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT
8203 GAAGGTTA
1 G-AGGTTA
8211 AAAAAAATTA
Statistics
Matches: 333, Mismatches: 72, Indels: 77
0.69 0.15 0.16
Matches are distributed among these distances:
37 2 0.01
38 26 0.08
39 1 0.00
40 2 0.01
41 1 0.00
42 21 0.06
43 12 0.04
44 164 0.49
45 58 0.17
46 46 0.14
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAAT
Found at i:8293 original size:22 final size:23
Alignment explanation
Indices: 8245--8298 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
8235 CCATAGTATC
*
8245 ATTATTAAAATTTCATAAGAAGG
1 ATTATAAAAATTTCATAAGAAGG
* *
8268 -TTATCAAAATTTCATAA-TAGG
1 ATTATAAAAATTTCATAAGAAGG
8289 ATTATAAAAA
1 ATTATAAAAA
8299 ATAGTGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (23 bp):
ATTATAAAAATTTCATAAGAAGG
Found at i:8522 original size:14 final size:15
Alignment explanation
Indices: 8498--8530 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
8488 AAGAAATTAA
8498 AAAATTAAGAGAGAG
1 AAAATTAAGAGAGAG
*
8513 AAAA-TAAGAGAGGG
1 AAAATTAAGAGAGAG
8527 AAAA
1 AAAA
8531 ATAGACATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (15 bp):
AAAATTAAGAGAGAG
Found at i:8636 original size:21 final size:21
Alignment explanation
Indices: 8611--8654 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
8601 TTTCGTTTCA
8611 CTCCCATTGTTCTTTTGAATT
1 CTCCCATTGTTCTTTTGAATT
8632 CTCCCATTGTTCTTTTGAATT
1 CTCCCATTGTTCTTTTGAATT
8653 CT
1 CT
8655 GACTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.25, G:0.09, T:0.52
Consensus pattern (21 bp):
CTCCCATTGTTCTTTTGAATT
Found at i:8942 original size:58 final size:58
Alignment explanation
Indices: 8860--8979 Score: 231
Period size: 58 Copynumber: 2.1 Consensus size: 58
8850 TATAAAATTT
8860 AACAAAATAACTAATTTTCTTAAACAAATAAAGTAGTTAAAATGGACAATTAAAAAGG
1 AACAAAATAACTAATTTTCTTAAACAAATAAAGTAGTTAAAATGGACAATTAAAAAGG
*
8918 AACAAAATAACTACTTTTCTTAAACAAATAAAGTAGTTAAAATGGACAATTAAAAAGG
1 AACAAAATAACTAATTTTCTTAAACAAATAAAGTAGTTAAAATGGACAATTAAAAAGG
8976 AACA
1 AACA
8980 TACGGAGTAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (58 bp):
AACAAAATAACTAATTTTCTTAAACAAATAAAGTAGTTAAAATGGACAATTAAAAAGG
Found at i:11278 original size:26 final size:26
Alignment explanation
Indices: 11244--11300 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
11234 TCATGAATAA
** *
11244 AAAAATGGTACATTAAATAAACAAAT
1 AAAAATGGTACAAAAAAAAAACAAAT
* *
11270 AAAATTGGTGCAAAAAAAAAACAAAT
1 AAAAATGGTACAAAAAAAAAACAAAT
11296 AAAAA
1 AAAAA
11301 ATAAAAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.18
Consensus pattern (26 bp):
AAAAATGGTACAAAAAAAAAACAAAT
Found at i:13054 original size:33 final size:31
Alignment explanation
Indices: 12980--13055 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
12970 CTATTCATCT
*
12980 TATGGAAAGTTATTTGGCAACTTTCAAAAAA
1 TATGGAAAGTTATTTGGCAACTGTCAAAAAA
*
13011 AATGGAAAGTTATTTGGCAA-TGT-AGAGAGAAA
1 TATGGAAAGTTATTTGGCAACTGTCA-A-A-AAA
13043 CTATGGAAAGTTA
1 -TATGGAAAGTTA
13056 GTAGGTGGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 1 0.03
30 3 0.08
31 20 0.53
32 3 0.08
33 11 0.29
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (31 bp):
TATGGAAAGTTATTTGGCAACTGTCAAAAAA
Found at i:14507 original size:133 final size:133
Alignment explanation
Indices: 14269--14671 Score: 727
Period size: 133 Copynumber: 3.0 Consensus size: 133
14259 CAAACAGAAA
*
14269 TACCTTGAAGCTCTTGACAAGTAAGGCATTTGAAATTTTTTAAAAGTTCGTTAAGTTTGGCGCGC
1 TACCTTGAAGCTCTTGACAAGTAAGGCCTTTGAAATTTTTTAAAAGTTCGTTAAGTTTGGCGCGC
*
14334 TGTGACCGTTTAATTAGTTGGTTAGCTTTCTTGTGGGTTGCCTTATATTACTTGTGAGTTAATTT
66 TGTGGCCGTTTAATTAGTTGGTTAGCTTTCTTGTGGGTTGCCTTATATTACTTGTGAGTTAATTT
14399 GGT
131 GGT
*
14402 TACCTTGAAGTTCTTGACAAGTAAGGCCTTTGAAATTTTTTAAAAGTTCGTTAAGTTTGGCGCGC
1 TACCTTGAAGCTCTTGACAAGTAAGGCCTTTGAAATTTTTTAAAAGTTCGTTAAGTTTGGCGCGC
* *
14467 TGTGGCCGTTTAATTAGTTGGTTAGCTTTTTTGTGGGTTGCCTTATATTACTTGTGAGTTATTTT
66 TGTGGCCGTTTAATTAGTTGGTTAGCTTTCTTGTGGGTTGCCTTATATTACTTGTGAGTTAATTT
14532 GGT
131 GGT
14535 TAACCTTGAAGCTCTTGACAAGTAAGGCCTTTGAAATTTTTT-AAAGTTCGTTAAGTTTGGCGCG
1 T-ACCTTGAAGCTCTTGACAAGTAAGGCCTTTGAAATTTTTTAAAAGTTCGTTAAGTTTGGCGCG
* *
14599 CTGTGGCCGTTTAATTAGTTGGTTAGCTTTCTTGTGGGTTGTCTTATATTACTTGAGAGTTAATT
65 CTGTGGCCGTTTAATTAGTTGGTTAGCTTTCTTGTGGGTTGCCTTATATTACTTGTGAGTTAATT
14664 TGGT
130 TGGT
14668 TACC
1 TACC
14672 ATAAAGGGAA
Statistics
Matches: 259, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
132 3 0.01
133 217 0.84
134 39 0.15
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.43
Consensus pattern (133 bp):
TACCTTGAAGCTCTTGACAAGTAAGGCCTTTGAAATTTTTTAAAAGTTCGTTAAGTTTGGCGCGC
TGTGGCCGTTTAATTAGTTGGTTAGCTTTCTTGTGGGTTGCCTTATATTACTTGTGAGTTAATTT
GGT
Found at i:25694 original size:42 final size:42
Alignment explanation
Indices: 25638--26102 Score: 495
Period size: 42 Copynumber: 10.9 Consensus size: 42
25628 CTTTAGGTTT
* * * **
25638 AGGTTTGCTTGCAGTCTCGCCCGATTCCGTGAATTTCACTTT
1 AGGTGTGCTTGCAGTCTCACCCGATTCCGTGAATTCCACTGG
25680 AGGTGTGCTTGCAGTCTCACCCGATTCCGTGAATTCCACTGG
1 AGGTGTGCTTGCAGTCTCACCCGATTCCGTGAATTCCACTGG
* *
25722 AGGTGTGCTTGCAATCTCACCCGATTCCGTGTATTCCACTGG
1 AGGTGTGCTTGCAGTCTCACCCGATTCCGTGAATTCCACTGG
*
25764 AGGTGTGCTTGCAGTCTCAGTCTCACCCGATTCCGTGAATTCCACAGG
1 AGGTGTGCTT---G---CAGTCTCACCCGATTCCGTGAATTCCACTGG
* *
25812 AGGTGTGCTTGCAATCTCACCCGATTCCGTGTATTCCACTGG
1 AGGTGTGCTTGCAGTCTCACCCGATTCCGTGAATTCCACTGG
25854 AGGTGTGCTTGCAGTCTCAGTCTCACCCGATTCCGTGAATTCCACTGG
1 AGGTGTGCTT---G---CAGTCTCACCCGATTCCGTGAATTCCACTGG
*
25902 AGGCGTGCTT---G-------C-A-TCCGTGAATTCCACTGG
1 AGGTGTGCTTGCAGTCTCACCCGATTCCGTGAATTCCACTGG
* *
25932 AGGTGTGCTTGCAGTCTCACCAGATTCCGTGTATTCCACTGG
1 AGGTGTGCTTGCAGTCTCACCCGATTCCGTGAATTCCACTGG
*
25974 AGGTGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGG
1 AGGTGTGCTTGCAGTCTCACCCGATTCCGTGAATTCCACTGG
* * *
26016 AGGTGTGCTTGCAATCTCACACGATTCAGATTCCATGTATTCCACTGG
1 AGGTGTGCTTGCAGTCTCAC-C----C-GATTCCGTGAATTCCACTGG
* * * *
26064 AGGTGTGCTTGCAATCTCACACGATTCAGTGTATTCCAC
1 AGGTGTGCTTGCAGTCTCACCCGATTCCGTGAATTCCAC
26103 AGAATGAGTA
Statistics
Matches: 366, Mismatches: 27, Indels: 60
0.81 0.06 0.13
Matches are distributed among these distances:
30 26 0.07
31 1 0.00
32 1 0.00
33 1 0.00
39 1 0.00
41 1 0.00
42 215 0.59
43 2 0.01
45 3 0.01
47 1 0.00
48 114 0.31
ACGTcount: A:0.18, C:0.28, G:0.24, T:0.30
Consensus pattern (42 bp):
AGGTGTGCTTGCAGTCTCACCCGATTCCGTGAATTCCACTGG
Found at i:25818 original size:90 final size:90
Alignment explanation
Indices: 25638--26102 Score: 550
Period size: 90 Copynumber: 5.4 Consensus size: 90
25628 CTTTAGGTTT
* * * * **
25638 AGGTTTGCTTGCAGTCTCGCCCGATTCCGTGAATTTCACTTTAGGTGTGCTT---G---CAGTCT
1 AGGTGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCAGTCT
25697 CACCCGATTCCGTGAATTCCACTGG
66 CACCCGATTCCGTGAATTCCACTGG
*
25722 AGGTGTGCTTGCAATCTCACCCGATTCCGTGTATTCCACTGGAGGTGTGCTTGCAGTCTCAGTCT
1 AGGTGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCAGTCT
*
25787 CACCCGATTCCGTGAATTCCACAGG
66 CACCCGATTCCGTGAATTCCACTGG
*
25812 AGGTGTGCTTGCAATCTCACCCGATTCCGTGTATTCCACTGGAGGTGTGCTTGCAGTCTCAGTCT
1 AGGTGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCAGTCT
25877 CACCCGATTCCGTGAATTCCACTGG
66 CACCCGATTCCGTGAATTCCACTGG
*
25902 AGGCGTGCTTG----------C-A-TCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCA--C-
1 AGGTGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCAGTCT
*
25952 CA---GATTCCGTGTATTCCACTGG
66 CACCCGATTCCGTGAATTCCACTGG
* *
25974 AGGTGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGGAGGTGTGCTTGCAATCTCA--CA
1 AGGTGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCAGTCT
* * * *
26037 CGATTCAGATTCCATGTATTCCACTGG
66 C-A-CCCGATTCCGTGAATTCCACTGG
* * *
26064 AGGTGTGCTTGCAATCTCACACGATTCAGTGTATTCCAC
1 AGGTGTGCTTGCAATCTCACCCGATTCCGTGAATTCCAC
26103 AGAATGAGTA
Statistics
Matches: 339, Mismatches: 18, Indels: 42
0.85 0.05 0.11
Matches are distributed among these distances:
72 29 0.09
75 2 0.01
76 1 0.00
78 35 0.10
79 1 0.00
80 1 0.00
82 1 0.00
83 1 0.00
84 81 0.24
85 1 0.00
86 1 0.00
87 1 0.00
90 184 0.54
ACGTcount: A:0.18, C:0.28, G:0.24, T:0.30
Consensus pattern (90 bp):
AGGTGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCAGTCT
CACCCGATTCCGTGAATTCCACTGG
Found at i:25921 original size:30 final size:30
Alignment explanation
Indices: 25885--25944 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
25875 CTCACCCGAT
25885 TCCGTGAATTCCACTGGAGGCGTGCTTGCA
1 TCCGTGAATTCCACTGGAGGCGTGCTTGCA
*
25915 TCCGTGAATTCCACTGGAGGTGTGCTTGCA
1 TCCGTGAATTCCACTGGAGGCGTGCTTGCA
25945 GTCTCACCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (30 bp):
TCCGTGAATTCCACTGGAGGCGTGCTTGCA
Found at i:25930 original size:78 final size:72
Alignment explanation
Indices: 25837--25986 Score: 219
Period size: 78 Copynumber: 2.0 Consensus size: 72
25827 CTCACCCGAT
*
25837 TCCGTGTATTCCACTGGAGGTGTGCTTGCAGTCTCAGTCTCACCCGATTCCGTGAATTCCACTGG
1 TCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCA--C-CA---GATTCCGTGAATTCCACTGG
25902 AGGCGTGCTTGCA
60 AGGCGTGCTTGCA
* *
25915 TCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCACCAGATTCCGTGTATTCCACTGGAGGTGT
1 TCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCACCAGATTCCGTGAATTCCACTGGAGGCGT
25980 GCTTGCA
66 GCTTGCA
25987 ATCTCACCCG
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
72 31 0.45
75 2 0.03
76 1 0.01
78 35 0.51
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (72 bp):
TCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCACCAGATTCCGTGAATTCCACTGGAGGCGT
GCTTGCA
Found at i:26060 original size:162 final size:164
Alignment explanation
Indices: 25747--26076 Score: 479
Period size: 162 Copynumber: 2.0 Consensus size: 164
25737 CTCACCCGAT
*
25747 TCCGTGTATTCCACTGGAGGTGTGCTTGCAGTCTCAGTCTCACCCGATTCCGTGAATTCCACAGG
1 TCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCAG-CTCA--CGATTCCGTGAATTCCACAGG
* * *
25812 AGGTGTGCTTGCAATCTCACCCGATTCCGTGTATTCCACTGGAGGTGTGCTTGCAGTCTCAGTCT
63 AGGTGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGGAGGTGTGCTTGCAATCTCAG-CA
* *
25877 CACCCGATTCCGTGAATTCCACTGGAGGCGTGCTTGCA
127 CACCAGATTCCATGAATTCCACTGGAGGCGTGCTTGCA
* *
25915 TCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCA-C-CA-GATTCCGTGTATTCCACTGGAGG
1 TCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCAGCTCACGATTCCGTGAATTCCACAGGAGG
25977 TGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGGAGGTGTGCTTGCAATCTCA-CACGAT
66 TGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGGAGGTGTGCTTGCAATCTCAGCAC-A-
* * *
26041 TCAGATTCCATGTATTCCACTGGAGGTGTGCTTGCA
129 CCAGATTCCATGAATTCCACTGGAGGCGTGCTTGCA
26077 ATCTCACACG
Statistics
Matches: 149, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
160 2 0.01
161 1 0.01
162 108 0.72
165 2 0.01
166 1 0.01
168 35 0.23
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (164 bp):
TCCGTGAATTCCACTGGAGGTGTGCTTGCAGTCTCAGCTCACGATTCCGTGAATTCCACAGGAGG
TGTGCTTGCAATCTCACCCGATTCCGTGAATTCCACTGGAGGTGTGCTTGCAATCTCAGCACACC
AGATTCCATGAATTCCACTGGAGGCGTGCTTGCA
Found at i:51884 original size:18 final size:19
Alignment explanation
Indices: 51861--51902 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
51851 TTGACGATGC
51861 TGATGAAGATGA-TAATAA
1 TGATGAAGATGAGTAATAA
* *
51879 TGATG-ATATTAGTAATAA
1 TGATGAAGATGAGTAATAA
51897 TGATGA
1 TGATGA
51903 TGAAACGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.33
Consensus pattern (19 bp):
TGATGAAGATGAGTAATAA
Found at i:79777 original size:125 final size:122
Alignment explanation
Indices: 79615--79848 Score: 360
Period size: 125 Copynumber: 1.9 Consensus size: 122
79605 GAGTTTAATG
* ***
79615 CACTTGAATTCGACGCACTTGTTTTTAGAATAATCAGGATTCAATATGACTATCGAACACCAAAG
1 CACTTGAATTCGACCCACTTACCTTTAGAATAATCAGGATTCAATATGACTATCGAACACCAAAG
* *
79680 GGTACCGTATAAAACAAAGAATCATGTTGGATCGAAACCCACTTTCTTACTTTTATATC
66 AGTACCGTA-AAAA-AAAGAATCATGTTGGATCCAAACCCACTTTCTTACTTTTATATC
*
79739 CACTTAGAATTCGACCCACTTACCTTTAGAATAATCAGGATTCAATATGACTATCGAACATCAAA
1 CACTT-GAATTCGACCCACTTACCTTTAGAATAATCAGGATTCAATATGACTATCGAACACCAAA
* *
79804 GATTACCGTACAAAAAAGAATCATGTTGGATCCAAACCCACTTTC
65 GAGTACCGTAAAAAAAAGAATCATGTTGGATCCAAACCCACTTTC
79849 CTAACGTTGT
Statistics
Matches: 100, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
123 30 0.30
124 8 0.08
125 62 0.62
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (122 bp):
CACTTGAATTCGACCCACTTACCTTTAGAATAATCAGGATTCAATATGACTATCGAACACCAAAG
AGTACCGTAAAAAAAAGAATCATGTTGGATCCAAACCCACTTTCTTACTTTTATATC
Found at i:83826 original size:29 final size:29
Alignment explanation
Indices: 83768--83832 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
83758 TGAAGCTTTT
*** **
83768 AAAACTTTATAACTAGACTTTTTTTTGAG
1 AAAACTTTATAACTAGACTAGATTAGGAG
83797 AAAACTTTATAACTAGACTAGATTAGGAG
1 AAAACTTTATAACTAGACTAGATTAGGAG
*
83826 ATAACTT
1 AAAACTT
83833 CATGCCACTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (29 bp):
AAAACTTTATAACTAGACTAGATTAGGAG
Found at i:85261 original size:31 final size:31
Alignment explanation
Indices: 85223--85283 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
85213 TTTTGTAAAG
85223 CTTTTGAAACGCCTATTATACCCTTATTTAA
1 CTTTTGAAACGCCTATTATACCCTTATTTAA
* *
85254 CTTTTGAAATGCCTATTATATCCTTATTTA
1 CTTTTGAAACGCCTATTATACCCTTATTTA
85284 TCTAACATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.46
Consensus pattern (31 bp):
CTTTTGAAACGCCTATTATACCCTTATTTAA
Done.