Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015205.1 Corchorus olitorius cultivar O-4 contig15238, 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: 39602
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1153 original size:254 final size:254
Alignment explanation
Indices: 703--1236 Score: 919
Period size: 254 Copynumber: 2.1 Consensus size: 254
693 TAAAAGTTAG
703 ACAGGGACCTCCCGGGTACTTTTACCAAAATAAATTTCAATAAAATAAAATATATTAAAAAAATA
1 ACAGGGACCTCCCGGGTACTTTTACCAAAATAAATTTCAATAAAATAAAATATATTAAAAAAATA
768 TTTAATTTTTATTCCACGTGTCACCTGCCACATCAGACAAAAAAGACGGTATTAGTGCCACGTCA
66 TTTAATTTTTATTCCACGTGTCACCTGCCACATCAGACAAAAAAGACGGTATTAGTGCCACGTCA
** *
833 GCAAATTTGACGGGTCTGTCACGGCATGCTAACGTGAGGGACCTCGGGTGATAGGCTCTGATAAT
131 GCAAATTTGACGGGTCTGTCACGGCACACTAACGTGAGGGACCTAGGGTGATAGGCTCTGATAAT
* *
898 AGAGGGACGAATTTGTAGAAAAAAAAAAGTACAGGGATCAAAATCAACATTTCGTATAGT
196 AGAGGGACGAATTTGTAG-AAAAAAAAAGTACAAGGACCAAAATCAACATTTCGTATAGT
958 ACAGGGACCTCCCGGGTACTTTTACCAAAATAAATTTCAATAAAATAAAATATATT-AAAAAATA
1 ACAGGGACCTCCCGGGTACTTTTACCAAAATAAATTTCAATAAAATAAAATATATTAAAAAAATA
* *
1022 TTTAATTTTTATTCCACGTGTCACCTGCCACGTCAG-CAAAAAACGACGGTATTAGTGTCACGTC
66 TTTAATTTTTATTCCACGTGTCACCTGCCACATCAGACAAAAAA-GACGGTATTAGTGCCACGTC
* * *
1086 AGCATATTTGACGGGTCTGTCACGGCACACTAACGTGAGGGACCTAGGGTGATAGGTTTTGATAA
130 AGCAAATTTGACGGGTCTGTCACGGCACACTAACGTGAGGGACCTAGGGTGATAGGCTCTGATAA
*
1151 TAGAGGGACGAATTTGTAGAAAAAAAAAGTACAAGGACCAAAATCAATATTTCGTATAGT
195 TAGAGGGACGAATTTGTAGAAAAAAAAAGTACAAGGACCAAAATCAACATTTCGTATAGT
**
1211 ACAGGGACCTCCCACGTACTTTTACC
1 ACAGGGACCTCCCGGGTACTTTTACC
1237 GCTTTTGAGA
Statistics
Matches: 265, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
253 69 0.26
254 140 0.53
255 56 0.21
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (254 bp):
ACAGGGACCTCCCGGGTACTTTTACCAAAATAAATTTCAATAAAATAAAATATATTAAAAAAATA
TTTAATTTTTATTCCACGTGTCACCTGCCACATCAGACAAAAAAGACGGTATTAGTGCCACGTCA
GCAAATTTGACGGGTCTGTCACGGCACACTAACGTGAGGGACCTAGGGTGATAGGCTCTGATAAT
AGAGGGACGAATTTGTAGAAAAAAAAAGTACAAGGACCAAAATCAACATTTCGTATAGT
Found at i:12651 original size:75 final size:75
Alignment explanation
Indices: 12475--12654 Score: 270
Period size: 75 Copynumber: 2.4 Consensus size: 75
12465 CGTCACTCCT
* * * *
12475 CGATTGATCTTGTGTCCCGTCAAAGTATTCCACTTCTTCATCAACTTCACTGTCACTCCTCGAAA
1 CGATTGATCTTGCGCCCCGTCAAAGTTTTCCACTTCTTCATCAACTTCACTGTCACTCCGCGAAA
12540 CGCTTCTTCC
66 CGCTTCTTCC
* **
12550 CGATCGATCTTGCGCCCCGTCAAAGTTTTCCACTTCTTCATCAACTTCACTGTCACTTGGCGAAA
1 CGATTGATCTTGCGCCCCGTCAAAGTTTTCCACTTCTTCATCAACTTCACTGTCACTCCGCGAAA
12615 CGCTTCTTCC
66 CGCTTCTTCC
* * *
12625 GGATTGATCTTCCGCCCCGTCCAAGTTTTC
1 CGATTGATCTTGCGCCCCGTCAAAGTTTTC
12655 TGTTGAAGAT
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.18, C:0.34, G:0.14, T:0.33
Consensus pattern (75 bp):
CGATTGATCTTGCGCCCCGTCAAAGTTTTCCACTTCTTCATCAACTTCACTGTCACTCCGCGAAA
CGCTTCTTCC
Found at i:13711 original size:3 final size:3
Alignment explanation
Indices: 13703--13734 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
13693 TAGTATGTAA
13703 ATT ATT ATT ATT AATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT A
13735 CTCTCATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:24699 original size:13 final size:13
Alignment explanation
Indices: 24681--24705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24671 TTAGAATTCC
24681 AAATAATATTTAT
1 AAATAATATTTAT
24694 AAATAATATTTA
1 AAATAATATTTA
24706 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:26355 original size:13 final size:13
Alignment explanation
Indices: 26337--26366 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
26327 AGTGCTATTG
26337 TTTAATGTAGTTA
1 TTTAATGTAGTTA
26350 TTTAATGTAGTTA
1 TTTAATGTAGTTA
26363 TTTA
1 TTTA
26367 GTACGTATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (13 bp):
TTTAATGTAGTTA
Found at i:29640 original size:42 final size:42
Alignment explanation
Indices: 29559--29643 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
29549 AATTTTATAG
* * *
29559 TGTGGTTATCAAAATTTCATAGGGAGGGAGGTTATCAAAATT
1 TGTGCTTATCAAAATTTCATAGGGAGGGAGATTAACAAAATT
*
29601 TGTGCTTATCAAAATTTCATAGGGAGGTTA-ATTAACAAAATT
1 TGTGCTTATCAAAATTTCATAGGGAGG-GAGATTAACAAAATT
29643 T
1 T
29644 CTTATGGAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.35
Consensus pattern (42 bp):
TGTGCTTATCAAAATTTCATAGGGAGGGAGATTAACAAAATT
Found at i:29678 original size:112 final size:108
Alignment explanation
Indices: 29498--29697 Score: 249
Period size: 112 Copynumber: 1.8 Consensus size: 108
29488 CATAAAAACT
* * * *
29498 TTATCAAAATTTCTTAGGGAGGTTAACAAAATCTCATACGAATGTTATTGAAATTTTATAGTGTG
1 TTATCAAAATTTCATAGGGAGGTTAACAAAATCTCATACGAAGGTTATTGAAATTTTATAGAGAG
* *
29563 GTTATCAAAATTTCATAGGGAGGGAGGTTATCAAAATTTGTGC
66 GTTATCAAAATTACATAGAGAGGGAGGTTATCAAAATTTGTGC
* * * * *
29606 TTATCAAAATTTCATAGGGAGGTTAATTAACAAAATTTCTTATGGAGGTTA-TGAAAATTTTATG
1 TTATCAAAATTTCATAGGGAGG----TTAACAAAATCTCATACGAAGGTTATTG-AAATTTTATA
29670 GAGAGGTTATCAAAATTACATAGAGAGG
61 GAGAGGTTATCAAAATTACATAGAGAGG
29698 ATATCACAGT
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
108 21 0.28
111 2 0.03
112 53 0.70
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.35
Consensus pattern (108 bp):
TTATCAAAATTTCATAGGGAGGTTAACAAAATCTCATACGAAGGTTATTGAAATTTTATAGAGAG
GTTATCAAAATTACATAGAGAGGGAGGTTATCAAAATTTGTGC
Found at i:29695 original size:22 final size:22
Alignment explanation
Indices: 29370--29961 Score: 169
Period size: 22 Copynumber: 26.5 Consensus size: 22
29360 ACAATCAAAC
* *
29370 CAAAATTACATAG-GAAAGTTAT
1 CAAAATTTCATAGAG-AGGTTAT
* * * *
29392 TAAAATTTCATAGTATA-GCTAC
1 CAAAATTTCATAG-AGAGGTTAT
29414 CAAAATTTCATATG-GAGGTTAT
1 CAAAATTTCATA-GAGAGGTTAT
* * * *
29436 CAACACTTCATTGTGTA-GTTAT
1 CAAAATTTCATAGAG-AGGTTAT
*
29458 CAAAATTTCATACAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * **
29480 CAAAATTTCATAAAAACTTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
29502 CAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAGAGAGGTTAT
* *
29524 CAAAATCTCATACGA-ATGTTAT
1 CAAAATTTCATA-GAGAGGTTAT
** * * *
29546 TGAAATTTTATAGTGTGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
29568 CAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCATA--GA--GAGGTTAT
* *
29594 CAAAA-TT--T---GTGCTTAT
1 CAAAATTTCATAGAGAGGTTAT
*
29610 CAAAATTTCATAGGGAGGTTAATT
1 CAAAATTTCATAGAGAGGTT-A-T
*
29634 AACAAAATTTCTTATG-GAGGTTAT
1 --CAAAATTTCATA-GAGAGGTTAT
* * *
29658 GAAAATTTTATGGAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
29680 CAAAATTACATAGAGAGGATAT
1 CAAAATTTCATAGAGAGGTTAT
*
29702 CACAGTTTCATTCTCATACGA-AGGTTATAT
1 CA-A----AATT-TCATA-GAGAGG-T-TAT
* * * * *
29732 CGAAATTTCATGGTGTGTTTAT
1 CAAAATTTCATAGAGAGGTTAT
* ** *
29754 CATAATTTTTTTGAGGAGGTTAT
1 CAAAATTTCATAGA-GAGGTTAT
* * **
29777 CAAAATTTTCATTGTGTTGTTA-
1 CAAAA-TTTCATAGAGAGGTTAT
* * * *
29799 C-CAATTTTATAGTATA-ATTAT
1 CAAAATTTCATAG-AGAGGTTAT
* * *
29820 CAAAATATCCTAG-GGGGATTAT
1 CAAAATTTCATAGAGAGG-TTAT
** ***
29842 CAAAATTTCATACTGAAAATAT
1 CAAAATTTCATAGAGAGGTTAT
* *
29864 CAAAATTTCATAGTGTGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
29886 CAAAATTTCATAGTGTGATTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
29908 CAAATTTTCATAGGGAGGTTAAT
1 CAAAATTTCATAGAGAGGTT-AT
*
29931 -GAAATTTCATA-ATGAGGTTAT
1 CAAAATTTCATAGA-GAGGTTAT
*
29952 CAAATTTTCA
1 CAAAATTTCA
29962 GTTTGGTTAT
Statistics
Matches: 406, Mismatches: 118, Indels: 92
0.66 0.19 0.15
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
19 1 0.00
20 9 0.02
21 10 0.02
22 279 0.69
23 27 0.07
24 14 0.03
25 6 0.01
26 29 0.07
27 4 0.01
28 7 0.02
29 3 0.01
30 4 0.01
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTTAT
Found at i:32559 original size:14 final size:14
Alignment explanation
Indices: 32540--32569 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
32530 AATGTATTAA
32540 GTAGGCATTGGAAC
1 GTAGGCATTGGAAC
32554 GTAGGCATTGGAAC
1 GTAGGCATTGGAAC
32568 GT
1 GT
32570 GTGTGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.13, G:0.37, T:0.23
Consensus pattern (14 bp):
GTAGGCATTGGAAC
Found at i:34417 original size:21 final size:21
Alignment explanation
Indices: 34339--34419 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
34329 ACTATAGCAT
* * *
34339 CAAAAAATTATAGGGAGATTAA
1 CAAAATATCATAGGAAGATT-A
*
34361 CAAAATCTCATAAGGAAG-TTA
1 CAAAATATCAT-AGGAAGATTA
34382 TCAAAA-ATCATAGGAAGATTA
1 -CAAAATATCATAGGAAGATTA
* *
34403 CAAAATTTTATAGGAAG
1 CAAAATATCATAGGAAG
34420 GTTTAATAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 11 0.23
21 17 0.35
22 15 0.31
23 5 0.10
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.25
Consensus pattern (21 bp):
CAAAATATCATAGGAAGATTA
Found at i:34452 original size:22 final size:22
Alignment explanation
Indices: 34361--34546 Score: 154
Period size: 22 Copynumber: 8.5 Consensus size: 22
34351 GGGAGATTAA
* *
34361 CAAAATCTCATAAGGAAG-TTAT
1 CAAAATTTCAT-AGGTAGTTTAT
* * *
34383 CAAAA-ATCATAGGAAGATTA-
1 CAAAATTTCATAGGTAGTTTAT
* *
34403 CAAAATTTTATAGGAAGGTTTAAT
1 CAAAATTTCATAGGTA-GTTT-AT
*
34427 -AAAATTTCATAGTTAGTTTAT
1 CAAAATTTCATAGGTAGTTTAT
34448 CAAAATTTCATATGG-AGTTTAT
1 CAAAATTTCATA-GGTAGTTTAT
*
34470 CACAATTTCATAGGT-GTTTAT
1 CAAAATTTCATAGGTAGTTTAT
* *
34491 CAGAATTTCATAGCGT-GATTAT
1 CAAAATTTCATAG-GTAGTTTAT
*
34513 CAAAATTTAATAGGGTAGTTTA-
1 CAAAATTTCATA-GGTAGTTTAT
34535 CAAAATTTCATA
1 CAAAATTTCATA
34547 AAAATATTTA
Statistics
Matches: 138, Mismatches: 15, Indels: 22
0.79 0.09 0.13
Matches are distributed among these distances:
20 11 0.08
21 37 0.27
22 71 0.51
23 19 0.14
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGGTAGTTTAT
Found at i:34489 original size:65 final size:65
Alignment explanation
Indices: 34400--34546 Score: 156
Period size: 65 Copynumber: 2.2 Consensus size: 65
34390 CATAGGAAGA
* * * * * *
34400 TTACAAAATTTTATAGGAAGGTTTAAT-AAAATTTCATAG-TTAGTTTATCAAAATTTCATATGG
1 TTACAAAATTTCATAGG--TGTTT-ATCAAAATTTCATAGCGT-GATTATCAAAATTTAATAGGG
34463 -AGT
62 TAGT
* *
34466 TTATCACAATTTCATAGGTGTTTATCAGAATTTCATAGCGTGATTATCAAAATTTAATAGGGTAG
1 TTA-CAAAATTTCATAGGTGTTTATCAAAATTTCATAGCGTGATTATCAAAATTTAATAGGGTAG
34531 T
65 T
34532 TTACAAAATTTCATA
1 TTACAAAATTTCATA
34547 AAAATATTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
64 2 0.03
65 44 0.65
66 10 0.15
67 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (65 bp):
TTACAAAATTTCATAGGTGTTTATCAAAATTTCATAGCGTGATTATCAAAATTTAATAGGGTAGT
Found at i:34500 original size:43 final size:44
Alignment explanation
Indices: 34427--34546 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 44
34417 AAGGTTTAAT
* *
34427 AAAATTTCATAGTTAGTTTATCAAAATTTCATATG-GAGTTTATC
1 AAAATTTCATAGGTAGTTTATCAAAATTTCATA-GCGAGATTATC
* * *
34471 ACAATTTCATAGGT-GTTTATCAGAATTTCATAGCGTGATTATC
1 AAAATTTCATAGGTAGTTTATCAAAATTTCATAGCGAGATTATC
*
34514 AAAATTTAATAGGGTAGTTTA-CAAAATTTCATA
1 AAAATTTCATA-GGTAGTTTATCAAAATTTCATA
34547 AAAATATTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 1 0.02
43 33 0.51
44 26 0.40
45 5 0.08
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (44 bp):
AAAATTTCATAGGTAGTTTATCAAAATTTCATAGCGAGATTATC
Found at i:35834 original size:22 final size:22
Alignment explanation
Indices: 35806--36039 Score: 122
Period size: 22 Copynumber: 10.5 Consensus size: 22
35796 TGTCTCTGTG
35806 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
35828 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
35851 -GATTATCAAAA-TTC-TATAGTG
1 TGGTTATCAAAATTTCATA-AG-A
* *
35872 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* **
35895 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* *
35916 AGGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
35938 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
35960 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
* ** *
35984 AGGTTATTGAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
36006 TGGTTATCATAAATTTTAT-AGAA
1 TGGTTATCA-AAATTTCATAAG-A
*
36029 AGGTTATCAAA
1 TGGTTATCAAA
36040 GAGATTATCA
Statistics
Matches: 162, Mismatches: 37, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
19 1 0.01
20 2 0.01
21 8 0.05
22 104 0.64
23 25 0.15
24 22 0.14
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:35909 original size:66 final size:68
Alignment explanation
Indices: 35803--36039 Score: 274
Period size: 66 Copynumber: 3.5 Consensus size: 68
35793 TCTTGTCTCT
* * * * *
35803 GTGTGGTTATCAAAATTTCATAAGAT-GGTTATTATAATTTCATGAGG-AGATTATCAAAA-TTC
1 GTGTGGTTACCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
35865 TATA
66 -ATA
35869 GTGTGGTTACCAAAATTTCATATGGA-A-GTTATCAAAATTTCATG-GGAAGGTTATCAAAATTT
1 GTGTGGTTACCAAAATTTCATA-GGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTT
35931 CATA
65 CATA
* * **
35935 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTC-TTAGGAAGGTTATTGAAATTT
1 GTGTGGTTACCAAAATTTCATAGGAT-AGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTT
35999 CATA
65 CATA
* * *
36003 GTGTGGTTATCATAAATTTTATA-GAAAGGTTATCAAA
1 GTGTGGTTACCA-AAATTTCATAGGATAGGTTATCAAA
36040 GAGATTATCA
Statistics
Matches: 149, Mismatches: 13, Indels: 17
0.83 0.07 0.09
Matches are distributed among these distances:
65 5 0.03
66 72 0.48
67 17 0.11
68 46 0.31
69 9 0.06
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (68 bp):
GTGTGGTTACCAAAATTTCATAGGATAGGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTC
ATA
Found at i:35989 original size:46 final size:44
Alignment explanation
Indices: 35807--37013 Score: 295
Period size: 44 Copynumber: 27.4 Consensus size: 44
35797 GTCTCTGTGT
* * * *
35807 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-A
1 GGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT-AGGAA
* * *
35851 GATTATCAAAA-TTCTATAGTG-TGGTTACCAAAATTTCATATGGAA
1 GGTTATCAAAATTTC-ATAG-GAAGGTTATCAAAATTTCATA-GGAA
* *
35896 -GTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATAGTG-T
1 GGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAG-GAA
* * *
35939 GGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAA
1 GGTTATCAAAATTTCATAGGA--AGGTTATCAAAATTTCATAGGAA
** * * *
35985 GGTTATTGAAATTTCATAGTG-TGGTTATCATAAATTTTATAGAAA
1 GGTTATCAAAATTTCATAG-GAAGGTTATCA-AAATTTCATAGGAA
* *
36030 GGTTATC---A----A-A-G-AGATTATCAAAATGTCATAGCG-A
1 GGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAG-GAA
* *
36064 GGTTAT-AAGAATTTCATAGTG-TGGTTAACAAAATTTCATAAGG-A
1 GGTTATCAA-AATTTCATAG-GAAGGTTATCAAAATTTCAT-AGGAA
* * *
36108 GGTTA-CAAATATTTCATGGGGAGGTTATCAAAATTTCATAAGAA
1 GGTTATCAAA-ATTTCATAGGAAGGTTATCAAAATTTCATAGGAA
* * * * *
36152 GGTTAT-AAAAGTCTCAATTTCA-TAAGGTGTACCAACATTTGATA-GAA
1 GGTTATCAAAA-TTTC-A--T-AGGAAGGT-TATCAAAATTTCATAGGAA
* * * * *
36199 GGTTATC-AAATCTCAGAGTG-A--TTATCGAAATTTTATAGAGATC
1 GGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAG-GA-A
* *
36242 GGATTATCAAAATTT-ATAGGAAGATTATCAAAATTTCATAGTG-T
1 GG-TTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAG-GAA
* * * *
36286 TGTTATCAAAATTTCAAAGCG-AGGTTATCAAAATTGCATA--AT
1 GGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAGGAA
* * * * *
36328 GTGATTATCAAAATTTTCATA-GAGGGTTCAACCAAATTTTATA-TAGA
1 G-G-TTATCAAAA-TTTCATAGGAAGGTT-ATCAAAATTTCATAGGA-A
* * * *
36375 GGTTATCAAAAATTCATA--AAGAGATTATCAAATTTTCAAAATGTAA
1 GGTTATCAAAATTTCATAGGAAG-G-TTATCAAAATTTC-ATA-GGAA
* * * * *
36421 --TTACCAAAATTTCATAGTGGTATTTCTGGTTATTAAACTTTTATTACGG-A
1 GGTTATCAAAATTTCATA--GG-A----AGGTTATCAAAATTTCA-TA-GGAA
* * * *
36471 -GTAATCAAAATTTC--AGGGAGGATATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGGAA
** *
36512 GGTTATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATAAGAGAA
1 GGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCAT-AG-GAA
* * * *
36558 --TTATCAAAATTTCATA-GTATGTAGATCATAATTTCATATGG-A
1 GGTTATCAAAATTTCATAGGAAGGT-TATCAAAATTTCATA-GGAA
* * * * ** *
36600 GATTAACAAAATTTCATAATG-AGGTTATAAAAAAATCATAGGGA
1 GGTTATCAAAATTTCAT-AGGAAGGTTATCAAAATTTCATAGGAA
* * * *
36644 GGTTAT-AAAAATT--T--GTA-GTTATCAAGATTTTATAAGG-A
1 GGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT-AGGAA
* *
36682 GGTTATCAAAATCTAATAGGAAGGTTTATCAAAATTTCATAGCG-A
1 GGTTATCAAAATTTCATAGGAAGG-TTATCAAAATTTCATAG-GAA
* * * * *
36727 GGTTATCACAATTTCATAGTG-TGATTATCAAAATTTCAGAGTG-T
1 GGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAG-GAA
* * * * * *
36771 GATTA-CTAACAA-TTCATATGG-AGGTTTTTAAATTTTCATAACG-T
1 GGTTATC-AA-AATTTCATA-GGAAGGTTATCAAAATTTCAT-AGGAA
* * *
36815 GGTTATCAATATATCATATGG-AGGTTATCAACATCTCAAAATTTCATTGGGAA
1 GGTTATCAAAATTTCATA-GGAAGG-T-T----A--TCAAAATTTCA-TAGGAA
* * * *
36868 -GTTATCAAAATTTCATAATG-AGG-TATTCAAAATTCCTTAGGGA
1 GGTTATCAAAATTTCAT-AGGAAGGTTA-TCAAAATTTCATAGGAA
* * * ** **
36911 GGTTAACAAAATTTCATAAGAAAGTTAAAAAAATTT-ATAAAAA
1 GGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGGAA
** * * ** *
36954 GGTTCCCAAAATTCCATAGTATCGTTATTAAAATTTCATA--AA
1 GGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGGAA
36996 GGTTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
37014 AAGAGGTCAT
Statistics
Matches: 862, Mismatches: 180, Indels: 244
0.67 0.14 0.19
Matches are distributed among these distances:
34 16 0.02
35 8 0.01
37 2 0.00
38 20 0.02
39 9 0.01
40 12 0.01
41 7 0.01
42 51 0.06
43 83 0.10
44 387 0.45
45 109 0.13
46 63 0.07
47 23 0.03
48 12 0.01
49 3 0.00
50 2 0.00
51 23 0.03
52 29 0.03
53 3 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGGAA
Found at i:36069 original size:22 final size:21
Alignment explanation
Indices: 36044--36412 Score: 153
Period size: 22 Copynumber: 16.7 Consensus size: 21
36034 ATCAAAGAGA
*
36044 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
36066 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
36088 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
36110 TTA-CAAATATTTCATGGGGAGG
1 TTATCAAA-ATTTCAT-AGGAGG
*
36132 TTATCAAAATTTCATAAGAAGG
1 TTATCAAAATTTCAT-AGGAGG
*
36154 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
36179 TGTACCAACATTTGATAGAAGG
1 T-TATCAAAATTTCATAGGAGG
* *
36201 TTATC-AAATCTCAGAGTGA--
1 TTATCAAAATTTCATAG-GAGG
* *
36220 TTATCGAAATTTTATAGAGATCGG
1 TTATCAAAATTTCATAG-GA--GG
*
36244 ATTATCAAAATTT-ATAGGAAGA
1 -TTATCAAAATTTCATAGG-AGG
**
36266 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
*
36288 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
36310 TTATCAAAATTGCATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
36332 TTATCAAAATTTTCATA-GAGGG
1 TTATCAAAA-TTTCATAGGA-GG
* * * *
36354 TTCAACCAAATTTTATATAGAGG
1 TT-ATCAAAATTTCATA-GGAGG
* * *
36377 TTATCAAAAATTCATAAAGAGA
1 TTATCAAAATTTCAT-AGGAGG
*
36399 TTATCAAATTTTCA
1 TTATCAAAATTTCA
36413 AAATGTAATT
Statistics
Matches: 264, Mismatches: 52, Indels: 62
0.70 0.14 0.16
Matches are distributed among these distances:
19 5 0.02
20 24 0.09
21 23 0.09
22 149 0.56
23 28 0.11
24 7 0.03
25 17 0.06
26 2 0.01
27 1 0.00
28 8 0.03
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:36269 original size:21 final size:23
Alignment explanation
Indices: 36243--36617 Score: 103
Period size: 22 Copynumber: 16.8 Consensus size: 23
36233 ATAGAGATCG
36243 GATTATCAAAATTT-ATAG-GAA
1 GATTATCAAAATTTCATAGTGAA
**
36264 GATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCATAGTGAA
* *
36287 G-TTATCAAAATTTCAAAGCG-A
1 GATTATCAAAATTTCATAGTGAA
* * * *
36308 GGTTATCAAAATTGCATAATG-T
1 GATTATCAAAATTTCATAGTGAA
*
36330 GATTATCAAAATTTTCATA--GAG
1 GATTATCAAAA-TTTCATAGTGAA
* * * *
36352 GGTTCAACCAAATTTTATA-T-AGA
1 GATT-ATCAAAATTTCATAGTGA-A
* * **
36375 GGTTATCAAAAATTCATAAAG-A
1 GATTATCAAAATTTCATAGTGAA
* * * *
36397 GATTATCAAATTTTCAAAATGTA
1 GATTATCAAAATTTCATAGTGAA
* *
36420 -ATTACCAAAATTTCATAGTGGTATTTCT
1 GATTATCAAAATTTCATAGT-G-A----A
* * * * * *
36448 GGTTATTAAACTTTTATTA-CGGA
1 GATTATCAAAATTTCA-TAGTGAA
* * *
36471 G-TAATCAAAATTTC--AGGGAG
1 GATTATCAAAATTTCATAGTGAA
36491 GA-TATCAAAATTTCATA-TGAA
1 GATTATCAAAATTTCATAGTGAA
* **
36512 GGTTATCAAAATTTCATAGTTTA
1 GATTATCAAAATTTCATAGTGAA
* *
36535 G-TTTTCAAAATTTCATA-AG-A
1 GATTATCAAAATTTCATAGTGAA
*
36555 GAATTATCAAAATTTCATAGT-AT
1 G-ATTATCAAAATTTCATAGTGAA
* * *
36578 G-TAGATCATAATTTCATA-TGGA
1 GAT-TATCAAAATTTCATAGTGAA
*
36600 GATTAACAAAATTTCATA
1 GATTATCAAAATTTCATA
36618 ATGAGGTTAT
Statistics
Matches: 254, Mismatches: 68, Indels: 63
0.66 0.18 0.16
Matches are distributed among these distances:
19 1 0.00
20 15 0.06
21 21 0.08
22 179 0.70
23 25 0.10
28 1 0.00
29 10 0.04
30 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (23 bp):
GATTATCAAAATTTCATAGTGAA
Found at i:36366 original size:67 final size:67
Alignment explanation
Indices: 36263--36412 Score: 164
Period size: 67 Copynumber: 2.3 Consensus size: 67
36253 ATTTATAGGA
* * * *
36263 AGATTATCAAAA-TTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTTATC-AAAATTGCATA
1 AGATTATCAAAATTTTCATAGAGTGGTTAACAAAATTTCAAAGAGAGGTTATCAAAAATT-CATA
*
36326 ATG
65 AAG
* * * * *
36329 TGATTATCAAAATTTTCATAGAG-GGTTCAACCAAATTTTATATAGAGGTTATCAAAAATTCATA
1 AGATTATCAAAATTTTCATAGAGTGGTT-AACAAAATTTCAAAGAGAGGTTATCAAAAATTCATA
36393 AAG
65 AAG
36396 AGATTATC-AAATTTTCA
1 AGATTATCAAAATTTTCA
36413 AAATGTAATT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
66 23 0.33
67 41 0.59
68 6 0.09
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (67 bp):
AGATTATCAAAATTTTCATAGAGTGGTTAACAAAATTTCAAAGAGAGGTTATCAAAAATTCATAA
AG
Found at i:36723 original size:23 final size:21
Alignment explanation
Indices: 36474--36845 Score: 186
Period size: 22 Copynumber: 17.2 Consensus size: 21
36464 TTACGGAGTA
* *
36474 ATCAAAATTTCA-GGGAGGAT
1 ATCAAAATTTCATAGGAGGTT
*
36494 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATA-GGAGGTT
*
36516 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG--GAGGTT
* * *
36538 TTCAAAATTTCATAAGAGAATT
1 ATCAAAATTTCATAGGAG-GTT
* * *
36560 ATCAAAATTTCATAGTATGTAG
1 ATCAAAATTTCATAGGAGGT-T
* *
36582 ATCATAATTTCATATGGAGATT
1 ATCAAAATTTCATA-GGAGGTT
* *
36604 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* **
36626 ATAAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATA-GGAGGTT
* *
36648 AT-AAAAATT--T-GTA-GTT
1 ATCAAAATTTCATAGGAGGTT
* *
36664 ATCAAGATTTTATAAGGAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* *
36686 ATCAAAATCTAATAGGAAGGTTT
1 ATCAAAATTTCATAGG-AGG-TT
36709 ATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAG-GAGGTT
* * *
36731 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAG-GAGGTT
* * *
36753 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAG-GAGGTT
36775 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATA-GGAGGTT
* * * * *
36797 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* *
36819 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATA-GGAGGTT
36841 ATCAA
1 ATCAA
36846 CATCTCAAAA
Statistics
Matches: 267, Mismatches: 59, Indels: 50
0.71 0.16 0.13
Matches are distributed among these distances:
16 5 0.02
17 7 0.03
19 2 0.01
20 13 0.05
21 17 0.06
22 195 0.73
23 27 0.10
24 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Found at i:36937 original size:22 final size:21
Alignment explanation
Indices: 36912--37015 Score: 68
Period size: 22 Copynumber: 4.9 Consensus size: 21
36902 CCTTAGGGAG
36912 GTTAACAAAATTTCATAAGAAA
1 GTTAACAAAATTTCATAA-AAA
*
36934 GTTAAAAAAATTT-ATAAAAA
1 GTTAACAAAATTTCATAAAAA
** * * **
36954 GGTTCCCAAAATTCCATAGTATC
1 -GTTAACAAAATTTCATA-AAAA
** *
36977 GTTATTAAAATTTCAT-AAAG
1 GTTAACAAAATTTCATAAAAA
*
36997 GTTATCAAAATTTCATAAA
1 GTTAACAAAATTTCATAAA
37016 GAGGTCATCA
Statistics
Matches: 62, Mismatches: 16, Indels: 9
0.71 0.18 0.10
Matches are distributed among these distances:
20 19 0.31
21 15 0.24
22 27 0.44
23 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.33
Consensus pattern (21 bp):
GTTAACAAAATTTCATAAAAA
Found at i:37006 original size:20 final size:20
Alignment explanation
Indices: 36977--37016 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
36967 CCATAGTATC
*
36977 GTTATTAAAATTTCATAAAG
1 GTTATCAAAATTTCATAAAG
36997 GTTATCAAAATTTCATAAAG
1 GTTATCAAAATTTCATAAAG
37017 AGGTCATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (20 bp):
GTTATCAAAATTTCATAAAG
Found at i:37025 original size:22 final size:20
Alignment explanation
Indices: 36983--37028 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
36973 TATCGTTATT
*
36983 AAAATTTCATAAAGGTTATC
1 AAAATTTCATAAAGGTCATC
37003 AAAATTTCATAAAGAGGTCATC
1 AAAATTTCAT-AA-AGGTCATC
37025 AAAA
1 AAAA
37029 ATAGTGTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 2 0.09
22 11 0.48
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (20 bp):
AAAATTTCATAAAGGTCATC
Found at i:37030 original size:65 final size:65
Alignment explanation
Indices: 36851--37028 Score: 159
Period size: 65 Copynumber: 2.7 Consensus size: 65
36841 ATCAACATCT
** * * * *
36851 CAAAATTTCATTGGGAAGTTATCAAAATTTCATAATGAGGTATTCAAAATTCCTTAGGGAGGTTA
1 CAAAATTTCATAAGAAAGTTATCAAAATTTCATAAAGAGGTA-TCAAAATTCCATAGGGACGTTA
36916 A
65 A
** * *
36917 CAAAATTTCATAAGAAAGTTAAAAAAATTT-ATAAAAAGGT-TCCCAAAATTCCATA-GTATCGT
1 CAAAATTTCATAAGAAAGTTATCAAAATTTCATAAAGAGGTAT--CAAAATTCCATAGGGA-CGT
*
36979 TAT
63 TAA
* *
36982 TAAAATTTCAT-A-AAGGTTATCAAAATTTCATAAAGAGGTCATCAAAA
1 CAAAATTTCATAAGAAAGTTATCAAAATTTCATAAAGAGGT-ATCAAAA
37029 ATAGTGTAAT
Statistics
Matches: 90, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
63 14 0.16
64 17 0.19
65 33 0.37
66 26 0.29
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (65 bp):
CAAAATTTCATAAGAAAGTTATCAAAATTTCATAAAGAGGTATCAAAATTCCATAGGGACGTTAA
Done.