Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015262.1 Corchorus olitorius cultivar O-4 contig15295, 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: 87001
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:230 original size:14 final size:13
Alignment explanation
Indices: 204--229 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
194 TATTGAAATT
204 TATTTTAAAAAAA
1 TATTTTAAAAAAA
217 TATTTTAAAAAAA
1 TATTTTAAAAAAA
230 AGAAATCTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTTTAAAAAAA
Found at i:1170 original size:251 final size:254
Alignment explanation
Indices: 681--1172 Score: 884
Period size: 250 Copynumber: 1.9 Consensus size: 254
671 TTTAAAAAAA
*
681 AAAAGTAAATTTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACGTGTCACC
1 AAAAGTAAATTTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACCTGTCACC
*
746 TGCTACGTCAGCAAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGC
66 TGCCACGTCAGCAAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGC
*
811 ATGCTAACGTGAGGGATCTCGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAA
131 ATGCTAACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAA
*
876 AGTACAGGGACCAAAATCAACATTTTGTATAGTACAGGGACCTCCCAGATACTTTTACC
196 AGTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCAGATACTTTTACC
*
935 AAAA-TAAATTTCAATAAAATAAAATATATT-AAAAAA-ATTTAATTTTTATTCCACCTGTCATC
1 AAAAGTAAATTTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACCTGTCACC
997 TGCCACGTCAGC-AAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGC
66 TGCCACGTCAGCAAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGC
*
1061 ATGCTAACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTATAGGGACGAATTTGTAGAAAAAAA
131 ATGCTAACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAG-AAAAAA
*
1126 AAGTACAGGGACCAAAATCAATATTTCGTATAGTACAGGGACCTCCC
195 AAGTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCC
1173 GGGTACGTTT
Statistics
Matches: 230, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
250 108 0.47
251 86 0.37
252 6 0.03
253 26 0.11
254 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (254 bp):
AAAAGTAAATTTCAATAAAATAAAATATATTAAAAAAATATTTAATTTTTATTCCACCTGTCACC
TGCCACGTCAGCAAAAAAAGACGGTGTTAGTGCCACGTCAGCATATTTGACGGGTCTGTCACGGC
ATGCTAACGTGAGGGACCTCGGGTGATAGGTTCTGATAGTAGAGGGACGAATTTGTAGAAAAAAA
AGTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCCCAGATACTTTTACC
Found at i:9901 original size:3 final size:3
Alignment explanation
Indices: 9893--9921 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9883 TGAAAACAGA
9893 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
9922 ATAGGACCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:11085 original size:1 final size:1
Alignment explanation
Indices: 11081--11106 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
11071 GGAAAAAGGG
11081 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
11107 GTGATTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26450 original size:18 final size:19
Alignment explanation
Indices: 26427--26491 Score: 77
Period size: 18 Copynumber: 3.6 Consensus size: 19
26417 ACACAATCAA
*
26427 ATTATATATATTCGTAT-T
1 ATTATATATATTCATATAT
26445 ATTATATATATTCATATAT
1 ATTATATATATTCATATAT
26464 A-TATATATA-T-ATATAT
1 ATTATATATATTCATATAT
26480 GATTAT-TATATT
1 -ATTATATATATT
26492 TGTACTAAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 6 0.14
17 6 0.14
18 28 0.67
19 2 0.05
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTATATATATTCATATAT
Found at i:26452 original size:2 final size:2
Alignment explanation
Indices: 26447--26479 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
26437 TTCGTATTAT
26447 TA TA TA TA T- TCA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA T
26480 GATTATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.93
3 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34192 original size:22 final size:22
Alignment explanation
Indices: 34164--34212 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
34154 ATTACTAAAA
34164 TATAGTGTGGTT-CTCAAAATTT
1 TATAGTGTGGTTAC-CAAAATTT
34186 TATAGTGTGGTTACCAAAATTT
1 TATAGTGTGGTTACCAAAATTT
*
34208 GATAG
1 TATAG
34213 GTAGAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (22 bp):
TATAGTGTGGTTACCAAAATTT
Found at i:34283 original size:22 final size:22
Alignment explanation
Indices: 34252--34492 Score: 195
Period size: 22 Copynumber: 10.8 Consensus size: 22
34242 TCCATGGGAT
* *
34252 GTTATCAAAATTTCATAATGTG
1 GTTATCAAAATTTCATAAGGAG
* *
34274 GTTATTAAAATAAAATTTCATAAGGAT
1 GTTA-T--CA-AAA-TTTCATAAGGAG
*
34301 GTTATCAAAATTTCATATGGAG
1 GTTATCAAAATTTCATAAGGAG
34323 GTTATCAAAATTTCATAAGGAG
1 GTTATCAAAATTTCATAAGGAG
* *
34345 GTTATCGAAA-TTCAT-GGGAAG
1 GTTATCAAAATTTCATAAGG-AG
* *
34366 GTTGTCAAAATTTCACAAGGAG
1 GTTATCAAAATTTCATAAGGAG
****
34388 GTTA-CTAAAATTTCATACTCTG
1 GTTATC-AAAATTTCATAAGGAG
*
34410 GTTATCAAAATTTCATAAGGCG
1 GTTATCAAAATTTCATAAGGAG
* * *
34432 ATTATCGAAATCTT-ATATGGAG
1 GTTATCAAAAT-TTCATAAGGAG
*
34454 GTTATTAAAATTTCAT-AGGAAG
1 GTTATCAAAATTTCATAAGG-AG
*
34476 ATTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
34493 GTGTGCTTAT
Statistics
Matches: 171, Mismatches: 34, Indels: 27
0.74 0.15 0.12
Matches are distributed among these distances:
20 2 0.01
21 20 0.12
22 121 0.71
23 9 0.05
24 1 0.01
25 1 0.01
26 4 0.02
27 13 0.08
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAG
Found at i:34304 original size:27 final size:27
Alignment explanation
Indices: 34258--34311 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
34248 GGATGTTATC
* *
34258 AAAATTTCATAATGTGGTTATTAAAAT
1 AAAATTTCATAAGGTGGTTATCAAAAT
34285 AAAATTTCATAAGGAT-GTTATCAAAAT
1 AAAATTTCATAAGG-TGGTTATCAAAAT
34312 TTCATATGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (27 bp):
AAAATTTCATAAGGTGGTTATCAAAAT
Found at i:34374 original size:43 final size:44
Alignment explanation
Indices: 34285--35195 Score: 248
Period size: 44 Copynumber: 20.7 Consensus size: 44
34275 TTATTAAAAT
* *
34285 AAAATTTCATAAGGATGTTATCAAAATTTCATATGGAGGTTATC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
* *
34329 AAAATTTCATAAGGAGGTTATCGAAA-TTCAT-GGGAAGGTTGTC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGG-AGGTTATC
* ****
34372 AAAATTTCACAAGGAGGTTA-CTAAAATTTCATACTCTGGTTATC
1 AAAATTTCATAAGGAGGTTATC-AAAATTTCATAGGGAGGTTATC
* * * * *
34416 AAAATTTCATAAGGCGATTATCGAAATCTT-ATATGGAGGTTATT
1 AAAATTTCATAAGGAGGTTATCAAAAT-TTCATAGGGAGGTTATC
* * * * *
34460 AAAATTTCAT-AGGAAGATTATCAAAATTTCATAGTGTGCTTATA
1 AAAATTTCATAAGG-AGGTTATCAAAATTTCATAGGGAGGTTATC
* * ** *
34504 AAAATTACATATTGAGATAGAGTGAGCTTATCAAAATTTCA-AGTGTTGTTACC
1 AAAATTTCATA---AG---GA--G-G-TTATCAAAATTTCATAGGGAGGTTATC
* * * *
34557 AAAATTTCAT-AGTGTA-ATAATCACAATTTCATA--GAGGTTAAC
1 AAAATTTCATAAG-G-AGGTTATCAAAATTTCATAGGGAGGTTATC
* * * * * * **
34599 AACATTTCAT-GGGAAGGTTATCGAAATTTTAGAGGTAATATTATC
1 AAAATTTCATAAGG-AGGTTATCAAAATTTCATAGG-GAGGTTATC
* * * **
34644 AAAA-TT--T-AGTGTGGTTATCAAAATTTTATA---ATGTGGT-
1 AAAATTTCATAAG-GAGGTTATCAAAATTTCATAGGGAGGTTATC
* * * * * * *
34681 ---ATTTCAGAGGGAGAGGTTATCAAATTTTCATTGTGTGG-TAGTT
1 AAAATTTCATA-AG-GAGGTTATCAAAATTTCATAGGGAGGTTA-TC
* * * * *
34724 AAAATTTCATAATGAGTTTATCAAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
* * * * **
34767 AAAATTTCATATGTAAGTTATCGTAAATTT-AT-GGTGTAATTAATTATC
1 AAAATTTCATAAGGAGGTTATC-AAAATTTCATAGG-G--A--GGTTATC
** * * * ***
34815 AAAATTTCATTGGGA-GTTATCAAAATTTAATTGTGTTCTTATC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
* * * * * *
34858 AAAATTT-AGT-AGAATGTTAACAAAATTTTATAAGGAGGTTATAAT
1 AAAATTTCA-TAAGGAGGTTATCAAAATTTCATAGGGAGGTTAT--C
* * *
34903 AAAATTT-ATAGGGATGTTATCAAAATTTCATA-AGATGGTTATC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGA-GGTTATC
* * * *
34946 AAAATTTCATGAGGTGGTTTTCAAAATTTC-T--TGAGGTTATC
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
* * *
34987 AAAATTTCA-AA--TGGTTATCAAAATTTTATAGGGAGTGGTTTATA
1 AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGA--GG-TTATC
* * * *
35031 AAAAGTTCAT-AGTGAGG-TATCACAATTTTAT-GGTATGGTTATC
1 AAAATTTCATAAG-GAGGTTATCAAAATTTCATAGGGA-GGTTATC
* * * * * * * *
35074 AAAAATTTCATAATGTGATTACCAATATTTTATCGGAAGGTTATC
1 -AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
* * * * * *
35119 AAAATATCATAATGTGCGCTTACCAACATTTCATTGGGAGGTTATC
1 AAAATTTCATAA-G-GAGGTTATCAAAATTTCATAGGGAGGTTATC
* *
35165 AAAATTTCAT-GGGTGGTTATCAAAATTTCAT
1 AAAATTTCATAAGGAGGTTATCAAAATTTCAT
35196 TAAGTAGTTA
Statistics
Matches: 641, Mismatches: 155, Indels: 143
0.68 0.17 0.15
Matches are distributed among these distances:
34 1 0.00
35 2 0.00
38 18 0.03
39 18 0.03
40 1 0.00
41 20 0.03
42 55 0.09
43 137 0.21
44 191 0.30
45 65 0.10
46 64 0.10
47 12 0.02
48 21 0.03
49 2 0.00
50 1 0.00
51 1 0.00
52 1 0.00
53 17 0.03
54 14 0.02
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (44 bp):
AAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGAGGTTATC
Found at i:34502 original size:22 final size:22
Alignment explanation
Indices: 34285--34521 Score: 102
Period size: 22 Copynumber: 10.8 Consensus size: 22
34275 TTATTAAAAT
34285 AAAATTTCATAAG-GATG-TTATC
1 AAAATTTCAT-AGTGA-GATTATC
*
34307 AAAATTTCATA-TGGAGGTTATC
1 AAAATTTCATAGT-GAGATTATC
*
34329 AAAATTTCATAAG-GAGGTTATC
1 AAAATTTCAT-AGTGAGATTATC
* * * *
34351 GAAA-TTCAT-GGGAAGGTTGTC
1 AAAATTTCATAGTG-AGATTATC
* *
34372 AAAATTTCACAAG-GAGGTTA-C
1 AAAATTTCA-TAGTGAGATTATC
* ** *
34393 TAAAATTTCATACTCTGGTTATC
1 -AAAATTTCATAGTGAGATTATC
*
34416 AAAATTTCATAAG-GCGATTATC
1 AAAATTTCAT-AGTGAGATTATC
* * *
34438 GAAATCTT-ATA-TGGAGGTTATT
1 AAAAT-TTCATAGT-GAGATTATC
34460 AAAATTTCATAG-GAAGATTATC
1 AAAATTTCATAGTG-AGATTATC
* * *
34482 AAAATTTCATAGTGTGCTTATA
1 AAAATTTCATAGTGAGATTATC
* *
34504 AAAATTACATATTGAGAT
1 AAAATTTCATAGTGAGAT
34522 AGAGTGAGCT
Statistics
Matches: 167, Mismatches: 27, Indels: 42
0.71 0.11 0.18
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 23 0.14
22 134 0.80
23 7 0.04
24 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAGTGAGATTATC
Found at i:34769 original size:21 final size:22
Alignment explanation
Indices: 34724--34777 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
34714 TGTGGTAGTT
* *
34724 AAAATTTCATAATGAGTTTATC
1 AAAATTTCATAATGAGATTAAC
*
34746 AAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAATGAGATTAAC
34767 AAAATTTCATA
1 AAAATTTCATA
34778 TGTAAGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAATGAGATTAAC
Found at i:34836 original size:21 final size:21
Alignment explanation
Indices: 34810--35214 Score: 87
Period size: 22 Copynumber: 18.6 Consensus size: 21
34800 GTGTAATTAA
34810 TTATCAAAATTTCATTGGGAG
1 TTATCAAAATTTCATTGGGAG
* ***
34831 TTATCAAAATTTAATTGTGTTC
1 TTATCAAAATTTCATTG-GGAG
* * *
34853 TTATCAAAATTT-AGTAGAATG
1 TTATCAAAATTTCATTGGGA-G
* * **
34874 TTAACAAAATTTTATAAGGAGG
1 TTATCAAAATTTCATTGGGA-G
* *
34896 TTATAATAAAATTT-ATAGGGATG
1 TTAT--CAAAATTTCATTGGGA-G
**
34919 TTATCAAAATTTCA-TAAGATGG
1 TTATCAAAATTTCATTGGGA--G
*
34941 TTATCAAAATTTCA-TGAGGTGG
1 TTATCAAAATTTCATTG-GG-AG
* *
34963 TTTTCAAAATTTC-TTGAG-G
1 TTATCAAAATTTCATTGGGAG
*
34982 TTATCAAAATTTCAAAT--G-G
1 TTATCAAAATTTC-ATTGGGAG
* *
35001 TTATCAAAATTTTATAGGGAGTGG
1 TTATCAAAATTTCATTGGGA---G
* * * *
35025 TTTATAAAAAGTTCATAGTGAG
1 -TTATCAAAATTTCATTGGGAG
* * * *
35047 GTATCACAATTTTA-TGGTATGG
1 TTATCAAAATTTCATTGGGA--G
*
35069 TTATCAAAAATTTCATAATGTGA-
1 TTATC-AAAATTTCAT--TGGGAG
* * * * *
35092 TTACCAATATTTTATCGGAAGG
1 TTATCAAAATTTCATTGGGA-G
* * *
35114 TTATCAAAATATCATAATGTGCG
1 TTATCAAAATTTCAT--TGGGAG
* *
35137 CTTACCAACATTTCATTGGGAGG
1 -TTATCAAAATTTCATTGGGA-G
*
35160 TTATCAAAATTTCA-TGGGTGG
1 TTATCAAAATTTCATTGGG-AG
* *
35181 TTATCAAAATTTCATTAAGTAG
1 TTATCAAAATTTCATT-GGGAG
*
35203 TTATTAAAATTT
1 TTATCAAAATTT
35215 TTATAGGGAT
Statistics
Matches: 274, Mismatches: 76, Indels: 67
0.66 0.18 0.16
Matches are distributed among these distances:
18 1 0.00
19 27 0.10
20 6 0.02
21 68 0.25
22 106 0.39
23 26 0.09
24 21 0.08
25 16 0.06
26 3 0.01
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (21 bp):
TTATCAAAATTTCATTGGGAG
Found at i:34927 original size:45 final size:45
Alignment explanation
Indices: 34858--34944 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 45
34848 TGTTCTTATC
*
34858 AAAATTTAGTAGAATGTTAACAAAATTTTATAAGGA-GGTTATAAT
1 AAAATTTAGTAGAATGTTAACAAAATTTCATAA-GATGGTTATAAT
* *
34903 AAAATTTA-TAGGGATGTTATCAAAATTTCATAAGATGGTTAT
1 AAAATTTAGTA-GAATGTTAACAAAATTTCATAAGATGGTTAT
34945 CAAAATTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 4 0.11
45 33 0.89
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.37
Consensus pattern (45 bp):
AAAATTTAGTAGAATGTTAACAAAATTTCATAAGATGGTTATAAT
Found at i:34953 original size:22 final size:22
Alignment explanation
Indices: 34918--35214 Score: 136
Period size: 22 Copynumber: 13.6 Consensus size: 22
34908 TTATAGGGAT
34918 GTTATCAAAATTTCATAAGATG
1 GTTATCAAAATTTCATAAGATG
* *
34940 GTTATCAAAATTTCATGAGGTG
1 GTTATCAAAATTTCATAAGATG
* *
34962 GTTTTCAAAATTTC-T-TGA-G
1 GTTATCAAAATTTCATAAGATG
34981 GTTATCAAAATTTC--AA-ATG
1 GTTATCAAAATTTCATAAGATG
* *
35000 GTTATCAAAATTTTATAGGGAGTG
1 GTTATCAAAATTTCATA-AGA-TG
* *
35024 GTTTATAAAAAGTTCAT-AG-TG
1 G-TTATCAAAATTTCATAAGATG
* * * *
35045 AGGTATCACAATTTTAT-GGTATG
1 -GTTATCAAAATTTCATAAG-ATG
35068 GTTATCAAAAATTTCATAATG-TG
1 GTTATC-AAAATTTCATAA-GATG
* * * * ** *
35091 ATTACCAATATTTTATCGGAAG
1 GTTATCAAAATTTCATAAGATG
*
35113 GTTATCAAAATATCATAATG-TG
1 GTTATCAAAATTTCATAA-GATG
* * **
35135 CGCTTACCAACATTTCATTGGGA-G
1 -G-TTATCAAAATTTCA-TAAGATG
* *
35159 GTTATCAAAATTTCAT-GGGTG
1 GTTATCAAAATTTCATAAGATG
*
35180 GTTATCAAAATTTCATTAAG-TA
1 GTTATCAAAATTTCA-TAAGATG
*
35202 GTTATTAAAATTT
1 GTTATCAAAATTT
35215 TTATAGGGAT
Statistics
Matches: 203, Mismatches: 49, Indels: 46
0.68 0.16 0.15
Matches are distributed among these distances:
18 1 0.00
19 28 0.14
20 3 0.01
21 33 0.16
22 86 0.42
23 22 0.11
24 16 0.08
25 14 0.07
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGATG
Found at i:35161 original size:46 final size:44
Alignment explanation
Indices: 35067--35174 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 44
35057 TTTATGGTAT
* *
35067 GGTTATCAAAAATTTCATAATGTGATTACCAATATTTTATCGGAA
1 GGTTATC-AAAATTTCATAATGTGATTACCAACATTTCATCGGAA
* * * *
35112 GGTTATCAAAATATCATAATGTGCGCTTACCAACATTTCATTGGGA
1 GGTTATCAAAATTTCATAATGT--GATTACCAACATTTCATCGGAA
35158 GGTTATCAAAATTTCAT
1 GGTTATCAAAATTTCAT
35175 GGGTGGTTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 14 0.26
45 7 0.13
46 33 0.61
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAATGTGATTACCAACATTTCATCGGAA
Found at i:35365 original size:20 final size:20
Alignment explanation
Indices: 35317--35367 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
35307 TCATAGTGTA
35317 ATTATCAAAACTTTATATGG
1 ATTATCAAAACTTTATATGG
*
35337 AGGTTATCAAAATTTTATAAT-G
1 A--TTATCAAAACTTTAT-ATGG
35359 ATTATCAAA
1 ATTATCAAA
35368 TTTCATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 9 0.33
22 16 0.59
23 2 0.07
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (20 bp):
ATTATCAAAACTTTATATGG
Found at i:41733 original size:13 final size:13
Alignment explanation
Indices: 41715--41741 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41705 ACAAAGTCCC
41715 TCTCTTACAAATT
1 TCTCTTACAAATT
41728 TCTCTTACAAATT
1 TCTCTTACAAATT
41741 T
1 T
41742 AAGGATCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (13 bp):
TCTCTTACAAATT
Found at i:43320 original size:41 final size:41
Alignment explanation
Indices: 43275--43356 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
43265 GCTTCTATGA
43275 AGCTTTCTTAAGAATAATAGTTTTCCCGTGCAAATGGATTC
1 AGCTTTCTTAAGAATAATAGTTTTCCCGTGCAAATGGATTC
43316 AGCTTTCTTAAGAATAATAGTTTTCCCGTGCAAATGGATTC
1 AGCTTTCTTAAGAATAATAGTTTTCCCGTGCAAATGGATTC
43357 TTGGAAACGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (41 bp):
AGCTTTCTTAAGAATAATAGTTTTCCCGTGCAAATGGATTC
Found at i:44517 original size:14 final size:14
Alignment explanation
Indices: 44500--44536 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
44490 TATAATCAAA
44500 TAATTAATAACAAG
1 TAATTAATAACAAG
44514 TAATTAATAACAAG
1 TAATTAATAACAAG
44528 TAA-TAATAA
1 TAATTAATAA
44537 TATATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (14 bp):
TAATTAATAACAAG
Found at i:45626 original size:5 final size:5
Alignment explanation
Indices: 45616--45646 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
45606 TTTTTACTTT
*
45616 ATATA ACATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA A
45647 GGATAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (5 bp):
ATATA
Found at i:48448 original size:22 final size:22
Alignment explanation
Indices: 48421--48462 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
48411 GGCAAACCCG
*
48421 TAACCCAAATGACCCGAGAAGT
1 TAACCCAAATGACCCAAGAAGT
**
48443 TAACCCGGATGACCCAAGAA
1 TAACCCAAATGACCCAAGAA
48463 TATTATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.29, G:0.19, T:0.12
Consensus pattern (22 bp):
TAACCCAAATGACCCAAGAAGT
Found at i:49789 original size:31 final size:30
Alignment explanation
Indices: 49748--49818 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
49738 TGACACGTGG
*
49748 ACTTTCAAAAT-TCAATCATTTTGCCCCCTAA
1 ACTTTTAAAATCTCAA-CATTTTG-CCCCTAA
**
49779 ACTTTTAAAATCTTGACATTTTGCCCCTAA
1 ACTTTTAAAATCTCAACATTTTGCCCCTAA
*
49809 ACTCTTAAAA
1 ACTTTTAAAA
49819 CTTTGTTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 16 0.46
31 17 0.49
32 2 0.06
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (30 bp):
ACTTTTAAAATCTCAACATTTTGCCCCTAA
Found at i:51596 original size:18 final size:18
Alignment explanation
Indices: 51549--51596 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
51539 TAGGGCAGAT
*
51549 AATAATATA-ATGATATA
1 AATAATATATATTATATA
*
51566 TATAAT-TATTATTATATA
1 AATAATATA-TATTATATA
51584 AATAATATATATT
1 AATAATATATATT
51597 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 2 0.08
17 5 0.20
18 16 0.64
19 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAATATATATTATATA
Found at i:55946 original size:23 final size:21
Alignment explanation
Indices: 55904--55949 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
55894 TGAACAAATA
*
55904 AAGAAAATTAAGAAAGCAATT
1 AAGAAAATTAAGAAAACAATT
55925 AAGAAAATTAAAGGAAAACAATT
1 AAGAAAATT-AA-GAAAACAATT
55948 AA
1 AA
55950 TCAGAGAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.65, C:0.04, G:0.13, T:0.17
Consensus pattern (21 bp):
AAGAAAATTAAGAAAACAATT
Found at i:66001 original size:19 final size:19
Alignment explanation
Indices: 65977--66017 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
65967 ACCCAATATT
65977 TCTGTCATGTCCAGTTAAG
1 TCTGTCATGTCCAGTTAAG
65996 TCTGTCATGTCCAGTTAAG
1 TCTGTCATGTCCAGTTAAG
66015 TCT
1 TCT
66018 CCCATAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (19 bp):
TCTGTCATGTCCAGTTAAG
Found at i:66436 original size:10 final size:11
Alignment explanation
Indices: 66413--66438 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
66403 ATGTGCTACC
66413 TTTTCTTTCTT
1 TTTTCTTTCTT
66424 TTTTCTTTCTT
1 TTTTCTTTCTT
66435 TTTT
1 TTTT
66439 TTTTAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:67837 original size:13 final size:13
Alignment explanation
Indices: 67819--67846 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
67809 TACCAACTTG
67819 AACGCAAAAGCTT
1 AACGCAAAAGCTT
67832 AACGCAAAAGCTT
1 AACGCAAAAGCTT
67845 AA
1 AA
67847 GACCTAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (13 bp):
AACGCAAAAGCTT
Found at i:68296 original size:110 final size:110
Alignment explanation
Indices: 68175--68390 Score: 380
Period size: 110 Copynumber: 2.0 Consensus size: 110
68165 TGAAAAACAG
*
68175 TTTTTTATCTCCAAACGCAATGTCAAACCTTTGATTTCTTGGGTCTT-TCAAGTATATGTGTCAT
1 TTTTTTATCTCCAAACGCAATGTCAAACCTTTGATTTCTTGGGTCTTAT-AAGTATATATGTCAT
*
68239 TCTTACAGCCCATCCCTTATGATATGGGATGCGACACTAACAGCTT
65 TCTTACAGCCCATCCCTTATGATATGGGATGCAACACTAACAGCTT
*
68285 TTTTTTATCTCCAAGCGCAATGTCAAACCTTTGATTTCTTGGGTCTTATAAGTATATATGTCATT
1 TTTTTTATCTCCAAACGCAATGTCAAACCTTTGATTTCTTGGGTCTTATAAGTATATATGTCATT
*
68350 CTTACAGCCCATCCCTTATGATGTGGGATGCAACACTAACA
66 CTTACAGCCCATCCCTTATGATATGGGATGCAACACTAACA
68391 TGTGAATTCC
Statistics
Matches: 101, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
110 100 0.99
111 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (110 bp):
TTTTTTATCTCCAAACGCAATGTCAAACCTTTGATTTCTTGGGTCTTATAAGTATATATGTCATT
CTTACAGCCCATCCCTTATGATATGGGATGCAACACTAACAGCTT
Found at i:75608 original size:24 final size:24
Alignment explanation
Indices: 75579--75627 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
75569 ATTTACCACT
* *
75579 TTGTCTTCATCATTTTCGGTGCAG
1 TTGTCTTCATCACTTTCAGTGCAG
*
75603 TTGTCTTTATCACTTTCAGTGCAG
1 TTGTCTTCATCACTTTCAGTGCAG
75627 T
1 T
75628 CATCACCTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (24 bp):
TTGTCTTCATCACTTTCAGTGCAG
Found at i:82749 original size:23 final size:23
Alignment explanation
Indices: 82719--82764 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
82709 TACCACTAAT
82719 CGATGATGAACCAAGTTTAACCG
1 CGATGATGAACCAAGTTTAACCG
82742 CGATGATGAACCAAGTTTAACCG
1 CGATGATGAACCAAGTTTAACCG
82765 TTTCTGTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (23 bp):
CGATGATGAACCAAGTTTAACCG
Found at i:86979 original size:1 final size:1
Alignment explanation
Indices: 86975--87001 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
86965 CTTTTTTACG
86975 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.