Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010039.1 Corchorus capsularis cultivar CVL-1 contig10060, 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: 84660
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1878 original size:2 final size:2
Alignment explanation
Indices: 1873--1919 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1863 CAGGAAAAAA
1873 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1915 AG AG A
1 AG AG A
1920 AGACAAGGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13275 original size:11 final size:11
Alignment explanation
Indices: 13261--13286 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13251 TTTCTTCTCC
13261 TTTTGTTTTGT
1 TTTTGTTTTGT
13272 TTTTGTTTTGT
1 TTTTGTTTTGT
13283 TTTT
1 TTTT
13287 TATTTCGAAT
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:0.00, G:0.15, T:0.85
Consensus pattern (11 bp):
TTTTGTTTTGT
Found at i:16754 original size:165 final size:164
Alignment explanation
Indices: 16439--16765 Score: 455
Period size: 165 Copynumber: 2.0 Consensus size: 164
16429 TAAAAGTACG
* *
16439 AATAATGGAAAACTTTATATTTTCCGATTGTATCCTTTTTTCAAATATATTTCTAAATTGACATT
1 AATAATGGAAAACTTTATATTTTCCGATTGCACCCTTTTTTCAAATATATTTCTAAATTGACATT
* *
16504 ATTAAAATTTATTATTTAAAAATTAATTATAAAAGTTCAATTTAGACCGAATTATAAGTTTGTAA
66 ATTAAAATTTATTATTT--AAATTAATTATAAAAGTTCAATTTAAACCAAATTATAAGTTTGTAA
*
16569 AATTGATTTTCATTGATGAACATGCAAATTTCTACA
129 AATTGATTTTCATCGATGAACATGCAAATTTCTACA
* * **
16605 AATAATGGGAAACTTTATGTTTTCCGATTGCACCCTTTTTTCTAAATATATTTCTAAATTTCCAT
1 AATAATGGAAAACTTTATATTTTCCGATTGCACCCTTTTTTC-AAATATATTTCTAAATTGACAT
* *
16670 TATTAAAATTTAGTATAATTT-TATT-ATTA-AAAATTTCAATTTAAACCAAATTATAAGTTTGT
65 TATTAAAATTTA-T-T-ATTTAAATTAATTATAAAAGTTCAATTTAAACCAAATTATAAGTTTGT
*
16732 CAAATTGATTTT-AGTCGATGAACATGCAAATTTC
127 AAAATTGATTTTCA-TCGATGAACATGCAAATTTC
16766 CTTTATTATT
Statistics
Matches: 144, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
164 1 0.01
165 60 0.42
166 42 0.29
167 35 0.24
168 1 0.01
169 1 0.01
170 4 0.03
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (164 bp):
AATAATGGAAAACTTTATATTTTCCGATTGCACCCTTTTTTCAAATATATTTCTAAATTGACATT
ATTAAAATTTATTATTTAAATTAATTATAAAAGTTCAATTTAAACCAAATTATAAGTTTGTAAAA
TTGATTTTCATCGATGAACATGCAAATTTCTACA
Found at i:16806 original size:19 final size:20
Alignment explanation
Indices: 16779--16816 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
16769 TATTATTATT
16779 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
16799 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
16817 AATGTTAATA
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:17011 original size:22 final size:22
Alignment explanation
Indices: 16983--17188 Score: 133
Period size: 22 Copynumber: 9.3 Consensus size: 22
16973 TGTCTCTATG
*
16983 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* * *
17005 TGGTTATTATAATTCCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
17028 -GGTTATCAAAA-TTC-TATGGTA
1 TGGTTATCAAAATTTCATA-GG-A
17049 TGGTTA-CTAAAATTTCATAGTGA
1 TGGTTATC-AAAATTTCATAG-GA
*
17072 -AGTTA-CTAAAATTTCATAGTGA
1 TGGTTATC-AAAATTTCATAG-GA
17094 -GGTTA-CTAAAATTTCATAGTG-
1 TGGTTATC-AAAATTTCATAG-GA
* *
17115 TAGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
17137 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
17161 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
17183 TGGTTA
1 TGGTTA
17189 ATTATCACAA
Statistics
Matches: 153, Mismatches: 18, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
19 1 0.01
20 3 0.02
21 5 0.03
22 115 0.75
23 9 0.06
24 20 0.13
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:17083 original size:44 final size:44
Alignment explanation
Indices: 17050--17154 Score: 156
Period size: 44 Copynumber: 2.3 Consensus size: 44
17040 TCTATGGTAT
*
17050 GGTTACTAAAATTTCATAGTGAAGTTACTAAAATTTCATAGTGA
1 GGTTACTAAAATTTCATAGTGAAGTTACCAAAATTTCATAGTGA
* *
17094 GGTTACTAAAATTTCATAGTGTAGTTACCAAAATTTCATAGGATCA
1 GGTTACTAAAATTTCATAGTGAAGTTACCAAAATTTCATA-G-TGA
*
17140 GGTTATTAAAATTTC
1 GGTTACTAAAATTTC
17155 TTAGGTTGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 38 0.69
45 1 0.02
46 16 0.29
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (44 bp):
GGTTACTAAAATTTCATAGTGAAGTTACCAAAATTTCATAGTGA
Found at i:17334 original size:22 final size:22
Alignment explanation
Indices: 17258--17362 Score: 74
Period size: 22 Copynumber: 4.8 Consensus size: 22
17248 TACGAATTAC
* *
17258 ATAGTGTGGTTAACAAAATTTT
1 ATAGTGAGGTTATCAAAATTTT
* *
17280 ATTAG-GAGGTTA-CTAATATTTC
1 A-TAGTGAGGTTATC-AAAATTTT
* *
17302 ATTGGGAGGTTATCAAAATTTT
1 ATAGTGAGGTTATCAAAATTTT
* * *
17324 ATAGTGTGGTTATTAAAATTTC
1 ATAGTGAGGTTATCAAAATTTT
17346 ATA-TGAAGGTTAT-AAAA
1 ATAGTG-AGGTTATCAAAA
17363 GTCTCAATTT
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
21 9 0.14
22 53 0.80
23 4 0.06
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (22 bp):
ATAGTGAGGTTATCAAAATTTT
Found at i:17356 original size:44 final size:44
Alignment explanation
Indices: 17265--17362 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
17255 TACATAGTGT
* * *
17265 GGTTAACAAAATTTTATTAGGAGGTTACTAATATTTCATTGGGA
1 GGTTATCAAAATTTTATTAGGAGGTTACTAAAATTTCATTGGAA
* *
17309 GGTTATCAAAATTTTA-TAGTGTGGTTATTAAAATTTCATAT-GAA
1 GGTTATCAAAATTTTATTAG-GAGGTTACTAAAATTTCAT-TGGAA
17353 GGTTAT-AAAA
1 GGTTATCAAAA
17363 GTCTCAATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
43 7 0.15
44 39 0.83
45 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (44 bp):
GGTTATCAAAATTTTATTAGGAGGTTACTAAAATTTCATTGGAA
Found at i:17410 original size:20 final size:22
Alignment explanation
Indices: 17387--17485 Score: 71
Period size: 21 Copynumber: 4.5 Consensus size: 22
17377 AGGAGTACCA
*
17387 AAATTTGATAG-GAGATTATC-
1 AAATTTCATAGAGAGATTATCG
* *
17407 AAATCTCATAGAGTGATTATCG
1 AAATTTCATAGAGAGATTATCG
* * *
17429 AAATTTCATAAAAATTGGATTATCA
1 AAATTTCATAGAGA---GATTATCG
*
17454 AAATTTACAT-GA-AGATTATCA
1 AAATTT-CATAGAGAGATTATCG
17475 AAATTTCATAG
1 AAATTTCATAG
17486 TGTTAACAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
20 12 0.19
21 23 0.37
22 10 0.16
24 1 0.02
25 14 0.22
26 3 0.05
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (22 bp):
AAATTTCATAGAGAGATTATCG
Found at i:17437 original size:22 final size:20
Alignment explanation
Indices: 17387--17438 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
17377 AGGAGTACCA
*
17387 AAATTTGATAGGAGATTATC
1 AAATTTCATAGGAGATTATC
* *
17407 AAATCTCATAGAGTGATTATC
1 AAATTTCATAG-GAGATTATC
17428 GAAATTTCATA
1 -AAATTTCATA
17439 AAAATTGGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 9 0.35
21 8 0.31
22 9 0.35
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (20 bp):
AAATTTCATAGGAGATTATC
Found at i:17592 original size:21 final size:21
Alignment explanation
Indices: 17368--17605 Score: 79
Period size: 22 Copynumber: 11.3 Consensus size: 21
17358 TAAAAGTCTC
*
17368 AATTTCATAAG-GAG-TACCAA
1 AATTTCATAAGAG-GTTATCAA
* * *
17388 AATTTGATAGGAGATTATC-A
1 AATTTCATAAGAGGTTATCAA
* *
17408 AATCTCAT-AGAGTGATTATCGA
1 AATTTCATAAGAG-G-TTATCAA
*
17430 AATTTCATAAAAATTGGATTATCAA
1 AATTTCAT-AAGA--GG-TTATCAA
17455 AATTTACATGAAGA--TTATCAA
1 AATTT-CAT-AAGAGGTTATCAA
* *
17476 AATTTCAT-AG-TGTTAACAA
1 AATTTCATAAGAGGTTATCAA
*
17495 AATTTCA-AAGCGAGGTTATCCA
1 AATTTCATAA--GAGGTTATCAA
* * * * *
17517 AATTACACAATGTGATTATCAT
1 AATTTCATAA-GAGGTTATCAA
* * *
17539 AATTTCATAGAGGGGTCAACAA
1 AATTTCATA-AGAGGTTATCAA
*
17561 AA--T-A-AAAAGGTTATCAA
1 AATTTCATAAGAGGTTATCAA
*
17578 AATTTCATAAGAGGTTAACAA
1 AATTTCATAAGAGGTTATCAA
*
17599 ATTTTCA
1 AATTTCA
17606 AAATATGATT
Statistics
Matches: 159, Mismatches: 37, Indels: 43
0.67 0.15 0.18
Matches are distributed among these distances:
17 10 0.06
18 3 0.02
19 19 0.12
20 21 0.13
21 39 0.25
22 42 0.26
23 3 0.02
24 2 0.01
25 13 0.08
26 7 0.04
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (21 bp):
AATTTCATAAGAGGTTATCAA
Found at i:17754 original size:22 final size:21
Alignment explanation
Indices: 17726--17997 Score: 119
Period size: 22 Copynumber: 12.5 Consensus size: 21
17716 TCAGGGAGGA
*
17726 TATCAAAATTTCATATGAATGT
1 TATCAAAATTTCATA-GTATGT
*
17748 TATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGTAT-GT
*
17770 TTTCAAAATTTCATAGTATGT
1 TATCAAAATTTCATAGTATGT
* *
17791 AGATCAAAATTTCATAGGGA-GAT
1 -TATCAAAATTTCATA-GTATG-T
* * *
17814 TAACAAAATTTCATAATCAGGT
1 TATCAAAATTTCATAGT-ATGT
** *
17836 TATCAAAAAATCATAGGGA-GCT
1 TATCAAAATTTCATA-GTATG-T
17858 TATCAAAA-TT--T-GTA-GT
1 TATCAAAATTTCATAGTATGT
* ** **
17874 TATCAAGATTTCATAACAAAAT
1 TATCAAAATTTCAT-AGTATGT
* * *
17896 TATCAAAATTTTATAGGGAGGCT
1 TATCAAAATTTCATA-GTATG-T
* *
17919 TATCAAAATTTTATGGGAAG-ATTT
1 TATCAAAATTTCAT----AGTATGT
* *
17943 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAG-TATGT
*
17965 TATCAAAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGTATG-T
17987 TATCAAAATTT
1 TATCAAAATTT
17998 TAAAGTGTGA
Statistics
Matches: 191, Mismatches: 36, Indels: 46
0.70 0.13 0.17
Matches are distributed among these distances:
16 8 0.04
17 5 0.03
19 2 0.01
20 2 0.01
21 9 0.05
22 129 0.68
23 19 0.10
24 14 0.07
25 1 0.01
26 1 0.01
27 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (21 bp):
TATCAAAATTTCATAGTATGT
Found at i:17821 original size:44 final size:43
Alignment explanation
Indices: 17707--18134 Score: 227
Period size: 44 Copynumber: 9.8 Consensus size: 43
17697 TTATGGAGTA
*
17707 ATCAAAATTTC--AGGGAGGA-TATCAAAATTTCATATGAATGTT
1 ATCAAAATTTCATAGGGA-GATTATCAAAATTTCATA-GTATGTT
** * *
17749 ATCAAAATTTCATAGTTTAG-TTTTCAAAATTTCATAGTATGTAG
1 ATCAAAATTTCATAG-GGAGATTATCAAAATTTCATAGTATGT-T
* * *
17793 ATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATCAGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGT-ATGTT
** *
17837 ATCAAAAAATCATAGGGAGCTTATCAAAA-TT--T-GTA-GTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTATGTT
* *** * * * *
17875 ATCAAGATTTCATAACAAAATTATCAAAATTTTATAGGGAGGCTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATA-GTATG-TT
* * *
17920 ATCAAAATTTTAT-GGGAAGATTTTATCAAAATTTCATAGCGAGGTT
1 ATCAAAATTTCATAGGG-AGA--TTATCAAAATTTCATAG-TATGTT
* * * * *
17966 ATCAAAATTTCATAGTGTGATTATCAAAATTTTAAAGTGTGATT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTATG-TT
* * * * * *
18010 A-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACGT-GGTT
1 ATC-AA-AATTTCATAGGGAGATTATCAAAATTTCAT-A-GTATGTT
* * * * * *
18054 ATCAATATATCATATGGAGATTATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGT-AT-GTT
*
18099 ATCAAAATTTCATTGGGA-AGTTATCAAAATTTCATA
1 ATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATA
18135 TTGAGATCTT
Statistics
Matches: 290, Mismatches: 66, Indels: 57
0.70 0.16 0.14
Matches are distributed among these distances:
38 24 0.08
39 3 0.01
40 1 0.00
41 2 0.01
42 13 0.04
43 15 0.05
44 137 0.47
45 55 0.19
46 19 0.07
47 21 0.07
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (43 bp):
ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTATGTT
Found at i:17850 original size:66 final size:66
Alignment explanation
Indices: 17727--17851 Score: 146
Period size: 66 Copynumber: 1.9 Consensus size: 66
17717 CAGGGAGGAT
* * * * * **
17727 ATCAAAATTTCATATGAATGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAGTATGTA
1 ATCAAAATTTCATAGGAATGTTAACAAAATTTCATAGATCAGTTATCAAAAAATCATAGTATGTA
17792 G
66 G
*
17793 ATCAAAATTTCATAGGGA-GATTAACAAAATTTCATA-ATCAGGTTATCAAAAAATCATAG
1 ATCAAAATTTCATAGGAATG-TTAACAAAATTTCATAGATCA-GTTATCAAAAAATCATAG
17852 GGAGCTTATC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
65 3 0.06
66 46 0.94
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (66 bp):
ATCAAAATTTCATAGGAATGTTAACAAAATTTCATAGATCAGTTATCAAAAAATCATAGTATGTA
G
Found at i:18004 original size:22 final size:22
Alignment explanation
Indices: 17942--18010 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
17932 TGGGAAGATT
* * * *
17942 TTATCAAAATTTCATAGCGAGG
1 TTATCAAAATTTCAAAGTGTGA
*
17964 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCAAAGTGTGA
*
17986 TTATCAAAATTTTAAAGTGTGA
1 TTATCAAAATTTCAAAGTGTGA
18008 TTA
1 TTA
18011 CTAACAATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCAAAGTGTGA
Found at i:18235 original size:22 final size:22
Alignment explanation
Indices: 18210--18270 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
18200 GTATAAGAAG
*
18210 ATTATTGAAA-TTCTATAGTATC
1 ATTATTAAAATTTC-ATAGTATC
18232 ATTATTAAAATTTCATAGTAAT-
1 ATTATTAAAATTTCATAGT-ATC
* *
18254 GTTATCAAAATTTCATA
1 ATTATTAAAATTTCATA
18271 ATGGGATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 29 0.85
23 5 0.15
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTATTAAAATTTCATAGTATC
Found at i:19030 original size:19 final size:20
Alignment explanation
Indices: 18989--19032 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
18979 TCCTAATGTG
*
18989 TAATTATTTTATTTGACTTA
1 TAATTAATTTATTTGACTTA
19009 TAATTAATTT-TTTG-CTTGA
1 TAATTAATTTATTTGACTT-A
19028 TAATT
1 TAATT
19033 GTAACTCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 10 0.45
20 9 0.41
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (20 bp):
TAATTAATTTATTTGACTTA
Found at i:57711 original size:111 final size:111
Alignment explanation
Indices: 57573--57773 Score: 384
Period size: 111 Copynumber: 1.8 Consensus size: 111
57563 AATTATATAG
*
57573 CATAAACCCTCTATCAGTCACTTTTTTGTCTGCATCGCTGCTTCCTTGTTTAAAGATTCCATTCA
1 CATAAACCCTCTATCAGTCACTTTTTTGTCTGCATCACTGCTTCCTTGTTTAAAGATTCCATTCA
57638 CATTTCCTTCAACTCATATTCTCTTCCTTGCAAATTTCCTTCAACT
66 CATTTCCTTCAACTCATATTCTCTTCCTTGCAAATTTCCTTCAACT
*
57684 CATAAACCCTCTGTCAGTCACTTTTTTGTCTGCATCACTGCTTCCTTGTTTAAAGATTCCATTCA
1 CATAAACCCTCTATCAGTCACTTTTTTGTCTGCATCACTGCTTCCTTGTTTAAAGATTCCATTCA
57749 CATTTCCTTCAACTCATATTCTCTT
66 CATTTCCTTCAACTCATATTCTCTT
57774 AGCACAATAT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 88 1.00
ACGTcount: A:0.21, C:0.29, G:0.07, T:0.42
Consensus pattern (111 bp):
CATAAACCCTCTATCAGTCACTTTTTTGTCTGCATCACTGCTTCCTTGTTTAAAGATTCCATTCA
CATTTCCTTCAACTCATATTCTCTTCCTTGCAAATTTCCTTCAACT
Found at i:65344 original size:12 final size:12
Alignment explanation
Indices: 65327--65353 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
65317 TCTTATTATA
65327 TTTTGTTCTTGT
1 TTTTGTTCTTGT
65339 TTTTGTTCTTGT
1 TTTTGTTCTTGT
65351 TTT
1 TTT
65354 CTTTTTATTT
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:0.00, C:0.07, G:0.15, T:0.78
Consensus pattern (12 bp):
TTTTGTTCTTGT
Found at i:66148 original size:20 final size:20
Alignment explanation
Indices: 66123--66161 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
66113 CTTAGGTTCA
66123 ACTCTCACGGAATGTGAGTC
1 ACTCTCACGGAATGTGAGTC
66143 ACTCTCACGGAATGTGAGT
1 ACTCTCACGGAATGTGAGT
66162 TTATTTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (20 bp):
ACTCTCACGGAATGTGAGTC
Found at i:73702 original size:19 final size:19
Alignment explanation
Indices: 73678--73714 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
73668 TTTGAGGGAA
73678 ATATATA-AATAT-ATAAT
1 ATATATATAATATAATAAT
73695 ATATATATAATATAATAAT
1 ATATATATAATATAATAAT
73714 A
1 A
73715 ACAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 5 0.28
19 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATATATAATATAATAAT
Found at i:78136 original size:48 final size:48
Alignment explanation
Indices: 78063--78160 Score: 135
Period size: 48 Copynumber: 2.0 Consensus size: 48
78053 CACCAATCTT
* * * *
78063 AAACATCATTCTGCGACAGAAGCCAACCATAATTCTACCGTAGAAGTC
1 AAACACCATTATGCGACAGAAGCCAACCACAATTCTACCGCAGAAGTC
*
78111 AAACACCATTATGCGGA-AGAAGCCAACCACAATTCTACTGCAGAAGTC
1 AAACACCATTATGC-GACAGAAGCCAACCACAATTCTACCGCAGAAGTC
78159 AA
1 AA
78161 GTATCATCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
48 42 0.95
49 2 0.05
ACGTcount: A:0.40, C:0.27, G:0.15, T:0.18
Consensus pattern (48 bp):
AAACACCATTATGCGACAGAAGCCAACCACAATTCTACCGCAGAAGTC
Found at i:78155 original size:24 final size:24
Alignment explanation
Indices: 78079--78156 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
78069 CATTCTGCGA
*
78079 CAGAAGCCAACCATAATTCTACCG
1 CAGAAGCCAACCACAATTCTACCG
* * * * * * *
78103 TAGAAGTCAAACACCATTATGCGG
1 CAGAAGCCAACCACAATTCTACCG
* *
78127 AAGAAGCCAACCACAATTCTACTG
1 CAGAAGCCAACCACAATTCTACCG
78151 CAGAAG
1 CAGAAG
78157 TCAAGTATCA
Statistics
Matches: 38, Mismatches: 16, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.40, C:0.27, G:0.17, T:0.17
Consensus pattern (24 bp):
CAGAAGCCAACCACAATTCTACCG
Done.