Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019808.1 Corchorus olitorius cultivar O-4 contig19841, 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: 134630
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:805 original size:3 final size:3
Alignment explanation
Indices: 797--821 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
787 GAAATTAGTG
797 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
822 ATTTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:6762 original size:19 final size:18
Alignment explanation
Indices: 6729--6764 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6719 TTGGAATAAT
6729 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
6747 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
6765 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:11457 original size:15 final size:15
Alignment explanation
Indices: 11427--11468 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
11417 TTACTTTGCT
11427 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
11443 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
11458 TTGCTTTCTGT
1 TTGTTTTCTGT
11469 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:30040 original size:22 final size:22
Alignment explanation
Indices: 30008--30220 Score: 135
Period size: 22 Copynumber: 9.6 Consensus size: 22
29998 CTCCAACATA
30008 AAAATATTGATAACCACACTGTG
1 AAAAT-TTGATAACCACACTGTG
* * * *
30031 AAAATTTGATAATCTCATTATG
1 AAAATTTGATAACCACACTGTG
* * * *
30053 -AAATTTCATTAACCTCCCTGCG
1 AAAATTTGA-TAACCACACTGTG
*
30075 AAATTTTGATAACCACACTGTG
1 AAAATTTGATAACCACACTGTG
* * * * *
30097 AAATTTTGATAATCTCATTATG
1 AAAATTTGATAACCACACTGTG
* * * *
30119 -AAATTTCAATAACCTCCCTATG
1 AAAATTT-GATAACCACACTGTG
* * *
30141 GAATTTTGATAACCATACTG-G
1 AAAATTTGATAACCACACTGTG
* *
30162 AAATTTTGATAATCACACTGTG
1 AAAATTTGATAACCACACTGTG
* * *
30184 AAATTTTGATAGCCACACTATG
1 AAAATTTGATAACCACACTGTG
30206 AAAATTTTGATAACC
1 AAAA-TTTGATAACC
30221 TTAGTGTAAA
Statistics
Matches: 146, Mismatches: 38, Indels: 12
0.74 0.19 0.06
Matches are distributed among these distances:
21 30 0.21
22 91 0.62
23 25 0.17
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (22 bp):
AAAATTTGATAACCACACTGTG
Found at i:30096 original size:66 final size:66
Alignment explanation
Indices: 30009--30241 Score: 270
Period size: 66 Copynumber: 3.5 Consensus size: 66
29999 TCCAACATAA
* * * *
30009 AAATATTGATAACCACACTGTGAAAATTTGATAATCTCATTATGAAATTTCATTAACCTCCCTGC
1 AAATTTTGATAACCACACTGTGAAATTTTGATAATCTCATTATGAAATTTCAATAACCTCCCTAC
30074 G
66 G
*
30075 AAATTTTGATAACCACACTGTGAAATTTTGATAATCTCATTATGAAATTTCAATAACCTCCCTAT
1 AAATTTTGATAACCACACTGTGAAATTTTGATAATCTCATTATGAAATTTCAATAACCTCCCTAC
30140 G
66 G
* * * * * ** * * * *
30141 GAATTTTGATAACCATACTG-GAAATTTTGATAATCACACTGTGAAATTTTGATAGCCACACTAT
1 AAATTTTGATAACCACACTGTGAAATTTTGATAATCTCATTATGAAATTTCAATAACCTCCCTAC
30205 G
66 G
** * *
30206 AAAATTTTGATAACCTTAGTGTAAAATTTTGATAAT
1 -AAATTTTGATAACCACACTGTGAAATTTTGATAAT
30242 TTTCGTATGA
Statistics
Matches: 146, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
65 37 0.25
66 96 0.66
67 13 0.09
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (66 bp):
AAATTTTGATAACCACACTGTGAAATTTTGATAATCTCATTATGAAATTTCAATAACCTCCCTAC
G
Found at i:30122 original size:44 final size:43
Alignment explanation
Indices: 30074--30269 Score: 171
Period size: 44 Copynumber: 4.5 Consensus size: 43
30064 ACCTCCCTGC
30074 GAAATTTTGATAACCACACTGTGAAATTTTGATAATCTCATTAT
1 GAAATTTTGATAACCACACTGTGAAATTTTGATAATCTCA-TAT
** * * * *
30118 GAAATTTCAATAACCTCCCTATGGAATTTTGATAA-C-CATACT
1 GAAATTTTGATAACCACACTGTGAAATTTTGATAATCTCATA-T
* ** *
30160 GGAAATTTTGATAATCACACTGTGAAATTTTGATAGCCACACTAT
1 -GAAATTTTGATAACCACACTGTGAAATTTTGATAATCTCA-TAT
** * * * *
30205 GAAAATTTTGATAACCTTAGTGTAAAATTTTGATAATTTTCGTAT
1 G-AAATTTTGATAACCACACTGTGAAATTTTGATAA-TCTCATAT
*
30250 GAAATTTTGATAATCACACT
1 GAAATTTTGATAACCACACT
30270 ATTGTTTATA
Statistics
Matches: 117, Mismatches: 28, Indels: 14
0.74 0.18 0.09
Matches are distributed among these distances:
41 2 0.02
42 3 0.03
43 28 0.24
44 46 0.39
45 35 0.30
46 3 0.03
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (43 bp):
GAAATTTTGATAACCACACTGTGAAATTTTGATAATCTCATAT
Found at i:30254 original size:22 final size:22
Alignment explanation
Indices: 30095--30264 Score: 81
Period size: 22 Copynumber: 7.7 Consensus size: 22
30085 AACCACACTG
* *
30095 TGAAATTTTGATAATCTCATTA
1 TGAAATTTTGATAATCTTAGTA
** * ***
30117 TGAAATTTCAATAACCTCCCTA
1 TGAAATTTTGATAATCTTAGTA
* * * *
30139 TGGAATTTTGATAACCATACT-
1 TGAAATTTTGATAATCTTAGTA
* ** * *
30160 GGAAATTTTGATAATCACACTG
1 TGAAATTTTGATAATCTTAGTA
** ** *
30182 TGAAATTTTGATAGCCACACTA
1 TGAAATTTTGATAATCTTAGTA
* *
30204 TGAAAATTTTGATAACCTTAGTG
1 TG-AAATTTTGATAATCTTAGTA
* * *
30227 TAAAATTTTGATAATTTTCGTA
1 TGAAATTTTGATAATCTTAGTA
30249 TGAAATTTTGATAATC
1 TGAAATTTTGATAATC
30265 ACACTATTGT
Statistics
Matches: 115, Mismatches: 31, Indels: 4
0.77 0.21 0.03
Matches are distributed among these distances:
21 17 0.15
22 82 0.71
23 16 0.14
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAATCTTAGTA
Found at i:32528 original size:22 final size:22
Alignment explanation
Indices: 32489--32700 Score: 123
Period size: 22 Copynumber: 9.6 Consensus size: 22
32479 TCTCCCTCCC
32489 TATGAAATTTTG-TAAACCTTCT
1 TATGAAATTTTGAT-AACCTTCT
* * *
32511 TATTAAATTTTGATAACC-ACAG
1 TATGAAATTTTGATAACCTTC-T
* * *
32533 TATAAAATTTCGATAACCTTCG
1 TATGAAATTTTGATAACCTTCT
* * * *
32555 AATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCT
*
32577 TAAGAAATTTTGATAACCTT-T
1 TATGAAATTTTGATAACCTTCT
* * *
32598 TGATGAAATTTCGGTAA-CTTTT
1 T-ATGAAATTTTGATAACCTTCT
32620 GTATGAAATTTTGATAA-CTATAC-
1 -TATGAAATTTTGATAACCT-T-CT
* * *
32643 TATGAAGTTTTGATAACCTCCA
1 TATGAAATTTTGATAACCTTCT
* * * *
32665 TATAAAATTTTGGTAACC-ACAC
1 TATGAAATTTTGATAACCTTC-T
32687 TATGAAATTTTGAT
1 TATGAAATTTTGAT
32701 TAGTGATTTT
Statistics
Matches: 147, Mismatches: 32, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
21 7 0.05
22 134 0.91
23 6 0.04
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCT
Found at i:32673 original size:66 final size:65
Alignment explanation
Indices: 32515--32682 Score: 167
Period size: 66 Copynumber: 2.5 Consensus size: 65
32505 CCTTCTTATT
* * * *
32515 AAATTTTGATAACCACAGTATAAAATTTCGATAACCTTCGAATGAAATTTTGTTAACCTCCCTAA
1 AAATTTTGATAACCTCA-TATAAAATTTCGGTAACCTTCGAATGAAATTTTGATAACCTCACTAA
32580 G
65 G
** * * * * *
32581 AAATTTTGATAACCTTTTGATGAAATTTCGGTAACTTTTGTATGAAATTTTGATAA-CTATACTA
1 AAATTTTGATAACCTCAT-ATAAAATTTCGGTAACCTTCGAATGAAATTTTGATAACCT-CACTA
*
32645 TG
64 AG
* *
32647 AAGTTTTGATAACCTCCATATAAAATTTTGGTAACC
1 AAATTTTGATAACCT-CATATAAAATTTCGGTAACC
32683 ACACTATGAA
Statistics
Matches: 81, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
65 3 0.04
66 77 0.95
67 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (65 bp):
AAATTTTGATAACCTCATATAAAATTTCGGTAACCTTCGAATGAAATTTTGATAACCTCACTAAG
Found at i:41239 original size:120 final size:120
Alignment explanation
Indices: 41082--41597 Score: 545
Period size: 120 Copynumber: 4.3 Consensus size: 120
41072 ATCATGGGTC
* * * *
41082 GTCACCAAATATGAGGAAAATGCTT-AATTATATGTGACGAAAATGT-GAACGTCACATGTATAG
1 GTCACAAAAAATGAGGAAAATG-TTCCATTATTTGTGACGAAAATGTGGAACGTCACATGTATAG
** * *
41145 GTGACGCCCATTTCGTCATAAAATATTAAAATATAACGTCACTAACAATTGTTGATT
65 GTGACG-GAATTTCGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATT
41202 GTCACAAAAAATGAGGAAAATGTTCCATTATTTGTGACGAAAAT-TGGAACGTCACATGTATAGG
1 GTCACAAAAAATGAGGAAAATGTTCCATTATTTGTGACGAAAATGTGGAACGTCACATGTATAGG
* *
41266 TGACGGAATTTGTGTCACAAAATACTACAATATAACGTCACTAACAATTGTTGATT
66 TGACGGAATTT-CGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATT
* *
41322 GTCACGAAAAATGATGAAAATGTTCCATTATTTGTGACGAAAA-GTGGAACGTCACATGTATAGG
1 GTCACAAAAAATGAGGAAAATGTTCCATTATTTGTGACGAAAATGTGGAACGTCACATGTATAGG
*
41386 TGACGGAATGTGT-GTCACAAAAT-CTAAAATATAACGTCACTTACAATTGTTGATT
66 TGACGGAAT-T-TCGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATT
* * * ** * * * *
41441 GTCACAAAATATGAGG-AAATTTTTCATTATTCCTGACG--AATTTCAGAACGTCACAAGAATAG
1 GTCACAAAAAATGAGGAAAATGTTCCATTATTTGTGACGAAAATGT-GGAACGTCACATGTATAG
* * * *** *
41503 GTGACGTAAGTTTCGTCATGCAATAT-GT-GTTTATAACGTCACTAA-AAGTTGTTGATC
65 GTGACGGAA-TTTCGTCA--CAAAATACTAAAATATAACGTCACTAACAA-TTGTTGATT
* * * *
41560 GTCACAAAAAAAT-AAGTAAATGTTCAATTATTCGTGAC
1 GTCAC-AAAAAATGAGGAAAATGTTCCATTATTTGTGAC
41598 ACAATGAGTA
Statistics
Matches: 342, Mismatches: 39, Indels: 30
0.83 0.09 0.07
Matches are distributed among these distances:
116 2 0.01
117 2 0.01
118 48 0.14
119 79 0.23
120 209 0.61
121 1 0.00
122 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (120 bp):
GTCACAAAAAATGAGGAAAATGTTCCATTATTTGTGACGAAAATGTGGAACGTCACATGTATAGG
TGACGGAATTTCGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATT
Found at i:41547 original size:238 final size:240
Alignment explanation
Indices: 41080--41597 Score: 583
Period size: 238 Copynumber: 2.2 Consensus size: 240
41070 ATATCATGGG
* * * *
41080 TCGTCACCAAATATGAGGAAAATGCTT-AATTATATGTGACGAAAATGTGAACGTCACATGTATA
1 TCGTCACAAAAAATGAAGAAAATG-TTCAATTATTTGTGACGAAAATGTGAACGTCACATGTATA
* * *
41144 GGTGACGCCCATTTCGTCATAAAATATTAAAATATAACGTCACTAACAATTGTTGATTGTCACAA
65 GGTGACGCCAATTTCGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATTGTCACAA
** * * *
41209 AAAATGAGGAAAATGTTCCATTATTTGTGACGAAAATTGGAACGTCACATGTATAGGTGACGGAA
130 AAAATGAGGAAAATGTTCCATTATTCCTGACGAAAATTAGAACGTCACAAGAATAGGTGACGGAA
*
41274 TTTGTGTCACAAAATACTACAATATAACGTCACTAACAA-TTGTTGA
195 TTTGCGTCACAAAATACTACAATATAACGTCACTAA-AAGTTGTTGA
* * * *
41320 TTGTCACGAAAAATGATGAAAATGTTCCATTATTTGTGACGAAAA-GTGGAACGTCACATGTATA
1 TCGTCACAAAAAATGAAGAAAATGTTCAATTATTTGTGACGAAAATGT-GAACGTCACATGTATA
* *
41384 GGTGACG-GAATGTGT-GTCACAAAAT-CTAAAATATAACGTCACTTACAATTGTTGATTGTCAC
65 GGTGACGCCAAT-T-TCGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATTGTCAC
* * * *
41446 AAAATATGAGG-AAATTTTTCATTATTCCTGACG-AATTTCAGAACGTCACAAGAATAGGTGACG
128 AAAAAATGAGGAAAATGTTCCATTATTCCTGACGAAAATT-AGAACGTCACAAGAATAGGTGACG
* * * ***
41509 TAAGTTT-CGTCATGCAATAT-GT-GTTTATAACGTCACTAAAAGTTGTTGA
192 GAA-TTTGCGTCA--CAAAATACTACAATATAACGTCACTAAAAGTTGTTGA
* *
41558 TCGTCACAAAAAAAT-AAGTAAATGTTCAATTATTCGTGAC
1 TCGTCAC-AAAAAATGAAGAAAATGTTCAATTATTTGTGAC
41598 ACAATGAGTA
Statistics
Matches: 235, Mismatches: 33, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
237 6 0.03
238 93 0.40
239 61 0.26
240 74 0.31
241 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (240 bp):
TCGTCACAAAAAATGAAGAAAATGTTCAATTATTTGTGACGAAAATGTGAACGTCACATGTATAG
GTGACGCCAATTTCGTCACAAAATACTAAAATATAACGTCACTAACAATTGTTGATTGTCACAAA
AAATGAGGAAAATGTTCCATTATTCCTGACGAAAATTAGAACGTCACAAGAATAGGTGACGGAAT
TTGCGTCACAAAATACTACAATATAACGTCACTAAAAGTTGTTGA
Found at i:46906 original size:65 final size:65
Alignment explanation
Indices: 46824--46953 Score: 217
Period size: 65 Copynumber: 2.0 Consensus size: 65
46814 GTGTATAAAA
*
46824 ATTTGGTGACATCACTTTATGTCACAAATAAT-TTAATACAATACGTGACATAAACAATATGTCA
1 ATTTGGTGACATCACTTTATGTCACAAATAATCAT-ATACAATACGTGACATAAACAATATGTCA
46888 C
65 C
* *
46889 ATTTGGTGACATTACTTTATGTCACAAATAATCATATACAATACGTGACATAAACAGTATGTCAC
1 ATTTGGTGACATCACTTTATGTCACAAATAATCATATACAATACGTGACATAAACAATATGTCAC
46954 GTATAAAAAC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 60 0.98
66 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (65 bp):
ATTTGGTGACATCACTTTATGTCACAAATAATCATATACAATACGTGACATAAACAATATGTCAC
Found at i:57652 original size:33 final size:34
Alignment explanation
Indices: 57584--57673 Score: 105
Period size: 33 Copynumber: 2.7 Consensus size: 34
57574 CAACTATTCG
*
57584 TGATGCAAAAGAAACTTTTTAATTTTTGGAGAAT
1 TGATGCAAAACAAACTTTTTAATTTTTGGAGAAT
* * *
57618 TGATGC-AAACAAACTTTTT-TTTTCTTTGATAAT
1 TGATGCAAAACAAACTTTTTAATTT-TTGGAGAAT
*
57651 TGATGCAAAACAAAC-CTTTAATT
1 TGATGCAAAACAAACTTTTTAATT
57674 GCCACTATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
32 3 0.06
33 28 0.60
34 16 0.34
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (34 bp):
TGATGCAAAACAAACTTTTTAATTTTTGGAGAAT
Found at i:58067 original size:7 final size:7
Alignment explanation
Indices: 58057--58123 Score: 62
Period size: 7 Copynumber: 8.4 Consensus size: 7
58047 TATACTATTA
58057 AATAAAT
1 AATAAAT
58064 AATAAAT
1 AATAAAT
58071 ATATTTTAAAT
1 A-A---TAAAT
58082 AATAAAT
1 AATAAAT
58089 AATAAAT
1 AATAAAT
58096 ATATTTTAAAT
1 A-A---TAAAT
58107 AATAAAT
1 AATAAAT
58114 AATAAAT
1 AATAAAT
58121 AAT
1 AAT
58124 GAGTTCAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
7 36 0.69
8 2 0.04
10 2 0.04
11 12 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AATAAAT
Found at i:58140 original size:25 final size:25
Alignment explanation
Indices: 58057--58121 Score: 130
Period size: 25 Copynumber: 2.6 Consensus size: 25
58047 TATACTATTA
58057 AATAAATAATAAATATATTTTAAAT
1 AATAAATAATAAATATATTTTAAAT
58082 AATAAATAATAAATATATTTTAAAT
1 AATAAATAATAAATATATTTTAAAT
58107 AATAAATAATAAATA
1 AATAAATAATAAATA
58122 ATGAGTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AATAAATAATAAATATATTTTAAAT
Found at i:58366 original size:18 final size:18
Alignment explanation
Indices: 58343--58377 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58333 CCTAAATACA
*
58343 TTTTCGACGTATATAATG
1 TTTTCGACGAATATAATG
58361 TTTTCGACGAATATAAT
1 TTTTCGACGAATATAAT
58378 AACCATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (18 bp):
TTTTCGACGAATATAATG
Found at i:59150 original size:26 final size:26
Alignment explanation
Indices: 59087--59188 Score: 159
Period size: 26 Copynumber: 3.8 Consensus size: 26
59077 AGCAAAAGTA
59087 TATAAATTAGTTACATTTTTTTTGAAT
1 TATAAATTAGTTACA-TTTTTTTGAAT
*
59114 TATAAATAATTAGTTACATTTTTTTAAAT
1 TAT--A-AATTAGTTACATTTTTTTGAAT
59143 TATAAATTAGTTACATTTTTTTGAAT
1 TATAAATTAGTTACATTTTTTTGAAT
59169 TATAAATTAGTTACATTTTT
1 TATAAATTAGTTACATTTTT
59189 GAATGATAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 7
0.89 0.03 0.09
Matches are distributed among these distances:
26 41 0.59
27 4 0.06
29 14 0.20
30 11 0.16
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (26 bp):
TATAAATTAGTTACATTTTTTTGAAT
Found at i:62495 original size:101 final size:101
Alignment explanation
Indices: 62320--62522 Score: 361
Period size: 101 Copynumber: 2.0 Consensus size: 101
62310 GGTTTTGTTT
*
62320 GTTTACAAGTTTATTTGGTAGGTAGGTTCTTAATGATAGTTTGTATATTTGTTTGTTGAATTTTC
1 GTTTACAAGTTTATTTGGTAGGTAGGTTCTTAATGATAGTCTGTATATTTGTTTGTTGAATTTTC
62385 ATTAGATAGATGGATATAAAAGAATGATTGTAATAA
66 ATTAGATAGATGGATATAAAAGAATGATTGTAATAA
* * *
62421 GTTTACAAGTTTATTTGGTAGGTAGGTTCTTAGTGATAGTCTGTTTGTTTGTTTGTTGAATTTTC
1 GTTTACAAGTTTATTTGGTAGGTAGGTTCTTAATGATAGTCTGTATATTTGTTTGTTGAATTTTC
*
62486 ATTAGATAGATGGATATATAAGAATGATTGTAATAA
66 ATTAGATAGATGGATATAAAAGAATGATTGTAATAA
62522 G
1 G
62523 ATTTTACTTG
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 97 1.00
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.45
Consensus pattern (101 bp):
GTTTACAAGTTTATTTGGTAGGTAGGTTCTTAATGATAGTCTGTATATTTGTTTGTTGAATTTTC
ATTAGATAGATGGATATAAAAGAATGATTGTAATAA
Found at i:64625 original size:31 final size:29
Alignment explanation
Indices: 64557--64625 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
64547 AACGTAAGGG
*
64557 ATTAATTTGTCCAAAAAAAAACATAAAGA
1 ATTATTTTGTCCAAAAAAAAACATAAAGA
64586 ATTATTTTGTCCCAAAAAAAAA-ATATAAGA
1 ATTATTTTGT-CCAAAAAAAAACATA-AAGA
*
64616 GATTTTTTTG
1 -ATTATTTTG
64626 GATATTTAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 12 0.34
30 15 0.43
31 8 0.23
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (29 bp):
ATTATTTTGTCCAAAAAAAAACATAAAGA
Found at i:65548 original size:11 final size:11
Alignment explanation
Indices: 65532--65556 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
65522 AAATCTGACA
65532 TATCTATATAC
1 TATCTATATAC
65543 TATCTATATAC
1 TATCTATATAC
65554 TAT
1 TAT
65557 ATAAGTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (11 bp):
TATCTATATAC
Found at i:65944 original size:28 final size:28
Alignment explanation
Indices: 65887--65944 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
65877 TTTTGAATTT
*** *
65887 TTAACGTGATGTATACTTTTTTTACCAA
1 TTAACGTGATGTATACTTTAAATAACAA
*
65915 TTAACGTGATGTATACTTTAAATAATAA
1 TTAACGTGATGTATACTTTAAATAACAA
65943 TT
1 TT
65945 TTCATTAAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (28 bp):
TTAACGTGATGTATACTTTAAATAACAA
Found at i:68629 original size:24 final size:24
Alignment explanation
Indices: 68583--68629 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
68573 ACTTAATTTG
*
68583 TTAATATTGTCAAAGTTTGTTTTT
1 TTAATATTGTCAAAGTATGTTTTT
68607 TTAATAATTGTCAAAGTAT-TTTT
1 TTAAT-ATTGTCAAAGTATGTTTT
68630 CTATAGCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (24 bp):
TTAATATTGTCAAAGTATGTTTTT
Found at i:76328 original size:75 final size:75
Alignment explanation
Indices: 76249--76422 Score: 172
Period size: 75 Copynumber: 2.3 Consensus size: 75
76239 GATGCTCAAA
* *
76249 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAGCTTCAAG-TTGTTG-CAAATCATCATC
1 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATT-TTGCCAAA-CACCATC
* * *
76312 ATAAAATTTAGT
64 AGAAAACTCAGT
* ** * * * * *
76324 ATTTGAATTCAAAAGAGGAATCTGGTCAAGTGAATCAACTTCAAGATTTTGCCTAACACCATCAG
1 ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATTTTGCCAAACACCATCAG
*
76389 AAAACTCATT
66 AAAACTCAGT
* *
76399 ATTTGAATTCGAATTAGCAACCTG
1 ATTTGAATTCGAATCAGAAACCTG
76423 TTGATACTTA
Statistics
Matches: 78, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
75 73 0.94
76 5 0.06
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (75 bp):
ATTTGAATTCGAATCAGAAACCTGATAAAGTGAATCAACTTCAAGATTTTGCCAAACACCATCAG
AAAACTCAGT
Found at i:80596 original size:13 final size:13
Alignment explanation
Indices: 80578--80602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
80568 GTATAGAACC
80578 ACCAAAACAATTG
1 ACCAAAACAATTG
80591 ACCAAAACAATT
1 ACCAAAACAATT
80603 TTGGTCGGCA
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:0.24, G:0.04, T:0.16
Consensus pattern (13 bp):
ACCAAAACAATTG
Found at i:83415 original size:351 final size:351
Alignment explanation
Indices: 82763--83444 Score: 1001
Period size: 351 Copynumber: 1.9 Consensus size: 351
82753 CAAAACATTT
* * *
82763 TCCAAGTCGGTTTAGGAGAAGATCAATTATGTCCAGAAATTTCAAGGGCAAAATCATCCACTAGA
1 TCCAAATCAGTTTAGGAGAAGATCAATTATATCCAGAAATTTCAAGGGCAAAATCATCCACTAGA
* * * * *
82828 ACTGAAGAATTAGGTCTCGAGGTAAACATAGAAGCTGTAGGTCTAGGAATCCTCTTTCCAACGCT
66 AATGAAGAATTAGATCTCGAGGTAAACATAAAAGCTGTAGATCTAGGAATCCTCTTTCCAACGAT
* *
82893 GTCTCATTTGCATTTTTCTGAGTTCTAGATAAAAAATTATGAAATTTCTTCGAAAACTGCACTTG
131 GTCTCATTTGCATTTTTCTGAGCTCTAGATAAAAAATTATGAAATTTCTTCCAAAACTGCACTTG
* *
82958 TGAAGTCCTCTTTTGAATAGGATTTAACAATGCTGCATCAGGACTAAACCATTACTGCATCATAA
196 TGAAGTCCTCCTTTGAATAGGATTTAACAATGCTGCATCAGGACTAAACCATTAATGCATCATAA
* * * * * * *
83023 TTACTGATTGGACTTGGACTCTTTTTTTGGGCTTCCATATTAACGAATTGGTTCTAAGAATATCA
261 TTACTAATTGGACTTGAACTCCTTCTTTGGGCGTCCATATTAACAAATTGGGTCTAAGAATATCA
83088 GATTTAGTTTTCAAGACATTTGGCTC
326 GATTTAGTTTTCAAGACATTTGGCTC
* *
83114 TCCAAATCAGTTTAGGAGAAGATCAATTCTATCTAGAAATTTCAAGGGCAAAATCATCCACT-GA
1 TCCAAATCAGTTTAGGAGAAGATCAATTATATCCAGAAATTTCAAGGGCAAAATCATCCACTAG-
* * * * *
83178 AAATGTAGAATTAGATCTTGAGTTAAACATAAAAG-TGGTAGATCTTGGAATTCTCTTTCCAACG
65 AAATGAAGAATTAGATCTCGAGGTAAACATAAAAGCT-GTAGATCTAGGAATCCTCTTTCCAACG
* * * * *
83242 ATGTCTCATTTGCATTTTTCTGAGCTCTGGATCAAAAGTTATGAATTTTCTTCCAAAACTGCTCT
129 ATGTCTCATTTGCATTTTTCTGAGCTCTAGATAAAAAATTATGAAATTTCTTCCAAAACTGCACT
* * *
83307 TGTGAAGTCCTCCTTTGAATATGATTTAACAATGCTGCATCAGCG-CTGAATCATTAATGCATCA
194 TGTGAAGTCCTCCTTTGAATAGGATTTAACAATGCTGCATCAG-GACTAAACCATTAATGCATCA
*
83371 TAATTACTAATTGGTCTTGAACTCCTTCTTTGGGCGTCCATATTAACAAATTGGGTCTAAGAATA
258 TAATTACTAATTGGACTTGAACTCCTTCTTTGGGCGTCCATATTAACAAATTGGGTCTAAGAATA
83436 TCAGATTTA
323 TCAGATTTA
83445 AACTTCAAGA
Statistics
Matches: 293, Mismatches: 35, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
350 2 0.01
351 290 0.99
352 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (351 bp):
TCCAAATCAGTTTAGGAGAAGATCAATTATATCCAGAAATTTCAAGGGCAAAATCATCCACTAGA
AATGAAGAATTAGATCTCGAGGTAAACATAAAAGCTGTAGATCTAGGAATCCTCTTTCCAACGAT
GTCTCATTTGCATTTTTCTGAGCTCTAGATAAAAAATTATGAAATTTCTTCCAAAACTGCACTTG
TGAAGTCCTCCTTTGAATAGGATTTAACAATGCTGCATCAGGACTAAACCATTAATGCATCATAA
TTACTAATTGGACTTGAACTCCTTCTTTGGGCGTCCATATTAACAAATTGGGTCTAAGAATATCA
GATTTAGTTTTCAAGACATTTGGCTC
Found at i:84017 original size:26 final size:26
Alignment explanation
Indices: 83988--84038 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
83978 ATTATGAAAA
*
83988 TATTTTATTTAGAAAAATTCAATTTT
1 TATTTTAATTAGAAAAATTCAATTTT
84014 TATTTTAATTAGAAAAATTCAATTT
1 TATTTTAATTAGAAAAATTCAATTT
84039 GTACAGTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (26 bp):
TATTTTAATTAGAAAAATTCAATTTT
Found at i:93447 original size:29 final size:29
Alignment explanation
Indices: 93391--93447 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
93381 CTCAACTTTG
** **
93391 ACAATTTATCTTAACTTTTTTTGGCCACA
1 ACAATTTATCTTAACTTAATTACGCCACA
*
93420 ACAATTTATCTTAACTTAATTACTCCAC
1 ACAATTTATCTTAACTTAATTACGCCAC
93448 TTTGGCAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (29 bp):
ACAATTTATCTTAACTTAATTACGCCACA
Found at i:95189 original size:33 final size:33
Alignment explanation
Indices: 95152--95256 Score: 90
Period size: 33 Copynumber: 3.2 Consensus size: 33
95142 AATTAATTTG
95152 TTTGATAAGTAGTTTATTTAAAATAAAAATTAT
1 TTTGATAAGTAGTTTATTTAAAATAAAAATTAT
** * * ** *
95185 TTTGATCTG-GGTTTTAGTT-AGTTAATTAATT-T
1 TTTGATAAGTAG-TTTATTTAAAATAA-AAATTAT
*
95217 GTTTGATAGGTAGTTTATTTAAAATAAAAATTAT
1 -TTTGATAAGTAGTTTATTTAAAATAAAAATTAT
95251 TTTGAT
1 TTTGAT
95257 CGTAATAAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
32 6 0.12
33 40 0.77
34 6 0.12
ACGTcount: A:0.35, C:0.01, G:0.14, T:0.50
Consensus pattern (33 bp):
TTTGATAAGTAGTTTATTTAAAATAAAAATTAT
Found at i:95205 original size:66 final size:66
Alignment explanation
Indices: 95123--95257 Score: 261
Period size: 66 Copynumber: 2.0 Consensus size: 66
95113 CTCACAGAAT
95123 ATCTGGGTTTTAGTTAGTTAATTAATTTGTTTGATAAGTAGTTTATTTAAAATAAAAATTATTTT
1 ATCTGGGTTTTAGTTAGTTAATTAATTTGTTTGATAAGTAGTTTATTTAAAATAAAAATTATTTT
95188 G
66 G
*
95189 ATCTGGGTTTTAGTTAGTTAATTAATTTGTTTGATAGGTAGTTTATTTAAAATAAAAATTATTTT
1 ATCTGGGTTTTAGTTAGTTAATTAATTTGTTTGATAAGTAGTTTATTTAAAATAAAAATTATTTT
95254 G
66 G
95255 ATC
1 ATC
95258 GTAATAAAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.50
Consensus pattern (66 bp):
ATCTGGGTTTTAGTTAGTTAATTAATTTGTTTGATAAGTAGTTTATTTAAAATAAAAATTATTTT
G
Found at i:98122 original size:17 final size:17
Alignment explanation
Indices: 98100--98133 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
98090 CCTTCCATCC
98100 TTTTATATTTAGCTTTA
1 TTTTATATTTAGCTTTA
* *
98117 TTTTATCTTTATCTTTA
1 TTTTATATTTAGCTTTA
98134 AATTATTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTATATTTAGCTTTA
Found at i:99212 original size:15 final size:15
Alignment explanation
Indices: 99194--99227 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
99184 AGTAACCAAC
99194 TAAAAAAGCAAAAAG
1 TAAAAAAGCAAAAAG
*
99209 TAAAAAAGGAAAAAG
1 TAAAAAAGCAAAAAG
99224 TAAA
1 TAAA
99228 CCAATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.15, T:0.09
Consensus pattern (15 bp):
TAAAAAAGCAAAAAG
Found at i:99925 original size:27 final size:26
Alignment explanation
Indices: 99879--99930 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
99869 TTTTTACTTT
*
99879 TTTTTTAAAATTAATAATTAGTTATTA
1 TTTTTAAAAATTAATAATTA-TTATTA
* *
99906 TTTTTAAAAATTAGTTATTATTATT
1 TTTTTAAAAATTAATAATTATTATT
99931 TTATATGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTTTAAAAATTAATAATTATTATTA
Found at i:99941 original size:23 final size:20
Alignment explanation
Indices: 99889--99927 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
99879 TTTTTTAAAA
*
99889 TTAATAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
99909 TTAAAAATTAGTTATTATT
1 TTAAAAATTAGTTATTATT
99928 ATTTTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAAAAATTAGTTATTATTT
Found at i:102007 original size:21 final size:22
Alignment explanation
Indices: 101961--102019 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
101951 TAATGATGTT
* *
101961 TTTTGTGGTTTGACTATCAAAC
1 TTTTGGGGTTTGACCATCAAAC
*
101983 -TTTGGGGTTTGACCATC-ATC
1 TTTTGGGGTTTGACCATCAAAC
* *
102003 TTTTGGGATTTTACCAT
1 TTTTGGGGTTTGACCAT
102020 ACATGCTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.46
Consensus pattern (22 bp):
TTTTGGGGTTTGACCATCAAAC
Found at i:102038 original size:76 final size:77
Alignment explanation
Indices: 101928--102074 Score: 242
Period size: 77 Copynumber: 1.9 Consensus size: 77
101918 ACTATCAAAC
* * **
101928 TTTGGGGTTTGACCATACATGTTTAATGATG-TTTTTTGTGGTTTGACTATCAAACTTTGGGGTT
1 TTTGGGATTTGACCATACATGCTTAATGATGTTTTTTTGTGGTTTGACTATCAAACTTTAAGGTT
101992 TGACCATCATCT
66 TGACCATCATCT
*
102004 TTTGGGATTTTACCATACATGCTTAATGATGTTTTTTTGTGGTTTGACTATCAAACTTTAAGGTT
1 TTTGGGATTTGACCATACATGCTTAATGATGTTTTTTTGTGGTTTGACTATCAAACTTTAAGGTT
102069 TGACCA
66 TGACCA
102075 CGCATGTACA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
76 28 0.43
77 37 0.57
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (77 bp):
TTTGGGATTTGACCATACATGCTTAATGATGTTTTTTTGTGGTTTGACTATCAAACTTTAAGGTT
TGACCATCATCT
Found at i:105473 original size:53 final size:53
Alignment explanation
Indices: 105410--105625 Score: 396
Period size: 53 Copynumber: 4.1 Consensus size: 53
105400 TGTTTATTCA
*
105410 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAACACACATACCAAATAATACAAAATGCAATGAACT
*
105463 ATTGAACCTATTAAATAAACACACATACCAAATAATATAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAACACACATACCAAATAATACAAAATGCAATGAACT
*
105516 ATTGAACCTATTAAATAAACACACATATCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAACACACATACCAAATAATACAAAATGCAATGAACT
*
105569 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAACACACATACCAAATAATACAAAATGCAATGAACT
105622 ATTG
1 ATTG
105626 GATTTAAAGA
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 157 1.00
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAACACACATACCAAATAATACAAAATGCAATGAACT
Found at i:106638 original size:2 final size:2
Alignment explanation
Indices: 106631--106660 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
106621 AAAATTTTGT
*
106631 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
106661 AATGCATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107639 original size:25 final size:25
Alignment explanation
Indices: 107592--107642 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
107582 TATTTTGAAC
*
107592 TTATTATTTATTATTTAAAATATAT
1 TTATTATTTATTATATAAAATATAT
*
107617 TTATTATTTATT-TAATAATATATAT
1 TTATTATTTATTAT-ATAAAATATAT
107642 T
1 T
107643 ATATCTAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATTATTTATTATATAAAATATAT
Found at i:107642 original size:21 final size:21
Alignment explanation
Indices: 107562--107644 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
107552 CGTTTAGTAA
107562 TTAAATATATATTATTTATTTATT
1 TTAAA-ATATATTA-TTATTTA-T
* *
107586 TTGAACT-TATTATT-TATTAT
1 TTAAAATATATTATTAT-TTAT
107606 TTAAAATATATTTATTATTTAT
1 TTAAAATATA-TTATTATTTAT
107628 TTAATAATATA-TATTAT
1 TTAA-AATATATTATTAT
107645 ATCTAAGATA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
20 7 0.14
21 13 0.26
22 18 0.36
23 8 0.16
24 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (21 bp):
TTAAAATATATTATTATTTAT
Found at i:124444 original size:3 final size:3
Alignment explanation
Indices: 124436--124488 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
124426 TTAGTTACGC
*
124436 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
124484 TTA TT
1 TTA TT
124489 GCTATTTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:129205 original size:3 final size:3
Alignment explanation
Indices: 129197--129261 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
129187 TTAGTTACGT
129197 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
129245 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
129262 GATATTTTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:132211 original size:40 final size:40
Alignment explanation
Indices: 132133--132267 Score: 200
Period size: 40 Copynumber: 3.4 Consensus size: 40
132123 TGGGCCTGCC
* * * * *
132133 CCAG-GCGTGGCCCAGGCGTGCCAAGCCAAGCACACTGGG
1 CCAGCGCGCGGCCCAGGCGCGCCAGGCCAGGCACGCTGGG
132172 CCAGCGCGCGGCCCAGGCGCGCCAGGCCAGGCACGCTGGG
1 CCAGCGCGCGGCCCAGGCGCGCCAGGCCAGGCACGCTGGG
*
132212 CCATCGCGCGGCCCAGGCGCGCCAGGCCAGGCACGCTGGG
1 CCAGCGCGCGGCCCAGGCGCGCCAGGCCAGGCACGCTGGG
*
132252 CCAGCGCGTGGCCCAG
1 CCAGCGCGCGGCCCAG
132268 CTGCCTTGCC
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 4 0.05
40 83 0.95
ACGTcount: A:0.15, C:0.41, G:0.39, T:0.05
Consensus pattern (40 bp):
CCAGCGCGCGGCCCAGGCGCGCCAGGCCAGGCACGCTGGG
Found at i:132253 original size:14 final size:14
Alignment explanation
Indices: 132167--132259 Score: 70
Period size: 14 Copynumber: 7.0 Consensus size: 14
132157 GCCAAGCACA
132167 CTGGGCCA-GCGCG
1 CTGGGCCAGGCGCG
*
132180 C-GGCCCAGGCGCG
1 CTGGGCCAGGCGCG
** *
132193 CCAGGCCAGGCACG
1 CTGGGCCAGGCGCG
*
132207 CTGGGCCA-TCGCG
1 CTGGGCCAGGCGCG
*
132220 C-GGCCCAGGCGCG
1 CTGGGCCAGGCGCG
** *
132233 CCAGGCCAGGCACG
1 CTGGGCCAGGCGCG
132247 CTGGGCCA-GCGCG
1 CTGGGCCAGGCGCG
132260 TGGCCCAGCT
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
12 10 0.17
13 20 0.33
14 30 0.50
ACGTcount: A:0.12, C:0.42, G:0.42, T:0.04
Consensus pattern (14 bp):
CTGGGCCAGGCGCG
Done.