Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011859.1 Corchorus capsularis cultivar CVL-1 contig11880, 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: 72100
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:13054 original size:2 final size:2
Alignment explanation
Indices: 13047--13072 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13037 GACAAACATC
13047 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13073 GGGTTATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14124 original size:2 final size:2
Alignment explanation
Indices: 14117--14148 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14107 AAATGTTTGG
14117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14149 GGAATTGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14905 original size:16 final size:16
Alignment explanation
Indices: 14884--14917 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
14874 AAAGTGTTTG
14884 AGTTGGTAGGGTTTTT
1 AGTTGGTAGGGTTTTT
14900 AGTTGGTAGGGTTTTT
1 AGTTGGTAGGGTTTTT
14916 AG
1 AG
14918 AGTTTAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (16 bp):
AGTTGGTAGGGTTTTT
Found at i:14914 original size:15 final size:15
Alignment explanation
Indices: 14879--14914 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
14869 TGGCCAAAGT
*
14879 GTTTGAGTTGGTAGG
1 GTTTTAGTTGGTAGG
14894 GTTTTTAGTTGGTAGG
1 G-TTTTAGTTGGTAGG
14910 GTTTT
1 GTTTT
14915 TAGAGTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.11, C:0.00, G:0.39, T:0.50
Consensus pattern (15 bp):
GTTTTAGTTGGTAGG
Found at i:16430 original size:22 final size:22
Alignment explanation
Indices: 16386--16430 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
16376 TGACACGATT
* *
16386 AAACACGAAACACGTTAAGCCC
1 AAACACGAAACACGTAAAACCC
16408 AAACAC-AAACACGGTAAAACCC
1 AAACACGAAACAC-GTAAAACCC
16430 A
1 A
16431 TATCATTCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.51, C:0.31, G:0.11, T:0.07
Consensus pattern (22 bp):
AAACACGAAACACGTAAAACCC
Found at i:16532 original size:2 final size:2
Alignment explanation
Indices: 16520--16552 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16510 TAATAGTAAG
*
16520 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16553 ATTGACCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21007 original size:3 final size:3
Alignment explanation
Indices: 20999--21035 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
20989 ACATTAGTTG
*
20999 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
21036 GATGAGTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:22868 original size:28 final size:28
Alignment explanation
Indices: 22836--22892 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
22826 TGATTTCTAT
22836 TAAAGTCATTATTATAAATTTATAACGG
1 TAAAGTCATTATTATAAATTTATAACGG
22864 TAAAGTCATTATTATAAATTTATAACGG
1 TAAAGTCATTATTATAAATTTATAACGG
22892 T
1 T
22893 TAATTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (28 bp):
TAAAGTCATTATTATAAATTTATAACGG
Found at i:24132 original size:35 final size:33
Alignment explanation
Indices: 24093--24162 Score: 113
Period size: 35 Copynumber: 2.1 Consensus size: 33
24083 AACCAAAGAT
24093 TCTACAAAACAAATAAATATGCAATTTCAGAATTA
1 TCTACAAAACAAATAAA-ATGCAA-TTCAGAATTA
*
24128 TCTACAAAACAAATAAAATGCAATTCTGAATTA
1 TCTACAAAACAAATAAAATGCAATTCAGAATTA
24161 TC
1 TC
24163 CTATGAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 11 0.32
34 6 0.18
35 17 0.50
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.29
Consensus pattern (33 bp):
TCTACAAAACAAATAAAATGCAATTCAGAATTA
Found at i:24171 original size:12 final size:12
Alignment explanation
Indices: 24154--24179 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24144 AATGCAATTC
24154 TGAATTATCCTA
1 TGAATTATCCTA
24166 TGAATTATCCTA
1 TGAATTATCCTA
24178 TG
1 TG
24180 GTACAGCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (12 bp):
TGAATTATCCTA
Found at i:25425 original size:3 final size:3
Alignment explanation
Indices: 25417--25442 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25407 ATAAATAAAA
25417 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
25443 ATTCCTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:26513 original size:15 final size:18
Alignment explanation
Indices: 26479--26515 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
26469 GGCTTATTTG
26479 TTTTTTATGAGTTATTAA
1 TTTTTTATGAGTTATTAA
26497 TTTTTTAT-A-TT-TTAA
1 TTTTTTATGAGTTATTAA
26512 TTTT
1 TTTT
26516 AAAAAGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 2 0.11
17 1 0.05
18 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTTATGAGTTATTAA
Found at i:26886 original size:2 final size:2
Alignment explanation
Indices: 26879--26904 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26869 CTAAGGTGGT
26879 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
26905 ATGAACTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32022 original size:18 final size:18
Alignment explanation
Indices: 31980--32022 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
31970 AGTCTACACC
*
31980 TTTAATTTAAATGTGACT
1 TTTAATTTAAATATGACT
31998 TTT-ATTTGAAATATGA-T
1 TTTAATTT-AAATATGACT
32015 TTTAATTT
1 TTTAATTT
32023 TTTCTCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (18 bp):
TTTAATTTAAATATGACT
Found at i:39584 original size:25 final size:25
Alignment explanation
Indices: 39546--39597 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
39536 ATGAATTCTC
*
39546 TCATAAAAAGACACTTTTTCATGTT
1 TCATAAAAAGACACCTTTTCATGTT
* *
39571 TCATAGAAATACACCTTTTCATGTT
1 TCATAAAAAGACACCTTTTCATGTT
39596 TC
1 TC
39598 TGCAGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (25 bp):
TCATAAAAAGACACCTTTTCATGTT
Found at i:40031 original size:3 final size:3
Alignment explanation
Indices: 40025--40075 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
40015 TTTTGTGAAA
40025 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40072 ATT A
1 ATT A
40076 AAACCAACCC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:41175 original size:31 final size:29
Alignment explanation
Indices: 41078--41177 Score: 103
Period size: 31 Copynumber: 3.3 Consensus size: 29
41068 GAGGGCTAAT
* *
41078 TGCTCAATTTGGTGCTAAACCTTTGACAAAA
1 TGCTCAATTTGGTCCTAAACCTTT--CAAAC
* *
41109 TGCTCGATTTGGTCCTAAACCTTT-AGAGC
1 TGCTCAATTTGGTCCTAAACCTTTCA-AAC
*
41138 TGCTCAAATTGGTCCTAAACCTTTCCAAATC
1 TGCTCAATTTGGTCCTAAACCTTT-CAAA-C
41169 TGCTCAATT
1 TGCTCAATT
41178 CAGTCCTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.02
29 23 0.40
30 1 0.02
31 32 0.56
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (29 bp):
TGCTCAATTTGGTCCTAAACCTTTCAAAC
Found at i:41184 original size:31 final size:29
Alignment explanation
Indices: 41120--41184 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
41110 GCTCGATTTG
* *
41120 GTCCTAAACCTTTAGAGCTGCTCAAATTG
1 GTCCTAAACCTTTAAAGCTGCTCAAATTA
*
41149 GTCCTAAACCTTTCCAAATCTGCTC-AATTCA
1 GTCCTAAACCTTT--AAAGCTGCTCAAATT-A
41180 GTCCT
1 GTCCT
41185 TTTTCTGACG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 13 0.43
30 4 0.13
31 13 0.43
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (29 bp):
GTCCTAAACCTTTAAAGCTGCTCAAATTA
Found at i:41341 original size:14 final size:15
Alignment explanation
Indices: 41319--41347 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41309 AGTTAAAAAT
41319 TAAAGACCAAAAACA
1 TAAAGACCAAAAACA
41334 TAAA-ACCAAAAACA
1 TAAAGACCAAAAACA
41348 CCTAACCCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.21, G:0.03, T:0.07
Consensus pattern (15 bp):
TAAAGACCAAAAACA
Found at i:43294 original size:29 final size:30
Alignment explanation
Indices: 43254--43337 Score: 107
Period size: 31 Copynumber: 2.8 Consensus size: 30
43244 GCAGATTTGG
* *
43254 AAAGGTTTAGGACCAATTTGAGCACCTCT-
1 AAAGGTTTAGGACCAAATTGAGCACCTATC
* **
43283 AAAGGTTTAGGACCAAATCGAGCTTTCTATC
1 AAAGGTTTAGGACCAAATTGAGC-ACCTATC
43314 AAAGGTTTAGGACCAAATTGAGCA
1 AAAGGTTTAGGACCAAATTGAGCA
43338 ATTAGCCCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 21 0.46
30 3 0.07
31 22 0.48
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (30 bp):
AAAGGTTTAGGACCAAATTGAGCACCTATC
Found at i:44924 original size:15 final size:15
Alignment explanation
Indices: 44904--44952 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
44894 AGCAAGTTGG
*
44904 TTTTTATTTTTTTTA
1 TTTTTATTTTTATTA
44919 TTTTTATTTTTATTA
1 TTTTTATTTTTATTA
* *
44934 TTATTATTATTATT-
1 TTTTTATTTTTATTA
44948 TTTTT
1 TTTTT
44953 GAGGATAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 4 0.13
15 26 0.87
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTTTATTA
Found at i:44930 original size:12 final size:12
Alignment explanation
Indices: 44907--44952 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
44897 AAGTTGGTTT
*
44907 TTATTTTTTTTA
1 TTATTATTTTTA
*
44919 TTTTTATTTTTA
1 TTATTATTTTTA
*
44931 TTATTATTATTA
1 TTATTATTTTTA
44943 TTATT-TTTTT
1 TTATTATTTTT
44953 GAGGATAAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 4 0.14
12 25 0.86
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TTATTATTTTTA
Found at i:47375 original size:6 final size:6
Alignment explanation
Indices: 47356--47406 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
47346 GACGCTGCGC
* *
47356 AAGGGG AAGCGG AAAGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG
47404 AAG
1 AAG
47407 AGCAAAGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.37, C:0.02, G:0.61, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:47998 original size:16 final size:16
Alignment explanation
Indices: 47933--47999 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
47923 GAGTATCCGG
*
47933 ACCCAAAATTACCCGA
1 ACCCAAAATGACCCGA
*
47949 ATCCAAACA--ACCCGA
1 ACCCAAA-ATGACCCGA
* **
47964 ACCCGAAATGACCAAA
1 ACCCAAAATGACCCGA
47980 ACCCAAAATGACCCGA
1 ACCCAAAATGACCCGA
47996 ACCC
1 ACCC
48000 GATCAACCCG
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
14 1 0.03
15 11 0.28
16 27 0.68
17 1 0.03
ACGTcount: A:0.45, C:0.39, G:0.09, T:0.07
Consensus pattern (16 bp):
ACCCAAAATGACCCGA
Found at i:48892 original size:11 final size:11
Alignment explanation
Indices: 48878--48902 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
48868 ATTATACTAC
48878 ATATATATAGT
1 ATATATATAGT
48889 ATATATATAGT
1 ATATATATAGT
48900 ATA
1 ATA
48903 AATCAGAGAC
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
ATATATATAGT
Found at i:49308 original size:15 final size:17
Alignment explanation
Indices: 49273--49310 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
49263 AACCAAAAAC
49273 GACCC-AACCCAGAATT
1 GACCCGAACCCAGAATT
49289 GACCCGAACCCA-AA-T
1 GACCCGAACCCAGAATT
49304 GACCCGA
1 GACCCGA
49311 CATTTGAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.37, C:0.39, G:0.16, T:0.08
Consensus pattern (17 bp):
GACCCGAACCCAGAATT
Found at i:49828 original size:15 final size:15
Alignment explanation
Indices: 49808--49844 Score: 60
Period size: 13 Copynumber: 2.6 Consensus size: 15
49798 CATCAGGATC
49808 AATTTTTTAAAAAAT
1 AATTTTTTAAAAAAT
49823 AA--TTTTAAAAAAT
1 AATTTTTTAAAAAAT
49836 AATTTTTTA
1 AATTTTTTA
49845 TGTTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.65
15 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATTTTTTAAAAAAT
Found at i:49938 original size:13 final size:13
Alignment explanation
Indices: 49922--50065 Score: 65
Period size: 13 Copynumber: 10.4 Consensus size: 13
49912 AAAATATTTT
49922 TTTGTAAGTAATA
1 TTTGTAAGTAATA
* * *
49935 TTTGAAAGAGACATG
1 TTTGTAAG-TA-ATA
* *
49950 TTTGTAATTATTA
1 TTTGTAAGTAATA
* *
49963 -TTGTATGTAATT
1 TTTGTAAGTAATA
*
49975 TTTGTAAGTAATT
1 TTTGTAAGTAATA
* *
49988 TTTTTATGTTAATTA
1 TTTGTAAG-TAA-TA
* *
50003 TTAGTGTATGTAATT
1 TT--TGTAAGTAATA
50018 TTTGTAAGTAATA
1 TTTGTAAGTAATA
* *
50031 TTTTTTTAAGTAATTTT
1 --TTTGTAAGTAA--TA
50048 TTTGTAAGTAATA
1 TTTGTAAGTAATA
50061 TTTGT
1 TTTGT
50066 TGTCCTCAGG
Statistics
Matches: 96, Mismatches: 24, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
12 8 0.08
13 40 0.42
14 5 0.05
15 34 0.35
16 3 0.03
17 6 0.06
ACGTcount: A:0.31, C:0.01, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTGTAAGTAATA
Found at i:50011 original size:43 final size:44
Alignment explanation
Indices: 49954--50036 Score: 150
Period size: 43 Copynumber: 1.9 Consensus size: 44
49944 GACATGTTTG
*
49954 TAATTATTATTGTATGTAATTTTTGTAAGTAAT-TTTTTTATGT
1 TAATTATTAGTGTATGTAATTTTTGTAAGTAATATTTTTTATGT
49997 TAATTATTAGTGTATGTAATTTTTGTAAGTAATATTTTTT
1 TAATTATTAGTGTATGTAATTTTTGTAAGTAATATTTTTT
50037 TAAGTAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
43 32 0.84
44 6 0.16
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (44 bp):
TAATTATTAGTGTATGTAATTTTTGTAAGTAATATTTTTTATGT
Found at i:50059 original size:43 final size:42
Alignment explanation
Indices: 49953--50065 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 42
49943 AGACATGTTT
*
49953 GTAATTATTATTGTATGTAATTTTTGTAAGTAATTTTTTTAT
1 GTAATTATTATTGTATGTAATTTTTGTAAGTAATTTTTTTAA
*
49995 GTTAATTATTAGTGTATGTAATTTTTGTAAGTAATATTTTTTTAA
1 G-TAATTATTATTGTATGTAATTTTTGTAAGT-A-ATTTTTTTAA
* * *
50040 GTAATT-TTTTTGTAAGTAATATTTGT
1 GTAATTATTATTGTATGTAATTTTTGT
50066 TGTCCTCAGG
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
42 1 0.02
43 45 0.73
44 6 0.10
45 10 0.16
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (42 bp):
GTAATTATTATTGTATGTAATTTTTGTAAGTAATTTTTTTAA
Found at i:50231 original size:10 final size:10
Alignment explanation
Indices: 50216--50240 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
50206 TTAGCTTGAA
50216 GATTTCAGAG
1 GATTTCAGAG
50226 GATTTCAGAG
1 GATTTCAGAG
50236 GATTT
1 GATTT
50241 GAAAGGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (10 bp):
GATTTCAGAG
Found at i:52866 original size:47 final size:47
Alignment explanation
Indices: 52700--53094 Score: 273
Period size: 47 Copynumber: 8.6 Consensus size: 47
52690 GATCATGGCA
** * * *
52700 AAACAACACCTTCCTATCGGGAAGGGC-AAAT-AAGGAATAAGACAAAATT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGAA--AATGAGAC--AACT
*** * * * *
52749 AAACAACACCTTCCGACCGGGAAGGGCAAAACGAGAATAAGACAAAATTT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGAAAATGAGAC--AA-CT
*
52799 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGAAAATGAGATAACT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGAAAATGAGACAACT
* * * * * * *
52846 AAACAACACCTTCTGATGGGGAAGGGCGAAATGAGAATAAGGCAATT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGAAAATGAGACAACT
* *
52893 AAACAACACCTTCCGGTGAGGAAGGGC------AAACTGAGA-AACT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGAAAATGAGACAACT
* ** * ** * *
52933 AAACAACACCTTCCGATGGGGAAGGGGTAAACGGGAATAAGGCAACT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGAAAATGAGACAACT
* * * *
52980 AAACAACACCTTCTGGTGAGGAAGGGCAAACTG-----G-GA-AGCT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAATGAAAATGAGACAACT
** *
53020 AAACAACACCTTCCGGTGGGGAAGGGCAAAACTGGTAATTAGACAACT
1 AAACAACACCTTCCGGTGGGGAAGGGCAAAA-TGAAAATGAGACAACT
53068 AAACAACACCTTCCGGTGGGGAAGGGC
1 AAACAACACCTTCCGGTGGGGAAGGGC
53095 GAACTTGGAA
Statistics
Matches: 277, Mismatches: 51, Indels: 37
0.76 0.14 0.10
Matches are distributed among these distances:
40 58 0.21
41 8 0.03
46 4 0.01
47 96 0.35
48 32 0.12
49 37 0.13
50 41 0.15
51 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (47 bp):
AAACAACACCTTCCGGTGGGGAAGGGCAAAATGAAAATGAGACAACT
Found at i:52947 original size:40 final size:40
Alignment explanation
Indices: 52892--53122 Score: 196
Period size: 40 Copynumber: 5.4 Consensus size: 40
52882 ATAAGGCAAT
*
52892 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGAGAAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGAGAAAC
* * * *
52932 TAAACAACACCTTCCGATGGGGAAGGGGTAAACGGGAATAAGGCAAC
1 TAAACAACACCTTCCGGTGGGGAA-GGGCAAAC-----TGA-GAAAC
* * * *
52979 TAAACAACACCTTCTGGTGAGGAAGGGCAAACTGGGAAGC
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGAGAAAC
53019 TAAACAACACCTTCCGGTGGGGAAGGGCAAAACTGGTAATTAGACAAC
1 TAAACAACACCTTCCGGTGGGGAAGGGC-AAACT-G-----AGA-AAC
*
53067 TAAACAACACCTTCCGGTGGGGAAGGGCGAACTTG-GAATA-
1 TAAACAACACCTTCCGGTGGGGAAGGGCAAAC-TGAGAA-AC
*
53107 AAAACAACACCTTCCG
1 TAAACAACACCTTCCG
53123 ACCTGGAAGG
Statistics
Matches: 155, Mismatches: 19, Indels: 34
0.75 0.09 0.16
Matches are distributed among these distances:
40 67 0.43
41 16 0.10
42 1 0.01
46 9 0.06
47 31 0.20
48 31 0.20
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (40 bp):
TAAACAACACCTTCCGGTGGGGAAGGGCAAACTGAGAAAC
Found at i:52988 original size:87 final size:87
Alignment explanation
Indices: 52748--53575 Score: 421
Period size: 87 Copynumber: 9.4 Consensus size: 87
52738 AAGACAAAAT
** *
52748 TAAACAACACCTTCCGACCGGGAAGGGCAAAACGAGAATAAGACAAAATTTAAACAACACCTTCC
1 TAAACAACACCTTCCGATGGGGAAGGGCAAAACGAGAATAAGAC--AA-CTAAACAACACCTTCC
* *
52813 GGTGGGGAAGGGCAAAATGAAAATGAGATAAC
63 GGTGAGGAAGGGC------AAACTGAGA-AAC
* * * * *
52845 TAAACAACACCTTCTGATGGGGAAGGGCGAAATGAGAATAAGGCAATTAAACAACACCTTCCGGT
1 TAAACAACACCTTCCGATGGGGAAGGGCAAAACGAGAATAAGACAACTAAACAACACCTTCCGGT
52910 GAGGAAGGGCAAACTGAGAAAC
66 GAGGAAGGGCAAACTGAGAAAC
** * * *
52932 TAAACAACACCTTCCGATGGGGAAGGGGTAAACGGGAATAAGGCAACTAAACAACACCTTCTGGT
1 TAAACAACACCTTCCGATGGGGAAGGGCAAAACGAGAATAAGACAACTAAACAACACCTTCCGGT
* *
52997 GAGGAAGGGCAAACTGGGAAGC
66 GAGGAAGGGCAAACTGAGAAAC
* *
53019 TAAACAACACCTTCCGGTGGGGAAGGGCAAAACTG-GTAATTAGACAACTAAACAACACCTTCCG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAAAC-GAG-AATAAGACAACTAAACAACACCTTCCG
* *
53083 GTGGGGAAGGGCGAACTTG-GAATA-
64 GTGAGGAAGGGCAAAC-TGAGAA-AC
* * **
53107 AAAACAACACCTTCCGACCTGGAAGGCCAAATTGG-AAATTGAGAATAAGACGAAACTAAACAAC
1 TAAACAACACCTTCCGA--TGG--GG---AA-GGGCAAAACGAGAATAAGAC--AACTAAACAAC
* * * * *
53171 ACCTTCTGATCG-GGAAGGCCGAACT-AGGAATAA
56 ACCTTCCGGT-GAGGAAGGGCAAACTGA-GAA-AC
* * ** **
53204 GAAGACAACACCTTTCGATGTTGAAGGGC-AAACTG-G--T---A-AACTAAACAACACCTTCTA
1 TAA-ACAACACCTTCCGATGGGGAAGGGCAAAAC-GAGAATAAGACAACTAAACAACACCTTCCG
*
53261 GTAAGGAAGGGCAAACTG-GTAAATC
64 GTGAGGAAGGGCAAACTGAG-AAA-C
* * * * *
53286 TAAACAACACCTTCTGGTGGGGAAGGGC-ATACTG-G---AA-A-AAGTAAACAACACCTTCCGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAAAC-GAGAATAAGACAACTAAACAACACCTTCCGG
* *
53344 TGAGGAAGGGCGAATTG-GTAAATC
65 TGAGGAAGGGCAAACTGAG-AAA-C
* * * ** * * *
53368 TAAACAATACTTTCCGGTGGGGAAGGGC-AAACTGCTAA-ATGTA-GACTTAACAACACCTTCCG
1 TAAACAACACCTTCCGATGGGGAAGGGCAAAAC-GAGAATAAG-ACAACTAAACAACACCTTCCG
* *
53430 GTGGGGAAGGGCAAACTGCTAAATGTAGAC
64 GTGAGGAAGGGCAAACTG----A-G-AAAC
* * * *
53460 TTAACAACACCTTCCGATGGGGAAAGAC-AAACTG-G-----GA-AACTAAACAACA-CTTCCGA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAAAC-GAGAATAAGACAACTAAACAACACCTTCCGG
*
53516 TGGGGAAGGGCAAACTGAGAATAAGCAAC
65 TGAGGAAGGGCAAACTGAG----A--AAC
* *
53545 TAAACAACACCTTTCGGTGGGGAAGGGCAAA
1 TAAACAACACCTTCCGATGGGGAAGGGCAAA
53576 TTAGGAATTT
Statistics
Matches: 593, Mismatches: 93, Indels: 101
0.75 0.12 0.13
Matches are distributed among these distances:
80 1 0.00
81 29 0.05
82 102 0.17
83 1 0.00
85 50 0.08
86 13 0.02
87 144 0.24
88 66 0.11
89 2 0.00
90 8 0.01
91 3 0.01
92 31 0.05
93 4 0.01
94 37 0.06
95 9 0.02
96 39 0.07
97 41 0.07
98 13 0.02
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (87 bp):
TAAACAACACCTTCCGATGGGGAAGGGCAAAACGAGAATAAGACAACTAAACAACACCTTCCGGT
GAGGAAGGGCAAACTGAGAAAC
Found at i:53310 original size:41 final size:41
Alignment explanation
Indices: 53208--53575 Score: 310
Period size: 41 Copynumber: 8.7 Consensus size: 41
53198 GAATAAGAAG
* * **
53208 ACAACACCTTTCGATGTTGAAGGGCAAACTGGTAAA-CTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAAATCTAA
** **
53248 ACAACACCTTCTAGTAAGGAAGGGCAAACTGGTAAATCTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAAATCTAA
* * * **
53289 ACAACACCTTCTGGTGGGGAAGGGCATACTGGAAAAAGTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAAATCTAA
* * * *
53330 ACAACACCTTCCGATGAGGAAGGGCGAATTGGTAAATCTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAAATCTAA
* * * *
53371 ACAATACTTTCCGGTGGGGAAGGGCAAACTGCTAAATGTAGACTTA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAAA--T---CTAA
* *
53417 ACAACACCTTCCGGTGGGGAAGGGCAAACTGCTAAATGTAGACTTA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAAA--T---CTAA
* * * *
53463 ACAACACCTTCCGATGGGGAAAGACAAACTGGGAAA-CTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAAATCTAA
* *
53503 ACAACA-CTTCCGATGGGGAAGGGCAAACTGAGAATAAGCAACTAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAACTG-G--TAA--ATCTAA
*
53548 ACAACACCTTTCGGTGGGGAAGGGCAAA
1 ACAACACCTTCCGGTGGGGAAGGGCAAA
53576 TTAGGAATTT
Statistics
Matches: 271, Mismatches: 44, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
39 22 0.08
40 39 0.14
41 99 0.37
42 2 0.01
43 1 0.00
44 1 0.00
45 10 0.04
46 97 0.36
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (41 bp):
ACAACACCTTCCGGTGGGGAAGGGCAAACTGGTAAATCTAA
Found at i:53437 original size:46 final size:46
Alignment explanation
Indices: 53243--53575 Score: 235
Period size: 46 Copynumber: 7.7 Consensus size: 46
53233 AAACTGGTAA
** ** *
53243 ACTAAACAACACCTTCTAGTAAGGAAGGGCAAACTGGTAAA--T--
1 ACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGCTAAATGTAG
* * *
53285 -CTAAACAACACCTTCTGGTGGGGAAGGGCATACTG-GAAA---A-
1 ACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGCTAAATGTAG
* * * * * *
53325 AGTAAACAACACCTTCCGATGAGGAAGGGCGAATTGGTAAA--T--
1 ACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGCTAAATGTAG
* *
53367 -CTAAACAATACTTTCCGGTGGGGAAGGGCAAACTGCTAAATGTAG
1 ACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGCTAAATGTAG
*
53412 ACTTAACAACACCTTCCGGTGGGGAAGGGCAAACTGCTAAATGTAG
1 ACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGCTAAATGTAG
* * * * * *
53458 ACTTAACAACACCTTCCGATGGGGAAAGACAAACTG------GGAA
1 ACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGCTAAATGTAG
* ** * *
53498 ACTAAACAACA-CTTCCGATGGGGAAGGGCAAACTGAGAATAAGCA-
1 ACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGCTAA-ATGTAG
*
53543 ACTAAACAACACCTTTCGGTGGGGAAGGGCAAA
1 ACTAAACAACACCTTCCGGTGGGGAAGGGCAAA
53576 TTAGGAATTT
Statistics
Matches: 239, Mismatches: 35, Indels: 30
0.79 0.12 0.10
Matches are distributed among these distances:
39 22 0.09
40 15 0.06
41 91 0.38
42 3 0.01
43 1 0.00
45 11 0.05
46 96 0.40
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.18
Consensus pattern (46 bp):
ACTAAACAACACCTTCCGGTGGGGAAGGGCAAACTGCTAAATGTAG
Found at i:53613 original size:47 final size:47
Alignment explanation
Indices: 53497--53715 Score: 212
Period size: 47 Copynumber: 4.7 Consensus size: 47
53487 CAAACTGGGA
* * **
53497 AACTAAACAACA-CTTCCGATGGGGAAGGGCAAACT-GAGAATAAG-C
1 AACTAGACAACACCTTCCGATGGGGAAGGGCAAATTAG-GAATTTGAC
* * *
53542 AACTAAACAACACCTTTCGGTGGGGAAGGGCAAATTAGGAATTTGAC
1 AACTAGACAACACCTTCCGATGGGGAAGGGCAAATTAGGAATTTGAC
* * * ** ** * *
53589 AACTAGACAGCACCTTCTGATGGGGAAGTGTGAA-CCGGAAATTGGC
1 AACTAGACAACACCTTCCGATGGGGAAGGGCAAATTAGGAATTTGAC
* * *
53635 AACTAGACAACACTTTCCGGTGGGGAAGGGCGAATTAGGAATTTGAC
1 AACTAGACAACACCTTCCGATGGGGAAGGGCAAATTAGGAATTTGAC
* *
53682 AACTAGACAACACCTTCCGTTTGGGAAGGGCAAA
1 AACTAGACAACACCTTCCGATGGGGAAGGGCAAA
53716 ACCGGAAATT
Statistics
Matches: 139, Mismatches: 31, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
45 12 0.09
46 61 0.44
47 66 0.47
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (47 bp):
AACTAGACAACACCTTCCGATGGGGAAGGGCAAATTAGGAATTTGAC
Found at i:53708 original size:93 final size:93
Alignment explanation
Indices: 53497--53709 Score: 272
Period size: 93 Copynumber: 2.3 Consensus size: 93
53487 CAAACTGGGA
* * * **
53497 AACTAAACAACA-CTTCCGATGGGGAAG-G-GCAAACTGAGAATAAGCAACTAAACAACACCTTT
1 AACTAGACAACACCTTCCGATGGGGAAGTGTG-AACCGGA-AATTGGCAACTAAACAACACCTTT
53559 CGGTGGGGAAGGGCAAATTAGGAATTTGAC
64 CGGTGGGGAAGGGCAAATTAGGAATTTGAC
* * *
53589 AACTAGACAGCACCTTCTGATGGGGAAGTGTGAACCGGAAATTGGCAACTAGACAACA-CTTTCC
1 AACTAGACAACACCTTCCGATGGGGAAGTGTGAACCGGAAATTGGCAACTAAACAACACCTTT-C
*
53653 GGTGGGGAAGGGCGAATTAGGAATTTGAC
65 GGTGGGGAAGGGCAAATTAGGAATTTGAC
* *
53682 AACTAGACAACACCTTCCGTTTGGGAAG
1 AACTAGACAACACCTTCCGATGGGGAAG
53710 GGCAAAACCG
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
92 14 0.13
93 83 0.80
94 6 0.06
95 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (93 bp):
AACTAGACAACACCTTCCGATGGGGAAGTGTGAACCGGAAATTGGCAACTAAACAACACCTTTCG
GTGGGGAAGGGCAAATTAGGAATTTGAC
Found at i:56562 original size:22 final size:22
Alignment explanation
Indices: 56536--56580 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
56526 AAGCAAATTG
56536 ATTCATATTAAGATAAGTAACT
1 ATTCATATTAAGATAAGTAACT
* *
56558 ATTCATGTTAAGATAAGTGACT
1 ATTCATATTAAGATAAGTAACT
56580 A
1 A
56581 AAGTGACCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
ATTCATATTAAGATAAGTAACT
Found at i:65216 original size:42 final size:42
Alignment explanation
Indices: 65170--65256 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
65160 ATGCATGGGA
*
65170 CATCGCACGGGCC-ATCGCAC-GAGCCATCCGGCCACAATCGGC
1 CATCGCACGGGCCAAT-GCACGGA-CCATCCGGCCACAACCGGC
65212 CATCGCACGGGCCAATGCACGGACCATCCGGCCACAACCGGC
1 CATCGCACGGGCCAATGCACGGACCATCCGGCCACAACCGGC
65254 CAT
1 CAT
65257 TCGACCCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.23, C:0.43, G:0.25, T:0.09
Consensus pattern (42 bp):
CATCGCACGGGCCAATGCACGGACCATCCGGCCACAACCGGC
Done.