Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013025.1 Kokia drynarioides strain JFW-HI SEQ_128043, 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: 53779
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:4840 original size:31 final size:29
Alignment explanation
Indices: 4801--4862 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
4791 ATAACATCGA
*
4801 TTTTAATAGTAT-AGTGACCTAAATAAAAAT
1 TTTTAATAGT-TGA-TGACCAAAATAAAAAT
4831 TTTTGAATAGTTGATGACCAAAATAAAAAT
1 TTTT-AATAGTTGATGACCAAAATAAAAAT
4861 TT
1 TT
4863 ACTTATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.37
Consensus pattern (29 bp):
TTTTAATAGTTGATGACCAAAATAAAAAT
Found at i:6357 original size:22 final size:24
Alignment explanation
Indices: 6314--6365 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
6304 ACAAACTGAA
* *
6314 AATAAAAAAAAAAATATGTAAT-G
1 AATAAGAAAAAAAAGATGTAATAG
*
6337 AATAAGAAAAAAAAGGT-TAATAG
1 AATAAGAAAAAAAAGATGTAATAG
6360 AA-AAGA
1 AATAAGA
6366 CGATAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.17
Consensus pattern (24 bp):
AATAAGAAAAAAAAGATGTAATAG
Found at i:10017 original size:4 final size:4
Alignment explanation
Indices: 10008--10032 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9998 GAAGTGCCTT
10008 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
10033 CTTGAGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:21575 original size:23 final size:23
Alignment explanation
Indices: 21543--21596 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
21533 TTGTGTATTT
21543 TTTA-TTTTTTAAATTATTTTTA
1 TTTATTTTTTTAAATTATTTTTA
*
21565 TTTATTTTTTTGAATTATTTTTA
1 TTTATTTTTTTAAATTATTTTTA
*
21588 ATT-TTTTTT
1 TTTATTTTTT
21597 ATTTTGCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTATTTTTTTAAATTATTTTTA
Found at i:23797 original size:12 final size:13
Alignment explanation
Indices: 23771--23802 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
23761 TTTTTCACTC
23771 ATTT-TCTCTCAA
1 ATTTCTCTCTCAA
23783 ATTTCTCTCTC-A
1 ATTTCTCTCTCAA
23795 ATTTCTCT
1 ATTTCTCT
23803 TTAAAGCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTCTCTCTCAA
Found at i:24026 original size:31 final size:29
Alignment explanation
Indices: 23987--24061 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
23977 GTTTTTATAA
*
23987 TTTA-ATTATTTTTTAATAATATTTAATTAT
1 TTTATATTATTTTTTAAT-ATAATTAATT-T
*
24017 TTTATATTATTTTTATAATTTAATTAATTT
1 TTTATATTATTTTT-TAATATAATTAATTT
*
24047 TTT-TAATATTTTTTA
1 TTTATATTATTTTTTA
24062 TTTGAATAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.05
29 9 0.22
30 8 0.20
31 17 0.43
32 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
TTTATATTATTTTTTAATATAATTAATTT
Found at i:24030 original size:48 final size:46
Alignment explanation
Indices: 23940--24064 Score: 148
Period size: 48 Copynumber: 2.7 Consensus size: 46
23930 TGGTAAGAGT
* * * * *
23940 TAATTTAA-T-TTTTTTATATTACTTATTTTTTTATTTTGTTTTTA
1 TAATTTAATTATTTTTTATAATATTTATTATTTTATATTATTTTTA
23984 TAATTTAATTATTTTTTAATAATATTTAATTATTTTATATTATTTTTA
1 TAATTTAATTATTTTTT-ATAATATTT-ATTATTTTATATTATTTTTA
*
24032 TAATTTAATTAATTTTTT-TAATATTTTTTATTT
1 TAATTTAATT-ATTTTTTATAATATTTATTATTT
24065 GAATAGTCGA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
44 8 0.11
45 1 0.01
46 12 0.17
47 15 0.21
48 27 0.39
49 7 0.10
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.69
Consensus pattern (46 bp):
TAATTTAATTATTTTTTATAATATTTATTATTTTATATTATTTTTA
Found at i:24038 original size:18 final size:17
Alignment explanation
Indices: 23978--24053 Score: 65
Period size: 18 Copynumber: 4.6 Consensus size: 17
23968 TTTTATTTTG
23978 TTTTTATAATTTAATTA
1 TTTTTATAATTTAATTA
23995 TTTTT-TAA--TAA-TA
1 TTTTTATAATTTAATTA
24008 TTTAATTAT--TTTATATTA
1 TTT--TTATAATTTA-ATTA
24026 TTTTTATAATTTAATTAA
1 TTTTTATAATTTAATT-A
*
24044 TTTTTTTAAT
1 TTTTTATAAT
24054 ATTTTTTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 19
0.71 0.01 0.28
Matches are distributed among these distances:
13 5 0.10
14 3 0.06
15 2 0.04
16 10 0.21
17 9 0.19
18 19 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTATAATTTAATTA
Found at i:24064 original size:27 final size:26
Alignment explanation
Indices: 24005--24064 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 26
23995 TTTTTTAATA
*
24005 ATATTTAATTATTTTATATTATTTTT
1 ATATTTAATTATTTTATAATATTTTT
*
24031 ATAATTTAATTAATTTTTTTAATATTTTT
1 AT-ATTTAATT-A-TTTTATAATATTTTT
24060 -TATTT
1 ATATTT
24065 GAATAGTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 2 0.07
27 12 0.41
28 2 0.07
29 13 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
ATATTTAATTATTTTATAATATTTTT
Found at i:25706 original size:18 final size:18
Alignment explanation
Indices: 25683--25724 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
25673 AGGAGCTCAA
25683 CTCAATCCCAATCGCCAC
1 CTCAATCCCAATCGCCAC
* *
25701 CTCAATTCTAATCGCCAC
1 CTCAATCCCAATCGCCAC
*
25719 ATCAAT
1 CTCAAT
25725 TTTCATCGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.40, G:0.05, T:0.24
Consensus pattern (18 bp):
CTCAATCCCAATCGCCAC
Found at i:26060 original size:59 final size:59
Alignment explanation
Indices: 25968--26109 Score: 223
Period size: 59 Copynumber: 2.4 Consensus size: 59
25958 ATTATTTTCA
* *
25968 AATATTTTTGTAAACATT-ATTGTTATATTGTTTCATTTAATAAAAGCGAAGTTCATTTG
1 AATATTTTTGTACACATTAATT-TTATATTGTTTCATTTAATAAAAGCGAAGTCCATTTG
* *
26027 AATATTTTTGTACACATTAATTTTATTTTGTTTCATTTAATAAAGGCGAAGTCCATTTG
1 AATATTTTTGTACACATTAATTTTATATTGTTTCATTTAATAAAAGCGAAGTCCATTTG
*
26086 AATGTTTTTGTACACATTAATTTT
1 AATATTTTTGTACACATTAATTTT
26110 GGGTAAAATT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
59 74 0.96
60 3 0.04
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (59 bp):
AATATTTTTGTACACATTAATTTTATATTGTTTCATTTAATAAAAGCGAAGTCCATTTG
Found at i:26521 original size:22 final size:21
Alignment explanation
Indices: 26499--26555 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
26489 ATAAATACTA
*
26499 AAATCATAATTTTAAAAA-CCT
1 AAATC-TAATTTAAAAAACCCT
*
26520 AAACCCTAATTTAAAAAACCCT
1 AAA-TCTAATTTAAAAAACCCT
26542 AAATCTAA-TTAAAA
1 AAATCTAATTTAAAA
26556 CAAAAGCACC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 6 0.19
21 18 0.58
22 7 0.23
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCTAATTTAAAAAACCCT
Found at i:29031 original size:29 final size:30
Alignment explanation
Indices: 28973--29039 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
28963 ATCTCAAAAC
*
28973 TATACATGAACTATGATTTAATATGCAATTA
1 TATACATGAACTATGATTT-ATATACAATTA
* * *
29004 TATACATGAACTTTGATTT-TGTACAATTT
1 TATACATGAACTATGATTTATATACAATTA
29033 TATACAT
1 TATACAT
29040 AAAAATTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.44
31 18 0.56
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.43
Consensus pattern (30 bp):
TATACATGAACTATGATTTATATACAATTA
Found at i:29974 original size:3 final size:3
Alignment explanation
Indices: 29961--29990 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
29951 TTATTGAGTT
29961 TTG TTG TTTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG -TTG TTG TTG TTG TTG TTG TTG TT
29991 ACAGTCGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (3 bp):
TTG
Found at i:38537 original size:6 final size:6
Alignment explanation
Indices: 38530--38587 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
38520 ATAACAAATT
* * *
38530 TTAATT TTAAT- TTTATA TTAATA TTAATA TTAA-A TAAATA TTATTATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTA--ATA
38578 TTAATA TTAA
1 TTAATA TTAA
38588 ATAAAATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 8 0.18
6 30 0.68
8 6 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAATA
Found at i:38556 original size:17 final size:16
Alignment explanation
Indices: 38530--38587 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
38520 ATAACAAATT
*
38530 TTAATTTTAATTTTATA
1 TTAATATTAA-TTTATA
*
38547 TTAATATTAATATTAAA
1 TTAATATTAAT-TTATA
*
38564 TAAATATT-A-TTATA
1 TTAATATTAATTTATA
38578 TTAATATTAA
1 TTAATATTAA
38588 ATAAAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 11 0.32
15 1 0.03
16 2 0.06
17 20 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAATATTAATTTATA
Found at i:44776 original size:22 final size:22
Alignment explanation
Indices: 44737--44784 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
44727 ATAACAGTTC
44737 AAAAATTTTCTTGCCATTTAAT
1 AAAAATTTTCTTGCCATTTAAT
* *
44759 AAAAGATTTTC-TGGCATTTATT
1 AAAA-ATTTTCTTGCCATTTAAT
44781 AAAA
1 AAAA
44785 TTATGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (22 bp):
AAAAATTTTCTTGCCATTTAAT
Found at i:45409 original size:44 final size:44
Alignment explanation
Indices: 45346--45437 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 44
45336 GAAACTACAT
*
45346 GAAAAAAGCCACATTCAAGAAACGACAAAGAAGGAAGCTACGTG
1 GAAAAAAACCACATTCAAGAAACGACAAAGAAGGAAGCTACGTG
* *
45390 GAAAAAAACCAC-TTCCAAGAAATGACAAAGAAGGAAGCTATGTG
1 GAAAAAAACCACATT-CAAGAAACGACAAAGAAGGAAGCTACGTG
45434 GAAA
1 GAAA
45438 TCACCCACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 2 0.05
44 42 0.95
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (44 bp):
GAAAAAAACCACATTCAAGAAACGACAAAGAAGGAAGCTACGTG
Found at i:46616 original size:96 final size:96
Alignment explanation
Indices: 46443--46623 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 96
46433 AGGATGTTCG
* * ** *
46443 ATTATTTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCATAAATTTTCAGAATCGAAGAT
1 ATTACTTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGAT
*
46508 AAGGAAACATTGCCTCGATTAAGGGTATTCT
66 AAAGAAACATTGCCTCGATTAAGGGTATTCT
*
46539 ATTACTTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTCGAA-
1 ATTACTTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-TCGAAG
*
46602 ATAAA-AGAATATTGCCTCGATT
64 ATAAAGA-AACATTGCCTCGATT
46624 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 2 0.03
96 67 0.91
97 5 0.07
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (96 bp):
ATTACTTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGAT
AAAGAAACATTGCCTCGATTAAGGGTATTCT
Found at i:46646 original size:96 final size:96
Alignment explanation
Indices: 46452--46647 Score: 204
Period size: 96 Copynumber: 2.0 Consensus size: 96
46442 GATTATTTCG
** * *
46452 ATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCATAAATTTTCAGAATCGAAGATAAGGAAACA
1 ATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGATAAAGAAACA
* * ***
46517 TTGCCTCGATTAAGGGTATTCTATTACTTCA
66 TTGCCTCGATTAAGAGTATTCTATGAAAACA
*
46548 ATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTCGAA-ATAAA-AGA
1 ATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-TCGAAGATAAAGA-A
* *
46610 ATATTGCCTCGATTTTAA-AGT-TTTTATGAAAACA
63 ACATTGCCTCGA--TTAAGAGTATTCTATGAAAACA
46644 ATTT
1 ATTT
46648 TGAAAACAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
95 2 0.02
96 70 0.84
97 7 0.08
98 4 0.05
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (96 bp):
ATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGATAAAGAAACA
TTGCCTCGATTAAGAGTATTCTATGAAAACA
Found at i:46882 original size:28 final size:28
Alignment explanation
Indices: 46840--46901 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
46830 AAATGAGACT
**
46840 TTTTGGATACACGGGGGCAAAATGGTAA
1 TTTTGGATACACGGGAACAAAATGGTAA
* *
46868 TTTTGGATTCTCGGGAACAAAATGGTAA
1 TTTTGGATACACGGGAACAAAATGGTAA
46896 TTTTGG
1 TTTTGG
46902 GAAAATTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (28 bp):
TTTTGGATACACGGGAACAAAATGGTAA
Found at i:47036 original size:59 final size:58
Alignment explanation
Indices: 46973--47224 Score: 183
Period size: 59 Copynumber: 4.3 Consensus size: 58
46963 ATCGTGATAA
*
46973 AAAAAAGGAATTTTTGGACATTCGGAGGT-AAAATGGTAATTTTT-GAGAGTTTTAG-GGTT
1 AAAAAAGGAATTTTTGGAGATTCGGAGGTAAAAAT-GTAATTTTTGGA-AG-TTTAGAGG-T
* * * * * *
47032 AAAAATGGATTTTTTTGAGGTTTAGG-GGTAAAAATGTAATTTTTGGAAGTTTCGAGGT
1 AAAAAAGGAATTTTTGGA-GATTCGGAGGTAAAAATGTAATTTTTGGAAGTTTAGAGGT
* ** *
47090 AAAAAATGGAATTTTTGGAGGTTC-GAGGGTAAAAATGTAATTTTTAAAAGTTTCGAGGT
1 AAAAAA-GGAATTTTTGGAGATTCGGA-GGTAAAAATGTAATTTTTGGAAGTTTAGAGGT
* * * * *** *
47149 AAAAAATGTAATTTTTGGAAGTTTAGG-GGTAAAAATATAATTTTCAAAAGTTTCGAGGTT
1 AAAAAA-GGAATTTTTGG-AGATTCGGAGGTAAAAATGTAATTTTTGGAAGTTTAGAGG-T
* *
47209 AAAAATGTAATTTTTG
1 AAAAAAGGAATTTTTG
47225 AAAGTTTCGA
Statistics
Matches: 163, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
57 1 0.01
58 13 0.08
59 127 0.78
60 21 0.13
61 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (58 bp):
AAAAAAGGAATTTTTGGAGATTCGGAGGTAAAAATGTAATTTTTGGAAGTTTAGAGGT
Found at i:47043 original size:29 final size:28
Alignment explanation
Indices: 47002--47184 Score: 134
Period size: 29 Copynumber: 6.2 Consensus size: 28
46992 ATTCGGAGGT
47002 AAAATGGTAATTTTTGAGAGTTTTAGGGTTA
1 AAAATGG-AATTTTTG-GAG-TTTAGGGTTA
* * *
47033 AAAATGGATTTTTTTGAGGTTTAGGGGTA
1 AAAATGGAATTTTTGGA-GTTTAGGGTTA
* * *
47062 AAAATGTAATTTTTGGAAGTTTCGAGGTAA
1 AAAATGGAATTTTTGG-AGTTTAG-GGTTA
*
47092 AAAATGGAATTTTTGGAGGTTCGAGGG-TA
1 AAAATGGAATTTTTGGA-GTT-TAGGGTTA
* ** * *
47121 AAAATGTAATTTTTAAAAGTTTCGAGGTAA
1 AAAATGGAATTTTT-GGAGTTTAG-GGTTA
* *
47151 AAAATGTAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGG-AGTTTAGGGTTA
47180 AAAAT
1 AAAAT
47185 ATAATTTTCA
Statistics
Matches: 119, Mismatches: 24, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
28 1 0.01
29 57 0.48
30 53 0.45
31 8 0.07
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.37
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAGTTTAGGGTTA
Found at i:47163 original size:89 final size:89
Alignment explanation
Indices: 47061--47236 Score: 248
Period size: 89 Copynumber: 2.0 Consensus size: 89
47051 GTTTAGGGGT
* ***
47061 AAAAATGTAATTTTTGGAAGTTTCGAGGTAAAAA-ATGGAATTTT-TGGAGGTTCGAGGGTAAAA
1 AAAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATAT--AATTTTCAAAAGGTTCGAGGGTAAAA
47124 ATGTAATTTTTAAAAGTTTCGAGGTA
64 ATGTAATTTTTAAAAGTTTCGAGGTA
* * *
47150 AAAAATGTAATTTTTGGAAGTTTAGGGGTAAAAATATAATTTTCAAAAGTTTCGAGGTTAAAAAT
1 AAAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATATAATTTTCAAAAGGTTCGAGGGTAAAAAT
*
47215 GTAATTTTTGAAAGTTTCGAGG
66 GTAATTTTTAAAAGTTTCGAGG
47237 ACCTCCAGGG
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
88 6 0.08
89 69 0.90
90 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (89 bp):
AAAAATGTAATTTTTGGAAGTTTAGAGGTAAAAATATAATTTTCAAAAGGTTCGAGGGTAAAAAT
GTAATTTTTAAAAGTTTCGAGGTA
Found at i:47230 original size:59 final size:58
Alignment explanation
Indices: 47032--47231 Score: 256
Period size: 59 Copynumber: 3.4 Consensus size: 58
47022 TTTTAGGGTT
* * **
47032 AAAAATGGATTTTTTTGAGGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTA
1 AAAAATGGA-ATTTTTGAAGTTTAGGGGTAAAAATGTAATTTTTAAAAGTTTCGAGGTA
* * *
47091 AAAAATGGAATTTTTGGAGGTTCGAGGGTAAAAATGTAATTTTTAAAAGTTTCGAGGTA
1 AAAAATGGAATTTTTGAAGTTTAG-GGGTAAAAATGTAATTTTTAAAAGTTTCGAGGTA
* * * *
47150 AAAAATGTAATTTTTGGAAGTTTAGGGGTAAAAATATAATTTTCAAAAGTTTCGAGGTT
1 AAAAATGGAATTTTT-GAAGTTTAGGGGTAAAAATGTAATTTTTAAAAGTTTCGAGGTA
*
47209 AAAAATGTAATTTTTGAAAGTTT
1 AAAAATGGAATTTTTG-AAGTTT
47232 CGAGGACCTC
Statistics
Matches: 124, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
58 11 0.09
59 107 0.86
60 6 0.05
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.38
Consensus pattern (58 bp):
AAAAATGGAATTTTTGAAGTTTAGGGGTAAAAATGTAATTTTTAAAAGTTTCGAGGTA
Found at i:47232 original size:30 final size:30
Alignment explanation
Indices: 47002--47236 Score: 219
Period size: 30 Copynumber: 7.9 Consensus size: 30
46992 ATTCGGAGGT
* *
47002 AAAATGGTAATTTTTGAGAGTTT-TAGGGTTA
1 AAAAT-GTAATTTTTGAAAGTTTCGA-GGTTA
* * * * *
47033 AAAATGGATTTTTTTG-AGGTTTAG-GGGTA
1 AAAATGTA-ATTTTTGAAAGTTTCGAGGTTA
* *
47062 AAAATGTAATTTTTGGAAGTTTCGAGGTAA
1 AAAATGTAATTTTTGAAAGTTTCGAGGTTA
* * * *
47092 AAAATGGAATTTTTG-GAGGTTCGAGGGTA
1 AAAATGTAATTTTTGAAAGTTTCGAGGTTA
* *
47121 AAAATGTAATTTTTAAAAGTTTCGAGGTAA
1 AAAATGTAATTTTTGAAAGTTTCGAGGTTA
* * *
47151 AAAATGTAATTTTTGGAAGTTTAG-GGGTA
1 AAAATGTAATTTTTGAAAGTTTCGAGGTTA
* **
47180 AAAATATAATTTTCAAAAGTTTCGAGGTTA
1 AAAATGTAATTTTTGAAAGTTTCGAGGTTA
47210 AAAATGTAATTTTTGAAAGTTTCGAGG
1 AAAATGTAATTTTTGAAAGTTTCGAGG
47237 ACCTCCAGGG
Statistics
Matches: 161, Mismatches: 37, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
28 6 0.04
29 62 0.39
30 82 0.51
31 11 0.07
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTGAAAGTTTCGAGGTTA
Found at i:48380 original size:21 final size:21
Alignment explanation
Indices: 48332--48390 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
48322 GGTTTTTTAT
* *
48332 TATTAATATTACTAATATTTT
1 TATTAATATTATTAATATTTC
*
48353 TACTAATATTATTAATATTTC
1 TATTAATATTATTAATATTTC
*
48374 TGTTAATACTTATTAAT
1 TATTAATA-TTATTAAT
48391 GCCATTCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 24 0.75
22 8 0.25
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTAATATTATTAATATTTC
Found at i:48419 original size:13 final size:12
Alignment explanation
Indices: 48403--48454 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
48393 CATTCATTGC
48403 TAACATTTATTAT
1 TAACA-TTATTAT
48416 TAACATTATTAT
1 TAACATTATTAT
*
48428 TAATATTTATTAT
1 TAACA-TTATTAT
* *
48441 CAATATTATTAT
1 TAACATTATTAT
48453 TA
1 TA
48455 TTATGACTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
12 19 0.54
13 16 0.46
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (12 bp):
TAACATTATTAT
Found at i:48437 original size:22 final size:22
Alignment explanation
Indices: 48412--48456 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
48402 CTAACATTTA
*
48412 TTATTAACATTATTATTAATAT
1 TTATTAACAATATTATTAATAT
* *
48434 TTATTATCAATATTATTATTAT
1 TTATTAACAATATTATTAATAT
48456 T
1 T
48457 ATGACTAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATTAACAATATTATTAATAT
Found at i:48448 original size:25 final size:25
Alignment explanation
Indices: 48407--48454 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
48397 CATTGCTAAC
*
48407 ATTTATTATTAACATTATTATTAAT
1 ATTTATTATCAACATTATTATTAAT
*
48432 ATTTATTATCAATATTATTATTA
1 ATTTATTATCAACATTATTATTA
48455 TTATGACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTATTATCAACATTATTATTAAT
Found at i:49195 original size:6 final size:6
Alignment explanation
Indices: 49184--49275 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
49174 TATAATAAGT
* * *
49184 TTTAAA TTTAAA TATAAA TCTAAA TTTATA -TTAAA TTTAAA TTTGAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
** * * * *
49232 -ACAAA TTTAAA TTT-AA TATAAA TTTATA TTCAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
49276 CCTTAAAAGA
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
5 14 0.22
6 47 0.73
7 3 0.05
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:49225 original size:35 final size:34
Alignment explanation
Indices: 49184--49271 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 34
49174 TATAATAAGT
49184 TTTAAATTTAAATATAAATCTAAATTT-ATATTAAA
1 TTTAAATTTAAA-ATAAATCTAAATTTAATA-TAAA
* *
49219 TTTAAATTTGAAAACAAATTTAAATTTAATATAAA
1 TTTAAATTT-AAAATAAATCTAAATTTAATATAAA
* *
49254 TTTATATTCAAAATAAAT
1 TTTAAATTTAAAATAAAT
49272 TTAACCTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
34 8 0.17
35 32 0.70
36 6 0.13
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATCTAAATTTAATATAAA
Found at i:49237 original size:29 final size:29
Alignment explanation
Indices: 49185--49257 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
49175 ATAATAAGTT
* * *
49185 TTAAATTTAAATATAAATCTAAATTTATA
1 TTAAATTTAAATTTAAAACTAAATTTAAA
49214 TTAAATTTAAATTTGAAAAC-AAATTTAAA
1 TTAAATTTAAATTT-AAAACTAAATTTAAA
* *
49243 TTTAATATAAATTTA
1 TTAAATTTAAATTTA
49258 TATTCAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 1 0.03
29 33 0.87
30 4 0.11
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (29 bp):
TTAAATTTAAATTTAAAACTAAATTTAAA
Found at i:49283 original size:17 final size:18
Alignment explanation
Indices: 49184--49275 Score: 84
Period size: 17 Copynumber: 5.3 Consensus size: 18
49174 TATAATAAGT
49184 TTTAAATTT-AAATATAAA
1 TTTAAATTTCAAA-ATAAA
* * *
49202 TCTAAATTT-ATATTAAA
1 TTTAAATTTCAAAATAAA
* *
49219 TTTAAATTTGAAAACAAA
1 TTTAAATTTCAAAATAAA
*
49237 TTTAAATTT-AATATAAA
1 TTTAAATTTCAAAATAAA
*
49254 TTTATA-TTCAAAATAAA
1 TTTAAATTTCAAAATAAA
49271 TTTAA
1 TTTAA
49276 CCTTAAAAGA
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
16 2 0.03
17 34 0.57
18 24 0.40
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (18 bp):
TTTAAATTTCAAAATAAA
Found at i:52004 original size:96 final size:96
Alignment explanation
Indices: 51840--52024 Score: 248
Period size: 96 Copynumber: 1.9 Consensus size: 96
51830 GAAAAGGATG
* * * *
51840 TTCGATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAAACGA
*
51905 AGAT-AAGGAAACATTACCTCGATTAAGGGTA
66 AGATAAAAG-AACATTACCTCGATTAAGGGTA
* * * *
51936 TTCGATTATTTCGATTTGAAGAAAATTTGCACCTAGTAAGTTAAGGCGCAAATTTT-TGAAACTT
1 TTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAAAC-G
*
52000 AAGATAAAAGAATATTACCTCGATT
65 AAGATAAAAGAACATTACCTCGATT
52025 TTAAAGTTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
95 4 0.05
96 70 0.91
97 3 0.04
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAAACGA
AGATAAAAGAACATTACCTCGATTAAGGGTA
Found at i:52468 original size:29 final size:28
Alignment explanation
Indices: 52433--52823 Score: 133
Period size: 29 Copynumber: 13.4 Consensus size: 28
52423 GTTAAAATTG
*
52433 GAAGTTTATGGGTAAAATAGTAATTTTT
1 GAAGTTTAGGGGTAAAATAGTAATTTTT
* *
52461 GAGAGTTTCGGGGTTAGAAAT-GAAATTTTT
1 GA-AGTTTAGGGG-TA-AAATAGTAATTTTT
** *
52491 GAAGGTTCGGGGGTAAAATGGTAATTTTT
1 GAA-GTTTAGGGGTAAAATAGTAATTTTT
* *
52520 GAAAGTTTTA-GGGTCAAAATTA-TGATTTTG
1 G-AAG-TTTAGGGGT-AAAA-TAGTAATTTTT
*
52550 GAAGTTTAGGGGT-AAATATTAATTTTT
1 GAAGTTTAGGGGTAAAATAGTAATTTTT
* * * *
52577 AAGAGTTTCGGAGTCAAAA-A-TAAGATTTTC
1 GA-AGTTTAGGGGT-AAAATAGT-A-ATTTTT
* * * * *
52607 GGAGGTTCGAGGGTAAAATGGCAATTTTT
1 GAAGTTTAG-GGGTAAAATAGTAATTTTT
* * *
52636 GAAAATTTTAGGGTTAAAATCG-AGATTTTT
1 G--AAGTTTAGGGGTAAAATAGTA-ATTTTT
* *
52666 GAAATTTAGGGGTAAAATGGTAATTTTT
1 GAAGTTTAGGGGTAAAATAGTAATTTTT
* * *
52694 GGAAGTTTCGGAGTCAAAATTG-AGATTTTT
1 -GAAGTTTAGGGGT-AAAATAGTA-ATTTTT
* * *
52724 AAAAG-TTCGAGGCTAAAA-ATGTAATTTTT
1 -GAAGTTTAG-GGGTAAAATA-GTAATTTTT
* * * *
52753 GGAAGTTTTAGGGTTAAAGT-GGAATTTTGGA
1 -GAAG-TTTAGGGGTAAAATAGTAATTTT--T
52784 GAAGTTTAGGGGTCAAAATA--AATTTTT
1 GAAGTTTAGGGGT-AAAATAGTAATTTTT
52811 GGATAGTTTAGGG
1 -GA-AGTTTAGGG
52824 ACCTTGAGGG
Statistics
Matches: 273, Mismatches: 52, Indels: 75
0.68 0.13 0.19
Matches are distributed among these distances:
26 2 0.01
27 10 0.04
28 44 0.16
29 111 0.41
30 94 0.34
31 12 0.04
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (28 bp):
GAAGTTTAGGGGTAAAATAGTAATTTTT
Found at i:52516 original size:59 final size:57
Alignment explanation
Indices: 52442--52753 Score: 236
Period size: 58 Copynumber: 5.4 Consensus size: 57
52432 GGAAGTTTAT
* * *
52442 GGGTAAAATAGTAATTTTTGAGAGTTTCGGGGTTAGAAATGAAATTTTTGAAGGTTCGG
1 GGGTAAAATGGTAATTTTTGAGAGTTTCGGGGTCA-AAATGAGATTTTTGAA-GTTCGG
* ** * * **
52501 GGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAATTATGATTTTGGAAGTTTAG
1 GGGTAAAATGGTAATTTTTGAGAGTTTCGGGGTCAAAATGA-GATTTTTGAAGTTCGG
* * * * * *
52559 GGGTAAATAT--TAATTTTTAAGAGTTTCGGAGTCAAAAATAAGATTTTCGGAGGTTCGA
1 GGGTAAA-ATGGTAATTTTTGAGAGTTTCGGGGTC-AAAATGAGATTTT-TGAAGTTCGG
* * * ** * * **
52617 GGGTAAAATGGCAATTTTTGAAAATTTTAGGGTTAAAATCGAGATTTTTGAAATTTAG
1 GGGTAAAATGGTAATTTTTGAGAGTTTCGGGGTCAAAAT-GAGATTTTTGAAGTTCGG
* * *
52675 GGGTAAAATGGTAATTTTTG-GAAGTTTCGGAGTCAAAATTGAGATTTTTAAAAGTTCGA
1 GGGTAAAATGGTAATTTTTGAG-AGTTTCGGGGTCAAAA-TGAGATTTTT-GAAGTTCGG
*
52734 GGCTAAAAAT-GTAATTTTTG
1 GGGT-AAAATGGTAATTTTTG
52754 GAAGTTTTAG
Statistics
Matches: 194, Mismatches: 48, Indels: 22
0.73 0.18 0.08
Matches are distributed among these distances:
57 26 0.13
58 83 0.43
59 80 0.41
60 5 0.03
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (57 bp):
GGGTAAAATGGTAATTTTTGAGAGTTTCGGGGTCAAAATGAGATTTTTGAAGTTCGG
Found at i:52614 original size:116 final size:115
Alignment explanation
Indices: 52430--52810 Score: 387
Period size: 116 Copynumber: 3.3 Consensus size: 115
52420 TGGGTTAAAA
* * * * *
52430 TTGGAAGTTTATGGGTAAAATAGTAATTTTTGAGAGTTTCGGGGTTAGAAATGAA-ATTTTTGAA
1 TTGGAAGTTTAGGGGT-AAATATTAATTTTT-AGAGTTTCGGAGTCAAAAAT-AAGATTTTTGAA
* *
52494 GGTTCGGGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAAT-TATGATT
63 GGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAATCGA-GATT
* *
52547 TTGGAAGTTTAGGGGTAAATATTAATTTTTAAGAGTTTCGGAGTCAAAAATAAGATTTTCGGAGG
1 TTGGAAGTTTAGGGGTAAATATTAATTTTT-AGAGTTTCGGAGTCAAAAATAAGATTTTTGAAGG
* * *
52612 TTCGAGGGTAAAATGGCAATTTTTGAAAATTTTAGGGTTAAAATCGAGATT
65 TTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAATCGAGATT
* * * * * *
52663 TTTGAAATTTAGGGGTAAA-ATGGTAATTTTTGGAAGTTTCGGAGTCAAAATTGAGATTTTTAAA
1 TTGGAAGTTTAGGGGTAAATAT--TAATTTTTAG-AGTTTCGGAGTCAAAAATAAGATTTTTGAA
* * * * * *
52727 AGTTCGAGGCTAAAAAT-GTAATTTTTGGAAGTTTTAGGGTTAAAGTGGA-ATT
63 GGTTCGAGGGT-AAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAATCGAGATT
*
52779 TTGGAGAAGTTTAGGGGTCAAA-ATAAATTTTT
1 TT-G-GAAGTTTAGGGGT-AAATATTAATTTTT
52811 GGATAGTTTA
Statistics
Matches: 224, Mismatches: 31, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
115 4 0.02
116 106 0.47
117 92 0.41
118 17 0.08
119 5 0.02
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (115 bp):
TTGGAAGTTTAGGGGTAAATATTAATTTTTAGAGTTTCGGAGTCAAAAATAAGATTTTTGAAGGT
TCGAGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAATCGAGATT
Done.