Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004342.1 Hibiscus syriacus cultivar Beakdansim tig00009515_pilon, 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: 99910
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:7118 original size:14 final size:16
Alignment explanation
Indices: 7089--7120 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
7079 TATGTAATAG
7089 TAATTTAGGACTATTT
1 TAATTTAGGACTATTT
7105 TAATTT-GG-CTATTT
1 TAATTTAGGACTATTT
7119 TA
1 TA
7121 GTTATAATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.53
Consensus pattern (16 bp):
TAATTTAGGACTATTT
Found at i:11144 original size:17 final size:17
Alignment explanation
Indices: 11119--11153 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
11109 AGATACACCA
11119 GTCAATTGTTTAAAATG
1 GTCAATTGTTTAAAATG
*
11136 GTCACTTGTTTAAAATG
1 GTCAATTGTTTAAAATG
11153 G
1 G
11154 GACATGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (17 bp):
GTCAATTGTTTAAAATG
Found at i:14078 original size:29 final size:31
Alignment explanation
Indices: 14046--14107 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
14036 GCGGCAAACA
*
14046 TGTAAAATTT-G-AAAGTTTAGTGG-CCAAAG
1 TGTAAAATTTGGAAAAATTTAG-GGACCAAAG
*
14075 TGTAAAGTTTGGAAAAATTTAGGGACCAAAG
1 TGTAAAATTTGGAAAAATTTAGGGACCAAAG
14106 TG
1 TG
14108 GTAATTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 9 0.32
30 3 0.11
31 16 0.57
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.29
Consensus pattern (31 bp):
TGTAAAATTTGGAAAAATTTAGGGACCAAAG
Found at i:16336 original size:13 final size:13
Alignment explanation
Indices: 16318--16342 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16308 ACAGACATGT
16318 ATATGAAGACTGC
1 ATATGAAGACTGC
16331 ATATGAAGACTG
1 ATATGAAGACTG
16343 TTCAACTATG
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:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATATGAAGACTGC
Found at i:24172 original size:45 final size:45
Alignment explanation
Indices: 23861--24170 Score: 478
Period size: 45 Copynumber: 6.9 Consensus size: 45
23851 ACCACTATAC
* *** *
23861 ACTTTTCTGTTGATAATGCATATATATGCATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
23906 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
* *
23951 AGTTTTCTGTTGATAATGTATCCATATACATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
* * *
23996 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
*
24041 ACTTTTCTGTTGATAAT-TCACCCATATGCATTTCAACTATAGTAT
1 ACTTTTCTGTTGATAATGT-ACCCATATACATTTCAACTATAGTAT
* * *
24086 ACTTTTCTATTGATAATATACCCATATACATTTCAACTATGGTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
24131 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTAT
1 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTAT
24171 GGCATCCTTT
Statistics
Matches: 244, Mismatches: 19, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
45 243 1.00
46 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (45 bp):
ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTAT
Found at i:24226 original size:135 final size:135
Alignment explanation
Indices: 23861--24208 Score: 446
Period size: 135 Copynumber: 2.6 Consensus size: 135
23851 ACCACTATAC
*** * * * *** *
23861 ACTTTTCTGTTGATAATGCATATATATGCATTTCAACTATAGTATACTTTTCTGTTGATAATGTA
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATACCTTTCTGCCAATAATGCA
* * * * *
23926 CCCATATACATTTCAACTATAGTATAGTTTTCTGTTGATAATGTATCCATATACATTTCAACTAT
66 CCCATATGCATTTCAACTATAGTATACTTTTCTATTGATAATATACCCATATACATTTCAACTAT
23991 AGTAT
131 AGTAT
* * *** *
23996 ACTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGATAATTCA
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATACCTTTCTGCCAATAATGCA
24061 CCCATATGCATTTCAACTATAGTATACTTTTCTATTGATAATATACCCATATACATTTCAACTAT
66 CCCATATGCATTTCAACTATAGTATACTTTTCTATTGATAATATACCCATATACATTTCAACTAT
*
24126 GGTAT
131 AGTAT
* *
24131 ACTTTTCTGTTGATAATGTACCCATATACATTTCAACTATGGCAT-CCTTTCAATGCCAATAATG
1 ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATACCTTTC--TGCCAATAATG
*
24195 CTCCCATATGCATT
64 CACCCATATGCATT
24209 ATTATTTTCA
Statistics
Matches: 190, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
134 5 0.03
135 165 0.87
136 20 0.11
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (135 bp):
ACTTTTCTGTTGATAATGCACCCATATACATTTCAACTATAGCATACCTTTCTGCCAATAATGCA
CCCATATGCATTTCAACTATAGTATACTTTTCTATTGATAATATACCCATATACATTTCAACTAT
AGTAT
Found at i:24653 original size:22 final size:22
Alignment explanation
Indices: 24628--24669 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
24618 GTATCAATAT
*
24628 CCCTACCA-TGGTATTGATACTA
1 CCCTA-CATTGGTATCGATACTA
24650 CCCTACATTGGTATCGATAC
1 CCCTACATTGGTATCGATAC
24670 CCCCTTCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (22 bp):
CCCTACATTGGTATCGATACTA
Found at i:24764 original size:95 final size:95
Alignment explanation
Indices: 24618--24834 Score: 253
Period size: 95 Copynumber: 2.3 Consensus size: 95
24608 TGGCCCTTCA
* * * *
24618 GTATCAATATCCC-TACCATGGTATTGATACTACCCTACATTGGTATCGATACCCCCT-TCCAGT
1 GTATCGATA-CCCTTACCATGGTATCGATACTACCATACATTGGTATCGATA-CCCCTATACAGT
* *
24681 ATCAATACCAAAATTAAATTCGATGTGGCCCG
64 ATCAATACCAAAATTAAACTCGATGTGACCCG
* **
24713 GTATCGATACCCTTACCATGGTATCGATACTACTATAC-TATGGTA-CTGATACCCCTATATGGT
1 GTATCGATACCCTTACCATGGTATCGATACTACCATACAT-TGGTATC-GATACCCCTATACAGT
* ** *
24776 ATCGATACCAAAATTAGGCTCGATGTTACCCG
64 ATCAATACCAAAATTAAACTCGATGTGACCCG
24808 GTATCGATACCCTTACCATGGTATCGA
1 GTATCGATACCCTTACCATGGTATCGA
24835 AACAACTTCG
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
94 10 0.10
95 95 0.90
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTACCATACATTGGTATCGATACCCCTATACAGTAT
CAATACCAAAATTAAACTCGATGTGACCCG
Found at i:34896 original size:18 final size:19
Alignment explanation
Indices: 34864--34905 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
34854 ACAATAGATG
34864 TTCTATACAAGTGTGACTA
1 TTCTATACAAGTGTGACTA
* *
34883 TTCTA-ACAATTGTGCCTA
1 TTCTATACAAGTGTGACTA
34901 TTCTA
1 TTCTA
34906 GATATAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (19 bp):
TTCTATACAAGTGTGACTA
Found at i:43342 original size:52 final size:52
Alignment explanation
Indices: 43280--43405 Score: 141
Period size: 51 Copynumber: 2.4 Consensus size: 52
43270 TATCATTCTG
* * *
43280 TTTTACTTTATTTTAATTTAGTCACTCTTTA-TTTCTGATTTAGCTAC-AGTTA
1 TTTTATTTTATTATATTTTAGTCACTCTTTACTTT-TGATTTAGCTACTA-TTA
** * *
43332 TTTTATTTTA-TGCATTTTAGTCACTGTTTACTTTTGATTTAGCTACTATTT
1 TTTTATTTTATTATATTTTAGTCACTCTTTACTTTTGATTTAGCTACTATTA
*
43383 TTTTATTTTGTTATATTTTAGTC
1 TTTTATTTTATTATATTTTAGTC
43406 CCCATCTAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
51 39 0.63
52 23 0.37
ACGTcount: A:0.21, C:0.11, G:0.09, T:0.60
Consensus pattern (52 bp):
TTTTATTTTATTATATTTTAGTCACTCTTTACTTTTGATTTAGCTACTATTA
Found at i:46003 original size:3 final size:3
Alignment explanation
Indices: 45989--46027 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
45979 TTGTCCGGGA
*
45989 TAT TAT TTT TAT TAT TAT TAT TA- TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
46028 ATAATAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:46003 original size:9 final size:9
Alignment explanation
Indices: 45989--46027 Score: 55
Period size: 8 Copynumber: 4.6 Consensus size: 9
45979 TTGTCCGGGA
*
45989 TATTATTTT
1 TATTATTAT
45998 TATTATTAT
1 TATTATTAT
46007 TATTA-TAT
1 TATTATTAT
46015 TATT-TTAT
1 TATTATTAT
46023 TATTA
1 TATTA
46028 ATAATAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
8 14 0.52
9 13 0.48
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TATTATTAT
Found at i:55614 original size:24 final size:24
Alignment explanation
Indices: 55567--55620 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
55557 TTAGTTACAA
* * *
55567 AATCTTGTGCTTTTATAGCCGATG
1 AATCTCGTGCTTTTACAGCAGATG
*
55591 AATCTCGTGCTTTTGCAGCAGATG
1 AATCTCGTGCTTTTACAGCAGATG
*
55615 AGTCTC
1 AATCTC
55621 CTTGAAGTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (24 bp):
AATCTCGTGCTTTTACAGCAGATG
Found at i:57742 original size:18 final size:18
Alignment explanation
Indices: 57719--57758 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
57709 CTTTACATCT
* *
57719 ACCCTACAACTTTTACTA
1 ACCCTACAACCTTTACCA
57737 ACCCTACAACCTTTACCA
1 ACCCTACAACCTTTACCA
57755 ACCC
1 ACCC
57759 ATTTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.42, G:0.00, T:0.25
Consensus pattern (18 bp):
ACCCTACAACCTTTACCA
Found at i:59327 original size:3 final size:3
Alignment explanation
Indices: 59319--59371 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
59309 TCCTAAAAAG
59319 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
59367 ATA AT
1 ATA AT
59372 TAAAAAGAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:61021 original size:10 final size:10
Alignment explanation
Indices: 60611--61019 Score: 737
Period size: 10 Copynumber: 40.9 Consensus size: 10
60601 AAATATACTA
60611 TAACATAACG
1 TAACATAACG
60621 TAACATAACG
1 TAACATAACG
60631 TAACATAACG
1 TAACATAACG
60641 TAACATAACG
1 TAACATAACG
60651 TAACATAACG
1 TAACATAACG
60661 TAACATAACG
1 TAACATAACG
60671 TAACATAACG
1 TAACATAACG
60681 TAACATAACG
1 TAACATAACG
60691 TAACATAACG
1 TAACATAACG
60701 TAACATAACG
1 TAACATAACG
60711 TAACATAACG
1 TAACATAACG
60721 TAACATAACG
1 TAACATAACG
60731 TAACATAACG
1 TAACATAACG
60741 TAACATAACG
1 TAACATAACG
60751 TAACATAACG
1 TAACATAACG
60761 TAACATAACG
1 TAACATAACG
60771 TAACATAACG
1 TAACATAACG
60781 TAACATAACG
1 TAACATAACG
60791 TAACATAACG
1 TAACATAACG
60801 TAACATAACG
1 TAACATAACG
60811 TAACATAACG
1 TAACATAACG
60821 TAACATAACG
1 TAACATAACG
60831 TAACATAACG
1 TAACATAACG
60841 TAACATAACG
1 TAACATAACG
60851 TAACATAACG
1 TAACATAACG
60861 TAACATAACG
1 TAACATAACG
60871 TAACATAACG
1 TAACATAACG
60881 TAACATAACG
1 TAACATAACG
60891 TAACATAACG
1 TAACATAACG
60901 TAACATAACG
1 TAACATAACG
60911 TAACATAACG
1 TAACATAACG
*
60921 TAACATAACA
1 TAACATAACG
*
60931 TAACATAACA
1 TAACATAACG
*
60941 TAACATAACA
1 TAACATAACG
*
60951 TAACATAACA
1 TAACATAACG
*
60961 TAACATAACA
1 TAACATAACG
*
60971 TAACATAACA
1 TAACATAACG
*
60981 TAACATAACA
1 TAACATAACG
*
60991 TAACATAACA
1 TAACATAACG
*
61001 TAACATAACA
1 TAACATAACG
61011 TAACATAAC
1 TAACATAAC
61020 ATCATATAAT
Statistics
Matches: 398, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 398 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
TAACATAACG
Found at i:61037 original size:5 final size:5
Alignment explanation
Indices: 60610--61021 Score: 545
Period size: 5 Copynumber: 82.4 Consensus size: 5
60600 AAAATATACT
* * * *
60610 ATAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * *
60660 GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * *
60710 GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * *
60760 GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * *
60810 GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * *
60860 GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC GTAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* *
60910 GTAAC ATAAC GTAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
60960 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
61010 ATAAC ATAAC AT
1 ATAAC ATAAC AT
61022 CATATAATAT
Statistics
Matches: 345, Mismatches: 62, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 345 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (5 bp):
ATAAC
Found at i:61095 original size:26 final size:27
Alignment explanation
Indices: 61059--61135 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 27
61049 ACTATTTAAC
*
61059 ATATAATATATTTTCAAAAATT-ATAT
1 ATATTATATATTTTCAAAAATTAATAT
*
61085 ATATTATATATGTTTTCAAAATTTAATAT
1 ATATTATATA--TTTTCAAAAATTAATAT
61114 ATATATATATATATATTCAAAA
1 ATAT-TATATAT-T-TTCAAAA
61136 TATGTTTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 9 0.21
28 12 0.28
29 9 0.21
30 13 0.30
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (27 bp):
ATATTATATATTTTCAAAAATTAATAT
Found at i:61100 original size:28 final size:30
Alignment explanation
Indices: 61059--61135 Score: 106
Period size: 28 Copynumber: 2.7 Consensus size: 30
61049 ACTATTTAAC
61059 ATATA-ATATATTTTCAAAAATT-ATATAT
1 ATATATATATATTTTCAAAAATTAATATAT
* *
61087 AT-TATATATGTTTTCAAAATTTAATATAT
1 ATATATATATATTTTCAAAAATTAATATAT
*
61116 ATATATATATATATTCAAAA
1 ATATATATATATTTTCAAAA
61136 TATGTTTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.05
28 17 0.40
29 8 0.19
30 15 0.36
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (30 bp):
ATATATATATATTTTCAAAAATTAATATAT
Found at i:61206 original size:38 final size:38
Alignment explanation
Indices: 61164--61398 Score: 300
Period size: 38 Copynumber: 6.2 Consensus size: 38
61154 TTATATAATT
* *
61164 TTTTTTAAAAAACAATATATTATATGTTTGCAGAAACC-
1 TTTTTTAAAAAACTATATATTATATGTTTTCA-AAACCG
** *
61202 TTTTTTTTAAAACTATATATTATATGTTTACAAAACC-
1 TTTTTTAAAAAACTATATATTATATGTTTTCAAAACCG
* *
61239 ATTTTTAAAAAACTATATATTATATGTTTTCAAACACTG
1 TTTTTTAAAAAACTATATATTATATGTTTTCAAA-ACCG
* *
61278 TTTTTT-AAAAATTATATATTATATATTTTCAAAACCG
1 TTTTTTAAAAAACTATATATTATATGTTTTCAAAACCG
*
61315 TTTTTT--TAAACTATATATTATATGTTTTCAAAAACCG
1 TTTTTTAAAAAACTATATATTATATGTTTTC-AAAACCG
* *
61352 TTTTTAAAAAAACTATATATTATATATTTTCAAAACCG
1 TTTTTTAAAAAACTATATATTATATGTTTTCAAAACCG
61390 TTTTTTAAA
1 TTTTTTAAA
61399 CTATACTATT
Statistics
Matches: 172, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
36 20 0.12
37 56 0.33
38 70 0.41
39 26 0.15
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (38 bp):
TTTTTTAAAAAACTATATATTATATGTTTTCAAAACCG
Found at i:61245 original size:75 final size:74
Alignment explanation
Indices: 61165--61412 Score: 306
Period size: 75 Copynumber: 3.3 Consensus size: 74
61155 TATATAATTT
* * * *
61165 TTTTTAAAAAACAATATATTATATGTTTGCAGAAACCTTTTTTTTAAAACTATATATTATATGTT
1 TTTTTAAAAAACTATATATTATATGTTTTCA-AAACCTTTTTTTAAAAACTATATATTATATATT
* *
61230 TACAAAACCA
65 TTCAAAACCG
*
61240 TTTTTAAAAAACTATATATTATATGTTTTC-AAACACTGTTTTTTAAAAATTATATATTATATAT
1 TTTTTAAAAAACTATATATTATATGTTTTCAAAAC-CT-TTTTTTAAAAACTATATATTATATAT
61304 TTTCAAAACCG
64 TTTCAAAACCG
** **
61315 TTTTT-TTAAACTATATATTATATGTTTTCAAAAACCGTTTTTAAAAAAACTATATATTATATAT
1 TTTTTAAAAAACTATATATTATATGTTTTC-AAAACC-TTTTTTTAAAAACTATATATTATATAT
61379 TTTCAAAACCG
64 TTTCAAAACCG
*
61390 TTTTT--TAAACTATACTATTATAT
1 TTTTTAAAAAACTATA-TATTATAT
61413 ATTATCATAT
Statistics
Matches: 155, Mismatches: 12, Indels: 12
0.87 0.07 0.07
Matches are distributed among these distances:
73 4 0.03
74 33 0.21
75 113 0.73
76 5 0.03
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (74 bp):
TTTTTAAAAAACTATATATTATATGTTTTCAAAACCTTTTTTTAAAAACTATATATTATATATTT
TCAAAACCG
Found at i:61414 original size:113 final size:114
Alignment explanation
Indices: 61164--61414 Score: 329
Period size: 113 Copynumber: 2.2 Consensus size: 114
61154 TTATATAATT
* *
61164 TTTTTTAAAAAACAATATAT-TATATGTTTGCAGAAACCTTTTTTTTAAAACTATATATTATATG
1 TTTTTT-AAAAACTATATATATATATGTTTGCAGAAACCGTTTTTTTAAAACTATATATTATATG
* *
61228 TTTACAAAACCATTTTTAAAAAACTATATATTATATGTTTTCAAACACTG
65 TTTACAAAACCATTTTTAAAAAACTATATATTATATATTTTCAAACACCG
*
61278 TTTTTTAAAAATTATATATTATATAT-TTT-CA-AAACCGTTTTTTT-AAACTATATATTATATG
1 TTTTTTAAAAACTATATA-TATATATGTTTGCAGAAACCGTTTTTTTAAAACTATATATTATATG
* *
61339 TTTTCAAAAACCGTTTTTAAAAAAACTATATATTATATATTTTCAAA-ACCG
65 TTTAC-AAAACCATTTTT-AAAAAACTATATATTATATATTTTCAAACACCG
61390 TTTTTT--AAACTATACTATTATATAT
1 TTTTTTAAAAACTATA-TA-TATATAT
61415 TATCATATAT
Statistics
Matches: 124, Mismatches: 8, Indels: 13
0.86 0.06 0.09
Matches are distributed among these distances:
110 7 0.06
111 31 0.25
112 32 0.26
113 39 0.31
114 10 0.08
115 5 0.04
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (114 bp):
TTTTTTAAAAACTATATATATATATGTTTGCAGAAACCGTTTTTTTAAAACTATATATTATATGT
TTACAAAACCATTTTTAAAAAACTATATATTATATATTTTCAAACACCG
Found at i:62076 original size:42 final size:42
Alignment explanation
Indices: 62017--62099 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
62007 GCCATATGAC
* * *
62017 ACCGGGGTGTTTCCATGCAAAATGCATTAAACACCATGCGTG
1 ACCGGGGTATTGCCATGCAAAATGCATGAAACACCATGCGTG
*
62059 ACCGGGGTATTGCCATGCAAAATGCATGGAACACCATGCGT
1 ACCGGGGTATTGCCATGCAAAATGCATGAAACACCATGCGT
62100 CACCCCTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (42 bp):
ACCGGGGTATTGCCATGCAAAATGCATGAAACACCATGCGTG
Found at i:62117 original size:42 final size:42
Alignment explanation
Indices: 62026--62118 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
62016 CACCGGGGTG
* * **
62026 TTTCCATGCAAAATGCATTAAACACCATGCGTGACCGGGGTA
1 TTTCCATGCAAAATGCATGAAACACCATGCGTCACCGCCGTA
* * *
62068 TTGCCATGCAAAATGCATGGAACACCATGCGTCACC-CCTTAA
1 TTTCCATGCAAAATGCATGAAACACCATGCGTCACCGCCGT-A
62110 TTTCCATGC
1 TTTCCATGC
62119 TTTCCATCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (42 bp):
TTTCCATGCAAAATGCATGAAACACCATGCGTCACCGCCGTA
Found at i:76844 original size:28 final size:30
Alignment explanation
Indices: 76813--76874 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
76803 TTATGTTAAT
76813 GGTTTA-GGTTTTAGGTT-AAAGGGTTTAG
1 GGTTTATGGTTTTAGGTTAAAAGGGTTTAG
** *
76841 GG-TTATGGTTTTTTGTTAAAATGGTTTAG
1 GGTTTATGGTTTTAGGTTAAAAGGGTTTAG
76870 GGTTT
1 GGTTT
76875 TTAGAGTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 3 0.11
28 11 0.39
29 12 0.43
30 2 0.07
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.48
Consensus pattern (30 bp):
GGTTTATGGTTTTAGGTTAAAAGGGTTTAG
Found at i:76866 original size:22 final size:22
Alignment explanation
Indices: 76841--76911 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 22
76831 AAGGGTTTAG
76841 GGTTATGGTTTTTTGTTAAAAT
1 GGTTATGGTTTTTTGTTAAAAT
* * *
76863 GGTTTAGGGTTTTTAGAGTAAAAT
1 GG-TTATGGTTTTTTG-TTAAAAT
* *
76887 GGTT-TAGTTTTTTGTTTAAAT
1 GGTTATGGTTTTTTGTTAAAAT
76908 GGTT
1 GGTT
76912 TAGGGTTAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
21 9 0.23
22 9 0.23
23 13 0.33
24 8 0.21
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (22 bp):
GGTTATGGTTTTTTGTTAAAAT
Found at i:76875 original size:21 final size:21
Alignment explanation
Indices: 76851--76918 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
76841 GGTTATGGTT
76851 TTTTGTTAAAATGGTTTAGGG
1 TTTTGTTAAAATGGTTTAGGG
* **
76872 TTTTTAGAGTAAAATGGTTTAGTT
1 -TTTT-G-TTAAAATGGTTTAGGG
*
76896 TTTTGTTTAAATGGTTTAGGG
1 TTTTGTTAAAATGGTTTAGGG
76917 TT
1 TT
76919 AGATTAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 14 0.38
22 5 0.14
23 5 0.14
24 13 0.35
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (21 bp):
TTTTGTTAAAATGGTTTAGGG
Found at i:76884 original size:24 final size:23
Alignment explanation
Indices: 76847--76918 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 23
76837 TTAGGGTTAT
* *
76847 GGTTTTTTGTTAAAATGGTTTAG
1 GGTTTTTAGGTAAAATGGTTTAG
76870 GGTTTTTAGAGTAAAATGGTTTA-
1 GGTTTTTAG-GTAAAATGGTTTAG
* * *
76893 -GTTTTTTGTTTAAATGGTTTAG
1 GGTTTTTAGGTAAAATGGTTTAG
76915 GGTT
1 GGTT
76919 AGATTAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 11 0.27
22 7 0.17
23 11 0.27
24 12 0.29
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.51
Consensus pattern (23 bp):
GGTTTTTAGGTAAAATGGTTTAG
Found at i:76928 original size:21 final size:21
Alignment explanation
Indices: 76856--76928 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
76846 TGGTTTTTTG
76856 TTAAAATGGTTTAGGGTTTTTAGA
1 TTAAAATGGTTTAGGG---TTAGA
* ** *
76880 GTAAAATGGTTTAGTTTTTTG-
1 TTAAAATGGTTTAG-GGTTAGA
*
76901 TTTAAATGGTTTAGGGTTAGA
1 TTAAAATGGTTTAGGGTTAGA
76922 TTAAAAT
1 TTAAAAT
76929 TAAAATCTTG
Statistics
Matches: 37, Mismatches: 10, Indels: 7
0.69 0.19 0.13
Matches are distributed among these distances:
20 3 0.08
21 18 0.49
22 3 0.08
24 13 0.35
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (21 bp):
TTAAAATGGTTTAGGGTTAGA
Found at i:77595 original size:20 final size:19
Alignment explanation
Indices: 77572--77633 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
77562 AGGTTTTATT
77572 TTTATGTCCTTAATGTAATG
1 TTTATGT-CTTAATGTAATG
* *
77592 TTTATGGT-TCATTGT--T-
1 TTTAT-GTCTTAATGTAATG
77608 TTTATGTCTTTAATGTAATG
1 TTTATGTC-TTAATGTAATG
77628 TTTATG
1 TTTATG
77634 GTTTAGGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
15 2 0.06
16 5 0.16
17 6 0.19
19 6 0.19
20 11 0.34
21 2 0.06
ACGTcount: A:0.21, C:0.06, G:0.16, T:0.56
Consensus pattern (19 bp):
TTTATGTCTTAATGTAATG
Found at i:77621 original size:36 final size:34
Alignment explanation
Indices: 77538--77637 Score: 139
Period size: 36 Copynumber: 2.9 Consensus size: 34
77528 TAATGGTATG
*
77538 TTTATGTCCTTAACGTAATGTGTTA-GGTTTTATT
1 TTTATGTCCTTAATGTAATGT-TTATGGTTTTATT
*
77572 TTTATGTCCTTAATGTAATGTTTATGGTTCATTGTT
1 TTTATGTCCTTAATGTAATGTTTATGGTT--TTATT
*
77608 TTTATGTCTTTAATGTAATGTTTATGGTTT
1 TTTATGTCCTTAATGTAATGTTTATGGTTT
77638 AGGATTTAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
33 3 0.05
34 25 0.42
36 32 0.53
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.56
Consensus pattern (34 bp):
TTTATGTCCTTAATGTAATGTTTATGGTTTTATT
Found at i:77952 original size:21 final size:21
Alignment explanation
Indices: 77926--77974 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
77916 TATCCTTATT
77926 GCAATCACCCTTTTATGAGAA
1 GCAATCACCCTTTTATGAGAA
*
77947 GCAATCACCCTTTTATGTGAA
1 GCAATCACCCTTTTATGAGAA
77968 GCAATCA
1 GCAATCA
77975 TATACCTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (21 bp):
GCAATCACCCTTTTATGAGAA
Found at i:95712 original size:7 final size:7
Alignment explanation
Indices: 95700--95730 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
95690 ACCTTATATA
95700 TTTAGGG
1 TTTAGGG
95707 TTTAGGG
1 TTTAGGG
95714 TTTAGGG
1 TTTAGGG
*
95721 TTTATGG
1 TTTAGGG
95728 TTT
1 TTT
95731 TTTTCAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (7 bp):
TTTAGGG
Done.