Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002398.1 Hibiscus syriacus cultivar Beakdansim tig00004903_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: 68129
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:10218 original size:30 final size:33
Alignment explanation
Indices: 10184--10259 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 33
10174 AAGAGCAATT
* *
10184 TAAAAGTTCAATGAGTAAATTTTAAAAA-A-A-
1 TAAAAGTTCAATGAGTAAAATATAAAAATAGAG
*
10214 TAAAAATAT-AATGAGTAAAATATAAAAATAGAG
1 TAAAAGT-TCAATGAGTAAAATATAAAAATAGAG
10247 T-AAAGTTCAATGA
1 TAAAAGTTCAATGA
10260 AGAATAGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
30 23 0.62
31 3 0.08
32 10 0.27
33 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.12, T:0.28
Consensus pattern (33 bp):
TAAAAGTTCAATGAGTAAAATATAAAAATAGAG
Found at i:14053 original size:18 final size:18
Alignment explanation
Indices: 14030--14066 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
14020 AGGGACGATA
14030 TGATGTTAAAGGGAGAAT
1 TGATGTTAAAGGGAGAAT
*
14048 TGATGTTAAAGGGTGAAT
1 TGATGTTAAAGGGAGAAT
14066 T
1 T
14067 TATAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (18 bp):
TGATGTTAAAGGGAGAAT
Found at i:18323 original size:25 final size:25
Alignment explanation
Indices: 18294--18345 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
18284 CATCTTATTC
*
18294 TTTTA-TTATATATTATTAGAAAGTG
1 TTTTAGTT-TATATTATTAGAAAATG
* *
18319 TTTTAGTTTATGTTATTATAAAATG
1 TTTTAGTTTATATTATTAGAAAATG
18344 TT
1 TT
18346 CTTTGGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (25 bp):
TTTTAGTTTATATTATTAGAAAATG
Found at i:22915 original size:23 final size:23
Alignment explanation
Indices: 22886--22938 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
22876 TATAATATTA
*
22886 TTTTAATTAAATTACATTTATAT
1 TTTTAATTAAATTACAATTATAT
*
22909 TTTTAATTAATTTACAATTATAT
1 TTTTAATTAAATTACAATTATAT
*
22932 GTTTAAT
1 TTTTAAT
22939 ACTTTATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAATTAAATTACAATTATAT
Found at i:22954 original size:15 final size:15
Alignment explanation
Indices: 22934--22968 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
22924 AATTATATGT
22934 TTAATACTTTATAAA
1 TTAATACTTTATAAA
*
22949 TTAATATTTTATAAA
1 TTAATACTTTATAAA
22964 TTAAT
1 TTAAT
22969 TTAATGATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAATACTTTATAAA
Found at i:24711 original size:13 final size:13
Alignment explanation
Indices: 24693--24717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24683 TGTGTTGTTA
24693 ATATTAATAATTG
1 ATATTAATAATTG
24706 ATATTAATAATT
1 ATATTAATAATT
24718 AAGAAAAGGT
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
ATATTAATAATTG
Found at i:25222 original size:113 final size:113
Alignment explanation
Indices: 25024--25236 Score: 349
Period size: 113 Copynumber: 1.9 Consensus size: 113
25014 TTCCTACTGT
*
25024 TAAGATCCTATTACACAATGTAAAACTCTTTTAGTTTTACACAGATTTAGGACCGTTGGATGGGT
1 TAAGATCCTATTACACAATGTAAAACTCTTTTAGTTTTACACAGATTTAGGACCGTTGGATGAGT
*
25089 GAAAATAGATGACTGAGATTAACAGTAAAAAATGAGAACATATAGAGA
66 GAAAATAGATGACTGAGATTAACAATAAAAAATGAGAACATATAGAGA
25137 TAAGATCCTATTACACAATGTAAAACT-TTTTAAGTTTTACACAGATTTAGGACTC-TTGGATGA
1 TAAGATCCTATTACACAATGTAAAACTCTTTT-AGTTTTACACAGATTTAGGAC-CGTTGGATGA
** *
25200 GTGAAAATAGATGGTTGAGATTAACAATAGAAAATGA
64 GTGAAAATAGATGACTGAGATTAACAATAAAAAATGA
25237 TAAGATATTC
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
112 4 0.04
113 88 0.95
114 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (113 bp):
TAAGATCCTATTACACAATGTAAAACTCTTTTAGTTTTACACAGATTTAGGACCGTTGGATGAGT
GAAAATAGATGACTGAGATTAACAATAAAAAATGAGAACATATAGAGA
Found at i:29207 original size:17 final size:18
Alignment explanation
Indices: 29182--29217 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
29172 GTTCAGAAAC
29182 ATTCATCACC-ATCCCGA
1 ATTCATCACCGATCCCGA
*
29199 ATTCTTCACCGATCCCGA
1 ATTCATCACCGATCCCGA
29217 A
1 A
29218 AAATTTGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.28, C:0.39, G:0.08, T:0.25
Consensus pattern (18 bp):
ATTCATCACCGATCCCGA
Found at i:33472 original size:36 final size:37
Alignment explanation
Indices: 33405--33474 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
33395 TTTTTATATT
33405 TTTAATTTTGTAAAAAAAATTATATAAATATTTTGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTTTGAA
* *
33442 TTTAATTTTTTAAAGAAAA-TATATAAATATTTT
1 TTTAATTTTGTAAAAAAAATTATATAAATATTTT
33475 ACAATTTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 14 0.45
37 17 0.55
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTTTGAA
Found at i:37007 original size:21 final size:21
Alignment explanation
Indices: 36970--37021 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
36960 TAATATTAAC
36970 TATTATAAATAT-T-TAAATCA
1 TATTATAAATATATCTAAAT-A
*
36990 T-TTATTAATATATCTAAATA
1 TATTATAAATATATCTAAATA
37010 TATTATAAATAT
1 TATTATAAATAT
37022 TATTTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 9 0.33
20 4 0.15
21 14 0.52
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTATAAATATATCTAAATA
Found at i:38269 original size:5 final size:4
Alignment explanation
Indices: 38248--38479 Score: 74
Period size: 4 Copynumber: 57.8 Consensus size: 4
38238 AAAAGGTAAG
* *
38248 AAAT AAAT AAAT AAATT AAATT AAAAT GAAG AAA- AAAT AAATT AAAT
1 AAAT AAAT AAAT AAA-T AAA-T -AAAT AAAT AAAT AAAT AAA-T AAAT
* * * * * *
38295 AAA- AGAT AAGAT AAAA AAAT TAA- AGAT AAA- ATAGT AAGT AAAAT AAAT
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT -AAAT AAAT
* * * * *
38343 ATAA- AAA- AAAT AAA- AAAA AAAA AGAAG AAAA AAAT ATAT AAAT AAAAT
1 A-AAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT -AAAT
* *
38391 AAAT AAA- AAAT -AA- AAAT AATAT ATAT ATAT ATAAT AAAT AAAT AAAAT
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT A-AAT AAAT AAAT -AAAT
* * * * * *
38439 AAA- AAAT -AGT AAAT ATAT ATAT ATAT ATAT AAAT TAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
38480 ACTGATAATA
Statistics
Matches: 179, Mismatches: 26, Indels: 46
0.71 0.10 0.18
Matches are distributed among these distances:
3 27 0.15
4 111 0.62
5 38 0.21
6 3 0.02
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:38352 original size:27 final size:26
Alignment explanation
Indices: 38256--38400 Score: 97
Period size: 26 Copynumber: 5.6 Consensus size: 26
38246 AGAAATAAAT
* * *
38256 AAATAAATTAAATTAAAAT-GAAGAAA
1 AAATAAATTAAA-AAAAATATAAGATA
* *
38282 AAATAAATTAAATAAAAGATAAGATA
1 AAATAAATTAAAAAAAATATAAGATA
38308 AAA-AAATTAAAGATAAAATAGTAAG-TA
1 AAATAAATTAAA-A-AAAATA-TAAGATA
38335 AAATAAATATAAAAAAAATA-AA-A-A
1 AAATAAAT-TAAAAAAAATATAAGATA
* ** *
38359 AAAAAAAGAAGAAAAAAATATATAAATA
1 AAATAAATTA-AAAAAAATATA-AGATA
38387 AAATAAA-TAAAAAA
1 AAATAAATTAAAAAA
38401 TAAAAATAAT
Statistics
Matches: 97, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
23 1 0.01
24 16 0.16
25 16 0.16
26 26 0.27
27 18 0.19
28 16 0.16
29 4 0.04
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (26 bp):
AAATAAATTAAAAAAAATATAAGATA
Found at i:38353 original size:11 final size:11
Alignment explanation
Indices: 38333--38413 Score: 58
Period size: 11 Copynumber: 7.2 Consensus size: 11
38323 AAATAGTAAG
*
38333 TAAAATAAATA
1 TAAAAAAAATA
38344 TAAAAAAAATA
1 TAAAAAAAATA
* *
38355 AAAAAAAAAAA
1 TAAAAAAAATA
*
38366 GAAGAAAAAAATA
1 -TA-AAAAAAATA
38379 TATAAATAAAATA
1 TA-AAA-AAAATA
*
38392 -AATAAAAA-A
1 TAAAAAAAATA
*
38401 TAAAAATAATA
1 TAAAAAAAATA
38412 TA
1 TA
38414 TATATATATA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
9 1 0.02
10 10 0.18
11 24 0.43
12 7 0.12
13 14 0.25
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
TAAAAAAAATA
Found at i:38382 original size:37 final size:37
Alignment explanation
Indices: 38305--38444 Score: 104
Period size: 38 Copynumber: 3.6 Consensus size: 37
38295 AAAAGATAAG
* * * * *
38305 ATAAAAAAATTAAAGATAAAATAGTAAGTAAAATAA-AT
1 ATAAAAAAAATAAAAAAAAAAAAG-AAG-AAAAAAATAT
38343 ATAAAAAAAATAAAAAAAAAAAAGAAGAAAAAAATAT
1 ATAAAAAAAATAAAAAAAAAAAAGAAGAAAAAAATAT
* * *
38380 ATAAATAAAATAAATAAAAAATAAA-AATAATATATATATAT
1 ATAAAAAAAATAAA-AAAAAA-AAAGAAGAA-A-A-AAATAT
*
38421 ATAATAAATAAATAAAATAAAAAA
1 ATAA-AAA-AAATAAAAAAAAAAA
38445 TAGTAAATAT
Statistics
Matches: 84, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
36 6 0.07
37 18 0.21
38 30 0.36
39 4 0.05
40 1 0.01
41 11 0.13
42 7 0.08
43 7 0.08
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (37 bp):
ATAAAAAAAATAAAAAAAAAAAAGAAGAAAAAAATAT
Found at i:38399 original size:35 final size:35
Alignment explanation
Indices: 38320--38432 Score: 97
Period size: 35 Copynumber: 3.1 Consensus size: 35
38310 AAAATTAAAG
*
38320 ATAAAATAGTAAGTAAAATAAATATA-AAA-AAAATAAAA
1 ATAAAAAAG-AAG-AAAA-AAATATATAAATAAAAT--AA
*
38358 AAAAAAAAGAAGAAAAAAATATATAAATAAAATAA
1 ATAAAAAAGAAGAAAAAAATATATAAATAAAATAA
* * * *
38393 ATAAAAAATAA-AAATAATATATATATATATAATAA
1 ATAAAAAAGAAGAAA-AAAATATATAAATAAAATAA
38428 ATAAA
1 ATAAA
38433 TAAAATAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
34 3 0.05
35 40 0.62
36 7 0.11
37 8 0.12
38 7 0.11
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (35 bp):
ATAAAAAAGAAGAAAAAAATATATAAATAAAATAA
Found at i:38456 original size:2 final size:2
Alignment explanation
Indices: 38451--38528 Score: 67
Period size: 2 Copynumber: 40.5 Consensus size: 2
38441 AAAATAGTAA
* * *
38451 AT AT AT AT AT AT AT AT AT AA AT -T A- AT A- AA ACT GAT A- AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT
*
38491 AA AT A- AT AT AT 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 AT AT AT A
38529 ATCTAAAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
1 5 0.08
2 57 0.89
3 1 0.02
4 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:39670 original size:35 final size:39
Alignment explanation
Indices: 39586--39675 Score: 125
Period size: 39 Copynumber: 2.4 Consensus size: 39
39576 CGAGGGTATG
* *
39586 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGT
1 GTGTTTCAAGAGAAACAATTTCAAAGGGTTTTTGTGTGT
*
39625 GTGTTTCAAGAGAAACAATTTC-GAGGGTTTTT-T-T-T
1 GTGTTTCAAGAGAAACAATTTCAAAGGGTTTTTGTGTGT
39660 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
39676 TGTCTCAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
35 17 0.35
36 1 0.02
37 1 0.02
38 8 0.17
39 21 0.44
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (39 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGGTTTTTGTGTGT
Found at i:39818 original size:37 final size:37
Alignment explanation
Indices: 39661--39826 Score: 178
Period size: 36 Copynumber: 4.5 Consensus size: 37
39651 GTTTTTTTTG
*
39661 TGTTTCAAGAGAAACTGTCTCAAGAGGGACA-AAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACACAAATT
* *
39697 TATTTCAAAAGAAACTGTCTCAAGAGAGACA-AAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACACAAA-TT
* * * *
39734 AGTTAT-AAAAGAAACTGTCTCAAGGGAGAC-GAAATT
1 TGTT-TCAAGAGAAACTGTCTCAAGAGAGACACAAATT
* * * *
39770 TGTTTCAAGGGAAACTGTCTCAAGAGATACACGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACACAAATT
*
39807 TGTTTCAAGGGAAACTGTCT
1 TGTTTCAAGAGAAACTGTCT
39827 TAAAACTCGT
Statistics
Matches: 111, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
35 1 0.01
36 56 0.50
37 53 0.48
38 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACACAAATT
Found at i:39821 original size:73 final size:73
Alignment explanation
Indices: 39661--39826 Score: 201
Period size: 73 Copynumber: 2.3 Consensus size: 73
39651 GTTTTTTTTG
39661 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATTTATTTCAAAAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATTTATTTCAAAAGAAACTGTCTCAAGAGAGA
39726 CAAAACTT
66 CAAAACTT
* * * * **
39734 AGTTAT-AAAAGAAACTGTCTCAAG-GGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TGTT-TCAAGAGAAACTGTCTCAAGAGG-GACAAAATTTATTTCAAAAGAAACTGTCTCAAGAGA
* ** *
39797 TACACGATTT
64 GACAAAACTT
*
39807 TGTTTCAAGGGAAACTGTCT
1 TGTTTCAAGAGAAACTGTCT
39827 TAAAACTCGT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
72 3 0.04
73 73 0.95
74 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATTTATTTCAAAAGAAACTGTCTCAAGAGAGA
CAAAACTT
Found at i:39945 original size:37 final size:37
Alignment explanation
Indices: 39894--39966 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
39884 TCAAGGTTTA
*
39894 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
*
39931 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
39967 AATTTCAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:39980 original size:36 final size:37
Alignment explanation
Indices: 39896--39980 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
39886 AAGGTTTATG
* **
39896 TTTC-AAGAGAAACTATCTCAAGGGAGACAAAATTTTG
1 TTTCAAAG-GAAACTATCTCAAGAGAGACAAAATTTAA
*
39933 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTAA
1 TTTCAAAGGAAACTATCTCAAGAGAGACAAAATTTAA
39969 TTTCAAAGGAAA
1 TTTCAAAGGAAA
39981 TGTTTTCAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 13 0.31
37 27 0.64
38 2 0.05
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.25
Consensus pattern (37 bp):
TTTCAAAGGAAACTATCTCAAGAGAGACAAAATTTAA
Found at i:39995 original size:102 final size:102
Alignment explanation
Indices: 39867--40106 Score: 381
Period size: 102 Copynumber: 2.4 Consensus size: 102
39857 ATATTTTGTG
* * *
39867 TTTCAAGGGAAATATTTTCAAGGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
1 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* *
39932 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
* * *
39969 TTTCAAAGGAAATGTTTTCAATGTTTATATTTCAAGAGAAGCTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* * *
40034 GTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTA
66 GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
40071 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAG
1 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAG
40107 GGAGACAAAA
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 126 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (102 bp):
TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTACCCCAAGAGAGACAAAATTAA
Found at i:40109 original size:87 final size:87
Alignment explanation
Indices: 40015--40193 Score: 297
Period size: 87 Copynumber: 2.1 Consensus size: 87
40005 AGAAGCTGTC
* *
40015 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAAGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTC-AAGG
40080 -AAATGTTTTCAATGTTTATGTT
65 AAAATGTTTTCAATGTTTATGTT
* * *
40102 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGA
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGA
40167 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
40189 TCAAG
1 TCAAG
40194 AGAAACTGTC
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
86 4 0.05
87 82 0.95
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGA
AAATGTTTTCAATGTTTATGTT
Found at i:40293 original size:189 final size:189
Alignment explanation
Indices: 39913--40294 Score: 500
Period size: 189 Copynumber: 2.0 Consensus size: 189
39903 AGAAACTATC
*
39913 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
* * * **
39978 AAATGTTTTCAATGTTTATATTTCAAGAGAAGCTGTCTCAAGGGAGACAAAATTTTGTTTCAAGG
66 AAATGTTTTCAATGTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAA
* * * * * * *
40043 GAAACTACCCCAAGCGAGATAAAATTTATTTCAAAGGAAATGTTTTCAATGTTTATGTT
131 GAAAATACCCCAAGCGAGACAAAATTTATTTCAAAGAAAAAGATTTAAATATTTATGTT
** * *
40102 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTC-AAGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
*
40166 AAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAA
66 -AAATGTTTTCAATGTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAA
** * * * *
40231 AGAAAATGTCTCAAGGGAGACGAAA-TTAGTTTCAATGAAAACAGATTTAAATATTT-TGTT
130 AGAAAATACCCCAAGCGAGACAAAATTTA-TTTCAAAGAAAA-AGATTTAAATATTTATGTT
40291 TCAA
1 TCAA
40295 TGGAAACTTG
Statistics
Matches: 166, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
188 7 0.04
189 149 0.90
190 10 0.06
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (189 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
AAATGTTTTCAATGTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAA
GAAAATACCCCAAGCGAGACAAAATTTATTTCAAAGAAAAAGATTTAAATATTTATGTT
Found at i:40635 original size:106 final size:106
Alignment explanation
Indices: 40450--40772 Score: 472
Period size: 106 Copynumber: 3.0 Consensus size: 106
40440 TGTATTGTTC
* * * * *
40450 CGAGTCCAATATCC-TCTGCTGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGCTGAC
1 CGAGTCCAATATCCTTCT-CTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGAC
* * * *
40514 AGCCAGCCG-CACCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 AACCAGCCGTC-CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
40556 CGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCCGAAATTAGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACA
40621 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
40662 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCTGAAATTAGG-AAATTGTTTGTTGAC
* *
40726 AACCAGCCGTCCCTTCATTGTGGAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
40768 CGAGT
1 CGAGT
40773 GGCACGATAT
Statistics
Matches: 198, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
105 2 0.01
106 192 0.97
107 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCTCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:41451 original size:32 final size:32
Alignment explanation
Indices: 41350--41439 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
41340 ATTCCCAAAG
* *
41350 ATGCCCCAATATTCGATGTTGAATCTAAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTAAAAAA
* *
41382 ATGGCCCAACATTTGATGTTAAATCTAAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTAAAAAA
41414 ATGCCCCAACATTTGATGTTGAATCT
1 ATGCCCCAACATTTGATGTTGAATCT
41440 TTAAAGATGC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATCTAAAAAA
Found at i:42491 original size:69 final size:68
Alignment explanation
Indices: 42371--42512 Score: 205
Period size: 69 Copynumber: 2.1 Consensus size: 68
42361 TATGTGTCTC
* *
42371 TCTC-TTTATGCTCCATGATCTTCGAGTGGAGTGATTCAATAATTCATAAATGATTGTGCTTGAT
1 TCTCATTTATGCTCCATGATCTTCGAGTGAAGTGATTCAATAATTCAGAAATGATTGTGCTTGAT
42435 CAA
66 CAA
* * * * *
42438 TCTCATTTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGA
1 TCTCATTT-ATGCTCCATGATCTTCGAGTGAAGTGATTCAATAATTCAGAAATGATTGTGCTTGA
42503 TCAA
65 TCAA
42507 TCTCAT
1 TCTCAT
42513 AGATTGAATC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 4 0.06
68 3 0.05
69 59 0.89
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (68 bp):
TCTCATTTATGCTCCATGATCTTCGAGTGAAGTGATTCAATAATTCAGAAATGATTGTGCTTGAT
CAA
Found at i:42599 original size:11 final size:11
Alignment explanation
Indices: 42595--42648 Score: 65
Period size: 11 Copynumber: 4.7 Consensus size: 11
42585 TTTTCCTTTG
42595 TTTTTTTTCTC
1 TTTTTTTTCTC
42606 TTTTTTTTCTC
1 TTTTTTTTCTC
*
42617 TTTGTTTTTTTC
1 TTT-TTTTTCTC
42629 TCTTTTTTTCT-
1 T-TTTTTTTCTC
42640 TTTTGTTTT
1 TTTT-TTTT
42649 GATTAAATCT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 3 0.08
11 19 0.50
12 14 0.37
13 2 0.05
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (11 bp):
TTTTTTTTCTC
Found at i:42607 original size:26 final size:25
Alignment explanation
Indices: 42573--42648 Score: 77
Period size: 24 Copynumber: 3.1 Consensus size: 25
42563 TCTTGTCTTC
*
42573 TTTTTTCT-TCAATTTTC-CTTTGTT
1 TTTTTTCTCTTAATTTTCTCTTTG-T
**
42597 TTTTTTCTCTTTTTTTTCTCTTTGT
1 TTTTTTCTCTTAATTTTCTCTTTGT
* *
42622 TTTTTTCTCTT-TTTTTCTTTTTGT
1 TTTTTTCTCTTAATTTTCTCTTTGT
42646 TTT
1 TTT
42649 GATTAAATCT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
24 23 0.50
25 18 0.39
26 5 0.11
ACGTcount: A:0.03, C:0.14, G:0.04, T:0.79
Consensus pattern (25 bp):
TTTTTTCTCTTAATTTTCTCTTTGT
Found at i:42612 original size:14 final size:14
Alignment explanation
Indices: 42585--42642 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
42575 TTTTCTTCAA
42585 TTTTC-CTTTGTTTT
1 TTTTCTCTTT-TTTT
42599 TTTTCTC---TTTT
1 TTTTCTCTTTTTTT
*
42610 TTTTCTCTTTGTTT
1 TTTTCTCTTTTTTT
42624 TTTTCTCTTTTTTT
1 TTTTCTCTTTTTTT
42638 CTTTT
1 -TTTT
42643 TGTTTTGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
11 11 0.30
14 21 0.57
15 5 0.14
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTCTCTTTTTTT
Found at i:42634 original size:24 final size:25
Alignment explanation
Indices: 42585--42648 Score: 96
Period size: 24 Copynumber: 2.6 Consensus size: 25
42575 TTTTCTTCAA
42585 TTTTC-CTTTGTTTTTTTTCTCTTTT
1 TTTTCTCTTTG-TTTTTTTCTCTTTT
42610 TTTTCTCTTTGTTTTTTTCTC-TTT
1 TTTTCTCTTTGTTTTTTTCTCTTTT
*
42634 TTTTCTTTTTGTTTT
1 TTTTCTCTTTGTTTT
42649 GATTAAATCT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
24 17 0.46
25 15 0.41
26 5 0.14
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.81
Consensus pattern (25 bp):
TTTTCTCTTTGTTTTTTTCTCTTTT
Found at i:50384 original size:2 final size:2
Alignment explanation
Indices: 50377--50412 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
50367 GAAGATAAAA
*
50377 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50413 TTGTATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50417 original size:12 final size:12
Alignment explanation
Indices: 50380--50418 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
50370 GATAAAAATA
*
50380 TATATATATATA
1 TATATATATATG
50392 TATATATATATG
1 TATATATATATG
*
50404 TATATATATTTG
1 TATATATATATG
50416 TAT
1 TAT
50419 TAAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (12 bp):
TATATATATATG
Found at i:50455 original size:31 final size:30
Alignment explanation
Indices: 50421--50480 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
50411 ATTTGTATTA
50421 AAAAATAAATTATA-TTTAATAAGTTAAGAC
1 AAAAATAAATTATATTTTAA-AAGTTAAGAC
50451 AAAAATAAATTATATTTTTAAAAGTTAAGA
1 AAAAATAAATTATA-TTTTAAAAGTTAAGA
50481 TATATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 14 0.50
31 9 0.32
32 5 0.18
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.35
Consensus pattern (30 bp):
AAAAATAAATTATATTTTAAAAGTTAAGAC
Found at i:58106 original size:25 final size:24
Alignment explanation
Indices: 58071--58130 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
58061 ATTTTATTTT
*
58071 AGATAGAAAATTTTTAAGTCTTAAG
1 AGAT-GAAAATTTATAAGTCTTAAG
* * *
58096 AGATGATAAATTTATAATTTTTAGG
1 AGATGA-AAATTTATAAGTCTTAAG
58121 AGATGAAAAT
1 AGATGAAAAT
58131 ATATTATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 6 0.20
25 24 0.80
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.37
Consensus pattern (24 bp):
AGATGAAAATTTATAAGTCTTAAG
Found at i:65938 original size:15 final size:16
Alignment explanation
Indices: 65913--65942 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
65903 AAATGCAATG
65913 ATAATGAGGATGAAGA
1 ATAATGAGGATGAAGA
65929 ATAA-GAGGATGAAG
1 ATAATGAGGATGAAG
65943 GCATAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (16 bp):
ATAATGAGGATGAAGA
Done.