Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002988.1 Hibiscus syriacus cultivar Beakdansim tig00006177_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: 96812
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:14491 original size:15 final size:16
Alignment explanation
Indices: 14471--14514 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
14461 CTATCTGTAT
14471 ATGTTAATAAAAAC-C
1 ATGTTAATAAAAACTC
* *
14486 ATGTTAATGACAACTC
1 ATGTTAATAAAAACTC
14502 ATGTTAATAAAAA
1 ATGTTAATAAAAA
14515 TACTAGGCCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (16 bp):
ATGTTAATAAAAACTC
Found at i:14985 original size:59 final size:59
Alignment explanation
Indices: 14901--15055 Score: 190
Period size: 59 Copynumber: 2.6 Consensus size: 59
14891 AAACTATAAA
* *
14901 TCTCATTCTAAATTCATCC-CTAAACTTTTGAACATTCTAATTTTGA-CCC-AAACAATGAC
1 TCTCATTCTAAATTAATCCAC-AAACTTTTGAACATTCTAATTTT-ATCCCAAAAC-ACGAC
* *
14960 TCTCATTCTAAATTAATCCACAAACTTTTGAACATTTTAATTTTATTCCAAAATCACGAC
1 TCTCATTCTAAATTAATCCACAAACTTTTGAACATTCTAATTTTATCCCAAAA-CACGAC
* * *
15020 TCTCATTCTAAATTAGTCTATAAACTTTTGAACATT
1 TCTCATTCTAAATTAATCCACAAACTTTTGAACATT
15056 TTAAACTCAT
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
58 1 0.01
59 42 0.49
60 41 0.48
61 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.39
Consensus pattern (59 bp):
TCTCATTCTAAATTAATCCACAAACTTTTGAACATTCTAATTTTATCCCAAAACACGAC
Found at i:15049 original size:60 final size:58
Alignment explanation
Indices: 14901--15059 Score: 196
Period size: 60 Copynumber: 2.7 Consensus size: 58
14891 AAACTATAAA
* * * *
14901 TCTCATTCTAAATTCATCCCTAAACTTTTGAACATTCTAATTTTGACCCAAACAATGAC
1 TCTCATTCTAAATT-ATCCATAAACTTTTGAACATTTTAATTTTGACCAAAACAACGAC
*
14960 TCTCATTCTAAATTAATCCACAAACTTTTGAACATTTTAATTTT-ATTCCAAAATC-ACGAC
1 TCTCATTCTAAATT-ATCCATAAACTTTTGAACATTTTAATTTTGA--CCAAAA-CAACGAC
*
15020 TCTCATTCTAAATTAGTCTATAAACTTTTGAACATTTTAA
1 TCTCATTCTAAATTA-TCCATAAACTTTTGAACATTTTAA
15060 ACTCATCCTA
Statistics
Matches: 88, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
58 1 0.01
59 41 0.47
60 45 0.51
61 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.39
Consensus pattern (58 bp):
TCTCATTCTAAATTATCCATAAACTTTTGAACATTTTAATTTTGACCAAAACAACGAC
Found at i:15302 original size:60 final size:59
Alignment explanation
Indices: 15224--15386 Score: 172
Period size: 59 Copynumber: 2.7 Consensus size: 59
15214 GAAAGCTTTG
* *
15224 AAAGTTTAGGGATCAATTTAGAATAAGGGTCATAATATGAGGATGA-AATTAGAATATTCA
1 AAAGTTTAGGGATCAATTTAGAAT-AGGGTCATAGT-TGAGGATAAGAATTAGAATATTCA
* * * * *
15284 AAAGTTATAGGAAT-AATTTAAAATAGGAGTCAT-GTTTAAGAAAAGAATTAGAATATTCA
1 AAAGTT-TAGGGATCAATTTAGAATAGG-GTCATAGTTGAGGATAAGAATTAGAATATTCA
*
15343 AAACTTTAGGGATCAATTTAGAATGAGGG-CATAGTTTGAGGATA
1 AAAGTTTAGGGATCAATTTAGAAT-AGGGTCATAG-TTGAGGATA
15387 TATGATGTAA
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
58 14 0.17
59 34 0.41
60 29 0.35
61 6 0.07
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (59 bp):
AAAGTTTAGGGATCAATTTAGAATAGGGTCATAGTTGAGGATAAGAATTAGAATATTCA
Found at i:21094 original size:3 final size:3
Alignment explanation
Indices: 21086--21123 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
21076 ATCCTATGTT
21086 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
21124 ATCATTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:32009 original size:13 final size:13
Alignment explanation
Indices: 31991--32034 Score: 88
Period size: 13 Copynumber: 3.4 Consensus size: 13
31981 ACCGGTCACA
31991 ACCCGTTTACCCG
1 ACCCGTTTACCCG
32004 ACCCGTTTACCCG
1 ACCCGTTTACCCG
32017 ACCCGTTTACCCG
1 ACCCGTTTACCCG
32030 ACCCG
1 ACCCG
32035 ACCCGTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGTTTACCCG
Found at i:32033 original size:18 final size:18
Alignment explanation
Indices: 32012--32052 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
32002 CGACCCGTTT
*
32012 ACCCGACCCGTTTACCCG
1 ACCCGACCCGTTGACCCG
32030 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
*
32048 GCCCG
1 ACCCG
32053 TTGACCGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.51, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:32045 original size:13 final size:13
Alignment explanation
Indices: 31991--32075 Score: 71
Period size: 13 Copynumber: 6.0 Consensus size: 13
31981 ACCGGTCACA
*
31991 ACCCGTTTACCCG
1 ACCCGTTGACCCG
*
32004 ACCCGTTTACCCG
1 ACCCGTTGACCCG
32017 ACCCGTTTACCCGACCCG
1 ACCCG-TT----GACCCG
32035 ACCCGTTGACCCG
1 ACCCGTTGACCCG
* *
32048 GCCCGTTGACCGTTG
1 ACCCGTTGACC--CG
32063 ACCCGTTGACCCG
1 ACCCGTTGACCCG
32076 TTGACCGGAG
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
13 35 0.58
14 2 0.03
15 11 0.18
17 2 0.03
18 10 0.17
ACGTcount: A:0.14, C:0.45, G:0.21, T:0.20
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:32058 original size:26 final size:26
Alignment explanation
Indices: 31991--32075 Score: 71
Period size: 31 Copynumber: 3.0 Consensus size: 26
31981 ACCGGTCACA
* *
31991 ACCCGTTTACCCGACCCGTTTACCCG
1 ACCCGTTGACCCGACCCGTTGACCCG
32017 ACCCGTTTACCCGACCCGACCCGTTGACCCG
1 ACCCG-TT----GACCCGACCCGTTGACCCG
* *
32048 GCCCGTTGACCGTTGACCCGTTGACCCG
1 ACCCGTTGACC--CGACCCGTTGACCCG
32076 TTGACCGGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
26 9 0.19
27 2 0.04
28 14 0.29
30 2 0.04
31 21 0.44
ACGTcount: A:0.14, C:0.45, G:0.21, T:0.20
Consensus pattern (26 bp):
ACCCGTTGACCCGACCCGTTGACCCG
Found at i:32062 original size:7 final size:8
Alignment explanation
Indices: 32034--32081 Score: 68
Period size: 8 Copynumber: 6.5 Consensus size: 8
32024 TACCCGACCC
32034 GACCCGTT
1 GACCCGTT
32042 GACCCG--
1 GACCCGTT
32048 G-CCCGTT
1 GACCCGTT
32055 GA-CCGTT
1 GACCCGTT
32062 GACCCGTT
1 GACCCGTT
32070 GACCCGTT
1 GACCCGTT
32078 GACC
1 GACC
32082 GGAGTTGACC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
5 4 0.11
6 1 0.03
7 8 0.22
8 23 0.64
ACGTcount: A:0.12, C:0.40, G:0.27, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:34834 original size:53 final size:52
Alignment explanation
Indices: 34728--34835 Score: 146
Period size: 53 Copynumber: 2.1 Consensus size: 52
34718 AAATGTTCCA
** *
34728 ATTTATCCCAAACTATGACCTTCATTCTAAATTAATCATTAAACTTTTGAAC
1 ATTTATCCCAAACTATGACCTTCATTCTAAATTAATCACCAAACTTTTAAAC
**
34780 ATTTCATCCCAAACTATGACCTTCATTCTAAATTGGTC-CCAAACTTTGTAAAC
1 ATTT-ATCCCAAACTATGACCTTCATTCTAAATTAATCACCAAACTTT-TAAAC
34833 ATT
1 ATT
34836 CCAATTTCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
52 11 0.22
53 38 0.78
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.37
Consensus pattern (52 bp):
ATTTATCCCAAACTATGACCTTCATTCTAAATTAATCACCAAACTTTTAAAC
Found at i:35289 original size:276 final size:279
Alignment explanation
Indices: 34734--35291 Score: 910
Period size: 276 Copynumber: 2.0 Consensus size: 279
34724 TCCAATTTAT
*
34734 CCCAAACTATGACCTTCATTCTAAATTAATCATTAAACTTTTGAACATTTCATCCCAAACTATGA
1 CCCAAACTATGACCTTCATTCTAAATTAATCATTAAACTTTTGAACATTTCATCCCAAACTATAA
*
34799 CCTTCATTCTAAATTGGTCCCAAACTTTGTAAACATTCCAATTTCATCCCAAACTATACATATAT
66 CCTTCATTCTAAATTGGTCCCAAACTTTGTAAACATTCCAATTTCATCCCAAACTATACACATAT
* * *
34864 ATTAATCACATCCATCGCTAATAAAATCTTAGGACAATTTATATTATTATGTGTTTGGAAAAAAA
131 ACTAATCACATCCATCACTAATAAAATCTTAGGACAA-TTATATTATTATGTGCTTGG---AAAA
*
34929 ACAAAATTTAGATTAAACTATGATTGAAACTAATTACATATTTGGATGAAATTGGAATATTCAAA
192 ACAAAATTTAGATTAAACTATGATTGAAACTAATTACATATTTGGATGAAATTGAAATATTCAAA
*
34994 AGTTTGAGAATCAATTTAAAATC
257 AGTTTGAGAACCAATTTAAAATC
* * *
35017 CCCAAACTATGACCTTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTCATCCCAAACTATAA
1 CCCAAACTATGACCTTCATTCTAAATTAATCATTAAACTTTTGAACATTTCATCCCAAACTATAA
* *
35082 CCTTCATTCTATATTGGTCCCCAAACTTTTTAAACATTCCAATTTCATCCCAAACTATACACATA
66 CCTTCATTCTAAATTGGT-CCCAAACTTTGTAAACATTCCAATTTCATCCCAAACTATACACATA
*
35147 TACTAATTACATCCATCACTAATAAAATCTTAGGACAA-TATATTATTATGTGCTT-G-AAAA-A
130 TACTAATCACATCCATCACTAATAAAATCTTAGGACAATTATATTATTATGTGCTTGGAAAAACA
35208 AAATTTA-AGTTAAACTATGATTGAAACTAATTACATATTTGGATGAAATTGAAATATTCAAAAG
195 AAATTTAGA-TTAAACTATGATTGAAACTAATTACATATTTGGATGAAATTGAAATATTCAAAAG
35272 TTTGAGAACCAATTTAAAAT
259 TTTGAGAACCAATTTAAAAT
35292 GAATGTTATA
Statistics
Matches: 260, Mismatches: 13, Indels: 11
0.92 0.05 0.04
Matches are distributed among these distances:
275 1 0.00
276 81 0.31
277 4 0.02
281 1 0.00
282 16 0.06
283 78 0.30
284 79 0.30
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.35
Consensus pattern (279 bp):
CCCAAACTATGACCTTCATTCTAAATTAATCATTAAACTTTTGAACATTTCATCCCAAACTATAA
CCTTCATTCTAAATTGGTCCCAAACTTTGTAAACATTCCAATTTCATCCCAAACTATACACATAT
ACTAATCACATCCATCACTAATAAAATCTTAGGACAATTATATTATTATGTGCTTGGAAAAACAA
AATTTAGATTAAACTATGATTGAAACTAATTACATATTTGGATGAAATTGAAATATTCAAAAGTT
TGAGAACCAATTTAAAATC
Found at i:35618 original size:2 final size:2
Alignment explanation
Indices: 35611--35637 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35601 GTTACAGTAT
35611 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
35638 TCTAACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37307 original size:2 final size:2
Alignment explanation
Indices: 37300--37353 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
37290 TAATTCTATC
37300 AT AT AT AT AT 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 AT AT AT AT AT
37342 AT AT AT AT AT AT
1 AT AT AT AT AT AT
37354 TCCCTACCTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46462 original size:31 final size:29
Alignment explanation
Indices: 46424--46488 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
46414 ATGATAATAA
* *
46424 AAAATATTTTAT-TTTATTAATTAATAAAAAT
1 AAAATATTTAATATTTAAT-ATT-AT-AAAAT
46455 AAAATATTTAATATTTAATATTATAAAAT
1 AAAATATTTAATATTTAATATTATAAAAT
46484 AAAAT
1 AAAAT
46489 TGAATCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 10 0.32
30 2 0.06
31 14 0.45
32 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAATATTTAATATTTAATATTATAAAAT
Found at i:47948 original size:128 final size:128
Alignment explanation
Indices: 47720--47955 Score: 454
Period size: 128 Copynumber: 1.8 Consensus size: 128
47710 GTGAAGAATG
*
47720 AAAATAATATTAATAAAATATTAATTTATTTTAAAAATTAATAAAATTTCCATGTCATCTTAAAG
1 AAAATAATATTAATAAAATATTAATTTAATTTAAAAATTAATAAAATTTCCATGTCATCTTAAAG
47785 TTATGAAAAAATTGATGGAGTGATAAAAAAATTCAATGTATAAGTGATGAATGAAAATAATAT
66 TTATGAAAAAATTGATGGAGTGATAAAAAAATTCAATGTATAAGTGATGAATGAAAATAATAT
47848 AAAATAATATTAATAAAATATTAATTTAATTTAAAAATTAATAAAATTTCCATGTCATCTTAAAG
1 AAAATAATATTAATAAAATATTAATTTAATTTAAAAATTAATAAAATTTCCATGTCATCTTAAAG
*
47913 TTATGGAAAAATTGATGGAGTGATAAAAAAATTCAATGTATAA
66 TTATGAAAAAATTGATGGAGTGATAAAAAAATTCAATGTATAA
47956 AGTTCAGTGA
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 106 1.00
ACGTcount: A:0.51, C:0.04, G:0.10, T:0.35
Consensus pattern (128 bp):
AAAATAATATTAATAAAATATTAATTTAATTTAAAAATTAATAAAATTTCCATGTCATCTTAAAG
TTATGAAAAAATTGATGGAGTGATAAAAAAATTCAATGTATAAGTGATGAATGAAAATAATAT
Found at i:49957 original size:22 final size:22
Alignment explanation
Indices: 49927--49970 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
49917 CCTTGAGGAG
49927 TTAAGCTTCACAATTATACAGA
1 TTAAGCTTCACAATTATACAGA
*
49949 TTAATCTTCACAATTATACAGA
1 TTAAGCTTCACAATTATACAGA
49971 GTGTATGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (22 bp):
TTAAGCTTCACAATTATACAGA
Found at i:53524 original size:248 final size:256
Alignment explanation
Indices: 53028--53541 Score: 828
Period size: 268 Copynumber: 2.0 Consensus size: 256
53018 GTGTTTGATG
* * *
53028 AAAATATGAAATGAGAAAAAGGCACATTTTTATATGTTTGTTTGATTTAAGTTCCAACATTGCTT
1 AAAATATGAAATGAAAAAAAGGCACATTTTTATACGTTTCTTTGATTTAAGTTCCAACATTGCTT
53093 GTTGGAAAGACAGTTTCCTGGTATAATTTTTTTTATCTGCATATTGTTGTATGTCTCATGTTTTT
66 GTTGGAAAGACAGTTTCCTGGTATAATTTTTTTTATCTGCATATTGTTGTATGTCTCATGTTTTT
*
53158 CACTCTTTCTGATCTCTTAATTGGGGTTTCCTGGTTACTTTTCATTTTTCATGTTTTTTTATTTC
131 CACTCTTTCTGATCTCCTAATTGGGGTTTCCTGGTTA----TCA-TTTTCA-GTTTTTTTATTTC
53223 ATAGTGTTGTATGTTTCTATCATGTTTCTACAGATTTTCCCACCTAGTGAGAAGATTGAGAATAT
190 ATAG-GTTGTATG----T-TCATGTTTCTACAGATTTTCCCACCTAGTGAGAAGATTGAGAATAT
53288 AAATGAGA
249 AAATGAGA
53296 AAAATATGAAATGAAAAAAAGGCACATTTTTATACGTTTCTTTGATTTAAGTTCCAACATTGCTT
1 AAAATATGAAATGAAAAAAAGGCACATTTTTATACGTTTCTTTGATTTAAGTTCCAACATTGCTT
53361 GTTGGAAAGACAGTTTCCTGGTATAATTTTTTTTATCTGCATATTGTTGTATGTCTCATGTTTTT
66 GTTGGAAAGACAGTTTCCTGGTATAATTTTTTTTATCTGCATATTGTTGTATGTCTCATGTTTTT
53426 CACTCTTTCTGATCTCCTAATTGGGGTTTCCTGGTTA-C-TTTTCA-TTTTTTTATTTCATA-G-
131 CACTCTTTCTGATCTCCTAATTGGGGTTTCCTGGTTATCATTTTCAGTTTTTTTATTTCATAGGT
53486 TGT-TG-T-ATGTTTCTACAGATTTTCCCACCTAGTGAGAAGATTGAGAATATAAATGA
196 TGTATGTTCATGTTTCTACAGATTTTCCCACCTAGTGAGAAGATTGAGAATATAAATGA
53542 CGAATACTGG
Statistics
Matches: 242, Mismatches: 4, Indels: 20
0.91 0.02 0.08
Matches are distributed among these distances:
248 50 0.21
249 1 0.00
255 2 0.01
256 3 0.01
257 1 0.00
259 15 0.06
261 6 0.02
263 1 0.00
268 163 0.67
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (256 bp):
AAAATATGAAATGAAAAAAAGGCACATTTTTATACGTTTCTTTGATTTAAGTTCCAACATTGCTT
GTTGGAAAGACAGTTTCCTGGTATAATTTTTTTTATCTGCATATTGTTGTATGTCTCATGTTTTT
CACTCTTTCTGATCTCCTAATTGGGGTTTCCTGGTTATCATTTTCAGTTTTTTTATTTCATAGGT
TGTATGTTCATGTTTCTACAGATTTTCCCACCTAGTGAGAAGATTGAGAATATAAATGAGA
Found at i:55482 original size:130 final size:130
Alignment explanation
Indices: 55309--55549 Score: 419
Period size: 130 Copynumber: 1.9 Consensus size: 130
55299 AAGTGCAAGA
* * * *
55309 AAGCTAATAGATATTTTGTCCAAATTAAACAAAATGGCAGGGTATGGTTCTGATGAAGAGAACAA
1 AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGCAGGGTATGCTCCTGATGAAGAGAACAA
* *
55374 TCTTTATGAGGTTAGCTTCTAGCAATATCTTTCTCAATGGAGCAATTCCACAGTCATTTTTCTCT
66 TCTTAATGAGGTTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATTCCACAGTCATTTTTCTCT
*
55439 AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGCAGGGTATGCTCCTGATGAAGATAACAA
1 AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGCAGGGTATGCTCCTGATGAAGAGAACAA
55504 TCTTAATGAGGTTAGCTTCTAGCAATATCTTTCTCAATAGAGCAAT
66 TCTTAATGAGGTTAGCTTCTAGCAATATCTTTCTCAATAGAGCAAT
55550 ACCAGTTCTC
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 104 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (130 bp):
AAGCCAATAGAAATTTTGTCCAAATTAAACAAAATGGCAGGGTATGCTCCTGATGAAGAGAACAA
TCTTAATGAGGTTAGCTTCTAGCAATATCTTTCTCAATAGAGCAATTCCACAGTCATTTTTCTCT
Found at i:73805 original size:30 final size:30
Alignment explanation
Indices: 73770--73828 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
73760 CTCGATCCCA
*
73770 CCACTTCCCTCCTTTCCCCTTCCTCTCCTC
1 CCACTTCCCTCCCTTCCCCTTCCTCTCCTC
*
73800 CCACTTCCTTCCCTTCCCCTTCCTCTCCT
1 CCACTTCCCTCCCTTCCCCTTCCTCTCCT
73829 TCCTCTCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.03, C:0.59, G:0.00, T:0.37
Consensus pattern (30 bp):
CCACTTCCCTCCCTTCCCCTTCCTCTCCTC
Found at i:73806 original size:15 final size:15
Alignment explanation
Indices: 73773--73842 Score: 74
Period size: 15 Copynumber: 4.6 Consensus size: 15
73763 GATCCCACCA
73773 CTTCC-CTCCTTTCCC
1 CTTCCTCTCC-TTCCC
73788 CTTCCTCTCC-TCCC
1 CTTCCTCTCCTTCCC
73802 ACTTCCT-TCCCTTCCC
1 -CTTCCTCT-CCTTCCC
*
73818 CTTCCTCTCCTTCCT
1 CTTCCTCTCCTTCCC
73833 CTCTCCTCTC
1 CT-TCCTCTC
73843 ATCTTCTTCC
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
14 5 0.10
15 27 0.56
16 16 0.33
ACGTcount: A:0.01, C:0.59, G:0.00, T:0.40
Consensus pattern (15 bp):
CTTCCTCTCCTTCCC
Found at i:73852 original size:41 final size:44
Alignment explanation
Indices: 73792--73878 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 44
73782 TTTCCCCTTC
*
73792 CTCTCCTCCCACTTCCTT-CCCTTCCCCT-TCCTCTCCTTC-CT
1 CTCTCCTCCCACTTCCTTCCCCTGCCCCTCTCCTCTCCTTCACT
* *
73833 CTCTCCTCTCATCTT-CTTCCCCTGCCCCTCTCCTCTTCTTCACT
1 CTCTCCTCCCA-CTTCCTTCCCCTGCCCCTCTCCTCTCCTTCACT
73877 CT
1 CT
73879 TGCATCCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
41 13 0.33
42 12 0.31
43 10 0.26
44 4 0.10
ACGTcount: A:0.03, C:0.55, G:0.01, T:0.40
Consensus pattern (44 bp):
CTCTCCTCCCACTTCCTTCCCCTGCCCCTCTCCTCTCCTTCACT
Found at i:74636 original size:15 final size:16
Alignment explanation
Indices: 74608--74638 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
74598 TGTGGGATAA
74608 GGTCATCAATGTTAGG
1 GGTCATCAATGTTAGG
74624 GGTCATC-ATGTTAGG
1 GGTCATCAATGTTAGG
74639 CCTTATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.32
Consensus pattern (16 bp):
GGTCATCAATGTTAGG
Found at i:80148 original size:16 final size:16
Alignment explanation
Indices: 80127--80158 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
80117 AAAAATAAAC
80127 GAACATAAACGAACAA
1 GAACATAAACGAACAA
80143 GAACATAAACGAACAA
1 GAACATAAACGAACAA
80159 ATTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.19, G:0.12, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAA
Found at i:80238 original size:10 final size:10
Alignment explanation
Indices: 80223--80281 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
80213 CATTTAATAA
80223 ATAAACGAAC
1 ATAAACGAAC
80233 ATAAACGAAC
1 ATAAACGAAC
** *
80243 ACGAAC-ATAA
1 ATAAACGA-AC
80253 ATGAACACGAAC
1 AT-AA-ACGAAC
80265 ATAAACGAAC
1 ATAAACGAAC
80275 ATAAACG
1 ATAAACG
80282 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.74
11 3 0.08
12 5 0.13
13 1 0.03
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:80248 original size:16 final size:16
Alignment explanation
Indices: 80227--80275 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
80217 TAATAAATAA
80227 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
80243 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
80259 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
80275 A
1 A
80276 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:81043 original size:14 final size:14
Alignment explanation
Indices: 81026--81055 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
81016 AATGAACATA
*
81026 AACGAACATAATCG
1 AACGAACATAAACG
81040 AACGAACATAAACG
1 AACGAACATAAACG
81054 AA
1 AA
81056 TATAACCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.20, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:81046 original size:24 final size:24
Alignment explanation
Indices: 81019--81067 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
81009 ATAAATGAAT
*
81019 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
*
81043 GAACATAAACGAATATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
81067 G
1 G
81068 TTCACGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.53, C:0.20, G:0.14, T:0.12
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:82481 original size:21 final size:21
Alignment explanation
Indices: 82455--82564 Score: 89
Period size: 21 Copynumber: 5.3 Consensus size: 21
82445 CTGTATTTCT
82455 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
* * ** ** *
82476 CGTTGCAAT-TTTCCATTTCA
1 CGTTGCGATAGTTGAAAATCG
82496 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
* * ** **
82517 CGTTGCGGT-TTTCCATTTCG
1 CGTTGCGATAGTTGAAAATCG
82537 CGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTTGAAAATCG
82558 CGTTGCG
1 CGTTGCG
82565 GTTTTTCATT
Statistics
Matches: 61, Mismatches: 26, Indels: 4
0.67 0.29 0.04
Matches are distributed among these distances:
20 27 0.44
21 34 0.56
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (21 bp):
CGTTGCGATAGTTGAAAATCG
Found at i:82494 original size:41 final size:41
Alignment explanation
Indices: 82476--82753 Score: 375
Period size: 41 Copynumber: 6.8 Consensus size: 41
82466 TTGAAAATCG
* * * *
82476 CGTTGCAATTTTCCATTTCACGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGT-GT
* * *
82517 CGTTGCGGTTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGT-GT
* *
82558 CGTTGCGGTTTTTCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
82599 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
* * *
82640 CGTTGCGGTTTTCCATTTCGTGTTACGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
82681 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
*
82722 CGTTGTGATTTTCCATTTCGCGTTGCGATAGT
1 CGTTGCGATTTTCCATTTCGCGTTGCGATAGT
82754 TTTAAAAATG
Statistics
Matches: 220, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
40 1 0.00
41 218 0.99
42 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
Found at i:82539 original size:20 final size:20
Alignment explanation
Indices: 82514--82584 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
82504 TAGTTGAAAA
82514 TCGCGTTGCGGTTTTCCATT
1 TCGCGTTGCGGTTTTCCATT
* * ** **
82534 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGGT-TTTCCATT
*
82555 TCGCGTTGCGGTTTTTCATT
1 TCGCGTTGCGGTTTTCCATT
82575 TCGCGTTGCG
1 TCGCGTTGCG
82585 ATAGTCTACA
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.11, C:0.21, G:0.28, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGGTTTTCCATT
Found at i:83592 original size:6 final size:6
Alignment explanation
Indices: 83581--83625 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
83571 TCTCGTCTCG
* *
83581 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GATCGT GATCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
83626 AATACGTGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.04, C:0.16, G:0.47, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:83736 original size:20 final size:20
Alignment explanation
Indices: 83711--83908 Score: 102
Period size: 20 Copynumber: 9.6 Consensus size: 20
83701 TTTTAAAACT
83711 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
83731 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
83752 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * **
83772 ATCACAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
83793 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* **
83813 ATCGCAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
*
83834 ATCACAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * ** *
83854 ACCGCAACGCGATATTTTCAACT
1 ATCGCAACGCGA-A-ATGGAA-A
83877 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
83897 ATCGCAACGCGA
1 ATCGCAACGCGA
83909 TTTTCAACTA
Statistics
Matches: 128, Mismatches: 32, Indels: 36
0.65 0.16 0.18
Matches are distributed among these distances:
18 9 0.07
19 9 0.07
20 48 0.38
21 29 0.23
22 13 0.10
23 20 0.16
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:83757 original size:21 final size:21
Alignment explanation
Indices: 83731--83842 Score: 74
Period size: 21 Copynumber: 5.4 Consensus size: 21
83721 GAAATGGAAA
83731 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
83752 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
*
83772 ATCACAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
* **
83793 ATCGCAACG-CGAAATG--GAAA
1 ATCGCAACGAC--ACTGTAGACT
83813 ATCGCAACGACACTGTAGACT
1 ATCGCAACGACACTGTAGACT
*
83834 ATCACAACG
1 ATCGCAACG
83843 CGAAATGGAA
Statistics
Matches: 66, Mismatches: 15, Indels: 20
0.65 0.15 0.20
Matches are distributed among these distances:
19 6 0.09
20 23 0.35
21 31 0.47
22 6 0.09
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (21 bp):
ATCGCAACGACACTGTAGACT
Found at i:83933 original size:41 final size:41
Alignment explanation
Indices: 83708--83905 Score: 308
Period size: 41 Copynumber: 4.8 Consensus size: 41
83698 CATTTTTAAA
83708 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
83749 ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
83790 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
* * * * *
83831 ACTATCACAACGCGAAATGGAAAACCGCAACGCGATATTTTCA-
1 ACTATCGCAACGCGAAATGGAAAATCGCAA--CGACACTGT-AG
83874 ACTATCGCAACGCGAAATGGAAAATCGCAACG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG
83906 CGATTTTCAA
Statistics
Matches: 145, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
41 110 0.76
43 34 0.23
44 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:85413 original size:23 final size:22
Alignment explanation
Indices: 85387--85431 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
85377 AGGTTGGACG
* *
85387 ATTTATTAAATGGTTATATAAAT
1 ATTTATT-AATAGCTATATAAAT
*
85410 ATTTGTTAATAGCTATATAAAT
1 ATTTATTAATAGCTATATAAAT
85432 GTTAGTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (22 bp):
ATTTATTAATAGCTATATAAAT
Found at i:89225 original size:23 final size:24
Alignment explanation
Indices: 89177--89225 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
89167 TGGTGGTTAG
*
89177 TTTAATGGATGTTTAGACTTTATT
1 TTTAATGGATATTTAGACTTTATT
* *
89201 TTTAATGGTTATTTA-AGTTTATT
1 TTTAATGGATATTTAGACTTTATT
89224 TT
1 TT
89226 GGTTCTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.59
Consensus pattern (24 bp):
TTTAATGGATATTTAGACTTTATT
Found at i:91812 original size:50 final size:50
Alignment explanation
Indices: 91733--91847 Score: 142
Period size: 50 Copynumber: 2.3 Consensus size: 50
91723 ATAAAAATAC
*
91733 TCATTAAATTTGTATACTTACTCTATTACAACGATTATTCTGTAACAGAT
1 TCATTAATTTTGTATACTTACTCTATTACAACGATTATTCTGTAACAGAT
* * * *
91783 TCATTAATTTTTTATACTTACTGC-GTTACAACGATTATTTTGTAATAGAT
1 TCATTAATTTTGTATACTTACT-CTATTACAACGATTATTCTGTAACAGAT
* * *
91833 TAATCAATTTAGTAT
1 TCATTAATTTTGTAT
91848 TATTTTATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 54 0.98
51 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (50 bp):
TCATTAATTTTGTATACTTACTCTATTACAACGATTATTCTGTAACAGAT
Found at i:93936 original size:13 final size:13
Alignment explanation
Indices: 93918--93942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93908 CATGATAAGA
93918 ATTAGAAAAAGGC
1 ATTAGAAAAAGGC
93931 ATTAGAAAAAGG
1 ATTAGAAAAAGG
93943 GAATCTCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.24, T:0.16
Consensus pattern (13 bp):
ATTAGAAAAAGGC
Done.