Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000368.1 Hibiscus syriacus cultivar Beakdansim tig00000669_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: 99581
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:486 original size:15 final size:15
Alignment explanation
Indices: 450--501 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
440 AGGTGATGCA
*
450 ATACATGCATGAAATT
1 ATACATGGATG-AATT
*
466 ACACATGGATGAATT
1 ATACATGGATGAATT
**
481 ATACATGGATGTTTT
1 ATACATGGATGAATT
496 ATACAT
1 ATACAT
502 CATAAGGAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
15 22 0.71
16 9 0.29
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (15 bp):
ATACATGGATGAATT
Found at i:1048 original size:45 final size:45
Alignment explanation
Indices: 958--1112 Score: 195
Period size: 45 Copynumber: 3.4 Consensus size: 45
948 GTAACCATGC
* *
958 AAATAAGCTTATGAGCTTACGGAAAT-ATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTACGAAAATAATGGCAAGTATATAGGAA
*
1002 AAATAAGCTTATGAGCTTACGAAAATAATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTACGAAAATAATGGCAAGTATATAGGAA
* ** * * * *
1047 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTA-CGAAAAT-AATGGCAAGTATATAGGAA
1094 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
1113 TGGGATAAAT
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
44 25 0.25
45 36 0.36
46 4 0.04
47 34 0.34
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTACGAAAATAATGGCAAGTATATAGGAA
Found at i:3737 original size:14 final size:14
Alignment explanation
Indices: 3718--3801 Score: 57
Period size: 14 Copynumber: 5.9 Consensus size: 14
3708 TTCCCTTTTT
3718 ATTTTATTTATTTA
1 ATTTTATTTATTTA
*
3732 ATTTTA-TTATATA
1 ATTTTATTTATTTA
* *
3745 TATATTATTAATTTA
1 -ATTTTATTTATTTA
* *
3760 ATTTAATTTAATTTTT
1 ATTTTATTT-A-TTTA
*
3776 ATTTT-TTTGTTTCA
1 ATTTTATTTATTT-A
3790 ATTTT-TTTATTT
1 ATTTTATTTATTT
3802 TCTATTCCTT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
13 9 0.17
14 28 0.53
15 9 0.17
16 7 0.13
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (14 bp):
ATTTTATTTATTTA
Found at i:4000 original size:15 final size:16
Alignment explanation
Indices: 3980--4012 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3970 TATTATTTAA
3980 TTTTTTTAT-TTTCAT
1 TTTTTTTATCTTTCAT
*
3995 TTTTTTTCTCTTTCAT
1 TTTTTTTATCTTTCAT
4011 TT
1 TT
4013 AGCTAATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTATCTTTCAT
Found at i:4020 original size:39 final size:41
Alignment explanation
Indices: 3942--4020 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 41
3932 GTTTTTAGGG
* **
3942 TTTTATATTTCATTTTGTTTTGTTTCCATATTATTTAATTT
1 TTTTATATTTCATTTTGTTTTCTTTCCATATTAGCTAATTT
*
3983 TTTTAT-TTTCATTTT-TTTTCTCTTTCAT-TTAGCTAATT
1 TTTTATATTTCATTTTGTTTTCT-TTCCATATTAGCTAATT
4021 CTTTGGAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
39 13 0.39
40 14 0.42
41 6 0.18
ACGTcount: A:0.18, C:0.10, G:0.04, T:0.68
Consensus pattern (41 bp):
TTTTATATTTCATTTTGTTTTCTTTCCATATTAGCTAATTT
Found at i:4036 original size:2 final size:2
Alignment explanation
Indices: 4029--4077 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
4019 TTCTTTGGAG
4029 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4071 TA TA TA T
1 TA TA TA T
4078 TATTTATGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4107 original size:15 final size:14
Alignment explanation
Indices: 4089--4131 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
4079 ATTTATGTAT
4089 TTTTTATTTGTTTTG
1 TTTTTATTT-TTTTG
4104 TTTTTA--TTTTTG
1 TTTTTATTTTTTTG
4116 TTTTTCATTTTTTTG
1 TTTTT-ATTTTTTTG
4131 T
1 T
4132 ATCTTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 2 0.08
15 13 0.52
ACGTcount: A:0.07, C:0.02, G:0.09, T:0.81
Consensus pattern (14 bp):
TTTTTATTTTTTTG
Found at i:4116 original size:12 final size:13
Alignment explanation
Indices: 4099--4127 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4089 TTTTTATTTG
4099 TTTTGTTTTT-AT
1 TTTTGTTTTTCAT
4111 TTTTGTTTTTCAT
1 TTTTGTTTTTCAT
4124 TTTT
1 TTTT
4128 TTGTATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTGTTTTTCAT
Found at i:7304 original size:29 final size:29
Alignment explanation
Indices: 7229--7373 Score: 166
Period size: 29 Copynumber: 5.0 Consensus size: 29
7219 ATTTTAACAT
* * *
7229 TAAAAATATATTTTATTTTTATATTGACT
1 TAAAAATATATTTTATTTTTATCTTAACC
* *
7258 TATTAAATATATTTTATTCTTATCTTAACC
1 TA-AAAATATATTTTATTTTTATCTTAACC
*
7288 TAAAAATATATTTTATTTTTATTTTAA-C
1 TAAAAATATATTTTATTTTTATCTTAACC
* * * *
7316 TTAAAATTTATTTTAGTCTTTATCTTAACT
1 TAAAAATATATTTTA-TTTTTATCTTAACC
*
7346 TAAAAATATATTCTATTTTTATCTTAAC
1 TAAAAATATATTTTATTTTTATCTTAAC
7374 TTATTACATA
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
28 14 0.15
29 46 0.48
30 36 0.38
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.54
Consensus pattern (29 bp):
TAAAAATATATTTTATTTTTATCTTAACC
Found at i:7363 original size:58 final size:58
Alignment explanation
Indices: 7222--7377 Score: 215
Period size: 58 Copynumber: 2.7 Consensus size: 58
7212 ATTTTACATT
* *
7222 TTAACATTAAAAATATATTTTATTTTTATATTGACTTATTAAATATATTTTATTCTTATC
1 TTAAC-TTAAAAATATATTTTATTTTTATATTAACTTA-TAAATATATTTTAGTCTTATC
* * *
7282 TTAACCTAAAAATATATTTTATTTTTATTTTAACTTA-AAATTTATTTTAGTCTTTATC
1 TTAACTTAAAAATATATTTTATTTTTATATTAACTTATAAATATATTTTAGTC-TTATC
* *
7340 TTAACTTAAAAATATATTCTATTTTTATCTTAACTTAT
1 TTAACTTAAAAATATATTTTATTTTTATATTAACTTAT
7378 TACATAAATT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
57 13 0.15
58 39 0.45
59 29 0.34
60 5 0.06
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.54
Consensus pattern (58 bp):
TTAACTTAAAAATATATTTTATTTTTATATTAACTTATAAATATATTTTAGTCTTATC
Found at i:7374 original size:29 final size:29
Alignment explanation
Indices: 7222--7421 Score: 197
Period size: 30 Copynumber: 6.8 Consensus size: 29
7212 ATTTTACATT
*
7222 TTAACATTAAAAATATATTTTATTTTTATA
1 TTAAC-TTAAAAATATATTTTATTTTTATC
* * *
7252 TTGACTTATTAAATATATTTTATTCTTATC
1 TTAACTTA-AAAATATATTTTATTTTTATC
* *
7282 TTAACCTAAAAATATATTTTATTTTTATT
1 TTAACTTAAAAATATATTTTATTTTTATC
* *
7311 TTAACTT-AAAATTTATTTTAGTCTTTATC
1 TTAACTTAAAAATATATTTTA-TTTTTATC
*
7340 TTAACTTAAAAATATATTCTATTTTTATC
1 TTAACTTAAAAATATATTTTATTTTTATC
* * * * *
7369 TTAACTTATTACATAAATTATATTTTTAAC
1 TTAACTTA-AAAATATATTTTATTTTTATC
*
7399 TT-ACATTATTAAATATATTTTAT
1 TTAAC-TTA-AAAATATATTTTAT
7422 ATCCTTTAGA
Statistics
Matches: 141, Mismatches: 24, Indels: 10
0.81 0.14 0.06
Matches are distributed among these distances:
28 12 0.09
29 57 0.40
30 72 0.51
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTTTTATC
Found at i:7480 original size:11 final size:11
Alignment explanation
Indices: 7464--7493 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
7454 AAAAATTTAT
7464 TAAATTAAAAA
1 TAAATTAAAAA
7475 TAAATT-AAAA
1 TAAATTAAAAA
7485 TAAATTAAA
1 TAAATTAAA
7494 TTATCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAATTAAAAA
Found at i:14234 original size:16 final size:16
Alignment explanation
Indices: 14209--14239 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14199 CTTCTAAATT
*
14209 TTTTTTGAGTTCAAGC
1 TTTTTCGAGTTCAAGC
14225 TTTTTCGAGTTCAAG
1 TTTTTCGAGTTCAAG
14240 TTTCAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCAAGC
Found at i:16805 original size:2 final size:2
Alignment explanation
Indices: 16798--16847 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
16788 AATTAAACAA
16798 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
16840 AT AT AT AT
1 AT AT AT AT
16848 TACTAAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17886 original size:18 final size:18
Alignment explanation
Indices: 17839--17890 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
17829 TTGCTATGTT
* * *
17839 CTTCGTTCTTGCTCGCTGC
1 CTTC-TTCTTGTTTGCTGA
17858 CTTCTTCTTGTTTGCTGA
1 CTTCTTCTTGTTTGCTGA
17876 CTTCTTCTTGTTTGC
1 CTTCTTCTTGTTTGC
17891 AGGTGAACCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.02, C:0.29, G:0.17, T:0.52
Consensus pattern (18 bp):
CTTCTTCTTGTTTGCTGA
Found at i:18294 original size:3 final size:3
Alignment explanation
Indices: 18286--18331 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
18276 AATATTTATT
* *
18286 TAA TAA TAA TAA TAA TAA TAA TGTA TAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
18332 AAACAAACTG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 36 0.95
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:18510 original size:45 final size:45
Alignment explanation
Indices: 18446--19068 Score: 933
Period size: 45 Copynumber: 13.8 Consensus size: 45
18436 GATGGAAATG
* * *
18446 TTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGC
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* *
18491 TTTGAAAACATCATGCACTGAAGGACTTACAGATTACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* *
18536 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
*
18581 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * * *
18626 TTTGAAAATATCAAGCAATGAAGGACTTATAGATGACCTGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
*
18671 TTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * *
18716 TTTGAAGACATTAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* *
18761 TTTGAAAACATCAAGAACTAAATGG-CTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAA-GGACTTACAGATGACCCGAAGGT
*
18806 TTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * *
18851 TTTGAAGACATCAAGCACTGAATGACTTACAGATGACCTGAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
* * * *
18896 TTTGAAAACATCATGCACTGAAGGGCTTAAAGATGACCCAAAGGT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
*
18941 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGG-T
* *
18987 TTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGG--T
*
19034 TTTGAAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGAAAACATCAAGCACTGAAGGACTTACAGATG
19069 TGAGAAATAG
Statistics
Matches: 533, Mismatches: 41, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
44 2 0.00
45 451 0.85
46 44 0.08
47 36 0.07
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (45 bp):
TTTGAAAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
Found at i:21254 original size:74 final size:75
Alignment explanation
Indices: 21128--21266 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 75
21118 AATACAAGCA
* * *
21128 TTCAAAATGCGTCAACATTCTTCATTCTGATTGAAAGAGGCTTTCAGCATGCCCCAGCATTTGCT
1 TTCAAAATACATCAACATTCATCATTCTGATTGAAAGAGGCTTTCAGCATGCCCCAGCATTTGCT
21193 GATATAAATG
66 GATATAAATG
* * * * *
21203 TTCAAAATACATCAACATT-ATGATTCTGATTGAGAGGGGCTTTCAGTATGCCCTAGCATTTGCT
1 TTCAAAATACATCAACATTCATCATTCTGATTGAAAGAGGCTTTCAGCATGCCCCAGCATTTGCT
21267 TCTTGTTAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
74 39 0.70
75 17 0.30
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (75 bp):
TTCAAAATACATCAACATTCATCATTCTGATTGAAAGAGGCTTTCAGCATGCCCCAGCATTTGCT
GATATAAATG
Found at i:29392 original size:28 final size:26
Alignment explanation
Indices: 29337--29394 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
29327 AAATATTAAT
*
29337 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
29363 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
29391 AAAA
1 AAAA
29395 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:31644 original size:3 final size:3
Alignment explanation
Indices: 31636--31702 Score: 125
Period size: 3 Copynumber: 22.0 Consensus size: 3
31626 AATATTTATT
31636 TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31682 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
31703 CAAACTGAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:38566 original size:21 final size:21
Alignment explanation
Indices: 38540--38584 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
38530 GCCTTAGGGC
38540 TTACAATTTTCTCAATGTTTA
1 TTACAATTTTCTCAATGTTTA
38561 TTACAATTTTCTCAATGTTTA
1 TTACAATTTTCTCAATGTTTA
38582 TTA
1 TTA
38585 TATAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.53
Consensus pattern (21 bp):
TTACAATTTTCTCAATGTTTA
Found at i:42858 original size:20 final size:20
Alignment explanation
Indices: 42833--42874 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
42823 ATTTTCGGGC
42833 TAAAATAATAATATTATGAT
1 TAAAATAATAATATTATGAT
* * *
42853 TAAAATATTATTATTATTAT
1 TAAAATAATAATATTATGAT
42873 TA
1 TA
42875 TTATTACTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TAAAATAATAATATTATGAT
Found at i:46455 original size:3 final size:3
Alignment explanation
Indices: 46449--46492 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
46439 AATAATAATA
* *
46449 ATT ATT ATT AATT ATT ATT ATT GTT ATCA ATT ATT ATT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
46493 GTTGAACCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 30 0.86
4 5 0.14
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:46475 original size:19 final size:19
Alignment explanation
Indices: 46453--46489 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
46443 ATAATAATTA
*
46453 TTATTAATTATTATTATTG
1 TTATCAATTATTATTATTG
46472 TTATCAATTATTATTATT
1 TTATCAATTATTATTATT
46490 ATTGTTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTATCAATTATTATTATTG
Found at i:50465 original size:17 final size:18
Alignment explanation
Indices: 50443--50482 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
50433 AAATTCTAGA
*
50443 ATACCGAAAT-GGTATTG
1 ATACCGAAATGGGTATCG
*
50460 ATACCGAAGTGGGTATCG
1 ATACCGAAATGGGTATCG
50478 ATACC
1 ATACC
50483 ATAGAATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (18 bp):
ATACCGAAATGGGTATCG
Found at i:50828 original size:24 final size:26
Alignment explanation
Indices: 50801--50850 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
50791 ATCGAAAACC
*
50801 TTTCAAT-TTCTATT-ATGTTATATT
1 TTTCAATGTTCTATTCAAGTTATATT
*
50825 TTTCAATGTTTTATTCAAGTTATATT
1 TTTCAATGTTCTATTCAAGTTATATT
50851 ATTTAAGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.26, C:0.08, G:0.06, T:0.60
Consensus pattern (26 bp):
TTTCAATGTTCTATTCAAGTTATATT
Found at i:51116 original size:23 final size:23
Alignment explanation
Indices: 51056--51123 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
51046 GTCAAGGGTT
51056 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
* * *
51079 TTAGGTGATCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
* *
51102 CTATGTGGTCATTCGAGACAAA
1 CTATGTGGTCCTTCGGGACAAA
51124 TATGTAGCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:55998 original size:3 final size:3
Alignment explanation
Indices: 55992--56107 Score: 207
Period size: 3 Copynumber: 38.7 Consensus size: 3
55982 AATAATAATA
*
55992 ATT ATT ATT ATCA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56038 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
56086 ATT A-T ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
56108 AGTTGTAAAC
Statistics
Matches: 109, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
2 2 0.02
3 105 0.96
4 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:59942 original size:11 final size:11
Alignment explanation
Indices: 59926--59951 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
59916 TTAGTATTCT
59926 TTGGAAAGGGG
1 TTGGAAAGGGG
59937 TTGGAAAGGGG
1 TTGGAAAGGGG
59948 TTGG
1 TTGG
59952 CGTGCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (11 bp):
TTGGAAAGGGG
Found at i:60521 original size:18 final size:19
Alignment explanation
Indices: 60498--60533 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
60488 CTCCTTTCTT
60498 AATATTAA-AAAATAAATA
1 AATATTAATAAAATAAATA
60516 AATATTAATAAAATAAAT
1 AATATTAATAAAATAAAT
60534 TAGTATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATATTAATAAAATAAATA
Found at i:60608 original size:110 final size:106
Alignment explanation
Indices: 60441--60636 Score: 293
Period size: 110 Copynumber: 1.8 Consensus size: 106
60431 TAAGATATTT
* ** * * *
60441 ATTTATTTAAAAATATCATAAAAGGGTTTCTATGTGCTTTAAGACAGCTCCTTTCTTAATATTAA
1 ATTTATTTAAAAATATCAAAAAAGGACTTCTAGGTGCTTTAAGACAACTCATTTCTTAATATTAA
60506 AAAATAAATAAATATTAATAAAATAAATTAGTATAGTTTATAAAA
66 AAAAT--ATAAATATT--TAAAATAAATTAGTATAGTTTATAAAA
*
60551 ATTTATTTAAGAATATCAAAAAAGGACTTCTAGGTGCTTTAAGACAACTCATTTCTTAATATTAA
1 ATTTATTTAAAAATATCAAAAAAGGACTTCTAGGTGCTTTAAGACAACTCATTTCTTAATATTAA
60616 AAAATATAAATATTTAAAATA
66 AAAATATAAATATTTAAAATA
60637 TGATTATTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
106 7 0.09
108 9 0.11
110 63 0.80
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (106 bp):
ATTTATTTAAAAATATCAAAAAAGGACTTCTAGGTGCTTTAAGACAACTCATTTCTTAATATTAA
AAAATATAAATATTTAAAATAAATTAGTATAGTTTATAAAA
Found at i:60813 original size:25 final size:28
Alignment explanation
Indices: 60758--60813 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
60748 TAATACTAAT
***
60758 AAAATAATAATAATTTAAACATATATAA
1 AAAATAATAATAAAACAAACATATATAA
60786 AAAATAATAATAAAACAAA-AT-TATAA
1 AAAATAATAATAAAACAAACATATATAA
60812 AA
1 AA
60814 TTAACTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.28
27 2 0.08
28 16 0.64
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.27
Consensus pattern (28 bp):
AAAATAATAATAAAACAAACATATATAA
Found at i:62133 original size:3 final size:3
Alignment explanation
Indices: 62120--62186 Score: 55
Period size: 3 Copynumber: 22.3 Consensus size: 3
62110 GTATTATTTG
* * * * *
62120 TAA TAA AAA TAA TAA TAA T-A TTA TTA TTA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
62167 TAA AAA TAA TTAA GAA TAA T
1 TAA TAA TAA -TAA TAA TAA T
62187 TTTAATGAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:62623 original size:45 final size:46
Alignment explanation
Indices: 62314--63066 Score: 978
Period size: 44 Copynumber: 16.7 Consensus size: 46
62304 GGACGAAATG
* * *
62314 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCAAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
62360 TTTGAAAACATCATGCACTAAAGG---TACAGATGACCCGAA-GTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
62402 TTTGAAAAAATCATGCA-TGAAGGACTTACAGA-GACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* **
62446 TTTGAAAACATCATGCACTGAAGGACTTACATATGACTTGAAGGTTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TT
*
62493 TTTGAAAACATCATGCACTGAAGGACTTTACAGA-GACCTGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGAC-TTACAGATGACCCGAAGGTT
*
62539 TTTGAAAACATCATGCACT----GACTTACAGATGACCTGAAGG-T
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
62580 TTTGAAAACATCATGCAGTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
62626 TTTAAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* **
62672 TTT-AAAA-ATCATGCACTGAAGGGCTTACAGATGACCTAAAGG-T
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* * *
62715 TTTGATAACATCATGCACTGAAGGGCTTACAGAAT-A-CCAAAGG-T
1 TTTGAAAACATCATGCACTGAAGGACTTACAG-ATGACCCGAAGGTT
* *
62759 TTTGAAAACATCATACACTGAAGGGCTTACAGATGACCC-AAGGTTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TT
* *
62805 TTTTATAACATCATGCACT-AAGGACTTACAGATGACCCGAAGG-T
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* * * *
62849 TTTGATAACATCATGTACTGAAAGAC-TACAGATTACCCGAAGGTTTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG--TT
*
62896 TTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-T
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
* **
62941 TTTGATAACATCATGCACTGAAGGACTT-GTGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
*
62986 TTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TT
* *
63033 TTTGATAACATCATGCATTGAAGGACTTACAGAT
1 TTTGAAAACATCATGCACTGAAGGACTTACAGAT
63067 TGGAAATAGT
Statistics
Matches: 639, Mismatches: 38, Indels: 59
0.87 0.05 0.08
Matches are distributed among these distances:
41 31 0.05
42 32 0.05
43 27 0.04
44 149 0.23
45 145 0.23
46 136 0.21
47 97 0.15
48 22 0.03
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (46 bp):
TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
Found at i:62822 original size:179 final size:183
Alignment explanation
Indices: 62314--63066 Score: 974
Period size: 179 Copynumber: 4.2 Consensus size: 183
62304 GGACGAAATG
*
62314 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGA-CTCAAAGGTTTTTGAAAACATCATGCAC
1 TTTGAAAA-ATCATGCACTGAAGGACTTACAGATGACCT-AAAGGTTTTTGAAAACATCATGCAC
* * *
62378 T-AAAGG--TACAGATGACCCGAAGTTTTTGAAAAAATCATGCA-TGAAGGACTTACAGA-GACC
64 TGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACC
* **
62438 CGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACATATGACTTGAAGGTTT
129 CGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
*
62493 TTTGAAAACATCATGCACTGAAGGACTTTACAGA-GACCTGAAGGTTTTTGAAAACATCATGCAC
1 TTTGAAAA-ATCATGCACTGAAGGAC-TTACAGATGACCTAAAGGTTTTTGAAAACATCATGCAC
* *
62557 TG-A---CTTACAGATGACCTGAAGGTTTTGAAAACATCATGCAGTGAAGGACTTACAGATGACC
64 TGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACC
*
62618 CGAAGGTTTTTAAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-TT
129 CGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
* *
62672 TTT-AAAAATCATGCACTGAAGGGCTTACAGATGACCTAAAGG-TTTTGATAACATCATGCACTG
1 TTTGAAAAATCATGCACTGAAGGACTTACAGATGACCTAAAGGTTTTTGAAAACATCATGCACTG
* * *
62735 AAGGGCTTACAGAAT-A-CCAAAGGTTTTGAAAACATCATACACTGAAGGGCTTACAGATGACCC
66 AAGGGCTTACAG-ATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCC
* *
62798 -AAGGTTTTTTTATAACATCATGCACT-AAGGACTTACAGATGACCCGAAGG--T
130 GAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
* * * * ** *
62849 TTTGATAACATCATGTACTGAAAGAC-TACAGATTACCCGAAGGTTTTTTTGATAACATCATGCA
1 TTTGA-AAAATCATGCACTGAAGGACTTACAGATGACCTAAAGG--TTTTTGAAAACATCATGCA
* * **
62913 CTGAAGGACTTACAGATGACCCGAAGGTTTTGATAACATCATGCACTGAAGGACTT-GTGATGAC
63 CTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
*
62977 CCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
128 CCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
* *
63033 TTTGATAACATCATGCATTGAAGGACTTACAGAT
1 TTTGA-AAAATCATGCACTGAAGGACTTACAGAT
63067 TGGAAATAGT
Statistics
Matches: 511, Mismatches: 37, Indels: 46
0.86 0.06 0.08
Matches are distributed among these distances:
176 27 0.05
177 30 0.06
178 79 0.15
179 150 0.29
180 71 0.14
181 63 0.12
182 60 0.12
184 24 0.05
185 7 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (183 bp):
TTTGAAAAATCATGCACTGAAGGACTTACAGATGACCTAAAGGTTTTTGAAAACATCATGCACTG
AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCG
AAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTT
Found at i:63788 original size:21 final size:19
Alignment explanation
Indices: 63764--63811 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 19
63754 CAATAAGCTT
63764 TCATCTTTAAAAGAAAATCTA
1 TCATCTTT--AAGAAAATCTA
*
63785 TCATCTTTGAGAAAATCTA
1 TCATCTTTAAGAAAATCTA
63804 TCATCTTT
1 TCATCTTT
63812 GAATATATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 18 0.69
21 8 0.31
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (19 bp):
TCATCTTTAAGAAAATCTA
Found at i:63799 original size:19 final size:19
Alignment explanation
Indices: 63775--63813 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
63765 CATCTTTAAA
63775 AGAAAATCTATCATCTTTG
1 AGAAAATCTATCATCTTTG
63794 AGAAAATCTATCATCTTTG
1 AGAAAATCTATCATCTTTG
63813 A
1 A
63814 ATATATAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (19 bp):
AGAAAATCTATCATCTTTG
Found at i:65286 original size:75 final size:75
Alignment explanation
Indices: 65147--65319 Score: 202
Period size: 75 Copynumber: 2.3 Consensus size: 75
65137 GATATAGGCC
* * * * *** * *
65147 TTCAACATGCCCCAACATTGGCTAATACAAGCATTCAAAATGCATCAACATTCTTCATTCTGATT
1 TTCAGCATGCCCCAACATTTGCTGATATAAATGTTCAAAATACATCAACATTCATCATTCTGATT
65212 GAAAGGGGCT
66 GAAAGGGGCT
* * *
65222 TTCAGCATGCCCCAGCATTTGCTGATATAAATGTTCAAAATACATCAACATTCATGATTTTGATT
1 TTCAGCATGCCCCAACATTTGCTGATATAAATGTTCAAAATACATCAACATTCATCATTCTGATT
*
65287 GAGAGGGGCT
66 GAAAGGGGCT
* * *
65297 TTTAGTATGCCCCAATATTTGCT
1 TTCAGCATGCCCCAACATTTGCT
65320 TTTTGTTAAT
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 81 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTGATATAAATGTTCAAAATACATCAACATTCATCATTCTGATT
GAAAGGGGCT
Found at i:66112 original size:113 final size:114
Alignment explanation
Indices: 65932--66161 Score: 453
Period size: 113 Copynumber: 2.0 Consensus size: 114
65922 TTTTCTGTGA
65932 AGGCTCTTGAAAAGTCTGCAACCATGCAACGTGTTGATTTTGATAACTACTCATCTGATTATGGA
1 AGGCTCTTGAAAAGTCTGCAACCATGCAACGTGTTGATTTTGATAACTACTCATCTGATTATGGA
65997 GCGACCTTTCAGGATGATTTCACAGATTTTGATAGTTCTTCTGATACCG
66 GCGACCTTTCAGGATGATTTCACAGATTTTGATAGTTCTTCTGATACCG
66046 AGGCTCTTGAAAAGTCTGCAACCATGCAACGTG-TGATTTTGATAACTACTCATCTGATTATGGA
1 AGGCTCTTGAAAAGTCTGCAACCATGCAACGTGTTGATTTTGATAACTACTCATCTGATTATGGA
66110 GCGACCTTTCAGGATGATTTCACAGATTTTGATAGTTCTTCTGATACCG
66 GCGACCTTTCAGGATGATTTCACAGATTTTGATAGTTCTTCTGATACCG
66159 AGG
1 AGG
66162 GGCTATGATT
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
113 83 0.72
114 33 0.28
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (114 bp):
AGGCTCTTGAAAAGTCTGCAACCATGCAACGTGTTGATTTTGATAACTACTCATCTGATTATGGA
GCGACCTTTCAGGATGATTTCACAGATTTTGATAGTTCTTCTGATACCG
Found at i:67589 original size:32 final size:32
Alignment explanation
Indices: 67548--67609 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
67538 GAAGAAATGA
*
67548 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTCGTAGAGATACTTCTCG
67580 TTGTTATGCTCATCTCGTAGAGATACTTCT
1 TTGTTATGCTCATCTCGTAGAGATACTTCT
67610 TGTGTCTCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTCGTAGAGATACTTCTCG
Found at i:68087 original size:19 final size:20
Alignment explanation
Indices: 68065--68105 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
68055 CTTGGTTCAA
68065 TTTTTT-CATTTTT-CCTTT
1 TTTTTTCCATTTTTCCCTTT
*
68083 TTTTTTCCTTTTTTCCCTTT
1 TTTTTTCCATTTTTCCCTTT
68103 TTT
1 TTT
68106 CAAGTATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 6 0.30
20 8 0.40
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTCCATTTTTCCCTTT
Found at i:68187 original size:121 final size:115
Alignment explanation
Indices: 68038--68274 Score: 402
Period size: 115 Copynumber: 2.0 Consensus size: 115
68028 TAACTCGAGG
68038 CTCTGTGAGTCACTCATCTTGGTTCAATTTTTTCATTTTTCCTTTTTTTTTCCTTTTTTCCCTTT
1 CTCTGTGAGTCACTCATCTTGGTTCAATTTTTTCATTTTTCC--TTTTTTTCCTTTTTT-CCTTT
*
68103 TTTCAAGTATAATATTTCTTGACAGAATCTGAGTTTATTTGGTTTCTCATAACTTT
63 TTTCAAG--T-ATATTTCTTGACAGAATCTGAGTTTATTTGGTTTCTCAGAACTTT
*
68159 CTCTGTGAGTCACTCATCTTGGTTCAATTTTTTCTTTTTTCCTTTTTTTCCTTTTTTCCTTTTTT
1 CTCTGTGAGTCACTCATCTTGGTTCAATTTTTTCATTTTTCCTTTTTTTCCTTTTTTCCTTTTTT
68224 CAAGTATATTTCTTGACAGAATCTGAGTTTATTTGGTTTCTCAGAACTTT
66 CAAGTATATTTCTTGACAGAATCTGAGTTTATTTGGTTTCTCAGAACTTT
68274 C
1 C
68275 CTTTATTTCT
Statistics
Matches: 114, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
115 45 0.39
116 1 0.01
118 12 0.11
119 15 0.13
121 41 0.36
ACGTcount: A:0.16, C:0.19, G:0.11, T:0.54
Consensus pattern (115 bp):
CTCTGTGAGTCACTCATCTTGGTTCAATTTTTTCATTTTTCCTTTTTTTCCTTTTTTCCTTTTTT
CAAGTATATTTCTTGACAGAATCTGAGTTTATTTGGTTTCTCAGAACTTT
Found at i:68203 original size:8 final size:8
Alignment explanation
Indices: 68186--68224 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
68176 CTTGGTTCAA
68186 TTTTTT-C
1 TTTTTTCC
68193 TTTTTTCC
1 TTTTTTCC
68201 TTTTTTTCC
1 -TTTTTTCC
68210 TTTTTTCC
1 TTTTTTCC
68218 TTTTTTC
1 TTTTTTC
68225 AAGTATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 6 0.20
8 16 0.53
9 8 0.27
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCC
Found at i:68205 original size:9 final size:9
Alignment explanation
Indices: 68193--68223 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
68183 CAATTTTTTC
68193 TTTTTTCCT
1 TTTTTTCCT
68202 TTTTTTCC-
1 TTTTTTCCT
68210 TTTTTTCCT
1 TTTTTTCCT
68219 TTTTT
1 TTTTT
68224 CAAGTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:68212 original size:17 final size:16
Alignment explanation
Indices: 68186--68223 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
68176 CTTGGTTCAA
68186 TTTTTTCTTTTTTCCT
1 TTTTTTCTTTTTTCCT
68202 TTTTTTCCTTTTTTCCT
1 TTTTTT-CTTTTTTCCT
68219 TTTTT
1 TTTTT
68224 CAAGTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTCTTTTTTCCT
Found at i:72613 original size:26 final size:25
Alignment explanation
Indices: 72556--72613 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
72546 TGAAATATTA
*
72556 ATAAAATAATATACATATAAATATT
1 ATAAAATAATATACATATAAAAATT
*
72581 ATGAAAATAATAAGTATATATAAAAATT
1 AT-AAAATAAT-A-TACATATAAAAATT
72609 -TAAAA
1 ATAAAA
72614 AAAAAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 2 0.07
26 12 0.43
27 2 0.07
28 12 0.43
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (25 bp):
ATAAAATAATATACATATAAAAATT
Found at i:73198 original size:18 final size:19
Alignment explanation
Indices: 73175--73210 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
73165 CTCCTTTCTT
73175 AATATTAA-AAAATAAATA
1 AATATTAATAAAATAAATA
73193 AATATTAATAAAATAAAT
1 AATATTAATAAAATAAAT
73211 TAGTATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATATTAATAAAATAAATA
Found at i:73244 original size:109 final size:105
Alignment explanation
Indices: 73118--73312 Score: 304
Period size: 109 Copynumber: 1.8 Consensus size: 105
73108 TAAGATATTT
*
73118 ATTTATTTAGAAATATCAGAAAATGGCTTCTAGGTGCTTTAAGACAGCTCC-TTTCTTAATATTA
1 ATTTATTTAGAAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAGC-CCATTTCTTAATATTA
73182 AAAAATAAATAAATATTAATAAAATAAATTAGTATGTTTATAAAA
65 AAAAAT--ATAAATATT--TAAAATAAATTAGTATGTTTATAAAA
*
73227 ATTTATTTA-AGAATATCAGAAAATGATTTCTAGGTGCTTTAAGACAGCCCATTTCTTAATATTA
1 ATTTATTTAGA-AATATCAGAAAATGACTTCTAGGTGCTTTAAGACAGCCCATTTCTTAATATTA
73291 AAAAATATAAATATTTAAAATA
65 AAAAATATAAATATTTAAAATA
73313 TTATTATTAT
Statistics
Matches: 82, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
105 7 0.09
107 9 0.11
108 3 0.04
109 63 0.77
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (105 bp):
ATTTATTTAGAAATATCAGAAAATGACTTCTAGGTGCTTTAAGACAGCCCATTTCTTAATATTAA
AAAATATAAATATTTAAAATAAATTAGTATGTTTATAAAA
Found at i:73478 original size:25 final size:26
Alignment explanation
Indices: 73425--73480 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
73415 GATAATACTA
* *
73425 ATAAAATAATAATAATTTAAACATAT
1 ATAAAATAATAATAATTAAAACAAAT
73451 ATAAAA-AATAATAA-TAAAACAAATT
1 ATAAAATAATAATAATTAAAACAAA-T
73476 ATAAA
1 ATAAA
73481 TTAACTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 7 0.26
25 14 0.52
26 6 0.22
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (26 bp):
ATAAAATAATAATAATTAAAACAAAT
Found at i:74761 original size:3 final size:3
Alignment explanation
Indices: 74747--74826 Score: 76
Period size: 3 Copynumber: 27.3 Consensus size: 3
74737 TATTTATTTG
* * * *
74747 TAA TAA -AA TAA TAA TAA T-A TAT TAA TAA TAA TAA T-G TTA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
74792 TAA TAA TAA TAA TAA AAA TAA TAA TTAA GAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA T
74827 TTTAATGAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
2 5 0.08
3 54 0.87
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:74778 original size:20 final size:20
Alignment explanation
Indices: 74753--74805 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
74743 TTTGTAATAA
74753 AATAATAATAATATATTAAT
1 AATAATAATAATATATTAAT
**
74773 AATAATAATGTTATATTAAT
1 AATAATAATAATATATTAAT
74793 AATAATAATAATA
1 AATAATAATAATA
74806 AAAATAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
AATAATAATAATATATTAAT
Found at i:82241 original size:89 final size:90
Alignment explanation
Indices: 82090--82264 Score: 282
Period size: 89 Copynumber: 2.0 Consensus size: 90
82080 ACAAGCCCAT
* * *
82090 CCAAAAGACGAGTAGGTGATGTGTTATTTTTTAAAATATAACTCTTAAAATATTTTATAATAAAA
1 CCAAAAGACGAGTAGGTCATGTGTTATTTTTTAAAATAAAAATCTTAAAATATTTTATAATAAAA
82155 ATTAATTTGTT-AATTTGAATCATA
66 ATTAATTTGTTAAATTTGAATCATA
* *
82179 CCAAAAG-CTGAGTATGTCATGTGTTATTTTTTAAAATAAAAATTTTAAAATATTTTATAATAAA
1 CCAAAAGAC-GAGTAGGTCATGTGTTATTTTTTAAAATAAAAATCTTAAAATATTTTATAATAAA
82243 AATTAATTTGTTAAATTTGAAT
65 AATTAATTTGTTAAATTTGAAT
82265 TATAAGATAT
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
88 1 0.01
89 69 0.87
90 9 0.11
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (90 bp):
CCAAAAGACGAGTAGGTCATGTGTTATTTTTTAAAATAAAAATCTTAAAATATTTTATAATAAAA
ATTAATTTGTTAAATTTGAATCATA
Found at i:83878 original size:23 final size:22
Alignment explanation
Indices: 83826--83878 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
83816 ATCCTTAAAT
*
83826 CCTTAAATTTCAATCCCTAATC
1 CCTTAAATCTCAATCCCTAATC
* *
83848 TCTAAAATCTCAAATACCC-AATC
1 CCTTAAATCTC-AAT-CCCTAATC
83871 CCTTAAAT
1 CCTTAAAT
83879 TCATTTGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 8 0.33
23 13 0.54
24 3 0.12
ACGTcount: A:0.38, C:0.30, G:0.00, T:0.32
Consensus pattern (22 bp):
CCTTAAATCTCAATCCCTAATC
Found at i:85127 original size:2 final size:2
Alignment explanation
Indices: 85120--85154 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
85110 ATGATGAATG
85120 AT 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 A
85155 AAGATTACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:86340 original size:20 final size:20
Alignment explanation
Indices: 86304--86344 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
86294 TAAGCCTTTT
*
86304 AGTATCGATGTCGACCATTG
1 AGTATCGATCTCGACCATTG
86324 AGTATCGATACTC-ACCATTG
1 AGTATCGAT-CTCGACCATTG
86344 A
1 A
86345 TACTGATACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (20 bp):
AGTATCGATCTCGACCATTG
Found at i:87424 original size:32 final size:32
Alignment explanation
Indices: 87384--87501 Score: 105
Period size: 32 Copynumber: 3.7 Consensus size: 32
87374 CTGTAACTTC
*
87384 TGTGCATTATTTAAATGCAACACTAATACTCT
1 TGTGCATTATCTAAATGCAACACTAATACTCT
* * * * * * *
87416 TATGCATTATCTGAATG-AGAGAATGACACTCC
1 TGTGCATTATCTAAATGCA-ACACTAATACTCT
* *
87448 TGTGCATTATTTAAATGCAACACTAACT-CTAT
1 TGTGCATTATCTAAATGCAACACTAA-TACTCT
*
87480 TGTGCATTATCTGAATGCAACA
1 TGTGCATTATCTAAATGCAACA
87502 TTACTAGTAT
Statistics
Matches: 64, Mismatches: 19, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
31 1 0.02
32 62 0.97
33 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (32 bp):
TGTGCATTATCTAAATGCAACACTAATACTCT
Found at i:93104 original size:32 final size:32
Alignment explanation
Indices: 93068--93140 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 32
93058 ATACATTCTT
93068 TAAATGCAACACTAACACTCATGTGCAATATC
1 TAAATGCAACACTAACACTCATGTGCAATATC
* * * ** *
93100 TAAATACAACACTGACTCTGTTGTGCACTATC
1 TAAATGCAACACTAACACTCATGTGCAATATC
*
93132 TAATTGCAA
1 TAAATGCAA
93141 TATTGATTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (32 bp):
TAAATGCAACACTAACACTCATGTGCAATATC
Found at i:95023 original size:189 final size:190
Alignment explanation
Indices: 94665--95044 Score: 658
Period size: 189 Copynumber: 2.0 Consensus size: 190
94655 ATCTTGGTGT
*
94665 TAGGATTCTGAAATGAAGCTCCTTGCTTAGCTACACTCTCTTCTCTAAGATTTGAATAAAATCTC
1 TAGGATCCTGAAATGAAGCTCCTTGCTTAGCTACACTCTCTTCTCTAAGATTTGAATAAAATCTC
* * *
94730 TCACTTTGTCTTTAGCTGTAAAGAACTCAAGTCTTTGAAACTTTAAAACAAGTTGCTGGAGGGAT
66 TCACTTTGTCTTTAGCTATAAAGAACCCAAGTCTTTGAAACTTTAAAACAAGTTGATGGAGGGAT
*
94795 TGAGGATGAAATTAAAGCTTAAAAGAAGTATAAAAGGTTCTCAAGATCTTACCTTTGAGC
131 TGAAGATGAAATTAAAGCTTAAAAGAAGTATAAAAGGTTCTCAAGATCTTACCTTTGAGC
*
94855 TAGGATCCTGAAATGAAGCTCCTTGCTTAGCTATACTCTCTTCTCTAAGATTTGAATGAAAA-CT
1 TAGGATCCTGAAATGAAGCTCCTTGCTTAGCTACACTCTCTTCTCTAAGATTTGAAT-AAAATCT
94919 CTCACTTTGTCTTTAGCTATAAA-AACCCAAGGT-TTTGAAACTTTAAAACAAGTTGATGGAGGG
65 CTCACTTTGTCTTTAGCTATAAAGAACCCAA-GTCTTTGAAACTTTAAAACAAGTTGATGGAGGG
*
94982 ATTGAAGATGAAATTGAAGCTTAAAAGAAGTATAAAAGGTTCTCAAGATCTTACCTTTGAGC
129 ATTGAAGATGAAATTAAAGCTTAAAAGAAGTATAAAAGGTTCTCAAGATCTTACCTTTGAGC
95044 T
1 T
95045 GGGCACTTGG
Statistics
Matches: 181, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
189 96 0.53
190 81 0.45
191 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (190 bp):
TAGGATCCTGAAATGAAGCTCCTTGCTTAGCTACACTCTCTTCTCTAAGATTTGAATAAAATCTC
TCACTTTGTCTTTAGCTATAAAGAACCCAAGTCTTTGAAACTTTAAAACAAGTTGATGGAGGGAT
TGAAGATGAAATTAAAGCTTAAAAGAAGTATAAAAGGTTCTCAAGATCTTACCTTTGAGC
Done.