Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002335.1 Hibiscus syriacus cultivar Beakdansim tig00004771_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: 123960
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6842 original size:18 final size:19
Alignment explanation
Indices: 6806--6843 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6796 AACCTAATTT
6806 GTGTACCGATACACCCATA
1 GTGTACCGATACACCCATA
*
6825 GTGTATCGATAC-CCCATA
1 GTGTACCGATACACCCATA
6843 G
1 G
6844 AAGAAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (19 bp):
GTGTACCGATACACCCATA
Found at i:13589 original size:19 final size:19
Alignment explanation
Indices: 13565--13614 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
13555 AACCTAATTT
13565 GTGTATCGATACACCCATA
1 GTGTATCGATACACCCATA
13584 GTGTATCGATACACCCATA
1 GTGTATCGATACACCCATA
13603 GTGTATCGATAC
1 GTGTATCGATAC
13615 CCCCTAGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (19 bp):
GTGTATCGATACACCCATA
Found at i:19458 original size:18 final size:19
Alignment explanation
Indices: 19423--19459 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
19413 CACGGAATGT
19423 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
19443 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
19460 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:21232 original size:18 final size:18
Alignment explanation
Indices: 21186--21234 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
21176 TCTAGAACCC
21186 AAAACATAAAAAAAAAGAG
1 AAAA-ATAAAAAAAAAGAG
*
21205 AAAAAGAAAAAAAAAGAG
1 AAAAATAAAAAAAAAGAG
* *
21223 AGAGATAAAAAA
1 AAAAATAAAAAA
21235 TGAAGAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAATAAAAAAAAAGAG
Found at i:21512 original size:32 final size:33
Alignment explanation
Indices: 21476--21539 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
21466 AATAATATCA
21476 TTTTGG-GTTTATATAACCCTCCTAAAATGATG
1 TTTTGGAGTTTATATAACCCTCCTAAAATGATG
* ** *
21508 TTTTGGAGTTTGTATAATTCTCTTAAAATGAT
1 TTTTGGAGTTTATATAACCCTCCTAAAATGAT
21540 TTTGATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 6 0.22
33 21 0.78
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (33 bp):
TTTTGGAGTTTATATAACCCTCCTAAAATGATG
Found at i:21903 original size:3 final size:3
Alignment explanation
Indices: 21895--21919 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
21885 ATTAATACTA
21895 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
21920 GATATTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27596 original size:24 final size:24
Alignment explanation
Indices: 27562--27630 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
27552 TGGGACACAC
* *
27562 TTTTCTTTACTCTTGTGGCA-TGTG
1 TTTTCTCTACTCTTGTGGCACT-CG
* *
27586 TTTTCTCTACTCTTCTGGTACTCG
1 TTTTCTCTACTCTTGTGGCACTCG
* *
27610 TTTTCTCTACTATTGTTGCAC
1 TTTTCTCTACTCTTGTGGCAC
27631 GATCCTTATG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
24 35 0.97
25 1 0.03
ACGTcount: A:0.10, C:0.23, G:0.14, T:0.52
Consensus pattern (24 bp):
TTTTCTCTACTCTTGTGGCACTCG
Found at i:31957 original size:11 final size:11
Alignment explanation
Indices: 31941--31965 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31931 TTGTACAAAG
31941 TTTCAAATAAT
1 TTTCAAATAAT
31952 TTTCAAATAAT
1 TTTCAAATAAT
31963 TTT
1 TTT
31966 GACATTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTCAAATAAT
Found at i:34002 original size:20 final size:20
Alignment explanation
Indices: 33967--34018 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
33957 GTTATATGTC
* *
33967 TAAAGAAAAGTAAAAAATCAA
1 TAAA-AAAATTAAAAGATCAA
*
33988 TAACAAAAATTAAAAGTTCAA
1 TAA-AAAAATTAAAAGATCAA
34009 TAAAAAAATT
1 TAAAAAAATT
34019 CAATTATTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.26
21 19 0.70
22 1 0.04
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (20 bp):
TAAAAAAATTAAAAGATCAA
Found at i:34776 original size:26 final size:26
Alignment explanation
Indices: 34747--34799 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
34737 GGTCTGAAGT
*
34747 GGCAATTTCGAGAAGGTCCAGTCAGC
1 GGCAATTTCGAGAAGATCCAGTCAGC
* ** *
34773 GGCAGTTTTTAGAAGATCTAGTCAGC
1 GGCAATTTCGAGAAGATCCAGTCAGC
34799 G
1 G
34800 TGCCTTTTGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (26 bp):
GGCAATTTCGAGAAGATCCAGTCAGC
Found at i:43942 original size:3 final size:3
Alignment explanation
Indices: 43934--43997 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
43924 CGTGGCAGAC
*
43934 TCA TCA TCA CCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
43982 T-A TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TC
43998 GTTATTATTC
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.33, C:0.34, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:44877 original size:25 final size:23
Alignment explanation
Indices: 44849--44900 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
44839 ATTTATAATA
* *
44849 TAATTTTACAACTTTTGAAAATTTC
1 TAATTATACAACCTTT-AAAA-TTC
*
44874 TAATTATACACCCTTTAAAATTC
1 TAATTATACAACCTTTAAAATTC
44897 TAAT
1 TAAT
44901 ATAACTTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.29
24 4 0.17
25 13 0.54
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.44
Consensus pattern (23 bp):
TAATTATACAACCTTTAAAATTC
Found at i:46265 original size:3 final size:3
Alignment explanation
Indices: 46257--46393 Score: 229
Period size: 3 Copynumber: 45.7 Consensus size: 3
46247 TTTTTATCCA
* *
46257 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
46305 TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
46353 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
46394 AATATATTAA
Statistics
Matches: 124, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 124 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:46935 original size:19 final size:18
Alignment explanation
Indices: 46898--46932 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
46888 ACAGAACCGG
46898 AGAGAAAGAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAC
46916 AGAGAAAGAAAAAAAAA
1 AGAGAAAGAAAAAAAAA
46933 ACAACTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (18 bp):
AGAGAAAGAAAAAAAAAC
Found at i:59197 original size:9 final size:9
Alignment explanation
Indices: 59183--59235 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
59173 ATTATGCTTG
59183 AAGAAAAGA
1 AAGAAAAGA
*
59192 AAGAAAAAA
1 AAGAAAAGA
59201 AAGAAAA-A
1 AAGAAAAGA
59209 AA-AAGAAG-
1 AAGAA-AAGA
59217 AA-AAAAGA
1 AAGAAAAGA
*
59225 GAGAAAAGA
1 AAGAAAAGA
59234 AA
1 AA
59236 AAAGGAGGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
7 5 0.14
8 10 0.27
9 22 0.59
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:59204 original size:13 final size:12
Alignment explanation
Indices: 59186--59222 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
59176 ATGCTTGAAG
59186 AAAAGAAAGAAAA
1 AAAAGAAA-AAAA
59199 AAAAGAAAAAAA
1 AAAAGAAAAAAA
59211 AAGAAGAAAAAA
1 AA-AAGAAAAAA
59223 GAGAGAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:59208 original size:10 final size:10
Alignment explanation
Indices: 59186--59238 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
59176 ATGCTTGAAG
*
59186 AAAAGAAAG-
1 AAAAAAAAGA
59195 AAAAAAAAGA
1 AAAAAAAAGA
59205 AAAAAAAAGA
1 AAAAAAAAGA
*
59215 AGAAAAAAG-
1 AAAAAAAAGA
* *
59224 AGAGAAAAGA
1 AAAAAAAAGA
59234 AAAAA
1 AAAAA
59239 GGAGGGTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
9 16 0.43
10 21 0.57
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:59213 original size:19 final size:18
Alignment explanation
Indices: 59183--59238 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
59173 ATTATGCTTG
*
59183 AAGAAAAGAAAGAAAAAA
1 AAGAAAAAAAAGAAAAAA
59201 AAGAAAAAAAAAGAAGAAAA
1 AAG-AAAAAAAAGAA-AAAA
* *
59221 AAGAGAGAAAAGAAAAAA
1 AAGAAAAAAAAGAAAAAA
59239 GGAGGGTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 7 0.21
19 19 0.58
20 7 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAAGAAAAAA
Found at i:59218 original size:31 final size:29
Alignment explanation
Indices: 59183--59238 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
59173 ATTATGCTTG
*
59183 AAGAA-AAGAAAGAAAAAAAAGAAAAAAA
1 AAGAAGAAAAAAGAAAAAAAAGAAAAAAA
* *
59211 AAGAAGAAAAAAGAGAGAAAAGAAAAAA
1 AAGAAGAAAAAAGAAAAAAAAGAAAAAA
59239 GGAGGGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (29 bp):
AAGAAGAAAAAAGAAAAAAAAGAAAAAAA
Found at i:59577 original size:16 final size:16
Alignment explanation
Indices: 59556--59595 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
59546 ATACAATTTT
59556 ATTTATTTCAAG-TTCA
1 ATTTATTT-AAGATTCA
*
59572 ATTTATTTGAGATTCA
1 ATTTATTTAAGATTCA
59588 ATTTATTT
1 ATTTATTT
59596 TTGGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (16 bp):
ATTTATTTAAGATTCA
Found at i:60576 original size:82 final size:82
Alignment explanation
Indices: 60378--61173 Score: 1400
Period size: 82 Copynumber: 9.7 Consensus size: 82
60368 TAAATGGAAT
*
60378 AGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGA
60442 ACCAATCAGTGAGTTTAGA
65 A-CAATCAGTGAGTTTAGA
60461 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
60526 CAATCAGTGAGTTTAGA
66 CAATCAGTGAGTTTAGA
60543 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
*
60608 CAATCAGTGAGTTTGGA
66 CAATCAGTGAGTTTAGA
*
60625 AGATGAATTTGCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGG-CAGA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGA
*
60689 ACCAATCAGTAAGTTTAGA
65 A-CAATCAGTGAGTTTAGA
60708 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
60773 CAATCAGTGAGTTTAGA
66 CAATCAGTGAGTTTAGA
60790 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
60855 CAATCAGTGAGTTTAGA
66 CAATCAGTGAGTTTAGA
60872 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
60937 CAATCAGTGAGTTTAGA
66 CAATCAGTGAGTTTAGA
* * *
60954 AGATGAGTTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
* * * *
61019 TCAAGCATTGAATTTGGA
66 -CAATCAGTGAGTTTAGA
*
61037 AGATGAATTTGCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGG-CAGA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGA
61101 ACCAATCAGTGAGTTTAGA
65 A-CAATCAGTGAGTTTAGA
61120 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
61174 ATTCAGTAGG
Statistics
Matches: 683, Mismatches: 24, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
82 407 0.60
83 272 0.40
84 4 0.01
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (82 bp):
AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA
CAATCAGTGAGTTTAGA
Found at i:60814 original size:247 final size:247
Alignment explanation
Indices: 60378--61173 Score: 1427
Period size: 247 Copynumber: 3.2 Consensus size: 247
60368 TAAATGGAAT
*
60378 AGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
60443 CCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
66 CCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
60508 TGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAA
131 TGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAA
*
60573 GTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTTGGA
196 GTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTTAGA
*
60625 AGATGAATTTGCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
*
60690 CCAATCAGTAAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
66 CCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
60755 TGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAA
131 TGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAA
60820 GTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTTAGA
196 GTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTTAGA
60872 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGA
* *
60936 A-CAATCAGTGAGTTTAGAAGATGAGTTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
65 ACCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* * * * *
61000 CTGATCTGATTGGACAGAATCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGG
130 CTGATCTGGTTGGACAGAA-CAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGG
*
61065 AAGTATTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCAGTGAGTTTAGA
194 AAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAA-CAATCAGTGAGTTTAGA
61120 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
61174 ATTCAGTAGG
Statistics
Matches: 531, Mismatches: 14, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
246 82 0.15
247 374 0.70
248 75 0.14
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (247 bp):
AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
CCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAA
GTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTTAGA
Found at i:60977 original size:329 final size:330
Alignment explanation
Indices: 60378--61173 Score: 1438
Period size: 329 Copynumber: 2.4 Consensus size: 330
60368 TAAATGGAAT
*
60378 AGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
60443 CCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
66 CCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
60508 TGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAA
131 TGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAA
*
60573 GTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTTGGAAGATGAATTTGCC
196 GTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCC
* *
60638 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCAGT-AA
261 AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCT-GATTGGACAGAACCAAGCAGTGAA
60701 GTTTAGA
325 -TTTAGA
60708 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGA
60772 A-CAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
65 ACCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
60836 CTGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGA
130 CTGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGA
* *
60901 AGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAGTTTGT
195 AGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGC
* * *
60966 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAA
260 CAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTGGACAGAACCAAGCAGTGAA
*
61031 TTTGGA
325 TTTAGA
*
61037 AGATGAATTTGCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
1 AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
61102 CCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
66 CCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
61167 TGATCTG
131 TGATCTG
61174 ATTCAGTAGG
Statistics
Matches: 450, Mismatches: 11, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
328 5 0.01
329 309 0.69
330 136 0.30
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (330 bp):
AGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
CCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAA
GTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAATCAGTGAGTTTAGAAGATGAATTTGCC
AATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGATTGGACAGAACCAAGCAGTGAAT
TTAGA
Found at i:62029 original size:113 final size:112
Alignment explanation
Indices: 61824--62786 Score: 1378
Period size: 113 Copynumber: 8.5 Consensus size: 112
61814 AAAGATCAGC
61824 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * *
61889 AAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATT
66 AAGAACTTGTTCAACCTTTTCT-TGAATTCATCACTTGATGGATCATT
61937 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * **
62002 AAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGC
66 AAGAACTTGTTCAACCTTTT-CTTGAATTCATCACTTGATGGATCATT
*
62050 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTATAATGAG
1 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * **
62115 AAGAGCTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGC
66 AAGAACTTGTTCAACCTTTT-CTTGAATTCATCACTTGATGGATCATT
62163 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * *
62228 AAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATT
66 AAGAACTTGTTCAACCTTTTCT-TGAATTCATCACTTGATGGATCATT
62276 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * *
62341 AAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATT
66 AAGAACTTGTTCAACCTTTTCT-TGAATTCATCACTTGATGGATCATT
62389 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* *
62454 AAGAACTTGTTCAATCTTTTGCTTGAATTCATCA-TTGGATGGATCAAT
66 AAGAACTTGTTCAACCTTTT-CTTGAATTCATCACTT-GATGGATCATT
* * *
62502 ATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAA
1 TTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAA
* *
62566 TGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCA-TTGGATGGATCAAT
62 TGAGAAGAACTTGTTCAACCTTTT-CTTGAATTCATCACTT-GATGGATCATT
* * * *
62618 ATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAGTTCATAA
1 TTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAA
* * *
62682 TGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCATC
62 TGAGAAGAACTTGTTCAACCTTTT-CTTGAATTCATCACTTGATGGATCATT
* ** *
62734 ATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAGAA
1 TTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
62787 TTTATTCAAT
Statistics
Matches: 807, Mismatches: 32, Indels: 22
0.94 0.04 0.03
Matches are distributed among these distances:
112 4 0.00
113 565 0.70
114 16 0.02
115 2 0.00
116 198 0.25
117 21 0.03
118 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (112 bp):
TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTTTCTTGAATTCATCACTTGATGGATCATT
Found at i:62426 original size:339 final size:339
Alignment explanation
Indices: 61801--62791 Score: 1521
Period size: 339 Copynumber: 2.9 Consensus size: 339
61791 CAAAGATTCA
* **
61801 AATCTATCATTTGAAAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
61866 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGG
61931 ATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
61996 AATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGA
196 AATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCATCTTTTCCAGAGA
*
62061 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTATAATGAGAAGAGCTTGTT
261 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTATAATGAGAAGAACTTGTT
62126 CAACCTTTTACTTG
326 CAACCTTTTACTTG
62140 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
62205 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGG
62270 ATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
62335 AATGAGAAGAATTTGTTCAACCTTTTG-TCTGAATTCATCACTTGATGGATTATTTTTTCCAGAG
196 AATGAGAAGAATTTGTTCAACCTTTTGCT-TGAATTCATCATTTGATGGATCATCTTTTCCAGAG
*
62399 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
260 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTATAATGAGAAGAACTTGT
* *
62464 TCAATCTTTTGCTTG
325 TCAACCTTTTACTTG
* * * * *
62479 AATTCATCATTGGATGGATCA-ATATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATCCATCATTTGATGGATCAGCT-TTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCT
* *
62542 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTG-CTTGAATTCATCA-T
61 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTC-TGAATTCATCACT
* * * * * *
62605 TGGATGGATCAATATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAG
125 T-GATGGATTATTTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAG
* *
62669 AAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATGGATCATC
185 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCATC
* ** *
62734 ATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAGAA-TTTAT
250 TTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTAT
62792 TCAATATCTC
Statistics
Matches: 602, Mismatches: 36, Indels: 23
0.91 0.05 0.03
Matches are distributed among these distances:
338 3 0.00
339 368 0.61
341 5 0.01
342 98 0.16
344 5 0.01
345 86 0.14
346 37 0.06
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (339 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGG
ATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCATCTTTTCCAGAGA
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTATAATGAGAAGAACTTGTT
CAACCTTTTACTTG
Found at i:62932 original size:3 final size:3
Alignment explanation
Indices: 62924--63040 Score: 209
Period size: 3 Copynumber: 39.0 Consensus size: 3
62914 TTTTTATCCA
62924 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
62972 TAT TAT TAT TAT TAC TAT TAT TAT TAT ATAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
63018 TAT TAT TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
63041 ATATATATAA
Statistics
Matches: 110, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
2 2 0.02
3 105 0.95
4 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:67868 original size:43 final size:43
Alignment explanation
Indices: 67813--67902 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
67803 ATATATTCTG
67813 TAAACTCATAACTATTATGAATTTTCTTTAACAAATAGAAACT
1 TAAACTCATAACTATTATGAATTTTCTTTAACAAATAGAAACT
*
67856 TAAACTCGTAACTATTATGAATTTTCTTTAACAAATAGAAACT
1 TAAACTCATAACTATTATGAATTTTCTTTAACAAATAGAAACT
67899 TAAA
1 TAAA
67903 AGATCTTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (43 bp):
TAAACTCATAACTATTATGAATTTTCTTTAACAAATAGAAACT
Found at i:68621 original size:13 final size:12
Alignment explanation
Indices: 68598--68627 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
68588 TGAGAATCTA
68598 AAAATAAAAAAT
1 AAAATAAAAAAT
68610 AAAATAATAAAAT
1 AAAATAA-AAAAT
68623 AAAAT
1 AAAAT
68628 TTCACTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:73849 original size:28 final size:29
Alignment explanation
Indices: 73817--73871 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
73807 AAGTTTAAGC
73817 TTCAATCAAACTAAGCGAAC-ATATAATA
1 TTCAATCAAACTAAGCGAACAATATAATA
73845 TTCAATCAAACTAAGCGAACAATATAA
1 TTCAATCAAACTAAGCGAACAATATAA
73872 GACTTTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (29 bp):
TTCAATCAAACTAAGCGAACAATATAATA
Found at i:75550 original size:50 final size:50
Alignment explanation
Indices: 75496--75618 Score: 149
Period size: 50 Copynumber: 2.5 Consensus size: 50
75486 TAGTAGAAAA
* * * *
75496 GCGCCCCCTGCACCGCGCTATATGTTGATTTGGCGCCACGTGGGTATAGC
1 GCGCCCCCTGCACCGCGCTATACGGTGATCTGGCGCCACGTGGGTATAAC
** * * *
75546 GCGCCTTCTGCCCCGCGATATACGGTGATCTGGTGCCACGTGGGTATAAC
1 GCGCCCCCTGCACCGCGCTATACGGTGATCTGGCGCCACGTGGGTATAAC
75596 GCGCCCCCTG-ATCCGCGCTATAC
1 GCGCCCCCTGCA-CCGCGCTATAC
75619 CTGGATATCT
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.23
Consensus pattern (50 bp):
GCGCCCCCTGCACCGCGCTATACGGTGATCTGGCGCCACGTGGGTATAAC
Found at i:75782 original size:12 final size:10
Alignment explanation
Indices: 75741--75781 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
75731 TTTATCACAC
75741 CAAATTCTCT
1 CAAATTCTCT
75751 CAAATTCTCT
1 CAAATTCTCT
75761 -AAATTTCTCT
1 CAAA-TTCTCT
*
75771 CAAATACTCT
1 CAAATTCTCT
75781 C
1 C
75782 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:75830 original size:13 final size:14
Alignment explanation
Indices: 75802--75830 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
75792 ATATTTTATA
75802 ATGTTTTTACTATT
1 ATGTTTTTACTATT
75816 ATGTTTTTACT-TT
1 ATGTTTTTACTATT
75829 AT
1 AT
75831 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (14 bp):
ATGTTTTTACTATT
Found at i:76099 original size:111 final size:111
Alignment explanation
Indices: 75905--76126 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
75895 TGGAAATCAT
* *
75905 ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
75970 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGCTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
*
76016 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
76081 TAATTAGCTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGCTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
76127 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGCTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:77660 original size:18 final size:18
Alignment explanation
Indices: 77633--77690 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
77623 CCAGCAGCCA
*
77633 CCGCAGCCATATATGATG
1 CCGCATCCATATATGATG
*
77651 TCGCATCCATATATGATG
1 CCGCATCCATATATGATG
77669 CCGC-TGCCATATATGATG
1 CCGCAT-CCATATATGATG
77687 CCGC
1 CCGC
77691 CATCGCCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 1 0.03
18 35 0.97
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (18 bp):
CCGCATCCATATATGATG
Found at i:78047 original size:21 final size:21
Alignment explanation
Indices: 78023--78062 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
78013 ACCTGCTCAG
78023 GACGACGACGATGACGATGGT
1 GACGACGACGATGACGATGGT
78044 GACGACGACGATGACGATG
1 GACGACGACGATGACGATG
78063 ATGATGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.38, T:0.12
Consensus pattern (21 bp):
GACGACGACGATGACGATGGT
Found at i:78323 original size:35 final size:33
Alignment explanation
Indices: 78284--78368 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
78274 ATATTTTAGT
78284 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
78319 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
78354 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
78369 TAAATATCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:80920 original size:31 final size:31
Alignment explanation
Indices: 80831--80923 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 31
80821 GAACCTCGAC
* *
80831 AACTGTCCATAGGTC-CCAAAGAACCTAGGT
1 AACTGTCCATATGTCTCCAAAGAACATAGGT
** *
80861 AACTGTCCATATGT-TCCTTAGAAAATAGGT
1 AACTGTCCATATGTCTCCAAAGAACATAGGT
*
80891 ATACTGTCCATATGTCTCGAAAG-ACATAGGT
1 A-ACTGTCCATATGTCTCCAAAGAACATAGGT
80922 AA
1 AA
80924 AACCCTCGAC
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
30 26 0.51
31 21 0.41
32 4 0.08
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCTCCAAAGAACATAGGT
Found at i:81088 original size:17 final size:19
Alignment explanation
Indices: 81058--81093 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
81048 CATATATGTC
81058 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
81077 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
81094 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:81714 original size:64 final size:64
Alignment explanation
Indices: 81582--81739 Score: 194
Period size: 64 Copynumber: 2.5 Consensus size: 64
81572 CAATGAATGT
* * ** *
81582 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTATTTAATGGGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTTATTTAATAAGC
* * *
81646 ATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAA-AAT
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTT-TATTTAATAAG
81709 C
64 C
* *
81710 ATGCATCGATGCACTGCATGTGCATCGATG
1 ATGCATCGATGCACTACTTGTGCATCGATG
81740 TACCTTAAAC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
63 5 0.06
64 69 0.85
65 7 0.09
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTTATTTAATAAGC
Found at i:84666 original size:31 final size:30
Alignment explanation
Indices: 84597--84689 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 30
84587 GAACCTCAGC
* *
84597 AACTGTCCATAGGTCCCAAAGAACCTAGGT
1 AACTGTCCATATGTCCCAAAGAACATAGGT
* **
84627 AACTGTCCATATGTTCCTTAGAACATAGGT
1 AACTGTCCATATGTCCCAAAGAACATAGGT
*
84657 ATACTGTCCATATGTCTCGAAAG-ACATAGGT
1 A-ACTGTCCATATGTC-CCAAAGAACATAGGT
84688 AA
1 AA
84690 AACCCTCGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
30 27 0.52
31 22 0.42
32 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (30 bp):
AACTGTCCATATGTCCCAAAGAACATAGGT
Found at i:84856 original size:17 final size:19
Alignment explanation
Indices: 84824--84859 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
84814 CATATATCTC
84824 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
84843 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
84860 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:85455 original size:63 final size:64
Alignment explanation
Indices: 85348--85506 Score: 189
Period size: 63 Copynumber: 2.5 Consensus size: 64
85338 CAATGAATGT
* * ** *
85348 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATG-TTT-TATTTAATGGGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAA-AAGC
* * *
85411 ATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAAAATC
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATTTAAAAGC
* *
85475 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACTTGTGCATCGATGCA
85507 CCTTAAACAA
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
62 5 0.06
63 38 0.46
64 32 0.39
65 7 0.09
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAAAGC
Found at i:88259 original size:50 final size:50
Alignment explanation
Indices: 88150--88272 Score: 147
Period size: 50 Copynumber: 2.5 Consensus size: 50
88140 CTACGTGGCG
* * * *
88150 TATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGACATCAGATCACCG
1 TATAGCGCGGAGCAGGGGGCGCGCTATACCCACGTGACACCAAATCACCA
* * * * *
88200 TATATCGCGGGGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAGCA
1 TATAGCGCGGAGCAGGGGGCGCGCTATACCCACGTGACACCAAATCACCA
* *
88250 TATAGCGCGGTGTAGGGGGCGCG
1 TATAGCGCGGAGCAGGGGGCGCG
88273 TTTTTCTGCT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.21, C:0.28, G:0.36, T:0.15
Consensus pattern (50 bp):
TATAGCGCGGAGCAGGGGGCGCGCTATACCCACGTGACACCAAATCACCA
Found at i:93086 original size:32 final size:32
Alignment explanation
Indices: 93036--93120 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
93026 AAAATTTAGA
*
93036 TACTAAAATGAAACAAAAAGTTAACAACGGAG
1 TACTGAAATGAAACAAAAAGTTAACAACGGAG
*
93068 TACTGAAATGAAATAAAAAGTTAACAACGGAG
1 TACTGAAATGAAACAAAAAGTTAACAACGGAG
93100 TACTGAAATGAAACAAAAAGT
1 TACTGAAATGAAACAAAAAGT
93121 AAATATTAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.18
Consensus pattern (32 bp):
TACTGAAATGAAACAAAAAGTTAACAACGGAG
Found at i:97535 original size:14 final size:16
Alignment explanation
Indices: 97507--97538 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
97497 CCCATGTGTT
97507 ATATATAATATATTTA
1 ATATATAATATATTTA
97523 ATATATAA-A-ATTTA
1 ATATATAATATATTTA
97537 AT
1 AT
97539 TTCGGTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATAATATATTTA
Found at i:99075 original size:42 final size:43
Alignment explanation
Indices: 98962--99082 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 43
98952 TTGCAATATG
* * **
98962 TTAGTTTGATGTATTTGTGGATTATTATTTTGATTGTAATATG
1 TTAGTTTGATGTATTTCTGGATTATTACTTTGATTGTAATAAC
* * * * *
99005 TTAGTTTGGTGTACTTCTGGGTTGTTACTTTGGTT-TAATAAC
1 TTAGTTTGATGTATTTCTGGATTATTACTTTGATTGTAATAAC
* *
99047 TTAGTTCGATGTATTTCTAGATTATTACTTTAGATT
1 TTAGTTTGATGTATTTCTGGATTATTACTTT-GATT
99083 TTGGAATTGT
Statistics
Matches: 61, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
42 30 0.49
43 31 0.51
ACGTcount: A:0.21, C:0.06, G:0.20, T:0.53
Consensus pattern (43 bp):
TTAGTTTGATGTATTTCTGGATTATTACTTTGATTGTAATAAC
Found at i:101644 original size:40 final size:40
Alignment explanation
Indices: 101589--101684 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
101579 TCTCAAGTTT
* * * *
101589 CAAACCACAATATTAACTTTATAATAATAAAATACATAAA
1 CAAACCATAATATTAACTCTAAAACAATAAAATACATAAA
* * * *
101629 CAAACCATTATATTAAGTCTAAAACAATAAAATCCGTAAA
1 CAAACCATAATATTAACTCTAAAACAATAAAATACATAAA
* *
101669 CAAACTATGATATTAA
1 CAAACCATAATATTAA
101685 AATGTCAAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.54, C:0.16, G:0.03, T:0.27
Consensus pattern (40 bp):
CAAACCATAATATTAACTCTAAAACAATAAAATACATAAA
Found at i:101950 original size:11 final size:11
Alignment explanation
Indices: 101936--101960 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
101926 TCCAATTCTC
101936 TTCTTTTTTTT
1 TTCTTTTTTTT
101947 TTCTTTTTTTT
1 TTCTTTTTTTT
101958 TTC
1 TTC
101961 CTTTAACCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:107611 original size:31 final size:31
Alignment explanation
Indices: 107573--107651 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 31
107563 CAAGAATTAC
107573 AGAGAAAAGAGAAGAGGAAAATAGGAGGAAA
1 AGAGAAAAGAGAAGAGGAAAATAGGAGGAAA
* *
107604 AGAGAAAAGAAGAAGAAGAAAGTAGGAGGAAA
1 AGAGAAAAG-AGAAGAGGAAAATAGGAGGAAA
* *
107636 A-AGAGAAGAGACGAGG
1 AGAGAAAAGAGAAGAGG
107652 GCGAGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 6 0.14
31 15 0.36
32 21 0.50
ACGTcount: A:0.59, C:0.01, G:0.37, T:0.03
Consensus pattern (31 bp):
AGAGAAAAGAGAAGAGGAAAATAGGAGGAAA
Found at i:123000 original size:21 final size:19
Alignment explanation
Indices: 122974--123028 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 19
122964 AACAATTTTT
122974 TTATTTTTCAATTTAGTCCC
1 TTATTTTTCAATTTA-TCCC
*
122994 TTAATTTTTC-ATTT-TTCC
1 TT-ATTTTTCAATTTATCCC
123012 TTATTTCTTCAATTTAT
1 TTATTT-TTCAATTTAT
123029 TTATTTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 4 0.13
18 8 0.27
19 4 0.13
20 7 0.23
21 7 0.23
ACGTcount: A:0.20, C:0.16, G:0.02, T:0.62
Consensus pattern (19 bp):
TTATTTTTCAATTTATCCC
Found at i:123018 original size:156 final size:151
Alignment explanation
Indices: 122754--123075 Score: 429
Period size: 156 Copynumber: 2.1 Consensus size: 151
122744 TTAAAACCAA
* * *
122754 ATGCTCATAAACCATATTAGAATGTATATGTTATTTCAATTCCTCTTTTTTTTATAACGATTTTT
1 ATGCTCATAAACCATATTAGAATATATATGTTATTTCAATTACTC-TTTTTTTATAACAATTTTT
*
122819 TATTTTTCAATTTAATCCCTTAATTTTTATATTTTCCTTATTTCTTCAATTCATCCTT-TTTTGA
65 TATTTTTCAATTTAATCCCTTAATTTTTATATTTTCCTTATTTCTTCAATTCAT--TTATTTTAA
*
122883 GTCCGTCTTTTACTAAATTTGAATCAC
128 GT--GTCTTTTACCAAA-TTGAATCAC
*
122910 ATGCTCATAAATCATCA-TAGAGATATATATG-TACTTTCAATTACTC-TTTTTTATAACAATTT
1 ATGCTCATAAACCAT-ATTAGA-ATATATATGTTA-TTTCAATTACTCTTTTTTTATAACAA-TT
* *
122972 TTTTATTTTTCAATTTAGTCCCTTAATTTTTCAT-TTTTCCTTATTTCTTCAATTTATTTATTTT
62 TTTTATTTTTCAATTTAATCCCTTAATTTTT-ATATTTTCCTTATTTCTTCAATTCATTTATTTT
123036 AAGTGTCTTTTACCAAATTGAATCAC
126 AAGTGTCTTTTACCAAATTGAATCAC
*
123062 ATGCTCATATACCA
1 ATGCTCATAAACCA
123076 CAATAAAATA
Statistics
Matches: 150, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
152 21 0.14
153 12 0.08
154 2 0.01
155 19 0.13
156 74 0.49
157 22 0.15
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (151 bp):
ATGCTCATAAACCATATTAGAATATATATGTTATTTCAATTACTCTTTTTTTATAACAATTTTTT
ATTTTTCAATTTAATCCCTTAATTTTTATATTTTCCTTATTTCTTCAATTCATTTATTTTAAGTG
TCTTTTACCAAATTGAATCAC
Found at i:123144 original size:152 final size:153
Alignment explanation
Indices: 122754--123152 Score: 387
Period size: 156 Copynumber: 2.6 Consensus size: 153
122744 TTAAAACCAA
* * *
122754 ATGCTCATAAACCAT-ATTAG-AATGTATATGTTA-TTTCAATTCCTCTTTTTTTTATAACGATT
1 ATGCTCATAAACCATCA-TAGAAATATATATG-TACTTTCAATTACTC--TTTTTTATAACAATT
* * *
122816 -TTTTATTTTTCAATTTAATCCCTTAATTTTTATATTTTCCTTATTTCTTCAATTCATCCTTTTT
62 ACTCTATTTTT-AATTTAGTCCCTTAATTTTTATATTTTCCTTATTTCTTCAATTCAT-CTTTTT
* *
122880 TGAGTCCGTCTTTTACTAAATTTGAATCAC
125 TAAGT-CGTCTTTTACCAAATTTGAATCAC
* * ** *
122910 ATGCTCATAAATCATCATAGAGATATATATGTACTTTCAATTACTCTTTTTTATAACAATTTTTT
1 ATGCTCATAAACCATCATAGAAATATATATGTACTTTCAATTACTCTTTTTTATAACAATTACTC
*
122975 TATTTTTCAATTTAGTCCCTTAATTTTTCAT-TTTTCCTTATTTCTTCAATTTAT-TTATTTTAA
66 TATTTTT-AATTTAGTCCCTTAATTTTT-ATATTTTCCTTATTTCTTCAATTCATCTT-TTTTAA
123038 GT-GTCTTTTACCAAA-TTGAATCAC
128 GTCGTCTTTTACCAAATTTGAATCAC
*
123062 ATGCTCATATACCA-CAATA-AAATACTATAT-TACTTT-AATT-CTTACTTTTTTACTAA-AAT
1 ATGCTCATAAACCATC-ATAGAAATA-TATATGTACTTTCAATTAC-T-CTTTTTTA-TAACAAT
*
123121 GGTACTCTACTTTTT-ATTTAGTCCTTTAATTT
61 --TACTCTA-TTTTTAATTTAGTCCCTTAATTT
123153 AGATTTACTC
Statistics
Matches: 213, Mismatches: 16, Indels: 32
0.82 0.06 0.12
Matches are distributed among these distances:
149 1 0.00
150 5 0.02
151 22 0.10
152 48 0.23
153 16 0.08
154 7 0.03
155 21 0.10
156 71 0.33
157 22 0.10
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (153 bp):
ATGCTCATAAACCATCATAGAAATATATATGTACTTTCAATTACTCTTTTTTATAACAATTACTC
TATTTTTAATTTAGTCCCTTAATTTTTATATTTTCCTTATTTCTTCAATTCATCTTTTTTAAGTC
GTCTTTTACCAAATTTGAATCAC
Found at i:123806 original size:2 final size:2
Alignment explanation
Indices: 123799--123825 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
123789 TTATAATGTG
123799 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 A
123826 ATTAGAGAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.