Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006289.1 Hibiscus syriacus cultivar Beakdansim tig00015010_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: 86763
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:5929 original size:22 final size:22
Alignment explanation
Indices: 5876--5957 Score: 86
Period size: 20 Copynumber: 4.0 Consensus size: 22
5866 AGTCGAGGGT
*
5876 TATACAGTGGTCATTCGGGAC-
1 TATACAGTGGTCCTTCGGGACA
* *
5897 -ATA-A-TGGTCCTTTGGGATA
1 TATACAGTGGTCCTTCGGGACA
5916 TATACAGTGGTCCTTCGGGACA
1 TATACAGTGGTCCTTCGGGACA
*
5938 TATACA--GGTCATTCGGGACA
1 TATACAGTGGTCCTTCGGGACA
5958 AATATTCAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
18 11 0.22
19 1 0.02
20 19 0.37
21 1 0.02
22 19 0.37
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (22 bp):
TATACAGTGGTCCTTCGGGACA
Found at i:5952 original size:20 final size:20
Alignment explanation
Indices: 5884--5957 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 20
5874 GTTATACAGT
*
5884 GGTCATTCGGGACATA-A-T
1 GGTCATTCGGGACATATACA
* * *
5902 GGTCCTTTGGGATATATACA
1 GGTCATTCGGGACATATACA
*
5922 GTGGTCCTTCGGGACATATACA
1 --GGTCATTCGGGACATATACA
5944 GGTCATTCGGGACA
1 GGTCATTCGGGACA
5958 AATATTCAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
18 13 0.29
19 1 0.02
20 13 0.29
22 18 0.40
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
GGTCATTCGGGACATATACA
Found at i:11266 original size:16 final size:16
Alignment explanation
Indices: 11245--11277 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11235 TAATAAATAA
*
11245 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
11261 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
11277 A
1 A
11278 ATTTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.24, G:0.09, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:11377 original size:16 final size:16
Alignment explanation
Indices: 11352--11410 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
11342 ATAAACGAAT
*
11352 ATAAATGAACACAAAC
1 ATAAACGAACACAAAC
*
11368 ATAAACGAACACAAAT
1 ATAAACGAACACAAAC
* *
11384 ATAAATGAACACGAAC
1 ATAAACGAACACAAAC
11400 ATAAACGAACA
1 ATAAACGAACA
11411 TAAAACGTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.61, C:0.19, G:0.08, T:0.12
Consensus pattern (16 bp):
ATAAACGAACACAAAC
Found at i:11385 original size:32 final size:32
Alignment explanation
Indices: 11349--11410 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
11339 TAAATAAACG
11349 AATATAAATGAACACAAACATAAACGAACACA
1 AATATAAATGAACACAAACATAAACGAACACA
*
11381 AATATAAATGAACACGAACATAAACGAACA
1 AATATAAATGAACACAAACATAAACGAACA
11411 TAAAACGTTG
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:0.61, C:0.18, G:0.08, T:0.13
Consensus pattern (32 bp):
AATATAAATGAACACAAACATAAACGAACACA
Found at i:12533 original size:14 final size:14
Alignment explanation
Indices: 12516--12569 Score: 80
Period size: 14 Copynumber: 4.1 Consensus size: 14
12506 TGAACATAAG
12516 CGAACATAACCGAA
1 CGAACATAACCGAA
12530 CGAACAT-A---AA
1 CGAACATAACCGAA
12540 CGAACATAACCGAA
1 CGAACATAACCGAA
12554 CGAACATAACCGAA
1 CGAACATAACCGAA
12568 CG
1 CG
12570 TTCACGAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 25 0.69
ACGTcount: A:0.50, C:0.28, G:0.15, T:0.07
Consensus pattern (14 bp):
CGAACATAACCGAA
Found at i:12534 original size:24 final size:24
Alignment explanation
Indices: 12507--12568 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
12497 ATAAATGAAT
*
12507 GAACATAAGCGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
12531 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
12555 GAACATAACCGAAC
1 GAACATAAACGAAC
12569 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.52, C:0.26, G:0.15, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:12577 original size:24 final size:25
Alignment explanation
Indices: 12507--12594 Score: 103
Period size: 24 Copynumber: 3.6 Consensus size: 25
12497 ATAAATGAAT
*
12507 GAACATAAGCGAAC-ATAACCGAAC
1 GAACATAAACGAACGATAACCGAAC
12531 GAACATAAACGAAC-ATAACCGAAC
1 GAACATAAACGAACGATAACCGAAC
* * *
12555 GAACATAACCGAACGTTCA-CGAAC
1 GAACATAAACGAACGATAACCGAAC
12579 GTAA-ATAAACGAACGA
1 G-AACATAAACGAACGA
12595 GACCTATGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
24 52 0.93
25 4 0.07
ACGTcount: A:0.50, C:0.24, G:0.16, T:0.10
Consensus pattern (25 bp):
GAACATAAACGAACGATAACCGAAC
Found at i:12592 original size:38 final size:38
Alignment explanation
Indices: 12516--12594 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
12506 TGAACATAAG
* *
12516 CGAACATAACCGAACGAACATAAACGAACATAACCGAA
1 CGAACATAACCGAACGAACACAAACGAACATAAACGAA
** *
12554 CGAACATAACCGAACGTTCACGAACGTAA-ATAAACGAA
1 CGAACATAACCGAACGAACACAAACG-AACATAAACGAA
12592 CGA
1 CGA
12595 GACCTATGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 33 0.94
39 2 0.06
ACGTcount: A:0.49, C:0.25, G:0.15, T:0.10
Consensus pattern (38 bp):
CGAACATAACCGAACGAACACAAACGAACATAAACGAA
Found at i:15114 original size:12 final size:12
Alignment explanation
Indices: 15094--15143 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
15084 AAAATTTGAT
*
15094 TTCATGGTACTG
1 TTCACGGTACTG
*
15106 TTCACGGTAATG
1 TTCACGGTACTG
*
15118 TTCA--TTACTG
1 TTCACGGTACTG
15128 TTCACGGTACTG
1 TTCACGGTACTG
15140 TTCA
1 TTCA
15144 TACCGTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 8 0.26
12 23 0.74
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (12 bp):
TTCACGGTACTG
Found at i:15127 original size:22 final size:22
Alignment explanation
Indices: 15101--15144 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15091 GATTTCATGG
15101 TACTGTTCACGGTAATGTTCAT
1 TACTGTTCACGGTAATGTTCAT
*
15123 TACTGTTCACGGTACTGTTCAT
1 TACTGTTCACGGTAATGTTCAT
15145 ACCGTATTTT
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:0.20, C:0.20, G:0.18, T:0.41
Consensus pattern (22 bp):
TACTGTTCACGGTAATGTTCAT
Found at i:15969 original size:15 final size:15
Alignment explanation
Indices: 15949--16014 Score: 105
Period size: 15 Copynumber: 4.4 Consensus size: 15
15939 TTCCAGAAAA
15949 TGAATTACTGGAATT
1 TGAATTACTGGAATT
15964 TGAATTACTGGAATT
1 TGAATTACTGGAATT
* **
15979 TGAATTACTGAAAAA
1 TGAATTACTGGAATT
15994 TGAATTACTGGAATT
1 TGAATTACTGGAATT
16009 TGAATT
1 TGAATT
16015 TTGGAAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:15983 original size:30 final size:30
Alignment explanation
Indices: 15949--16030 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 30
15939 TTCCAGAAAA
* **
15949 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGAAAAATGAATTACTGGAATT
15979 TGAATTACTGAAAAATGAATTACTGGAATT
1 TGAATTACTGAAAAATGAATTACTGGAATT
* *
16009 TGAATT-TTGGAAAATGAATTAC
1 TGAATTACTGAAAAATGAATTAC
16031 ATTTCTGTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 14 0.30
30 33 0.70
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (30 bp):
TGAATTACTGAAAAATGAATTACTGGAATT
Found at i:16026 original size:14 final size:15
Alignment explanation
Indices: 15944--16030 Score: 95
Period size: 15 Copynumber: 5.9 Consensus size: 15
15934 TGGTTTTCCA
15944 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
15959 GAATTTGAATTACTG
1 GAAAATGAATTACTG
**
15974 GAATTTGAATTACTG
1 GAAAATGAATTACTG
*
15989 AAAAATGAATTACTG
1 GAAAATGAATTACTG
** *
16004 GAATTTGAATT-TTG
1 GAAAATGAATTACTG
16018 GAAAATGAATTAC
1 GAAAATGAATTAC
16031 ATTTCTGTAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.19
15 48 0.81
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.34
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:16042 original size:20 final size:20
Alignment explanation
Indices: 16012--16082 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
16002 TGGAATTTGA
16012 ATTT-TGGAAAATGAATTAC
1 ATTTCTGGAAAATGAATTAC
*
16031 ATTTCTGTAAAATGAATTAC
1 ATTTCTGGAAAATGAATTAC
16051 ATTTCTGGAAAATGAATTAC
1 ATTTCTGGAAAATGAATTAC
16071 ATTTCTGGAAAA
1 ATTTCTGGAAAA
16083 CATATGGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 4 0.08
20 45 0.92
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (20 bp):
ATTTCTGGAAAATGAATTAC
Found at i:16312 original size:30 final size:27
Alignment explanation
Indices: 16248--16404 Score: 99
Period size: 30 Copynumber: 5.6 Consensus size: 27
16238 CTTTACTAAA
16248 ATATTATTGAAATATATAAATATATTAT
1 ATATTATT-AAATATATAAATATATTAT
*
16276 -TCATTATTAAATATATAAAAAATTTATTAT
1 AT-ATTATTAAATATAT---AAATATATTAT
16306 ATATTATTAAA-ATA-AAATATA-TAT
1 ATATTATTAAATATATAAATATATTAT
* * * *
16330 CTTATTATTATAATATAATTGATTATTTTAT
1 -ATATTATTA-AATAT-A-TAAATATATTAT
* * *
16361 ATAATATTAAAAATATATAT-TATTAT
1 ATATTATTAAATATATAAATATATTAT
*
16387 AAATATTAATAAATATAT
1 --ATATTATTAAATATAT
16405 TTTAAATATT
Statistics
Matches: 99, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
24 3 0.03
25 14 0.14
26 7 0.07
27 13 0.13
28 21 0.21
29 7 0.07
30 30 0.30
31 4 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
ATATTATTAAATATATAAATATATTAT
Found at i:16379 original size:16 final size:16
Alignment explanation
Indices: 16358--16397 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
16348 TTGATTATTT
16358 TATATAATATTAAAAA
1 TATATAATATTAAAAA
* *
16374 TATATATTATTATAAA
1 TATATAATATTAAAAA
16390 TAT-TAATA
1 TATATAATA
16398 AATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATATAATATTAAAAA
Found at i:16391 original size:25 final size:25
Alignment explanation
Indices: 16248--16404 Score: 85
Period size: 25 Copynumber: 6.1 Consensus size: 25
16238 CTTTACTAAA
* *
16248 ATATTATT-GAAATA-TATAAATAT
1 ATATTATTATAAATATTAAAAATAT
*
16271 ATTATTCATTATTAAATATATAAAAAATTT
1 A-TATT-ATTA-TAAATAT-T-AAAAATAT
16301 ATTATATATTATTAAA-A-TAAAATATAT
1 A-TAT-TATTA-TAAATATTAAAA-ATAT
* * * * *
16328 ATCTTATTAT-TATAATATAATTGAT
1 ATATTATTATAAATATTAAAAAT-AT
16353 -TATT-TTATATAATATTAAAAATAT
1 ATATTATTATA-AATATTAAAAATAT
16377 ATATTATTATAAATATTAATAAATAT
1 ATATTATTATAAATATTAA-AAATAT
16403 AT
1 AT
16405 TTTAAATATT
Statistics
Matches: 104, Mismatches: 13, Indels: 31
0.70 0.09 0.21
Matches are distributed among these distances:
23 6 0.06
24 12 0.12
25 34 0.33
26 19 0.18
27 10 0.10
29 2 0.02
30 20 0.19
31 1 0.01
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (25 bp):
ATATTATTATAAATATTAAAAATAT
Found at i:16410 original size:21 final size:22
Alignment explanation
Indices: 16372--16414 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
16362 TAATATTAAA
*
16372 AATATATATTATTATAAATATT
1 AATAAATATTATTATAAATATT
*
16394 AATAAATA-TATTTTAAATATT
1 AATAAATATTATTATAAATATT
16415 TTAATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAAATATTATTATAAATATT
Found at i:16660 original size:42 final size:42
Alignment explanation
Indices: 16601--16720 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
16591 ATGAATTACA
*
16601 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
16643 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
16685 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
16721 TTCGGGGAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:33704 original size:24 final size:25
Alignment explanation
Indices: 33652--33705 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
33642 ATAATATATT
* * *
33652 TTTATAGTTTTAGATGTAAATATAC
1 TTTATAATCTTAGATGTAAATATAA
*
33677 TTTATAATCTTAGATG-ATATATAA
1 TTTATAATCTTAGATGTAAATATAA
33701 TTTAT
1 TTTAT
33706 TAAATAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (25 bp):
TTTATAATCTTAGATGTAAATATAA
Found at i:34492 original size:20 final size:21
Alignment explanation
Indices: 34467--34518 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
34457 TTTTCCCAAT
*
34467 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
34487 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
34508 TCGCAATGCGA
1 TCGCAATGCGA
34519 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:34532 original size:20 final size:20
Alignment explanation
Indices: 34507--34560 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
34497 AATTGGGAAA
34507 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
34527 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
*
34547 ATCGCAATACGATA
1 ATCGCAATGCGATA
34561 ATACAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:34605 original size:20 final size:20
Alignment explanation
Indices: 34582--34621 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
34572 CAACAAGATA
*
34582 CTGACTTTCTCAACGCGATT
1 CTGACTTTCGCAACGCGATT
34602 CTGACTTTCGCAACGCGATT
1 CTGACTTTCGCAACGCGATT
34622 TACATAGCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (20 bp):
CTGACTTTCGCAACGCGATT
Found at i:35211 original size:19 final size:19
Alignment explanation
Indices: 35175--35216 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
35165 ACGAGAGAAT
*
35175 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
* *
35194 CGCAACGCGAAACCAAAAT
1 CGCAACGCGAAACAAAAAA
35213 CGCA
1 CGCA
35217 TTACGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.29, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:35234 original size:19 final size:19
Alignment explanation
Indices: 35220--35395 Score: 138
Period size: 19 Copynumber: 9.7 Consensus size: 19
35210 AATCGCATTA
35220 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
*
35239 CAATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
* *
35258 CGATTTTTATTTTGCGTTG
1 CGATTTTCATTTCGCGTTG
35277 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
* *
35296 CGA--TTC---TCTCGTCG
1 CGATTTTCATTTCGCGTTG
** *
35310 CGATAGTCATTTCACGTTG
1 CGATTTTCATTTCGCGTTG
*
35329 CGA--TTC---TCTCGTTG
1 CGATTTTCATTTCGCGTTG
**
35343 CGATAGTCATTTCCGCGTTG
1 CGATTTTCATTT-CGCGTTG
* * *
35363 TGATTCTCATTATCTCGTTG
1 CGATTTTCATT-TCGCGTTG
35383 CGATTTTCATTTC
1 CGATTTTCATTTC
35396 AACCAAAAGA
Statistics
Matches: 124, Mismatches: 21, Indels: 24
0.73 0.12 0.14
Matches are distributed among these distances:
14 19 0.15
16 4 0.03
17 5 0.04
19 66 0.53
20 29 0.23
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTG
Found at i:35320 original size:33 final size:33
Alignment explanation
Indices: 35283--35370 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
35273 GTTGCGATTT
35283 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
35316 TCATTTCACGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
35349 TCATTTCCGCGTTGTGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
35371 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 37 0.74
34 13 0.26
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:35372 original size:20 final size:20
Alignment explanation
Indices: 35338--35395 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
35328 GCGATTCTCT
**
35338 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
* *
35358 CGTTGTGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
35378 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
35396 AACCAAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:37201 original size:30 final size:30
Alignment explanation
Indices: 37135--37223 Score: 126
Period size: 30 Copynumber: 3.0 Consensus size: 30
37125 CCCGAAGGAC
* * *
37135 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
37164 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
37194 TTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
37224 ACTGTCCATA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 18 0.33
30 36 0.67
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:37280 original size:31 final size:31
Alignment explanation
Indices: 37219--37286 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
37209 AAAGATCCTC
**
37219 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCAAAGAACATA
* *
37250 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCAAAGAACATA
37281 GGTAAA
1 GGTAAA
37287 ACCCTCGACT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCAAAGAACATA
Found at i:38035 original size:21 final size:21
Alignment explanation
Indices: 38011--38055 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
38001 CTATGTTCGT
* * *
38011 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
38032 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
38053 TTG
1 TTG
38056 CCCAGAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:41342 original size:30 final size:30
Alignment explanation
Indices: 41283--41371 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
41273 CCCGAAGGAC
* * *
41283 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
41312 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
41342 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
41372 ATTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:42179 original size:21 final size:21
Alignment explanation
Indices: 42155--42199 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42145 CTATGTTCGT
* * *
42155 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
42176 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
42197 TTG
1 TTG
42200 CCCAGAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:42836 original size:29 final size:29
Alignment explanation
Indices: 42794--42852 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
42784 TTAGGAAATA
42794 TTTCCGAACAAATCATTAAACTATTAAAC
1 TTTCCGAACAAATCATTAAACTATTAAAC
42823 TTTCCGAACAAATCATTAAACTATTAAAC
1 TTTCCGAACAAATCATTAAACTATTAAAC
42852 T
1 T
42853 ATTATACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.32
Consensus pattern (29 bp):
TTTCCGAACAAATCATTAAACTATTAAAC
Found at i:45502 original size:30 final size:30
Alignment explanation
Indices: 45443--45531 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
45433 CCCGAAGGAC
* * *
45443 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
45472 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
45502 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
45532 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:49594 original size:14 final size:14
Alignment explanation
Indices: 49575--49610 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
49565 ATTGTTTAAT
49575 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
49589 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
49603 TGATTTGT
1 TGATTTGT
49611 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:49755 original size:14 final size:14
Alignment explanation
Indices: 49736--49792 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
49726 GTGAAATGAA
49736 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
49750 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
49769 AATCGCAATGAGAG
1 AATCGCAACGAGAG
49783 AATCGCAACG
1 AATCGCAACG
49793 CGAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:49765 original size:33 final size:33
Alignment explanation
Indices: 49718--49807 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
49708 AAAAAGTACT
* *
49718 ATCGCAATGTGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
49751 ATCGCAACGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
49784 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
49808 GTTGCGATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:49774 original size:19 final size:18
Alignment explanation
Indices: 49718--49776 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
49708 AAAAAGTACT
*
49718 ATCGCAATGTGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
49737 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
49751 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
49770 ATCGCAA
1 ATCGCAA
49777 TGAGAGAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 17 0.53
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:49853 original size:20 final size:19
Alignment explanation
Indices: 49803--49856 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
49793 CGAAATTAAA
** *
49803 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATAGTAAT
*
49822 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATAGTAAT
49841 TTCCGCGTTGCGATAG
1 TT-CGCGTTGCGATAG
49857 ACATTAAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (19 bp):
TTCGCGTTGCGATAGTAAT
Found at i:52142 original size:12 final size:12
Alignment explanation
Indices: 52125--52149 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52115 TCTTCGGGGA
52125 CTTTTTCTTCTT
1 CTTTTTCTTCTT
52137 CTTTTTCTTCTT
1 CTTTTTCTTCTT
52149 C
1 C
52150 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:53147 original size:20 final size:20
Alignment explanation
Indices: 53122--53172 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
53112 TGTATTATCT
53122 CGTTGCGAAAGTCAGAATCA
1 CGTTGCGAAAGTCAGAATCA
*
53142 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCA
53162 CGTTGCGAAAG
1 CGTTGCGAAAG
53173 GCAATCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCA
Found at i:53442 original size:20 final size:20
Alignment explanation
Indices: 53385--53435 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
53375 ATTCATTTGA
53385 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
53405 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
53425 CTATCGCAACG
1 CTATCGCAACG
53436 ACAAAATCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:53502 original size:19 final size:19
Alignment explanation
Indices: 53461--53544 Score: 133
Period size: 19 Copynumber: 4.7 Consensus size: 19
53451 GAAATGAAAA
53461 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
53477 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
53494 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
53513 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
53532 TCGCATTGCGATT
1 TCGCATTGCGATT
53545 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 46 0.73
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:53531 original size:38 final size:33
Alignment explanation
Indices: 53461--53557 Score: 140
Period size: 38 Copynumber: 2.8 Consensus size: 33
53451 GAAATGAAAA
53461 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
53494 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
*
53532 TCGCATTGCGATTCTCTCGTTGCGAT
1 TCGCATTGCGATTTTCTCGTTGCGAT
53558 AGTCAGTTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
33 23 0.40
35 3 0.05
36 3 0.05
38 29 0.50
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:53575 original size:20 final size:20
Alignment explanation
Indices: 53550--53588 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53540 CGATTCTCTC
53550 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
53570 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
53589 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:53690 original size:14 final size:14
Alignment explanation
Indices: 53671--53707 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
53661 CATCAATTAA
53671 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
53685 ACAAATCATCTTTT
1 ACAAATCAACATTT
53699 ACAAATCAA
1 ACAAATCAA
53708 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:55600 original size:20 final size:20
Alignment explanation
Indices: 55577--55644 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
55567 GAAACTTAAA
55577 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
55597 ATCGCAACGC-AGAAATGGCT
1 ATCGCAACGCGA-AAATGACT
* **
55617 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
55636 ATCGCAACG
1 ATCGCAACG
55645 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:55652 original size:14 final size:14
Alignment explanation
Indices: 55633--55690 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
55623 ATGCGAAATG
55633 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
55647 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
55663 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
55679 AAAATCGCAACG
1 AAAATCGCAACG
55691 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:55675 original size:32 final size:33
Alignment explanation
Indices: 55617--55695 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
55607 AGAAATGGCT
55617 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
55650 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
55682 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
55696 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:55744 original size:14 final size:14
Alignment explanation
Indices: 55725--55781 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
55715 TTCATTTCGT
55725 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
*
55739 GTTGCGATTTCATTTC
1 GTTGCGATTT--TGTC
55755 GCATTGCGATTTTGTC
1 G--TTGCGATTTTGTC
55771 GTTGCGATTTT
1 GTTGCGATTTT
55782 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.49
Consensus pattern (14 bp):
GTTGCGATTTTGTC
Found at i:55788 original size:33 final size:33
Alignment explanation
Indices: 55707--55797 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
55697 ACAAATCGCA
**
55707 TTGCGATTTTCATTTCGTGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
55740 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
55772 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
55798 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:55816 original size:20 final size:19
Alignment explanation
Indices: 55782--55836 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
55772 TTGCGATTTT
*
55782 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
55801 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
55821 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
55837 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:56346 original size:18 final size:18
Alignment explanation
Indices: 56320--56364 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
56310 GTCGATCAGA
*
56320 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
56338 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
56356 TGATGGCTC
1 TGATGGCTC
56365 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:57732 original size:20 final size:20
Alignment explanation
Indices: 57684--57742 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
57674 AATAGTTTCT
** *
57684 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
57704 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
57724 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
57743 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:58296 original size:61 final size:61
Alignment explanation
Indices: 58216--58353 Score: 213
Period size: 61 Copynumber: 2.3 Consensus size: 61
58206 CGCTTTGAAA
* *
58216 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
* * * * *
58277 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
58338 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
58354 CCCAATTCGC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGT
Found at i:58322 original size:20 final size:20
Alignment explanation
Indices: 58216--58350 Score: 139
Period size: 20 Copynumber: 6.7 Consensus size: 20
58206 CGCTTTGAAA
*
58216 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
58237 ATCGCATTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
58257 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
58277 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
58298 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
58318 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
58338 ATCGCATTGCGAT
1 ATCGCATTGCGAT
58351 TTTCCCAATT
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.68
21 24 0.25
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:58369 original size:61 final size:61
Alignment explanation
Indices: 58216--58371 Score: 170
Period size: 61 Copynumber: 2.6 Consensus size: 61
58206 CGCTTTGAAA
* ** * * *
58216 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTCAGAATCGCATTGCGAAAGTCAGT
* * ** * * *
58277 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTCAGAATCGCATTGCGAAAGTCAGT
*
58338 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCATTGCGAT
58372 TTACTTATTC
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
61 79 0.98
62 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCATTGCGATAGTCAGAATCGCATTGCGAAAGTCAGT
Found at i:58461 original size:21 final size:21
Alignment explanation
Indices: 58421--58461 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58411 ACTGTAGACC
**
58421 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
58442 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
58462 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:58491 original size:20 final size:20
Alignment explanation
Indices: 58468--58513 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
58458 CAACGCGAAT
*
58468 TTGCGATAATGGAGATCGCG
1 TTGCGATAATAGAGATCGCG
* *
58488 TTGCGA-ATTAGCGATCGCG
1 TTGCGATAATAGAGATCGCG
58507 TTGCGAT
1 TTGCGAT
58514 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (20 bp):
TTGCGATAATAGAGATCGCG
Found at i:63595 original size:59 final size:57
Alignment explanation
Indices: 63528--63642 Score: 151
Period size: 57 Copynumber: 2.0 Consensus size: 57
63518 TTGATTTTGT
* * * *
63528 TACTATGAGTATATGTGTTCAATGTGA-ATAAATGATCATTTGAATAATGCTATGTGAAA
1 TACTATGAGTATA--TGCTCAATGTGAGA-AAATAATAAGTTGAATAATGCTATGTGAAA
*
63587 TACTATGAGTATATGCTCTATGTGAGAAAATAATAAGTTGAATAATGCTATGTGAA
1 TACTATGAGTATATGCTCAATGTGAGAAAATAATAAGTTGAATAATGCTATGTGAA
63643 TAATTATATG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 36 0.72
58 1 0.02
59 13 0.26
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (57 bp):
TACTATGAGTATATGCTCAATGTGAGAAAATAATAAGTTGAATAATGCTATGTGAAA
Found at i:63748 original size:23 final size:24
Alignment explanation
Indices: 63717--63802 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 24
63707 AGTCGATGGT
* *
63717 TCTACGTGGTC-CTTCAGGACAAT
1 TCTATGTGGTCACTTCAGGACAAA
* *
63740 TCTATGTGGT-GCTTCGGGACAAA
1 TCTATGTGGTCACTTCAGGACAAA
* *
63763 TCTATGT-GACACTTCGGGACAAA
1 TCTATGTGGTCACTTCAGGACAAA
63786 TCTATGTGG-CACTTCAG
1 TCTATGTGGTCACTTCAG
63803 TGCATATTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.02
23 52 0.96
24 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (24 bp):
TCTATGTGGTCACTTCAGGACAAA
Found at i:63818 original size:24 final size:24
Alignment explanation
Indices: 63782--63838 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
63772 CACTTCGGGA
*
63782 CAAA-TCTATGTGGCACTTCAGTG
1 CAAATTCTACGTGGCACTTCAGTG
* *
63805 CATATTCTACGTGGCACTTCGGTG
1 CAAATTCTACGTGGCACTTCAGTG
63829 CAAATTCTAC
1 CAAATTCTAC
63839 ACGTCAGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (24 bp):
CAAATTCTACGTGGCACTTCAGTG
Found at i:63961 original size:2 final size:2
Alignment explanation
Indices: 63954--63987 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
63944 TCAGTGAATA
63954 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
63988 TGAAATGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67625 original size:5 final size:5
Alignment explanation
Indices: 67610--67643 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
67600 GTCCGTCCGT
* *
67610 CTCGT CTCGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
67644 TAACTTAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.03, C:0.41, G:0.35, T:0.21
Consensus pattern (5 bp):
CTCGG
Found at i:68033 original size:2 final size:2
Alignment explanation
Indices: 68026--68056 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68016 TACTTCATAG
68026 TA TA 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 TA TA T
68057 TAGATTCGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:77136 original size:17 final size:17
Alignment explanation
Indices: 77114--77152 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
77104 AGACAAGAGC
77114 AATATCAAAGACTGAGT
1 AATATCAAAGACTGAGT
77131 AATATCAAAGACTGAGT
1 AATATCAAAGACTGAGT
77148 AATAT
1 AATAT
77153 AGTGGACTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (17 bp):
AATATCAAAGACTGAGT
Found at i:81962 original size:29 final size:29
Alignment explanation
Indices: 81917--81974 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
81907 GTGTTGGTCG
* *
81917 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGAACTAC
*
81946 TAGGTCGCCATGTCTTCCCGGCGAACTAC
1 TAGGTCGCCATGCCTTCCCGGCGAACTAC
81975 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGAACTAC
Found at i:82038 original size:14 final size:14
Alignment explanation
Indices: 82019--82101 Score: 65
Period size: 14 Copynumber: 6.2 Consensus size: 14
82009 CTGGGTATCT
82019 GAGGCCATCCGACC
1 GAGGCCATCCGACC
82033 GAGGCCATCCGA--
1 GAGGCCATCCGACC
82045 GA-G-CATCCGA--
1 GAGGCCATCCGACC
82055 GA--CCATCCGAGCATCC
1 GAGGCCATCC--G-A-CC
82071 GAGGCCATCCGACC
1 GAGGCCATCCGACC
*
82085 GAGGCCATCCGAAC
1 GAGGCCATCCGACC
82099 GAG
1 GAG
82102 CTATGCGAGG
Statistics
Matches: 59, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
10 14 0.24
11 1 0.02
12 3 0.05
13 1 0.02
14 30 0.51
15 1 0.02
16 3 0.05
18 6 0.10
ACGTcount: A:0.25, C:0.37, G:0.29, T:0.08
Consensus pattern (14 bp):
GAGGCCATCCGACC
Found at i:82068 original size:18 final size:18
Alignment explanation
Indices: 82031--82082 Score: 77
Period size: 18 Copynumber: 2.8 Consensus size: 18
82021 GGCCATCCGA
82031 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCC--GAGCAT
*
82051 CCGAGACCATCCGAGCAT
1 CCGAGGCCATCCGAGCAT
82069 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
82083 CCGAGGCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 19 0.63
20 11 0.37
ACGTcount: A:0.25, C:0.38, G:0.27, T:0.10
Consensus pattern (18 bp):
CCGAGGCCATCCGAGCAT
Found at i:82096 original size:10 final size:10
Alignment explanation
Indices: 82031--82082 Score: 65
Period size: 10 Copynumber: 5.4 Consensus size: 10
82021 GGCCATCCGA
82031 CCGAGGCCAT
1 CCGAGGCCAT
82041 CCGAGAG-CAT
1 CCGAG-GCCAT
*
82051 CCGAGACCAT
1 CCGAGGCCAT
82061 CCGA-G-CAT
1 CCGAGGCCAT
82069 CCGAGGCCAT
1 CCGAGGCCAT
82079 CCGA
1 CCGA
82083 CCGAGGCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 27 0.75
11 1 0.03
ACGTcount: A:0.25, C:0.38, G:0.27, T:0.10
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:82135 original size:33 final size:33
Alignment explanation
Indices: 82083--82167 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
82073 GGCCATCCGA
* * *
82083 CCGAGGCCATCCGAACGAGCTATGCGA-GGACAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGA-AT
82116 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
82149 CCGAGGG-AAGCCGAGCGAG
1 CCGAGGGCAA-CCGAGCGAG
82168 GATAGGTTGC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
32 2 0.04
33 42 0.89
34 3 0.06
ACGTcount: A:0.27, C:0.27, G:0.38, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:82208 original size:29 final size:29
Alignment explanation
Indices: 82171--82226 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
82161 GAGCGAGGAT
* *
82171 AGGTTGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
82200 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
82227 TGTGTCGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.38, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:83654 original size:29 final size:30
Alignment explanation
Indices: 83599--83663 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
83589 TAATATTTTG
* *
83599 TTTATAATATTATTATGTTATATTTTTTATA
1 TTTATAATATTATTA-GTAATATTTTTAATA
83630 TTTATAATATTAATTA-TAAT-TTTTTAATA
1 TTTATAATATT-ATTAGTAATATTTTTAATA
83659 TTTAT
1 TTTAT
83664 CAAATGAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 13 0.42
30 3 0.10
31 11 0.35
32 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTATAATATTATTAGTAATATTTTTAATA
Done.