Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005017.1 Hibiscus syriacus cultivar Beakdansim tig00011261_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: 139654
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3650 original size:24 final size:21
Alignment explanation
Indices: 3616--3659 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
3606 TCAACAAGAC
*
3616 ATGTCCTTTGACATTTCAAAAT
1 ATGTCCTTTGA-AATTCAAAAT
3638 ATGTACCTCTTGAAATTCAAAA
1 ATGT-CCT-TTGAAATTCAAAA
3660 GAATGTGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAAT
Found at i:13403 original size:20 final size:21
Alignment explanation
Indices: 13378--13418 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13368 GTAGGAGTTC
13378 TTTCTT-TTGTTTTTGATTTT
1 TTTCTTCTTGTTTTTGATTTT
* *
13398 TTTCTTCTTTTTTTTTATTTT
1 TTTCTTCTTGTTTTTGATTTT
13419 GTTGCAGCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.83
Consensus pattern (21 bp):
TTTCTTCTTGTTTTTGATTTT
Found at i:14584 original size:192 final size:192
Alignment explanation
Indices: 14257--14643 Score: 720
Period size: 192 Copynumber: 2.0 Consensus size: 192
14247 GAGCATGACC
*
14257 ATTCGGTTGGGATTGAAGATGCATCCCCCTTGGCTGAATGATTAGATGTATCTTCACTTTGGCGC
1 ATTCGGTTGGGATTGAAGATGCATCCCCCTTGGCTGAATGATTAGATGCATCTTCACTTTGGCGC
*
14322 CAAGCATTGGGTATGTTCTAGGCGTGTACCAAGGCTGTGGCTGAATGGTTGTAAGGGTTGCCTCA
66 CAAGCATTGGGTATGTTCTAGGCGTGTACCAAGGCTGTAGCTGAATGGTTGTAAGGGTTGCCTCA
*
14387 TGTCTCCTCGCAAATTAGGCTCCCTTTGGCTACAACAAGCTCACCAACGTGCATCTAGGTTT
131 TGTCTCCTCGCAAATTAGGCTCCCTTTGGCTACAACAAGCTCACCAACGTGCATCTAGGTGT
*
14449 ATTCGGTTGGGATTGAAGATGCATCCCCCTTGGTTGAATGATTAGATGCATCTTCACTTTGGCGC
1 ATTCGGTTGGGATTGAAGATGCATCCCCCTTGGCTGAATGATTAGATGCATCTTCACTTTGGCGC
* *
14514 CAAGCATTGGGTATGTTCTAGGCGTGTGCCAAGGCTGTAGTTGAATGGTTGTAAGGGTTGCCTCA
66 CAAGCATTGGGTATGTTCTAGGCGTGTACCAAGGCTGTAGCTGAATGGTTGTAAGGGTTGCCTCA
14579 TGTCTCCTCGCAAATTAGGCTCCCTTTGGCTACAACAAGCTCACCAACGTGCATCTAGGTGT
131 TGTCTCCTCGCAAATTAGGCTCCCTTTGGCTACAACAAGCTCACCAACGTGCATCTAGGTGT
14641 ATT
1 ATT
14644 AGCATCTAAT
Statistics
Matches: 189, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
192 189 1.00
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (192 bp):
ATTCGGTTGGGATTGAAGATGCATCCCCCTTGGCTGAATGATTAGATGCATCTTCACTTTGGCGC
CAAGCATTGGGTATGTTCTAGGCGTGTACCAAGGCTGTAGCTGAATGGTTGTAAGGGTTGCCTCA
TGTCTCCTCGCAAATTAGGCTCCCTTTGGCTACAACAAGCTCACCAACGTGCATCTAGGTGT
Found at i:15736 original size:16 final size:15
Alignment explanation
Indices: 15712--15749 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
15702 TGAAGCACTC
*
15712 AAAAAAAAAGTAAAG
1 AAAAAAAAAGAAAAG
15727 AAAAAGAAAAGAAAAG
1 AAAAA-AAAAGAAAAG
15743 AAAAAAA
1 AAAAAAA
15750 GAAAAGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:16946 original size:24 final size:21
Alignment explanation
Indices: 16912--16954 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
16902 CCCACAAGAC
*
16912 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AGTTCAAAGG
16934 ATGTACCTCTTGAAGTTCAAA
1 ATGT-CCT-TTGAAGTTCAAA
16955 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAGTTCAAAGG
Found at i:18390 original size:17 final size:17
Alignment explanation
Indices: 18365--18404 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
18355 GTATGTTGTT
*
18365 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
18382 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
18399 CATTTA
1 CATTTA
18405 GGGAAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:18487 original size:18 final size:18
Alignment explanation
Indices: 18464--18505 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
18454 ATGCATTTAG
18464 TTCATTGAATAAAGTTAT
1 TTCATTGAATAAAGTTAT
* *
18482 TTCATTGAATTATGTTAT
1 TTCATTGAATAAAGTTAT
18500 TTCATT
1 TTCATT
18506 ACTCAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52
Consensus pattern (18 bp):
TTCATTGAATAAAGTTAT
Found at i:22018 original size:17 final size:17
Alignment explanation
Indices: 21996--22030 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21986 TTGTTTATTA
21996 AAGCATGCATTGCATTT
1 AAGCATGCATTGCATTT
* *
22013 AAGCATGTATTTCATTT
1 AAGCATGCATTGCATTT
22030 A
1 A
22031 TGGAAGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (17 bp):
AAGCATGCATTGCATTT
Found at i:22109 original size:18 final size:18
Alignment explanation
Indices: 22086--22131 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
22076 ATTAATGCAT
22086 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
22104 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
22122 TTATTTCATT
1 TTAGTTCATT
22132 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:38472 original size:22 final size:22
Alignment explanation
Indices: 38429--38475 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
38419 AATTTTATCC
* *
38429 TTTTTTGGCTTTTTGATATTTT
1 TTTTTTGCCTTTTTCATATTTT
38451 TTTTTTGCCTTTTTC-T-TTTT
1 TTTTTTGCCTTTTTCATATTTT
38471 TTTTT
1 TTTTT
38476 GAAAAATAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
21 1 0.04
22 13 0.57
ACGTcount: A:0.04, C:0.09, G:0.09, T:0.79
Consensus pattern (22 bp):
TTTTTTGCCTTTTTCATATTTT
Found at i:41329 original size:19 final size:20
Alignment explanation
Indices: 41280--41334 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
41270 GTACCTTTCT
*
41280 AAAATGACATGATTTTTAATG
1 AAAAT-ACATGATCTTTAATG
41301 AAAA-AGCATGA-CTTTAATG
1 AAAATA-CATGATCTTTAATG
*
41320 AAAATACATGCTCTT
1 AAAATACATGATCTT
41335 GGCTGAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 16 0.55
20 9 0.31
21 4 0.14
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (20 bp):
AAAATACATGATCTTTAATG
Found at i:43452 original size:24 final size:23
Alignment explanation
Indices: 43425--43479 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
43415 TTCAATTGGC
43425 ACATTCTTTTGAATT-TCAAGAGG
1 ACATTCTTTTGAATTGTCAA-AGG
*
43448 TACA-TCCTTTGAATTGTCAAAGG
1 -ACATTCTTTTGAATTGTCAAAGG
43471 ACATGTCTT
1 ACAT-TCTT
43480 GTGGATCACC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 3 0.12
23 13 0.50
24 10 0.38
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (23 bp):
ACATTCTTTTGAATTGTCAAAGG
Found at i:43462 original size:23 final size:22
Alignment explanation
Indices: 43432--43474 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
43422 GGCACATTCT
43432 TTTGAATT-TCAAGAGGTACATCC
1 TTTGAATTGTCAA-AGG-ACATCC
43455 TTTGAATTGTCAAAGGACAT
1 TTTGAATTGTCAAAGGACAT
43475 GTCTTGTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (22 bp):
TTTGAATTGTCAAAGGACATCC
Found at i:51529 original size:14 final size:14
Alignment explanation
Indices: 51512--51538 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51502 TTAAGGATTT
51512 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
51526 ATGGTGATGGAAA
1 ATGGTGATGGAAA
51539 TAGTATCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:65898 original size:24 final size:21
Alignment explanation
Indices: 65863--65905 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
65853 GGCACATTCT
*
65863 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
65886 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
65906 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:73859 original size:14 final size:14
Alignment explanation
Indices: 73842--73868 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
73832 TTAAGGATTT
73842 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
73856 ATGGTGATGGAAA
1 ATGGTGATGGAAA
73869 TAGTATCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:77195 original size:16 final size:16
Alignment explanation
Indices: 77162--77210 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
77152 TAAGGTAATG
77162 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
77180 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
77196 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
77211 GATAACTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:77694 original size:15 final size:16
Alignment explanation
Indices: 77651--77699 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
77641 ATATAAATAA
*
77651 GAAATGGAAGAAGAAAA
1 GAAATGG-AGAAGAAAT
*
77668 GAAAT-GATAAGAAAT
1 GAAATGGAGAAGAAAT
77683 GAAATGGA-AAGAAAT
1 GAAATGGAGAAGAAAT
77698 GA
1 GA
77700 TATCAAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 21 0.72
16 3 0.10
17 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (16 bp):
GAAATGGAGAAGAAAT
Found at i:79510 original size:14 final size:14
Alignment explanation
Indices: 79486--79520 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
79476 TAACTATTAA
79486 AACATTATATAACAT
1 AACA-TATATAACAT
79501 AACATATATAACAT
1 AACATATATAACAT
79515 AACATA
1 AACATA
79521 GGAGGGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (14 bp):
AACATATATAACAT
Found at i:92594 original size:13 final size:13
Alignment explanation
Indices: 92572--92601 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
92562 ACTAAACACC
92572 TTTC-ACATACCT
1 TTTCAACATACCT
92584 TTTCAACATACCT
1 TTTCAACATACCT
92597 TTTCA
1 TTTCA
92602 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:100683 original size:15 final size:16
Alignment explanation
Indices: 100640--100685 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
100630 ATATAAATAA
100640 GAAATGGAAGAAGAAAG
1 GAAATGG-AGAAGAAAG
*
100657 GAAAT-GATAAGAAAG
1 GAAATGGAGAAGAAAG
100672 GAAATGGA-AAGAAA
1 GAAATGGAGAAGAAA
100686 TAATATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 19 0.70
16 3 0.11
17 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (16 bp):
GAAATGGAGAAGAAAG
Found at i:106954 original size:202 final size:202
Alignment explanation
Indices: 106581--106954 Score: 565
Period size: 202 Copynumber: 1.9 Consensus size: 202
106571 CCTTAACAAA
* *
106581 TTGATTGTGGATATAGGAAGAAAGCAAACAACCTGTACAAGTGAATGACTCAAAAAGAGATGGTT
1 TTGATTGTGGATATAGGAAGAAAGCAAACAACCTGCACAAGTGAATGACTCAAAAAGAGATGGGT
*
106646 TAAGGTGGTAAACGTATAGGTGAATAGGTGGGCTGCTTAAAATGAGAGATGGAAGCGGAAGATGG
66 TAAGGTGGTAAACGTATAGGTGAATAGGTGGGCTGCTTAAAATGAGAGATGGAAGCGGAAGATGA
* * * *
106711 TTGATAAGGCTATGGTTATGTCTTATGAAATAAAGGGATGGTAGTTATTGTTAGGTAATTCTACC
131 TTGAAAAGGCTATGGTTATGTCTGATGAAACAAAAGGATGGTAGTTATTGTTAGGTAATTCTACC
106776 TTCTCGT
196 TTCTCGT
* * *
106783 TTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCACAAGTGAATGGCTCAAAAAGAGA-GGG
1 TTGATTGTGGATATAGGAAGAAAGC-AAACAACCTGCACAAGTGAATGACTCAAAAAGAGATGGG
** *
106847 TTAACGGTGGTGGACGTATA-GTGAATAGGTGGGCTGTTTAAAATGAGAGATGGAAGCGGAAGAT
65 TTAA-GGTGGTAAACGTATAGGTGAATAGGTGGGCTGCTTAAAATGAGAGATGGAAGCGGAAGAT
* *
106911 GATTGAAAATGGTTATGGTTATG-GTGATGAAACAAAAGGATGGT
129 GATTGAAAA-GGCTATGGTTATGTCTGATGAAACAAAAGGATGGT
106955 TATGAGGATA
Statistics
Matches: 154, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
202 96 0.62
203 58 0.38
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (202 bp):
TTGATTGTGGATATAGGAAGAAAGCAAACAACCTGCACAAGTGAATGACTCAAAAAGAGATGGGT
TAAGGTGGTAAACGTATAGGTGAATAGGTGGGCTGCTTAAAATGAGAGATGGAAGCGGAAGATGA
TTGAAAAGGCTATGGTTATGTCTGATGAAACAAAAGGATGGTAGTTATTGTTAGGTAATTCTACC
TTCTCGT
Found at i:115159 original size:26 final size:25
Alignment explanation
Indices: 115115--115164 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
115105 TGAGATACAA
*
115115 CAACACCACCATCTCCATTTCATCAT
1 CAACACCACCAACTCCA-TTCATCAT
* *
115141 CAACACCATCAACTTCATTCATCA
1 CAACACCACCAACTCCATTCATCA
115165 AGACCATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.34, C:0.40, G:0.00, T:0.26
Consensus pattern (25 bp):
CAACACCACCAACTCCATTCATCAT
Found at i:115165 original size:22 final size:21
Alignment explanation
Indices: 115133--115174 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
115123 CCATCTCCAT
115133 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
115154 TTCATTCATCAAGACCATCAA
1 TTCA-TCATCAACACCATCAA
115175 TTTCGTAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.38, C:0.33, G:0.02, T:0.26
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:125194 original size:19 final size:20
Alignment explanation
Indices: 125156--125205 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
125146 GAAACCCCTT
125156 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
*
125176 TGAATATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
125195 TGAAGATACAT
1 TGAAAATACAT
125206 AGTCTTGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:127482 original size:21 final size:21
Alignment explanation
Indices: 127432--127484 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
127422 AATGTTCTCC
* *
127432 TTCAGTTTCATTGTCTTTAAG
1 TTCATTTTCATTGTCTTCAAG
*
127453 TTACTTTTTCATT-TCTTCAATG
1 TT-CATTTTCATTGTCTTCAA-G
127475 TTCATTTTCA
1 TTCATTTTCA
127485 AATGCGTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.19, C:0.17, G:0.08, T:0.57
Consensus pattern (21 bp):
TTCATTTTCATTGTCTTCAAG
Found at i:128291 original size:18 final size:18
Alignment explanation
Indices: 128268--128312 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
128258 GGTAATGAAT
128268 AGGAAATGATGAAAGAAA
1 AGGAAATGATGAAAGAAA
128286 AGGAAATGATGAAAGAAA
1 AGGAAATGATGAAAGAAA
128304 AGGAAATGA
1 AGGAAATGA
128313 AGTAAAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (18 bp):
AGGAAATGATGAAAGAAA
Found at i:128576 original size:6 final size:6
Alignment explanation
Indices: 128530--128573 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
128520 GACTTAGGAG
* *
128530 TTCTTT TTC-TT TTCTTT TTGTTT TTCTTCT TTCTTT TTGTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTT-T TTCTTT TTCTTT TT
128574 GTTGCAGCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:128769 original size:12 final size:12
Alignment explanation
Indices: 128752--128796 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
128742 AAAATGGATT
128752 AATGAAATAAAA
1 AATGAAATAAAA
*
128764 AATGAAAGAAAGA
1 AATGAAATAAA-A
*
128777 AATGAAATGAAA
1 AATGAAATAAAA
128789 AATGAAAT
1 AATGAAAT
128797 GAATGAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AATGAAATAAAA
Found at i:129383 original size:19 final size:20
Alignment explanation
Indices: 129333--129375 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
129323 GAAATCCCTT
129333 TGAAAATACATGATATTTAA
1 TGAAAATACATGATATTTAA
129353 TGAAAATACATGAT-TTTAA
1 TGAAAATACATGATATTTAA
129372 TGAA
1 TGAA
129376 GTTACATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATATTTAA
Done.