Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000009.1 Hibiscus syriacus cultivar Beakdansim tig00000015_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: 78307
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Found at i:4309 original size:26 final size:26
Alignment explanation
Indices: 4275--4334 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
4265 ATTAATGTGC
* * *
4275 ATTAT-ATTATATGAATTTTAATTTTT
1 ATTATAATTAAAT-AATTTTAAGTTTA
4301 ATT-TAATTAAATAATTTTAAGTTTA
1 ATTATAATTAAATAATTTTAAGTTTA
4326 ATTATAATT
1 ATTATAATT
4335 TCATAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (26 bp):
ATTATAATTAAATAATTTTAAGTTTA
Found at i:5636 original size:69 final size:70
Alignment explanation
Indices: 5556--5690 Score: 218
Period size: 70 Copynumber: 1.9 Consensus size: 70
5546 AATACAATAC
* * * *
5556 CAAATGAACTGATGAA-AAATTTGGATAAAATACAATGGTAGTATTGATATTGTTTATAGAGTAT
1 CAAATGAACTGATGAAGAAATCTAGATAAAATACAATCGTAGTATCGATATTGTTTATAGAGTAT
5620 CTATA
66 CTATA
*
5625 CAAATGAACTGATGAAGAAATCTAGATAAAATACAATCGTAGTATCGGTATTGTTTATAGAGTAT
1 CAAATGAACTGATGAAGAAATCTAGATAAAATACAATCGTAGTATCGATATTGTTTATAGAGTAT
5690 C
66 C
5691 GGGACTCCTC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 16 0.27
70 44 0.73
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (70 bp):
CAAATGAACTGATGAAGAAATCTAGATAAAATACAATCGTAGTATCGATATTGTTTATAGAGTAT
CTATA
Found at i:7567 original size:21 final size:24
Alignment explanation
Indices: 7542--7589 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
7532 TGTACATGTG
7542 ATATGTGA-TA-AA-AGAAAAGAT
1 ATATGTGATTACAAGAGAAAAGAT
*
7563 ATATGTGATTACAAGAGAAATGAT
1 ATATGTGATTACAAGAGAAAAGAT
7587 ATA
1 ATA
7590 AATACATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
22 2 0.09
23 2 0.09
24 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.19, T:0.27
Consensus pattern (24 bp):
ATATGTGATTACAAGAGAAAAGAT
Found at i:9337 original size:42 final size:41
Alignment explanation
Indices: 9268--9346 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 41
9258 AGTCAACACC
* * * *
9268 GATCAATGGTCGTTCAACGGTGATCAACACTCGGTTAATAAT
1 GATCAACGGTCGATCAACGATGATCAACAAT-GGTTAATAAT
* *
9310 GATCAACGGTCGATCAATGATGGTCAACAATGGTTAA
1 GATCAACGGTCGATCAACGATGATCAACAATGGTTAA
9347 CAAATGGTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
41 6 0.19
42 25 0.81
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (41 bp):
GATCAACGGTCGATCAACGATGATCAACAATGGTTAATAAT
Found at i:11616 original size:23 final size:21
Alignment explanation
Indices: 11523--11624 Score: 125
Period size: 21 Copynumber: 4.8 Consensus size: 21
11513 AGGGTGTCAA
11523 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTAC
* * *
11544 AGTGCATCCATACACCCTTGC
1 AGTGCATCCATGCACCCCTAC
*
11565 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTAC
11586 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCACC--CCTAC
*
11608 TAGTGCATCGATGCACC
1 -AGTGCATCCATGCACC
11625 ATGTATTGCA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
21 53 0.75
22 1 0.01
23 17 0.24
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:14240 original size:2 final size:2
Alignment explanation
Indices: 14233--14263 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14223 AATTATTATT
14233 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
14264 TTGATTAAGG
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:20210 original size:31 final size:31
Alignment explanation
Indices: 20172--20244 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
20162 TGTTTCAAAA
* *
20172 GTAACAAATTGGTCACCATCGTTATCTATTT
1 GTAACAAATTGGTCACCAACGTTATCGATTT
* * *
20203 GTAACAAATTAGTCACTAACTTTATCGATTT
1 GTAACAAATTGGTCACCAACGTTATCGATTT
*
20234 ATAACAAATTG
1 GTAACAAATTG
20245 ACCACTCGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (31 bp):
GTAACAAATTGGTCACCAACGTTATCGATTT
Found at i:23565 original size:18 final size:19
Alignment explanation
Indices: 23542--23584 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
23532 CAGTAATCCT
23542 ATTCC-CTGGTAATATTAC
1 ATTCCACTGGTAATATTAC
*
23560 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATATTAC
23580 ATTCC
1 ATTCC
23585 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATATTAC
Found at i:23572 original size:20 final size:20
Alignment explanation
Indices: 23547--23584 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
23537 ATCCTATTCC
23547 CTGGTAATATTACATTCCCA
1 CTGGTAATATTACATTCCCA
*
23567 CTGGTAATCTTACATTCC
1 CTGGTAATATTACATTCC
23585 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATATTACATTCCCA
Found at i:23681 original size:37 final size:37
Alignment explanation
Indices: 23639--23716 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
23629 TACATGACAA
23639 TCAAGAATACTCATTTCATAACTAATTGATCACAAAC
1 TCAAGAATACTCATTTCATAACTAATTGATCACAAAC
*
23676 TCAAGAATACTCATTTCGTAACTAATTGATCACAAAC
1 TCAAGAATACTCATTTCATAACTAATTGATCACAAAC
23713 TCAA
1 TCAA
23717 ATCTTACTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.29
Consensus pattern (37 bp):
TCAAGAATACTCATTTCATAACTAATTGATCACAAAC
Found at i:23953 original size:26 final size:26
Alignment explanation
Indices: 23899--23954 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
23889 ATTCCTTTGG
*
23899 AACAGCAGAAAACAACAACAGTAGTA
1 AACAGCAGAAAACAACAACAGTAGCA
* *
23925 AACAGTAGCAAACAACAACA-TCAGCA
1 AACAGCAGAAAACAACAACAGT-AGCA
23951 AACA
1 AACA
23955 TCAACACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.07
Consensus pattern (26 bp):
AACAGCAGAAAACAACAACAGTAGCA
Found at i:28040 original size:45 final size:45
Alignment explanation
Indices: 27975--28311 Score: 494
Period size: 45 Copynumber: 7.5 Consensus size: 45
27965 TTTTATTAAG
* * *
27975 GGCACCCTTTAATGCCTTTAATGCACCGGTATGCATTTCATTTAT
1 GGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTAT
* ** ** *
28020 GGCATCATTTCAAACCTTTAATTAACCGTTATGCATTACATTTAT
1 GGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTAT
* *
28065 GACATCCTTTCATGCCTTTAATTCACCGTTATGCATTTCATTTAT
1 GGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTAT
* *
28110 GACATCCTTTCATGCCTTTAATGCACTGTTATGCATTTCATTTAT
1 GGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTAT
* *
28155 GGCATCCTTTCATGCCTTTAATGCACCGTTATACTTTTCATTTAT
1 GGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTAT
* *
28200 GGCATCCTTTCAAGCCTTTAATGCTCCGTTATGCATTTCATTTAT
1 GGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTAT
**
28245 GGCATCCTTTCATGCCTTTAATGCATAGTTATGCATTTCATTTAT
1 GGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTAT
*
28290 GGCATCCTTTCATGCTTTTAAT
1 GGCATCCTTTCATGCCTTTAAT
28312 CTTTTATTTT
Statistics
Matches: 262, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 262 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (45 bp):
GGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTAT
Found at i:28458 original size:45 final size:45
Alignment explanation
Indices: 28403--28524 Score: 208
Period size: 45 Copynumber: 2.7 Consensus size: 45
28393 TTGTACACGT
28403 AGTGCCCATATGGAAATTCATAAATTTATTAGTTTTTGCACACAC
1 AGTGCCCATATGGAAATTCATAAATTTATTAGTTTTTGCACACAC
28448 AGTGCCCATATGGAAATTCATAAATTTATTAGTTTTTGCACACAC
1 AGTGCCCATATGGAAATTCATAAATTTATTAGTTTTTGCACACAC
* * *
28493 AGTGCCCATACGAAAAATTCATAAACTTATTA
1 AGTGCCCATATG-GAAATTCATAAATTTATTA
28525 TAAATTTCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 56 0.77
46 17 0.23
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (45 bp):
AGTGCCCATATGGAAATTCATAAATTTATTAGTTTTTGCACACAC
Found at i:28592 original size:56 final size:57
Alignment explanation
Indices: 28467--28604 Score: 233
Period size: 56 Copynumber: 2.4 Consensus size: 57
28457 ATGGAAATTC
* * *
28467 ATAAATTTATTAGTTTTTGCACACACAGTGCCCATACGAAAAATTCATAAACTTATT
1 ATAAATTTCTTAGTTTTTGCACACACAATGCCCATACGAAAAATTCATAAACTCATT
28524 ATAAATTTCTTAGTTTTTGCACACACAATGCCCATACG-AAAATTCATAAACTCATT
1 ATAAATTTCTTAGTTTTTGCACACACAATGCCCATACGAAAAATTCATAAACTCATT
*
28580 ATGAATTTCTTAGTTTTTGCACACA
1 ATAAATTTCTTAGTTTTTGCACACA
28605 AAGTGTCCAT
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
56 41 0.53
57 36 0.47
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (57 bp):
ATAAATTTCTTAGTTTTTGCACACACAATGCCCATACGAAAAATTCATAAACTCATT
Found at i:31572 original size:2 final size:2
Alignment explanation
Indices: 31565--31610 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
31555 ACCAGAAAAG
31565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31607 AT AT
1 AT AT
31611 TGACATCATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33456 original size:45 final size:45
Alignment explanation
Indices: 33326--33468 Score: 209
Period size: 45 Copynumber: 3.2 Consensus size: 45
33316 TAGTCATTAT
*
33326 TTTCATTTAGGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
** * *
33371 -TT-ATTTATGGCATCCTTTCATGATTTTAATGTACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
33414 TTTCATTTATGGCATCCTTTTATGCCTTGAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
33459 TTTCATTTAT
1 TTTCATTTAT
33469 AGTATCTGTC
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
43 36 0.42
44 4 0.05
45 45 0.53
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:34111 original size:12 final size:12
Alignment explanation
Indices: 34090--34122 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
34080 GCTTGTAAAC
34090 TAAA-AAATATA
1 TAAAGAAATATA
34101 TAAAGAAATATA
1 TAAAGAAATATA
*
34113 TTAAGAAATA
1 TAAAGAAATA
34123 ACGTAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (12 bp):
TAAAGAAATATA
Found at i:35787 original size:106 final size:106
Alignment explanation
Indices: 35602--36027 Score: 660
Period size: 106 Copynumber: 4.0 Consensus size: 106
35592 TGTATTGTTC
* * *
35602 CGAGTCCAATATCC-TCTGC-CGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTATTGA
1 CGAGTCCAATATCCTTC-GCTC-TGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGA
* *
35665 CAACCAGCCATCCCTTCATTGTGAAGTTGAACTTATGTTGTCT
64 CAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
35708 CGAGTCCAATATCCTTCGCTCTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTCTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
*
35773 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
66 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * *
35814 CGAGTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTTTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTCTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
*
35879 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
35920 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTT-TGAAATTGGGAAGTTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCTCTGAAGTTGAAATTGG-TTCTGAAATTGGGAAATTGTTTGTTGAC
*
35984 AACCAGCCATCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
36026 CG
1 CG
36028 GGTGGCGCGA
Statistics
Matches: 295, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
106 291 0.99
107 4 0.01
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTCTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:36704 original size:37 final size:37
Alignment explanation
Indices: 36656--36762 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 37
36646 TTGTTTCATG
* * *
36656 AGAAACGGTCTCAAGGGAGATAAAATTTTGTTTTAAGA
1 AGAAACTGTCTCAAGGGAGATAAAATTTAGTTCTAA-A
* * *
36694 A-AAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAA
1 AGAAACTGTCTCAAGGGAGATAAAATTTAGTTCTAAA
* * *
36730 AGAAATTGTCTCATGGTGAGATGAAA-TTAGTTC
1 AGAAACTGTCTCAAGG-GAGATAAAATTTAGTTC
36763 CAAGGAAAAC
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
36 2 0.04
37 46 0.82
38 8 0.14
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (37 bp):
AGAAACTGTCTCAAGGGAGATAAAATTTAGTTCTAAA
Found at i:37481 original size:18 final size:18
Alignment explanation
Indices: 37455--37489 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
37445 GTTGAATCCC
*
37455 CAAAGATGCCCCAATATA
1 CAAAAATGCCCCAATATA
37473 CAAAAATGCCCCAATAT
1 CAAAAATGCCCCAATAT
37490 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.29, G:0.09, T:0.17
Consensus pattern (18 bp):
CAAAAATGCCCCAATATA
Found at i:38567 original size:5 final size:5
Alignment explanation
Indices: 38557--38613 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
38547 TGATTTTTGA
*
38557 TTCTT TTCTT TTCTT TTCTT TT-TT GTTCTT GT-TT TTCTT TT-TT GCTTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT -TTCTT TTCTT TTCTT TTCTT --TTCTT
38607 TTCTT TT
1 TTCTT TT
38614 TTGTTTTTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 7 0.16
5 31 0.70
6 4 0.09
7 2 0.05
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (5 bp):
TTCTT
Found at i:38592 original size:19 final size:18
Alignment explanation
Indices: 38567--38618 Score: 72
Period size: 16 Copynumber: 2.9 Consensus size: 18
38557 TTCTTTTCTT
38567 TTCTTTTCTTTTTTGTTC
1 TTCTTTTCTTTTTTGTTC
*
38585 TTGTTTTTCTTTTTTG--C
1 TT-CTTTTCTTTTTTGTTC
38602 TTCTTTTCTTTTTTGTT
1 TTCTTTTCTTTTTTGTT
38619 TTTGATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 12 0.41
17 3 0.10
18 2 0.07
19 12 0.41
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (18 bp):
TTCTTTTCTTTTTTGTTC
Found at i:38608 original size:29 final size:29
Alignment explanation
Indices: 38560--38621 Score: 67
Period size: 29 Copynumber: 2.1 Consensus size: 29
38550 TTTTTGATTC
38560 TTTTCTTTTCTTTTCTTTTT-TGTTCTTGT
1 TTTTCTTTTCTTTTCTTTTTCT-TTCTTGT
*
38589 TTTTCTTTT-TTGCTTC-TTTTCTTTTTTGT
1 TTTTCTTTTCTT--TTCTTTTTCTTTCTTGT
38618 TTTT
1 TTTT
38622 GATTGAATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
28 2 0.07
29 23 0.79
30 4 0.14
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (29 bp):
TTTTCTTTTCTTTTCTTTTTCTTTCTTGT
Found at i:42085 original size:15 final size:15
Alignment explanation
Indices: 42065--42102 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
42055 AATAGTTAGT
42065 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
*
42080 AAAATAATAATAAAA
1 AAAATAAAAATAAAA
*
42095 TAAATAAA
1 AAAATAAA
42103 TGGTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATAAAAATAAAA
Found at i:42752 original size:38 final size:39
Alignment explanation
Indices: 42695--42781 Score: 149
Period size: 39 Copynumber: 2.2 Consensus size: 39
42685 CAACCGTCTT
*
42695 TCGGACACCCTATCATTTATTTTAAAGAAAA-TGGGTTGA
1 TCGGACA-CCGATCATTTATTTTAAAGAAAATTGGGTTGA
42734 TCGGACACCGATCATTTATTTTAAAGAAAATTGGGTTGA
1 TCGGACACCGATCATTTATTTTAAAGAAAATTGGGTTGA
42773 TCGGACACC
1 TCGGACACC
42782 CTATTTCTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 22 0.48
39 24 0.52
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (39 bp):
TCGGACACCGATCATTTATTTTAAAGAAAATTGGGTTGA
Found at i:44162 original size:45 final size:45
Alignment explanation
Indices: 44098--44251 Score: 263
Period size: 45 Copynumber: 3.4 Consensus size: 45
44088 TGTCTACAAT
* *
44098 ATCCTTTCATGCCTTTAATGCATCGTTATGCATTTTATTTATGAC
1 ATCCTTTCATGCCTTTAATGCATCGTTATGCATTTCATTTATGGC
44143 ATCCTTTCATGCCTTTAATGCATCGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCATCGTTATGCATTTCATTTATGGC
* *
44188 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCACTTATGGC
1 ATCCTTTCATGCCTTTAATGCATCGTTATGCATTTCATTTATGGC
*
44233 ATCATTTCATGCCTTTAAT
1 ATCCTTTCATGCCTTTAAT
44252 CTTTTATTTT
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 104 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (45 bp):
ATCCTTTCATGCCTTTAATGCATCGTTATGCATTTCATTTATGGC
Found at i:44429 original size:57 final size:57
Alignment explanation
Indices: 44337--44520 Score: 273
Period size: 56 Copynumber: 3.3 Consensus size: 57
44327 TATAGTTTAT
* * * *
44337 ACACATAGTGTCCGTACGG-AAATTCATAAATTTATTATAAATTTCTTAGTTTTTGC
1 ACACACAGTGCCCATACGGAAAATTCATAAACTTATTATAAATTTCTTAGTTTTTGC
*
44393 ACACACAGTGCCCATACGGAAAATTCATAAACTTATTATAAACTTCTTAGTTTTTGC
1 ACACACAGTGCCCATACGGAAAATTCATAAACTTATTATAAATTTCTTAGTTTTTGC
* *
44450 ACACACAGTGCCCATAC-GAAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGC
1 ACACACAGTGCCCATACGGAAAATTCATAAACTTATTATAAATTTCTTAGTTTTTGC
* *
44506 ACACAAAGTGTCCAT
1 ACACACAGTGCCCAT
44521 TTGGTAATCA
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
56 65 0.56
57 52 0.44
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (57 bp):
ACACACAGTGCCCATACGGAAAATTCATAAACTTATTATAAATTTCTTAGTTTTTGC
Found at i:44476 original size:113 final size:111
Alignment explanation
Indices: 44316--44520 Score: 286
Period size: 113 Copynumber: 1.8 Consensus size: 111
44306 CTTTCAATTC
* * * * * *
44316 ATTATAAACTCTATAGTTTATACACATAGTGTCCGTACGGAAATTCATAAATTTATTATAAATTT
1 ATTATAAACTCTATAGTTTATACACACAGTGCCCATACGAAAATTCATAAACTCATTATAAATTT
*
44381 CTTAGTTTTTGCACACACAGTGCCCATACGGAAAATTCATAAACTT
66 CTTAGTTTTTGCACACAAAGTGCCCATACGGAAAATTCATAAACTT
* *
44427 ATTATAAACTTCT-TAGTTTTTGCACACACAGTGCCCATACGAAAATTCATAAACTCATTATGAA
1 ATTATAAAC-TCTATAGTTTAT--ACACACAGTGCCCATACGAAAATTCATAAACTCATTATAAA
*
44491 TTTCTTAGTTTTTGCACACAAAGTGTCCAT
63 TTTCTTAGTTTTTGCACACAAAGTGCCCAT
44521 TTGGTAATCA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
111 16 0.20
112 3 0.04
113 62 0.77
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.36
Consensus pattern (111 bp):
ATTATAAACTCTATAGTTTATACACACAGTGCCCATACGAAAATTCATAAACTCATTATAAATTT
CTTAGTTTTTGCACACAAAGTGCCCATACGGAAAATTCATAAACTT
Found at i:46628 original size:20 final size:22
Alignment explanation
Indices: 46583--46637 Score: 78
Period size: 20 Copynumber: 2.6 Consensus size: 22
46573 TGCTCGGGGA
* *
46583 AGTATCGATACCACAAGAGGGG
1 AGTATCAATACCACAAGAGAGG
46605 AGTATCAATACCA-AA-AGAGG
1 AGTATCAATACCACAAGAGAGG
46625 AGTATCAATACCA
1 AGTATCAATACCA
46638 TTGTGGTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 17 0.55
21 2 0.06
22 12 0.39
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (22 bp):
AGTATCAATACCACAAGAGAGG
Found at i:52306 original size:25 final size:26
Alignment explanation
Indices: 52255--52307 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
52245 GATATTAATC
* * * *
52255 AGATAAAAACATTCATATTTTTGATA
1 AGATAAAAACAATCATATATATCATA
52281 AGAT-AAAACAATCATATATATCATA
1 AGATAAAAACAATCATATATATCATA
52306 AG
1 AG
52308 GAATGCACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.32
Consensus pattern (26 bp):
AGATAAAAACAATCATATATATCATA
Found at i:53716 original size:17 final size:17
Alignment explanation
Indices: 53694--53727 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53684 TGGGAAATTT
*
53694 AAACTTTTATTAACATA
1 AAACTTATATTAACATA
*
53711 AAACTTATATTTACATA
1 AAACTTATATTAACATA
53728 CTAAATTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (17 bp):
AAACTTATATTAACATA
Found at i:54270 original size:31 final size:31
Alignment explanation
Indices: 54235--54295 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
54225 CCCGAAAGAC
* *
54235 CTATCCATATGT-TCTAGAGAACATAGGTAAA
1 CTATCCATATGTCTCAAAAG-ACATAGGTAAA
54266 CTATCCATATGTCTCAAAAGACATAGGTAA
1 CTATCCATATGTCTCAAAAGACATAGGTAA
54296 CCATCGACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (31 bp):
CTATCCATATGTCTCAAAAGACATAGGTAAA
Found at i:63377 original size:24 final size:24
Alignment explanation
Indices: 63350--63400 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
63340 ATAACATCAA
*
63350 TTCCTCTTATATTTGCTTTACCAG
1 TTCCTCCTATATTTGCTTTACCAG
63374 TTCCTCCTATATTTGCTTTACCAG
1 TTCCTCCTATATTTGCTTTACCAG
63398 TTC
1 TTC
63401 GTTCGATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.27, G:0.08, T:0.49
Consensus pattern (24 bp):
TTCCTCCTATATTTGCTTTACCAG
Found at i:64519 original size:17 final size:19
Alignment explanation
Indices: 64477--64519 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
64467 GGGAGCATAG
64477 GTGTATCGGTACACTATCAAA
1 GTGTATCGGTACAC-ATC-AA
64498 GTGTATCGGTACAC-TC-A
1 GTGTATCGGTACACATCAA
64515 GTGTA
1 GTGTA
64520 AAATTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.27
19 2 0.09
21 14 0.64
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (19 bp):
GTGTATCGGTACACATCAA
Found at i:67295 original size:23 final size:23
Alignment explanation
Indices: 67267--67369 Score: 117
Period size: 23 Copynumber: 4.7 Consensus size: 23
67257 TACACCTTGA
67267 AGTGTATCGATACACATTCAAGG
1 AGTGTATCGATACACATTCAAGG
67290 AGTGTATCGATACACATTCAAGG
1 AGTGTATCGATACACATTCAAGG
* *
67313 AATGTATC-AGTACACATTC-A-T
1 AGTGTATCGA-TACACATTCAAGG
* * *
67334 AGTGTATCGATACATAGT-GAGG
1 AGTGTATCGATACACATTCAAGG
67356 A-TGTATCGATACAC
1 AGTGTATCGATACAC
67370 TTTGCACAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
21 26 0.38
22 4 0.06
23 39 0.57
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (23 bp):
AGTGTATCGATACACATTCAAGG
Found at i:67384 original size:67 final size:66
Alignment explanation
Indices: 67249--67384 Score: 150
Period size: 67 Copynumber: 2.0 Consensus size: 66
67239 ACCCGATGGG
* * * * **
67249 TGTATCGGTACACCTTGAAGTGTATCGATACACATTCAAGGAGTGTATCGATACACATTCAAGGA
1 TGTATCAGTACACATTCAAGTGTATCGATACACAGTCAAGGAGTGTATCGATACACATTCAAAAA
67314 A
66 A
* * *
67315 TGTATCAGTACACATTCATAGTGTATCGATACATAGT-GAGGA-TGTATCGATACACTTTGCACA
1 TGTATCAGTACACATTCA-AGTGTATCGATACACAGTCAAGGAGTGTATCGATACACATT-CA-A
67378 AAAA
63 AAAA
67382 TGT
1 TGT
67385 CAAAATCTGC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
65 15 0.26
66 21 0.36
67 22 0.38
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (66 bp):
TGTATCAGTACACATTCAAGTGTATCGATACACAGTCAAGGAGTGTATCGATACACATTCAAAAA
A
Found at i:69752 original size:34 final size:33
Alignment explanation
Indices: 69687--69757 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 33
69677 CCTTTACAAC
* *
69687 TCCCTAGTTTTTCACGGGTTAAACTAGAACCTT
1 TCCCTAGTTTTACACGGGTTAAACTAAAACCTT
*
69720 TCCCTAGCTTTTACACGGGCTT-AGCTAAAACCTT
1 TCCCTAG-TTTTACACGGG-TTAAACTAAAACCTT
69754 TCCC
1 TCCC
69758 CTTTACAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 24 0.73
35 2 0.06
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.34
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGTTAAACTAAAACCTT
Found at i:70138 original size:17 final size:18
Alignment explanation
Indices: 70089--70139 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
70079 CGTTGTAGCC
*
70089 AGGGGGTATGGATACCCCT
1 AGGGGGTATGGATA-CACT
* *
70108 AGGGGATATCGATA-ACT
1 AGGGGGTATGGATACACT
*
70125 GGGGGGTATGGATAC
1 AGGGGGTATGGATAC
70140 CCTTTTTGCA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
17 13 0.52
19 12 0.48
ACGTcount: A:0.25, C:0.14, G:0.39, T:0.22
Consensus pattern (18 bp):
AGGGGGTATGGATACACT
Found at i:70445 original size:21 final size:21
Alignment explanation
Indices: 70421--70461 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
70411 TGTTTAATGA
70421 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
70442 AAAATGATATCAATTGTTAA
1 AAAAAGATACCAATTGTTAA
70462 AATGATACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:70476 original size:17 final size:18
Alignment explanation
Indices: 70442--70477 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
70432 AATTGTTAAC
70442 AAAATGATATCAATTGTT
1 AAAATGATATCAATTGTT
*
70460 AAAATGATA-CCATTGTT
1 AAAATGATATCAATTGTT
70477 A
1 A
70478 CCAATTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (18 bp):
AAAATGATATCAATTGTT
Found at i:72154 original size:17 final size:18
Alignment explanation
Indices: 72127--72160 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
72117 TGCTTACCTC
*
72127 CTTCTTCTTCATGTTTTT
1 CTTCTTCTTCATATTTTT
72145 CTTC-TCTTCATATTTT
1 CTTCTTCTTCATATTTT
72161 CCCTCTTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.09, C:0.24, G:0.03, T:0.65
Consensus pattern (18 bp):
CTTCTTCTTCATATTTTT
Found at i:76384 original size:27 final size:27
Alignment explanation
Indices: 76348--76399 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
76338 ATCCTAAAAT
76348 TTTCATAGCTATGAGTAAGAAGACTAA
1 TTTCATAGCTATGAGTAAGAAGACTAA
*
76375 TTTCATAGCTATGAGTACGAAGACT
1 TTTCATAGCTATGAGTAAGAAGACT
76400 TATAGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (27 bp):
TTTCATAGCTATGAGTAAGAAGACTAA
Done.