Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006951.1 Hibiscus syriacus cultivar Beakdansim tig00017866_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: 74643
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:4540 original size:24 final size:24
Alignment explanation
Indices: 4494--4564 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
4484 GCTTAGGGTT
*
4494 GGGCTTGGTTTGGG-TCCCGGGTCG
1 GGGCTTGGTTTGGGCT-CTGGGTCG
* *
4518 GGGCTTGGTTTGGGCTCTAGGTCT
1 GGGCTTGGTTTGGGCTCTGGGTCG
* * *
4542 GAGTTTAGTTTGGGCTCTGGGTC
1 GGGCTTGGTTTGGGCTCTGGGTC
4565 TTTTGGGTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 38 0.97
25 1 0.03
ACGTcount: A:0.04, C:0.17, G:0.44, T:0.35
Consensus pattern (24 bp):
GGGCTTGGTTTGGGCTCTGGGTCG
Found at i:4684 original size:17 final size:17
Alignment explanation
Indices: 4657--4696 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4647 GTTATTGGTT
* *
4657 TAATAATAATAATCTTTA
1 TAAT-ATAATAATATTAA
4675 TAATATAATAATATTAA
1 TAATATAATAATATTAA
4692 TAATA
1 TAATA
4697 ATATATAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATATAATAATATTAA
Found at i:11476 original size:19 final size:19
Alignment explanation
Indices: 11454--11495 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11444 CTCTAAACTT
11454 TGATATTTATTCGGATCTC
1 TGATATTTATTCGGATCTC
* * *
11473 TGATTTTTGTTCTGATCTC
1 TGATATTTATTCGGATCTC
11492 TGAT
1 TGAT
11496 CTCTGCTATG
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:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (19 bp):
TGATATTTATTCGGATCTC
Found at i:17513 original size:2 final size:2
Alignment explanation
Indices: 17506--17550 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
17496 AAATAAGCAA
17506 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
17548 AT A
1 AT A
17551 AAATAAGACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18027 original size:20 final size:20
Alignment explanation
Indices: 18004--18071 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
17994 AACTTCAATT
18004 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
** * * **
18024 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATATGTAAA
* *
18044 TTTGCAACGCGAATCTGTAAA
1 -TCGCAACGCGAATATGTAAA
18065 TCGCAAC
1 TCGCAAC
18072 ACAGAAGTCA
Statistics
Matches: 33, Mismatches: 14, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
20 20 0.61
21 13 0.39
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:18088 original size:20 final size:20
Alignment explanation
Indices: 18065--18126 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
18055 AATCTGTAAA
*
18065 TCGCAACACAGAAGTCAAAT
1 TCGCAACGCAGAAGTCAAAT
18085 TCGCAACGCA-ATAGTCAAAT
1 TCGCAACGCAGA-AGTCAAAT
*
18105 TCGCAACGCGGAAGTCAAAT
1 TCGCAACGCAGAAGTCAAAT
18125 TC
1 TC
18127 ACAAAGCGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
TCGCAACGCAGAAGTCAAAT
Found at i:18109 original size:40 final size:40
Alignment explanation
Indices: 18040--18136 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 40
18030 TGCGATTTTC
* *
18040 CAAATTTGCAACGCGAATCTGTAAATCGCAACACAGAAGT
1 CAAATTCGCAACGCGAATCAGTAAATCGCAACACAGAAGT
* *
18080 CAAATTCGCAACGC-AAT-AGTCAAATTCGCAACGCGGAAGT
1 CAAATTCGCAACGCGAATCAGT-AAA-TCGCAACACAGAAGT
* *
18120 CAAATTCACAAAGCGAA
1 CAAATTCGCAACGCGAA
18137 CTCCAATTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
38 2 0.04
39 6 0.12
40 38 0.79
41 2 0.04
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (40 bp):
CAAATTCGCAACGCGAATCAGTAAATCGCAACACAGAAGT
Found at i:18177 original size:20 final size:20
Alignment explanation
Indices: 18152--18206 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
18142 ATTTCGCAAC
18152 GTGAATAGTAAAATTAC-AAA
1 GTGAATAGTAAAATT-CGAAA
* *
18172 GTGAATAGTAAAAATCGTAAT
1 GTGAATAGTAAAATTCG-AAA
18193 GTGAATAGTAAAAT
1 GTGAATAGTAAAAT
18207 CGCAACGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 14 0.47
21 15 0.50
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (20 bp):
GTGAATAGTAAAATTCGAAA
Found at i:18207 original size:20 final size:20
Alignment explanation
Indices: 18145--18211 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
18135 AACTCCAATT
*
18145 TCGCAACGTGAATAGTAAAA
1 TCGCAAAGTGAATAGTAAAA
**
18165 TTACAAAGTGAATAGTAAAAA
1 TCGCAAAGTGAATAGT-AAAA
* *
18186 TCGTAATGTGAATAGTAAAA
1 TCGCAAAGTGAATAGTAAAA
18206 TCGCAA
1 TCGCAA
18212 CGAATCTATA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAAAGTGAATAGTAAAA
Found at i:21612 original size:12 final size:12
Alignment explanation
Indices: 21597--21637 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
21587 TTTATATATA
21597 TATTTAAAAAAT
1 TATTTAAAAAAT
21609 TATTTAAAAAA-
1 TATTTAAAAAAT
*
21620 TAATTAAAAATAT
1 TATTTAAAAA-AT
21633 TATTT
1 TATTT
21638 GTTTCCCCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.36
12 12 0.48
13 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATTTAAAAAAT
Found at i:23468 original size:19 final size:20
Alignment explanation
Indices: 23432--23469 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
23422 TTGATTAAAA
**
23432 TAAATTTAAAATTGAATAAC
1 TAAATTTAAAATAAAATAAC
23452 TAAA-TTAAAATAAAATAA
1 TAAATTTAAAATAAAATAA
23470 AAAAAGTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
TAAATTTAAAATAAAATAAC
Found at i:23507 original size:22 final size:21
Alignment explanation
Indices: 23457--23507 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
23447 ATAACTAAAT
*
23457 TAAAA-TAAAATAAAAAAAGT
1 TAAAACTAAAATAAAAAAAGC
**
23477 TAGTGACTAAAATATAAAAAAGC
1 TA-AAACTAAAATA-AAAAAAGC
23500 TAAAACTA
1 TAAAACTA
23508 TAGAGATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 4
0.72 0.16 0.12
Matches are distributed among these distances:
20 2 0.09
21 1 0.04
22 11 0.48
23 9 0.39
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.22
Consensus pattern (21 bp):
TAAAACTAAAATAAAAAAAGC
Found at i:25197 original size:117 final size:117
Alignment explanation
Indices: 24988--25218 Score: 363
Period size: 117 Copynumber: 2.0 Consensus size: 117
24978 TAGGATCAAG
* *
24988 CTAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATT
1 CTAAGATTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCAGATGAGTTCTTCTCATT
* *
25053 ACGAACTCTCCACTAGAAATGTCGATCCATCTCCTTCTGTGGTGGAATCGAA
66 ACGAACTCTCCACTAGAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAA
* * *
25105 CTAAGATTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCTTCTTCAGATGAGTTCTTCTCATT
1 CTAAGATTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCAGATGAGTTCTTCTCATT
* * * *
25170 ATGAACTCTTCACTAGAAATGTTGATCCACCTTCTTCTGTGATGGAATC
66 ACGAACTCTCCACTAGAAATGTCGATCCACCTCCTTCTGTGATGGAATC
25219 AAACAAAGTG
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
117 103 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (117 bp):
CTAAGATTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCAGATGAGTTCTTCTCATT
ACGAACTCTCCACTAGAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAA
Found at i:25736 original size:17 final size:15
Alignment explanation
Indices: 25696--25738 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
25686 TTTTGACTTC
25696 TTTTATTTTTTGCAT
1 TTTTATTTTTTGCAT
*
25711 TTCTCATTTTTTAGCAT
1 TT-TTATTTTTT-GCAT
25728 ATTTTATTTTT
1 -TTTTATTTTT
25739 CTCTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 8 0.35
17 11 0.48
18 2 0.09
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (15 bp):
TTTTATTTTTTGCAT
Found at i:25880 original size:42 final size:41
Alignment explanation
Indices: 25825--25906 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
25815 TCCGGATGAC
* * *
25825 TTATCATCTTGCTCGAAAGGCTTATAGATGACCTGAAGGAT
1 TTATCATCATGCTCGAAAGACTTATAGATGACCCGAAGGAT
* *
25866 TTATGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGA
1 TTAT-CATCATGCTCGAAAGACTTATAGATGACCCGAAGGA
25907 CTTACTAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 4 0.11
42 31 0.89
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (41 bp):
TTATCATCATGCTCGAAAGACTTATAGATGACCCGAAGGAT
Found at i:26353 original size:239 final size:237
Alignment explanation
Indices: 25781--26516 Score: 1010
Period size: 239 Copynumber: 3.1 Consensus size: 237
25771 TAACACCATA
* * *
25781 TGAAAACATCATGCCCAAAAAGTCTTACAGATGGTCCGGATGACTTATCATCTTGCTCGAAAGGC
1 TGAAAACATCATGCCC-AAAAGTCTTATAGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGC
* * *
25846 TTATAGATGACCTGAAGGATTTATGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGGACTTA
65 TTATAGATGACCTAAAGGATTTATGCATCATGCTTGAAAGACTTAATGATGG-CCGAAGGACTTA
*
25911 CTAAGTAAGAAACTTTGAAAATCATTTTCTTTCTTTTTAAAAATCAATTTTCAGAAAAGATTTAA
129 CTAAGTAAGAAACTTTGAAAATCATTTTCTTTCTTTTAAAAAATCAATTTTCAGAAAAGATTTAA
* *
25976 ATGAGAAACTTTGGAAATTGCTTTCTCA-TTTTCAAAAATCATG
194 ATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATG
* * * *
26019 TGAAAACATCTTGCCCCAAGGTTTTATAGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCT
1 TGAAAACATCATGCCCAAAAGTCTTATAGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCT
* *
26084 TATAGATGAACC-AAAAGATTTATGCATCATGCTTAAAAGACTTAATGATGGTCCGAAGGACTTA
66 TATAGATG-ACCTAAAGGATTTATGCATCATGCTTGAAAGACTTAATGATGG-CCGAAGGACTTA
* *
26148 CTAAGAAAGAAACTTTGGAAATCATTTTCTTTCTTTTCAAAAAATCAATTTTCAGAAAAGATTTA
129 CTAAGTAAGAAACTTTGAAAATCATTTTCTTTCTTTT-AAAAAATCAATTTTCAGAAAAGATTTA
* *
26213 AATGAGAAACTTTGGAAACCGCTTTCTCATTTTTCGAAAATCATT
193 AATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATG
* *
26258 TGGAAACATCATGCCCAAAAGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCT
1 TGAAAACATCATGCCCAAAAGTCTTATAGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCT
* * * * *
26323 TATAGATGACCTTAAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGGCTCGAAGGATTTGC
66 TATAGATGACCTAAAGGATTTATGCATCATGCTTGAAAGACTTAATGATGGC-CGAAGGACTTAC
* ** ** *
26388 TAAGTAAGAAACTTTGTAAATTGTTTTCGTACCTTTTTAAAAAAAATCAGTTTTCAGAAAATG-T
130 TAAGTAAGAAACTTTGAAAATCATTTTC-TTTC-TTTT--AAAAAATCAATTTTCAGAAAA-GAT
** * *
26452 TTAAATGAGAATTTTTGGAAATCGATTTCTCATTTTTTTGAAAATCATG
190 TTAAATGAGAAACTTTGGAAATCGCTTTCTCA-TTTTTCGAAAATCATG
*
26501 TGAAAACATCCTGCCC
1 TGAAAACATCATGCCC
26517 GAAGGACTTA
Statistics
Matches: 439, Mismatches: 49, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
237 132 0.30
238 75 0.17
239 148 0.34
240 2 0.00
241 4 0.01
242 49 0.11
243 29 0.07
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (237 bp):
TGAAAACATCATGCCCAAAAGTCTTATAGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCT
TATAGATGACCTAAAGGATTTATGCATCATGCTTGAAAGACTTAATGATGGCCGAAGGACTTACT
AAGTAAGAAACTTTGAAAATCATTTTCTTTCTTTTAAAAAATCAATTTTCAGAAAAGATTTAAAT
GAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATG
Found at i:29064 original size:11 final size:11
Alignment explanation
Indices: 29039--29075 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
29029 ATATTTATTG
*
29039 TTATT-ATAAA
1 TTATTAATATA
29049 TTATTAATATA
1 TTATTAATATA
29060 TTATTAATATA
1 TTATTAATATA
29071 TTATT
1 TTATT
29076 TATCAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTATTAATATA
Found at i:29071 original size:13 final size:13
Alignment explanation
Indices: 29029--29096 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
29019 TAAAGATTTT
* *
29029 ATATTTATTGTTA
1 ATATATATTATTA
* *
29042 TTATAAATTATT-
1 ATATATATTATTA
29054 A-ATATATTATTA
1 ATATATATTATTA
*
29066 ATATATTATTTATCA
1 ATATA-TA-TTATTA
*
29081 ATATAAATTATTA
1 ATATATATTATTA
29094 ATA
1 ATA
29097 ATAAAGATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
11 9 0.21
12 1 0.02
13 19 0.45
14 3 0.07
15 10 0.24
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (13 bp):
ATATATATTATTA
Found at i:29426 original size:20 final size:20
Alignment explanation
Indices: 29398--29439 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29388 GGAATTATTT
*
29398 TAATATTTTAAAATTAATAA
1 TAATATTTTAAAATAAATAA
* *
29418 TAATTTTTTATAATAAATAA
1 TAATATTTTAAAATAAATAA
29438 TA
1 TA
29440 TTAATTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATATTTTAAAATAAATAA
Found at i:29456 original size:22 final size:22
Alignment explanation
Indices: 29425--29468 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29415 TAATAATTTT
29425 TTATAATAAAT-AATATTAATTA
1 TTATAATAAATAAATA-TAATTA
*
29447 TTATATTAAATAAATATAATTA
1 TTATAATAAATAAATATAATTA
29469 ATCATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATAATAAATAAATATAATTA
Found at i:29483 original size:26 final size:26
Alignment explanation
Indices: 29408--29498 Score: 71
Period size: 26 Copynumber: 3.5 Consensus size: 26
29398 TAATATTTTA
* *
29408 AAAT-TAA-TAATAATTTTTTATAAT
1 AAATATAATTAATAATTTTATAAAAT
* * *
29432 AAATA-ATATTAATTATTATATTAAAT
1 AAATATA-ATTAATAATTTTATAAAAT
*
29458 AAATATAATTAATCATTTTATAAAATT
1 AAATATAATTAATAATTTTATAAAA-T
*
29485 ACAATATAAATAAT
1 A-AATATAATTAAT
29499 TTATATAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
24 5 0.10
25 1 0.02
26 32 0.62
27 3 0.06
28 11 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATATAATTAATAATTTTATAAAAT
Found at i:30308 original size:23 final size:23
Alignment explanation
Indices: 30282--30344 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
30272 ATGTGAAGTT
30282 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
30305 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
* *
30328 TGGATAAATTGAATAAA
1 TGAATAAATTGGATAAA
30345 TGTGAAGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAATAAATTGGATAAAATGTTA
Found at i:30401 original size:23 final size:23
Alignment explanation
Indices: 30285--30407 Score: 107
Period size: 23 Copynumber: 5.6 Consensus size: 23
30275 TGAAGTTTGA
*
30285 ATAAATTGGATAAAATGTTATGA
1 ATAAATTGGATAAAATGTTATGG
30308 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGGATAAAATGTTATGG
* * *
30331 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGGATAAAATGTTATG-G
* * *
30354 ATCAGTTGG-T----TGTT-TGA
1 ATAAATTGGATAAAATGTTATGG
*
30371 ATATATTGGATAAAATGTTATGG
1 ATAAATTGGATAAAATGTTATGG
*
30394 ATAAATTGAATAAA
1 ATAAATTGGATAAA
30408 TGTGAAGTGA
Statistics
Matches: 77, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
17 6 0.08
18 2 0.03
19 3 0.04
22 13 0.17
23 53 0.69
ACGTcount: A:0.43, C:0.01, G:0.20, T:0.36
Consensus pattern (23 bp):
ATAAATTGGATAAAATGTTATGG
Found at i:30404 original size:63 final size:63
Alignment explanation
Indices: 30300--30492 Score: 341
Period size: 63 Copynumber: 3.0 Consensus size: 63
30290 TTGGATAAAA
*
30300 TGTTATGAATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGT
1 TGTT-TGAATATATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGT
30364 TGTTTGAATATATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGT
1 TGTTTGAATATATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGT
* * *
30427 TGTTTGAATATATTGGATAAAATGTTATGGATAAACTGAATAAATGTGAAGTGATAAGTTAGT
1 TGTTTGAATATATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGT
30490 TGT
1 TGT
30493 GAGCATGAAA
Statistics
Matches: 125, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
63 121 0.97
64 4 0.03
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (63 bp):
TGTTTGAATATATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGT
Found at i:30436 original size:31 final size:31
Alignment explanation
Indices: 30336--30436 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 31
30326 TATGGATAAA
30336 TTGAATAAATGTGAAGTGATCAGTTGGTTGT
1 TTGAATAAATGTGAAGTGATCAGTTGGTTGT
* * ** ***
30367 TTGAATATAT-TGGA-T-AAAATGTTATGGATAAA
1 TTGAATAAATGTGAAGTGATCA-G-T-TGG-TTGT
30399 TTGAATAAATGTGAAGTGATCAGTTGGTTGT
1 TTGAATAAATGTGAAGTGATCAGTTGGTTGT
30430 TTGAATA
1 TTGAATA
30437 TATTGGATAA
Statistics
Matches: 49, Mismatches: 14, Indels: 14
0.64 0.18 0.18
Matches are distributed among these distances:
28 2 0.04
29 2 0.04
30 4 0.08
31 20 0.41
32 13 0.27
33 4 0.08
34 2 0.04
35 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.39
Consensus pattern (31 bp):
TTGAATAAATGTGAAGTGATCAGTTGGTTGT
Found at i:30577 original size:14 final size:14
Alignment explanation
Indices: 30558--30599 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
30548 TGATAAGTTG
30558 GTTTTAATGTATAT
1 GTTTTAATGTATAT
30572 GTTTTAATGTATAT
1 GTTTTAATGTATAT
*
30586 GTTTCAATGTATAT
1 GTTTTAATGTATAT
30600 ATTATCAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.55
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:31267 original size:21 final size:20
Alignment explanation
Indices: 31240--31309 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
31230 GTCATAAAAC
*
31240 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
31260 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
31281 CCCTGAGGGCTAGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
31302 CCCTGCGG
1 -CCTGCGG
31310 AGATGACATA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:46818 original size:51 final size:51
Alignment explanation
Indices: 46754--47116 Score: 433
Period size: 51 Copynumber: 7.0 Consensus size: 51
46744 GACACGATTG
* * *
46754 TTGAAGATATTCGAGTTCTATTCTCCTTAATGAAAGAAGGAGCGAACCCGT
1 TTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
* **
46805 TTGAAGATGTTCGAGTTCTATACTCTTTAAAGTGAGAAGGAGCGAACCCGT
1 TTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
* * * *
46856 TTGAAGATTTTTGAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGT
1 TTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
** * * * * *
46907 AAGAAGAAGATTTTTGAGTTCTATACTCCCTGAAGAAA-AATGGAGCAAACCCAG-
1 ---TTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAA-GGAGCGAACCC-GT
*
46961 TCGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
1 TTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
47012 TTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
1 TTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
* * * * *
47063 TTGCAGAAGATTTTCAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGT
1 TT---GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
47117 AGGCAAAAGA
Statistics
Matches: 273, Mismatches: 29, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
50 1 0.00
51 184 0.67
52 2 0.01
53 2 0.01
54 83 0.30
55 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (51 bp):
TTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT
Found at i:46967 original size:105 final size:105
Alignment explanation
Indices: 46701--47117 Score: 393
Period size: 105 Copynumber: 4.0 Consensus size: 105
46691 AACAATCGTT
* * * * * * ** *
46701 GAAGATCGTTCGAG-TCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATATT
1 GAAGAT-GTTCGAGTTCT-ATACTCCCTAAAGAAAGAAGGAGCAAACCCG-TTGCAGAAGATTTT
* * **
46765 CGAGTTCTATTCTCCTTAATGAAAGAAGGAGCGAACCCGT-TT
63 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTAAA
** ** * * *
46807 GAAGATGTTCGAGTTCTATACTCTTTAAAGTGAGAAGGAGCGAACCCGTT--TGAAGATTTTTGA
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAAGGAGCAAACCCGTTGCAGAAGATTTTCGA
* *
46870 GTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAGAA
66 GTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT-A-AA
* * * *
46912 GAAGATTTTTGAGTTCTATACTCCCTGAAGAAA-AATGGAGCAAACCCAG-T-C-GAAGATGTTC
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAA-GGAGCAAACCC-GTTGCAGAAGATTTTC
**
46973 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT-TT
64 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTAAA
* * *
47014 GAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGCAGAAGATTTTCA
1 GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAAGGAGCAAACCCG-TTGCAGAAGATTTTCG
* * *
47079 AGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTA
65 AGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTA
47118 GGCAAAAGAT
Statistics
Matches: 257, Mismatches: 41, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
101 1 0.00
102 83 0.32
103 3 0.01
104 5 0.02
105 155 0.60
106 10 0.04
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (105 bp):
GAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGAAGGAGCAAACCCGTTGCAGAAGATTTTCGA
GTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTAAA
Found at i:47003 original size:156 final size:155
Alignment explanation
Indices: 46756--47116 Score: 501
Period size: 156 Copynumber: 2.3 Consensus size: 155
46746 CACGATTGTT
* * * *
46756 GAAGATATTCGAGTTCTATTCT-CCTTAATGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAG
1 GAAGATTTTCGAGTTCTATACTCCCTGAA-GAAA-AAGGAGCGAACCCGTTCGAAGATGTTCGAG
* ** * * *
46820 TTCTATACTCTTTAAAGTGAGAAGGAGCGAACCCGTTTGAAGATTTTTGAGTTCTATACTCTTTA
64 TTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTA
*
46885 AAGAGAGAAGGAGCGAACCCGTAAGAA
129 AAGAAAGAAGGAGCGAACCCGTAAGAA
* *
46912 GAAGATTTTTGAGTTCTATACTCCCTGAAGAAAAATGGAGCAAACCCAG-TCGAAGATGTTCGAG
1 GAAGATTTTCGAGTTCTATACTCCCTGAAGAAAAA-GGAGCGAACCC-GTTCGAAGATGTTCGAG
46976 TTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTA
64 TTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTA
** *
47041 AAGAAAGAAGGAGCGAACCCGTTTGCA
129 AAGAAAGAAGGAGCGAACCCGTAAGAA
* *
47068 GAAGATTTTCAAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGT
1 GAAGATTTTCGAGTTCTATACTCCCTGAAGAAA-AAGGAGCGAACCCGT
47117 AGGCAAAAGA
Statistics
Matches: 180, Mismatches: 20, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
155 3 0.02
156 170 0.94
157 7 0.04
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (155 bp):
GAAGATTTTCGAGTTCTATACTCCCTGAAGAAAAAGGAGCGAACCCGTTCGAAGATGTTCGAGTT
CTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAA
GAAAGAAGGAGCGAACCCGTAAGAA
Found at i:47160 original size:54 final size:54
Alignment explanation
Indices: 46869--47167 Score: 186
Period size: 54 Copynumber: 5.6 Consensus size: 54
46859 AAGATTTTTG
** * * * * ***
46869 AGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAG-AAGAAGATTTTTG
1 AGTTCTATACTCCATGAAGAAAGAGGGAGCGAACCCGTAGGCAA-AAGATTTACA
* * * * * * *
46923 AGTTCTATACTCCCTGAAGAAAAATGGAGCAAACCC--AGTC-GAAGATGTT-CG
1 AGTTCTATACTCCATGAAGAAAGAGGGAGCGAACCCGTAGGCAAAAGAT-TTACA
* * * ** *
46974 AGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG---AAGATGTT-CG
1 AGTTCTATACTCCATGAAGAAAGAGGGAGCGAACCCGTAGGCAAAAGAT-TTACA
* * * ** * *
47025 AGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGCAGAAGATTTTCA
1 AGTTCTATACTCCATGAAGAAAGAGGGAGCGAACCCGTAGGCAAAAGATTTACA
* *
47079 AGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCGTAGGCAAAAGATTGTACG
1 AGTTCTATACTCCATGAAGAAAGAGGGAGCGAACCCGTAGGCAAAAGATT-TACA
* * *
47134 AGTT-TCTACTCCATGAAGGAATAGGGAGCGAACC
1 AGTTCTATACTCCATGAAGAAAGAGGGAGCGAACC
47168 TGTTGTCTGA
Statistics
Matches: 204, Mismatches: 32, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
51 88 0.43
52 3 0.01
53 2 0.01
54 105 0.51
55 6 0.03
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (54 bp):
AGTTCTATACTCCATGAAGAAAGAGGGAGCGAACCCGTAGGCAAAAGATTTACA
Found at i:51326 original size:31 final size:28
Alignment explanation
Indices: 51259--51327 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
51249 TAATAAGTAC
*
51259 AAAAAATAATTAATTAACTAATTTAAAT
1 AAAAAATAATTAATAAACTAATTTAAAT
* * *
51287 AAATAATAATTATATAAACATTATTTTAAT
1 AAAAAATAATTA-ATAAAC-TAATTTAAAT
51317 AAAAAAATAAT
1 -AAAAAATAAT
51328 ATTTATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 11 0.33
29 5 0.15
30 8 0.24
31 9 0.27
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (28 bp):
AAAAAATAATTAATAAACTAATTTAAAT
Found at i:51345 original size:17 final size:17
Alignment explanation
Indices: 51287--51345 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
51277 TAATTTAAAT
*
51287 AAATAATAATTATATAA
1 AAATAATATTTATATAA
* * *
51304 ACATTAT-TTTAATAAAA
1 AAATAATATTT-ATATAA
51321 AAATAATATTTATATAA
1 AAATAATATTTATATAA
*
51338 ATATAATA
1 AAATAATA
51346 ATAAAAAATA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
16 2 0.06
17 27 0.84
18 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATAATATTTATATAA
Found at i:63946 original size:27 final size:26
Alignment explanation
Indices: 63894--63946 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
63884 GTCTGATGTG
*
63894 GCAGTTTCTAGAAGGTCCAGTCAGCA
1 GCAGTTTCTAGAAGATCCAGTCAGCA
* *
63920 GCAGTTTTCTAGAAGATCTAGTTAGCA
1 GCAG-TTTCTAGAAGATCCAGTCAGCA
63947 CATTCTGGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (26 bp):
GCAGTTTCTAGAAGATCCAGTCAGCA
Found at i:64195 original size:25 final size:24
Alignment explanation
Indices: 64157--64212 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
64147 TAGTTTTATA
* * * *
64157 AAGTTATTTCTTTTATTTTCTTTT
1 AAGTTTTTTATTTTACTTTATTTT
64181 CAAGTTTTTTATTTTACTTTATTTT
1 -AAGTTTTTTATTTTACTTTATTTT
64206 AAGTTTT
1 AAGTTTT
64213 ATTTTTAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 7 0.26
25 20 0.74
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (24 bp):
AAGTTTTTTATTTTACTTTATTTT
Found at i:69746 original size:13 final size:13
Alignment explanation
Indices: 69728--69752 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69718 TCAAAAATTA
69728 TATATTATATATG
1 TATATTATATATG
69741 TATATTATATAT
1 TATATTATATAT
69753 TAAATAACCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TATATTATATATG
Done.