Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007060.1 Hibiscus syriacus cultivar Beakdansim tig00018327_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: 78347
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:8049 original size:88 final size:88
Alignment explanation
Indices: 7864--8049 Score: 234
Period size: 88 Copynumber: 2.1 Consensus size: 88
7854 GTTCATAGAA
*
7864 TTTTACTGTAAAATATAATAATTAAACTTGTATCCTTTCTTTACCTATATTTATCTTTTTTTCAG
1 TTTT-CTGTAAAATATAATAATTAAACTTGTATCCTTTCTTTACCTATACTTATCTTTTTTTCAG
*
7929 TACTAATCCTTAGTGTACTATTAC
65 TACTAATCCTTAATGTACTATTAC
* * * * *
7953 GTTTCTGTAAAATATAGTAATTAAACTTTTATCGTTTCTTTTCCTATACTTATC-TTTTTT-A-T
1 TTTTCTGTAAAATATAATAATTAAACTTGTATCCTTTCTTTACCTATACTTATCTTTTTTTCAGT
* *
8015 ACTAATTCTTTCAATGTACTATTAT
66 ACTAA-TCCTT-AATGTACTATTAC
8040 TTTTCCTGTA
1 TTTT-CTGTA
8050 TCGTTTCTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
85 6 0.07
86 5 0.06
87 20 0.24
88 50 0.60
89 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.06, T:0.52
Consensus pattern (88 bp):
TTTTCTGTAAAATATAATAATTAAACTTGTATCCTTTCTTTACCTATACTTATCTTTTTTTCAGT
ACTAATCCTTAATGTACTATTAC
Found at i:9064 original size:19 final size:19
Alignment explanation
Indices: 9040--9077 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
9030 AACTAGTCCA
9040 AAATCAATATTTCAATATT
1 AAATCAATATTTCAATATT
*
9059 AAATCAATATTTTAATATT
1 AAATCAATATTTCAATATT
9078 CGATTCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATCAATATTTCAATATT
Found at i:13020 original size:20 final size:20
Alignment explanation
Indices: 12995--13032 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12985 TTCTTCGGAG
*
12995 ATTGCTTCAATCGATAAAAC
1 ATTGCTTCAATCCATAAAAC
13015 ATTGCTTCAATCCATAAA
1 ATTGCTTCAATCCATAAA
13033 GCAACTTGTT
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:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (20 bp):
ATTGCTTCAATCCATAAAAC
Found at i:21303 original size:29 final size:29
Alignment explanation
Indices: 21269--21356 Score: 176
Period size: 29 Copynumber: 3.0 Consensus size: 29
21259 CCTAAATTAA
21269 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
21298 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
21327 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
21356 T
1 T
21357 AGGTGAAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:23884 original size:19 final size:19
Alignment explanation
Indices: 23860--23897 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23850 AACTAGTCCA
23860 AAATCAACATTTCAATATT
1 AAATCAACATTTCAATATT
* *
23879 AAATCAATATTTTAATATT
1 AAATCAACATTTCAATATT
23898 CGATTCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATCAACATTTCAATATT
Found at i:29482 original size:22 final size:24
Alignment explanation
Indices: 29457--29500 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
29447 CTTGATTTTT
*
29457 TAAAATCTAA-TTAAT-TAATATA
1 TAAAACCTAATTTAATATAATATA
29479 TAAAACCTAATTTAATATAATA
1 TAAAACCTAATTTAATATAATA
29501 ATATTTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 5 0.26
24 5 0.26
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAAACCTAATTTAATATAATATA
Found at i:30331 original size:22 final size:22
Alignment explanation
Indices: 30303--30345 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
30293 CCCAATAACA
30303 TTCATGATAAATATCATATATT
1 TTCATGATAAATATCATATATT
*
30325 TTCATGATAAATATTATATAT
1 TTCATGATAAATATCATATAT
30346 ATTAACCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (22 bp):
TTCATGATAAATATCATATATT
Found at i:35969 original size:23 final size:24
Alignment explanation
Indices: 35920--35970 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
35910 ACTTGTTCAT
* *
35920 GAACACGTTCGTGAACATATAAAC
1 GAACACATTCGCGAACATATAAAC
35944 GAACACATTCGCGAACAT-TAAAC
1 GAACACATTCGCGAACATATAAAC
35967 GAAC
1 GAAC
35971 GCTAAACGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.18
Consensus pattern (24 bp):
GAACACATTCGCGAACATATAAAC
Found at i:37353 original size:89 final size:89
Alignment explanation
Indices: 37252--37429 Score: 263
Period size: 89 Copynumber: 2.0 Consensus size: 89
37242 TCCCCCTTTG
*
37252 CCCCATGAAATTACGTCTATGTAAAAAGGTATTATATTTT-ATGGTAAATATTAC-AATTTGAAC
1 CCCCATGAAATTACATCTATGTAAAAAGGTATTATATTTTGA-GGTAAATATTACGAA-TTGAAC
*
37315 CAACA-AAGAGAGAGATAATATAAACA
64 CAACACAA-AGAGAGACAATATAAACA
* *
37341 CCCCATGAAATTACATCTATGTAAAGAGGTATTATATTTTGAGGTAAATATTACGAATTGAACCT
1 CCCCATGAAATTACATCTATGTAAAAAGGTATTATATTTTGAGGTAAATATTACGAATTGAACCA
*
37406 ACACAAAGTGAGACAATATAAACA
66 ACACAAAGAGAGACAATATAAACA
37430 TCTTGACCAC
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
89 76 0.94
90 5 0.06
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (89 bp):
CCCCATGAAATTACATCTATGTAAAAAGGTATTATATTTTGAGGTAAATATTACGAATTGAACCA
ACACAAAGAGAGACAATATAAACA
Found at i:44448 original size:36 final size:36
Alignment explanation
Indices: 44407--44544 Score: 240
Period size: 36 Copynumber: 3.8 Consensus size: 36
44397 ATTTATAAGT
* * *
44407 TGGTGATAATATAGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
44443 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
44479 TGGTGATGATATAGGCGCGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
44515 TGGTGATGATATAGGCGTGATAATGGTGAT
1 TGGTGATGATATAGGCGTGATAATGGTGAT
44545 AGACAGATTG
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:49384 original size:19 final size:19
Alignment explanation
Indices: 49360--49396 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
49350 AAAAAATTGA
49360 AAAAAAAAAAGAACAAAAG
1 AAAAAAAAAAGAACAAAAG
49379 AAAAAAAAAAGAACAAAA
1 AAAAAAAAAAGAACAAAA
49397 AATAAGGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAACAAAAG
Found at i:50703 original size:32 final size:32
Alignment explanation
Indices: 50618--50695 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
50608 CTTACTTGGA
50618 TTTCAACTTCACGACAGAGGGACCACTCGCGG
1 TTTCAACTTCACGACAGAGGGACCACTCGCGG
50650 TTTCAACTTCACGACAGAGGGACCACTCGCGG
1 TTTCAACTTCACGACAGAGGGACCACTCGCGG
50682 TTTCAACTTCACGA
1 TTTCAACTTCACGA
50696 TGAAGGGAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (32 bp):
TTTCAACTTCACGACAGAGGGACCACTCGCGG
Found at i:51865 original size:27 final size:26
Alignment explanation
Indices: 51849--51901 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
51839 TTTTGTTTCT
51849 TTATTCATTACTATTATTTTTTTAATAC
1 TTATT-ATTACTATTATTTTTTT-ATAC
51877 TTATTATTACTATTA-TTTTTTATAC
1 TTATTATTACTATTATTTTTTTATAC
51902 CTTGTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 4 0.16
26 6 0.24
27 10 0.40
28 5 0.20
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.62
Consensus pattern (26 bp):
TTATTATTACTATTATTTTTTTATAC
Found at i:59706 original size:239 final size:240
Alignment explanation
Indices: 59243--60192 Score: 1559
Period size: 239 Copynumber: 4.0 Consensus size: 240
59233 TAGCTGCCTA
* * * * *
59243 AACCTAGCCTCAAAATTGTCCAGATTCATTCACAAATTAGTTGTTGACACGATTTTTAAATCAGC
1 AACCTAGCCTCAAAACTGTCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGC
* * * *
59308 AAAACAAATTGTTGAAATCAAGCCCCGAAAATAAGTTGTTATCTGTTGTGATAAATATTCAAACC
66 AAAACGAATTGTTGAAAT-AAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCGAACC
* ** * * *
59373 TAGCCCCAAAAAACATACAAGTTCAAATAGTGGTGCTAGTTGTTAAACAACGAGTAGATTAATTT
130 TAGCCCC-AGAAAGGTTCAGGTTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTT
* *
59438 TAGGCTTTCCACAATTCTTACGTATTTTCTCTAAACATAGCTAGTTG
194 TAGGATTTCCACAATTCTTCCGTATTTTCTCTAAACATAGCTAGTTG
59485 AACCTAGCCTCAAAACTGTCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGC
1 AACCTAGCCTCAAAACTGTCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGC
*
59550 AAAACGAATTATTGAAATAAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCGAACCT
66 AAAACGAATTGTTGAAATAAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCGAACCT
*
59615 A-TCCCAGAAAGGTTCAGGTTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTTTA
131 AGCCCCAGAAAGGTTCAGGTTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTTTA
*
59679 GGATTTCCACAATTCTTCCGTATTTTCTCTAAACATAGCTAGCTG
196 GGATTTCCACAATTCTTCCGTATTTTCTCTAAACATAGCTAGTTG
* * *
59724 AACCTAGCCTCAAAACTATCCATATTCATTTACAAATTAGTTGTTGACACTACATTTAAATCAGA
1 AACCTAGCCTCAAAACTGTCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGC
*
59789 AAAACGAATTGTTGAAATAAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCTAACCT
66 AAAACGAATTGTTGAAATAAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCGAACCT
59854 AGCCCCAGAAAGGTTCAGGTTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTTTA
131 AGCCCCAGAAAGGTTCAGGTTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTTTA
59919 GGATTTCCACAATTCTTCCGTATTTTCTCTAAACATAGCTAGTTG
196 GGATTTCCACAATTCTTCCGTATTTTCTCTAAACATAGCTAGTTG
59964 AACCTAGCCTCAAAACTGTCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGC
1 AACCTAGCCTCAAAACTGTCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGC
* *
60029 AAAACGAATTGTTGAAATTAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTTGAACCT
66 AAAACGAATTGTTGAAATAAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCGAACCT
* *
60094 A-TCCTAGAAAGGTTCAGGTTCAAATAGTGGTGCTAGCTGTT--A-AACGAGTAGATTAATTTTA
131 AGCCCCAGAAAGGTTCAGGTTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTTTA
* * * *
60155 AGATTTCCATAATTCTTCCATATTTTCTCTAAAAATAG
196 GGATTTCCACAATTCTTCCGTATTTTCTCTAAACATAG
60193 AACACATGCA
Statistics
Matches: 668, Mismatches: 39, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
236 53 0.08
237 1 0.00
239 259 0.39
240 234 0.35
241 45 0.07
242 76 0.11
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (240 bp):
AACCTAGCCTCAAAACTGTCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGC
AAAACGAATTGTTGAAATAAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCGAACCT
AGCCCCAGAAAGGTTCAGGTTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTTTA
GGATTTCCACAATTCTTCCGTATTTTCTCTAAACATAGCTAGTTG
Found at i:60130 original size:479 final size:478
Alignment explanation
Indices: 59243--60192 Score: 1607
Period size: 479 Copynumber: 2.0 Consensus size: 478
59233 TAGCTGCCTA
* * ** *
59243 AACCTAGCCTCAAAATTGTCCAGATTCATTCACAAATTAGTTGTTGACACGATTTTTAAATCAGC
1 AACCTAGCCTCAAAACTATCCAGATTCATTCACAAATTAGTTGTTGACACGACATTTAAATCAGA
*
59308 AAAACAAATTGTTGAAATCAAGCCCCGAAAATAAGTTGTTATCTGTTGTGATAAATATTCAAACC
66 AAAACAAATTGTTGAAATCAAGCCCCGAAAATAAGTTGTTATCTATTGTGATAAATATTCAAACC
*
59373 TAGCCCCAAAAAACATACAAGTTCAAATAGTGGTGCTAGTTGTTAAACAACGAGTAGATTAATTT
131 TAGCCCCAAAAAACATACAAGTTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTT
*
59438 TAGGCTTTCCACAATTCTTACGTATTTTCTCTAAACATAGCTAGTTGAACCTAGCCTCAAAACTG
196 TAGGATTTCCACAATTCTTACGTATTTTCTCTAAACATAGCTAGTTGAACCTAGCCTCAAAACTG
59503 TCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGCAAAACGAATTATTGAAAT
261 TCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGCAAAACGAATTATTGAAAT
59568 AAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCGAACCTATCCCAGAAAGGTTCAGG
326 AAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCGAACCTATCCCAGAAAGGTTCAGG
*
59633 TTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTTTAGGATTTCCACAATTCTTCC
391 TTCAAATAGTGGTGCTAGCTGTT--A-AACGAGTAGATTAATTTTAAGATTTCCACAATTCTTCC
* *
59698 GTATTTTCTCTAAACATAGCTAGCTG
453 ATATTTTCTCTAAAAATAGCTAGCTG
* * *
59724 AACCTAGCCTCAAAACTATCCATATTCATTTACAAATTAGTTGTTGACACTACATTTAAATCAGA
1 AACCTAGCCTCAAAACTATCCAGATTCATTCACAAATTAGTTGTTGACACGACATTTAAATCAGA
* * *
59789 AAAACGAATTGTTGAAAT-AAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCTAACC
66 AAAACAAATTGTTGAAATCAAGCCCCGAAAATAAGTTGTTATCTATTGTGATAAATATTCAAACC
* ** * *
59853 TAGCCCC-AGAAAGGTTCAGGTTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTT
131 TAGCCCCAAAAAACATACAAGTTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTT
*
59917 TAGGATTTCCACAATTCTTCCGTATTTTCTCTAAACATAGCTAGTTGAACCTAGCCTCAAAACTG
196 TAGGATTTCCACAATTCTTACGTATTTTCTCTAAACATAGCTAGTTGAACCTAGCCTCAAAACTG
*
59982 TCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGCAAAACGAATTGTTGAAAT
261 TCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGCAAAACGAATTATTGAAAT
* * *
60047 TAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTTGAACCTATCCTAGAAAGGTTCAGG
326 AAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCGAACCTATCCCAGAAAGGTTCAGG
*
60112 TTCAAATAGTGGTGCTAGCTGTTAAACGAGTAGATTAATTTTAAGATTTCCATAATTCTTCCATA
391 TTCAAATAGTGGTGCTAGCTGTTAAACGAGTAGATTAATTTTAAGATTTCCACAATTCTTCCATA
60177 TTTTCTCTAAAAATAG
456 TTTTCTCTAAAAATAG
60193 AACACATGCA
Statistics
Matches: 441, Mismatches: 28, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
476 53 0.12
477 1 0.00
479 263 0.60
480 50 0.11
481 74 0.17
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (478 bp):
AACCTAGCCTCAAAACTATCCAGATTCATTCACAAATTAGTTGTTGACACGACATTTAAATCAGA
AAAACAAATTGTTGAAATCAAGCCCCGAAAATAAGTTGTTATCTATTGTGATAAATATTCAAACC
TAGCCCCAAAAAACATACAAGTTCAAATAGTGGTGCTAGCTGTTAAACAACGAGTAGATTAATTT
TAGGATTTCCACAATTCTTACGTATTTTCTCTAAACATAGCTAGTTGAACCTAGCCTCAAAACTG
TCCATATTCATTTACAAATTAGTTGTTGACACTACTTTTAAATCAGCAAAACGAATTATTGAAAT
AAGCCCCGACAATAAGTTGTTATCTATTGTGATAAATATTCGAACCTATCCCAGAAAGGTTCAGG
TTCAAATAGTGGTGCTAGCTGTTAAACGAGTAGATTAATTTTAAGATTTCCACAATTCTTCCATA
TTTTCTCTAAAAATAGCTAGCTG
Found at i:67878 original size:115 final size:119
Alignment explanation
Indices: 67719--68035 Score: 315
Period size: 115 Copynumber: 2.6 Consensus size: 119
67709 ATTATAATTA
* * * * *
67719 TAAAGAAGAAACTAATTCCTTATTTTTTATTAAGGCGATTATTTTTCATTTTTAATTAAAATATT
1 TAAAGAAGAAACTAATTCC-TAATTTTCATTAA-ACAATTATTTTTCATTTTTAATTAAAATAAT
*
67784 AAAA-TTT-CA-TAAAAATTT-AAAA-A-AAATATAAATTATTATTTATTTTTAAT
64 AAAATTTTACATTAAAAATTTAAAAACAGAAATATAAATTATTATTTATTTTCAAT
* *
67834 TAAATAAGAAACTAATTCTCTAATTTTCATTAAACCAATTATTTTTCATTTTTAATTTAAATAAT
1 TAAAGAAGAAACTAATTC-CTAATTTTCATTAAA-CAATTATTTTTCATTTTTAATTAAAATAAT
* * *
67899 AAAATTTTGACATTTCTTAAACATTTAGAAAATCAGGAAATGTATATTATTATTTATTTTCAAT
64 AAAATTTT-ACA----TTAAAAATTTA-AAAA-CA-GAAATATAAATTATTATTTATTTTCAAT
* * *
67963 TAAAGAAGAAACTAATTCCTAATTTTCATTAAGATAATCATTTCTCATTTTTTAATTGAAAATAA
1 TAAAGAAGAAACTAATTCCTAATTTTCATTAA-ACAATTATTTTTCA-TTTTTAATT-AAAATAA
*
68028 -AATATTTT
63 TAAAATTTT
68036 TTGGATAATT
Statistics
Matches: 166, Mismatches: 17, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
115 59 0.36
116 4 0.02
118 2 0.01
123 8 0.05
125 4 0.02
127 1 0.01
128 24 0.14
129 58 0.35
130 6 0.04
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.45
Consensus pattern (119 bp):
TAAAGAAGAAACTAATTCCTAATTTTCATTAAACAATTATTTTTCATTTTTAATTAAAATAATAA
AATTTTACATTAAAAATTTAAAAACAGAAATATAAATTATTATTTATTTTCAAT
Found at i:71709 original size:3 final size:3
Alignment explanation
Indices: 71701--71747 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
71691 GGAATTAGAT
*
71701 ATA ATA ATA ATA ATA ATA ATA ATA A-A AT- ATA A-A ATAA ATA AAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
71744 ATA A
1 ATA A
71748 AAAAAGACCC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 6 0.16
3 29 0.76
4 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:71740 original size:22 final size:22
Alignment explanation
Indices: 71707--71749 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
71697 AGATATAATA
*
71707 ATAATAATAATAATAATAAAAT
1 ATAATAATAATAAAAATAAAAT
71729 ATAA-AATAAATAAAAATAAAA
1 ATAATAAT-AATAAAAATAAAA
71750 AAAGACCCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAATAATAATAAAAATAAAAT
Found at i:74601 original size:16 final size:16
Alignment explanation
Indices: 74589--74618 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
74579 CTAATATATT
74589 AATAA-AAATATATAA
1 AATAATAAATATATAA
74604 AATAATAAATATATA
1 AATAATAAATATATA
74619 GCATGTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAATAAATATATAA
Found at i:75766 original size:31 final size:31
Alignment explanation
Indices: 75718--75792 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
75708 TCAAAAAACA
* *
75718 TAAGCTTTGGTCACTTTCATTTCATTTTAAT
1 TAAGATTTGATCACTTTCATTTCATTTTAAT
*
75749 TAAGATTTGATCACTTTCATTTCGTTTTAAT
1 TAAGATTTGATCACTTTCATTTCATTTTAAT
*
75780 TAAGATGTGATCA
1 TAAGATTTGATCA
75793 TTGAATGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (31 bp):
TAAGATTTGATCACTTTCATTTCATTTTAAT
Found at i:75998 original size:31 final size:31
Alignment explanation
Indices: 75960--76039 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
75950 AAAAAAGACA
* * **
75960 TAAGTTTTGATCACTTACGTTATTGTTTTAT
1 TAAGTTTTGGTCACTTACGCTATCATTTTAT
*
75991 TAAGTTTTGGTCACTTATGCTATCATTTTAT
1 TAAGTTTTGGTCACTTACGCTATCATTTTAT
*
76022 TAAGTTTGGGTCACTTAC
1 TAAGTTTTGGTCACTTAC
76040 ATTAAATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACGCTATCATTTTAT
Done.