Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003720.1 Hibiscus syriacus cultivar Beakdansim tig00007956_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: 54706
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:1200 original size:3 final size:3
Alignment explanation
Indices: 1186--1223 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
1176 AATATGTAGA
1186 AAT AATT AAT AAT AAT AAT AAT AA- AAT AAAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A
1224 TTATTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 24 0.75
4 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1231 original size:21 final size:20
Alignment explanation
Indices: 1193--1235 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
1183 AGAAATAATT
1193 AATAATAATAATAATAAAATA
1 AATAATAATAATAAT-AAATA
* *
1214 AATAATAATATTATTAAATA
1 AATAATAATAATAATAAATA
1234 AA
1 AA
1236 AAAGAAGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAATAATAATAATAAATA
Found at i:7439 original size:86 final size:86
Alignment explanation
Indices: 7274--7439 Score: 197
Period size: 86 Copynumber: 1.9 Consensus size: 86
7264 CATATCGGAT
* ** **
7274 CGTACTAAAAGATACCTAGTGCGAGTCAGTACTAAAGGATACCTAGTGCTGATGGTGGGAACAAC
1 CGTACTAAAAGATACCTAGTGCGAGTCAGTACTAAAGAATACCTAGTGCTGATGACGAAAACAAC
* *
7339 CTTATGTGTCATATTCGAGAC
66 CTCACGTGTCATATTCGAGAC
* * * * **
7360 CGTACTAAATGATATCTAGTGCGGGTTAGTACTAAAGAATACCTAGTGCTGATGACGAAAATGAC
1 CGTACTAAAAGATACCTAGTGCGAGTCAGTACTAAAGAATACCTAGTGCTGATGACGAAAACAAC
* *
7425 CTCCCGTGTTATATT
66 CTCACGTGTCATATT
7440 GGTTTAGCAT
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
86 65 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (86 bp):
CGTACTAAAAGATACCTAGTGCGAGTCAGTACTAAAGAATACCTAGTGCTGATGACGAAAACAAC
CTCACGTGTCATATTCGAGAC
Found at i:10302 original size:22 final size:22
Alignment explanation
Indices: 10274--10325 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
10264 ACCCGACCCG
*
10274 ACCCGAGAACAAGGAGCCCTCC
1 ACCCGAGAACAAGAAGCCCTCC
10296 ACCCGAGAACAAGAAGCCCTCC
1 ACCCGAGAACAAGAAGCCCTCC
10318 ACCCGAGA
1 ACCCGAGA
10326 CCCAACCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.40, G:0.21, T:0.04
Consensus pattern (22 bp):
ACCCGAGAACAAGAAGCCCTCC
Found at i:12789 original size:43 final size:43
Alignment explanation
Indices: 12741--12826 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
12731 CTAGAGATAG
*
12741 AACATACATTGAGAACCCCAGCATACAACTTGATTAGGGAGCA
1 AACATACATTGAGAACCCCAGCATACAACTTGATTAGAGAGCA
* *
12784 AACATACATTGAGAATCCCGGCATACAACTTGATTAGAGAGCA
1 AACATACATTGAGAACCCCAGCATACAACTTGATTAGAGAGCA
12827 CAAAGTGCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.20
Consensus pattern (43 bp):
AACATACATTGAGAACCCCAGCATACAACTTGATTAGAGAGCA
Found at i:19319 original size:2 final size:2
Alignment explanation
Indices: 19314--19345 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19304 TTTTTAACAT
19314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19346 GCATCCCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19551 original size:81 final size:81
Alignment explanation
Indices: 19429--19637 Score: 235
Period size: 81 Copynumber: 2.6 Consensus size: 81
19419 TATTTAGCTT
* * * *
19429 TTCATTTAACTTA-CATATTTGACA-CTTTCCTGTAAAATGCACAGTTAATCCATTATTCTTTTA
1 TTCATTTAAC-TAGCATAATTGACACCTTT-CTGTCAATTGCACAGTTAAGCCATTATTCTTTTA
* * *
19492 TTCAATAGTGTTTAACCG
64 CTCAACAGTATTTAACCG
* * *
19510 TTCATCTAACTAGCATAATTGACACCTTTCTGTCAATTGCACAGTTAGGCCTTTATTCTTTTACT
1 TTCATTTAACTAGCATAATTGACACCTTTCTGTCAATTGCACAGTTAAGCCATTATTCTTTTACT
*
19575 CAACGGTATTTAACCG
66 CAACAGTATTTAACCG
* * * *
19591 TTCATTTAACT-GACATAAATGACACATTTCTGCCATTTGCACAGTTA
1 TTCATTTAACTAG-CATAATTGACACCTTTCTGTCAATTGCACAGTTA
19638 GGCCTCAAAA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
80 3 0.03
81 102 0.94
82 4 0.04
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.40
Consensus pattern (81 bp):
TTCATTTAACTAGCATAATTGACACCTTTCTGTCAATTGCACAGTTAAGCCATTATTCTTTTACT
CAACAGTATTTAACCG
Found at i:22158 original size:33 final size:33
Alignment explanation
Indices: 22115--22187 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
22105 TTAAACTTTG
* *
22115 TTTC-ATTTATCAAACTTGGAAGTTTTTAAGTA
1 TTTCAATTTATCAAACTTGGAAGTATTTAAATA
* *
22147 TTTGAATTTATCGAACTTGGAAGTATTTAAATA
1 TTTCAATTTATCAAACTTGGAAGTATTTAAATA
22180 TTTCAATT
1 TTTCAATT
22188 ATCGTAAACT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 3 0.09
33 32 0.91
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (33 bp):
TTTCAATTTATCAAACTTGGAAGTATTTAAATA
Found at i:22517 original size:68 final size:68
Alignment explanation
Indices: 22408--22750 Score: 521
Period size: 68 Copynumber: 5.0 Consensus size: 68
22398 TGCATGTCTA
* * * *
22408 CCTCAAAAGCACTTAGCCTTTCATCTATCTGTCATAAATGACATC-TTTCTGTCAAATCCACA-T
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACA-CATTTCTGTCAAATGCACAGT
22471 ATAGG
65 -TAGG
* *
22476 CCTCAAAGGCACTTAGCATTTCATCTAAGC-GGCATAAATGACACCTTTCTGTCAAATGCACAGT
1 CCTCAAAGGCACTTAGCCTTTCATCTAA-CTGGCATAAATGACACATTTCTGTCAAATGCACAGT
22540 TAGG
65 TAGG
* * *
22544 CCTCAAAGGCACTTAGCCTTTCATCTAACCGACATAAATGACACATTTCTGTCAAATGTACAGTT
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTT
22609 AGG
66 AGG
* * *
22612 CTTTAAAGGCACTTAACCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTT
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTT
22677 AGG
66 AGG
*
22680 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTATCAAATGCACAGTT
1 CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTT
22745 AGG
66 AGG
22748 CCT
1 CCT
22751 TAAATATTTT
Statistics
Matches: 252, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
67 2 0.01
68 248 0.98
69 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (68 bp):
CCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTT
AGG
Found at i:23167 original size:59 final size:59
Alignment explanation
Indices: 23092--23861 Score: 1119
Period size: 59 Copynumber: 13.1 Consensus size: 59
23082 TACATATTTT
* * * * * * *
23092 CCTATACGAAAATTCATACACTTAGGATGAATTTCTTATCATTTTAGCACAC-ATGGTAC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGA-AGTGC
* * * * * *
23151 CCCATTTGAAAATTCATACACTTAGTATGAATTCCTTCCCATGTTAGCACACGAATTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
* * *
23210 CCTATATGGAAATTCACACACTTAGTATGAATTCCTTCCCATGTTAGCACACGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
* * *
23269 CCTATATGAAAATTCATACACTTAGTATGAATTCCTTCCCATGTTAGCACACGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
* * * *
23328 CCTATATGGAAATTCACACACTTAGTATGAATTCCTTCTCATGGTAGCACAAGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
*
23387 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCAAACGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
* *
23446 CCTATATGGAAATTCCTACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
* ** *
23505 CCTATATAGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
*
23564 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAACACACGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
* *
23623 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCGTGTTAGTACACGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
** *
23682 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
* * **
23741 TCTATATGGAAATTCATACACTTAGTATGAATTTCTTTTCATGTTAGCACACGACTTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
* * ** *
23800 CCTATATGGAAATCCATACACTTAGTATGAATTTATTAACATTTTAGCACACGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
23859 CCT
1 CCT
23862 TTTTGTAATT
Statistics
Matches: 646, Mismatches: 64, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
59 645 1.00
60 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (59 bp):
CCTATATGGAAATTCATACACTTAGTATGAATTTCTTCTCATGTTAGCACACGAAGTGC
Found at i:28311 original size:14 final size:14
Alignment explanation
Indices: 28292--28319 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28282 GTAGCTCCTA
28292 CCACCCCTAGACGG
1 CCACCCCTAGACGG
28306 CCACCCCTAGACGG
1 CCACCCCTAGACGG
28320 ATGGCCAGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
CCACCCCTAGACGG
Found at i:39670 original size:95 final size:94
Alignment explanation
Indices: 39579--39767 Score: 256
Period size: 94 Copynumber: 2.0 Consensus size: 94
39569 CGATACTTTT
** * *
39579 ATGCTATGGTACCGATACCCCCTTTTGGTATCGATA-CAAATTTTAGGTTCGATG-TTGCATGGT
1 ATGCTATGGTACCGATA-CCCCTTCCGGTATCGATACCAAA-TTTAGATTCGATGATT-CATGCT
39642 ATCGATACCCTTACCATGGTATGGATACTACC
63 ATCGATACCCTTACCATGGTATGGATACTACC
* * *
39674 ATGTTATGGTATCGATACCCCTTCCGGTATCGATACCAAATTTAGATTCGATGATTCTTGCTATC
1 ATGCTATGGTACCGATACCCCTTCCGGTATCGATACCAAATTTAGATTCGATGATTCATGCTATC
* *
39739 GATACCCTTACCATGGTATCGAAACTACC
66 GATACCCTTACCATGGTATGGATACTACC
39768 TCTTCGGTAT
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
94 62 0.75
95 21 0.25
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.33
Consensus pattern (94 bp):
ATGCTATGGTACCGATACCCCTTCCGGTATCGATACCAAATTTAGATTCGATGATTCATGCTATC
GATACCCTTACCATGGTATGGATACTACC
Found at i:41351 original size:65 final size:67
Alignment explanation
Indices: 41195--41352 Score: 187
Period size: 65 Copynumber: 2.4 Consensus size: 67
41185 TTATTTGTTT
*
41195 AAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTTGGTTAATTTGATTCAGTTAATAAT
1 AAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAA-TT-GTTAATTTGATTCAGTTAATAAT
41260 TTGC
64 TTGC
* * * * *
41264 AAATAAATTTTGGTTCGTTTAACGGTTAAGGAAAAATAA-T-TT-ATTTTATTCGGTTAATAATT
1 AAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAA-AATTGTTAATTTGATTCAGTTAATAATT
*
41326 TTC
65 TGC
* *
41329 AAATAAATTTCGATACGATTAACG
1 AAATAAATTTCGGTTCGATTAACG
41353 ATCAAATAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
65 40 0.52
66 2 0.03
68 1 0.01
69 32 0.42
70 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.40
Consensus pattern (67 bp):
AAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAATTGTTAATTTGATTCAGTTAATAATTT
GC
Found at i:41371 original size:91 final size:93
Alignment explanation
Indices: 41263--41446 Score: 230
Period size: 94 Copynumber: 2.0 Consensus size: 93
41253 TAATAATTTG
* * * *
41263 CAAATAAATTTTGGTTCGTTTAACGGTTAAGGAAAAATAAT-TT-ATTTTATTCGGTTAATAATT
1 CAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAA-AATGTTGATTTGATTCGGTTAATAATT
41326 TTCAAATAAATTTCGATACGATTAACGAT
65 TTCAAATAAATTTCGATACGATTAACGAT
* *
41355 CAAAT-AATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAAT
1 CAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAAT--GTTGATTTGATTCGGTTAATAAT
* * * *
41419 TTTCAAATATATTTTGGTTCGATTAACG
64 TTTCAAATAAATTTCGATACGATTAACG
41447 GTTAAAGAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
90 3 0.04
91 27 0.35
92 5 0.06
93 2 0.03
94 41 0.53
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.40
Consensus pattern (93 bp):
CAAATAAATTTCGGTTCGATTAACGGTTAAAGAAAAAAATGTTGATTTGATTCGGTTAATAATTT
TCAAATAAATTTCGATACGATTAACGAT
Found at i:41443 original size:68 final size:64
Alignment explanation
Indices: 41354--41513 Score: 214
Period size: 65 Copynumber: 2.4 Consensus size: 64
41344 CGATTAACGA
*
41354 TCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAA-AATCGGTTGATTTGGTTCGGTTAATAA
1 TCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAATAA----TTGATTTGATTCGGTTAATAA
41418 TTT
62 TTT
* * *
41421 TCAAATATATTTTGGTTCGATTAACGGTTAAAGAAAAATAATTGATTTTATTCGGTTAATAATTT
1 TCAAATA-ATTTCGGTTCGATTAATGGTTAAAGAAAAATAATTGATTTGATTCGGTTAATAATTT
*
41486 TCAAATAAATTTGGGTTCGATTAATGGT
1 TCAAAT-AATTTCGGTTCGATTAATGGT
41514 CAAATAATTT
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
65 46 0.55
66 1 0.01
67 7 0.08
68 28 0.33
69 2 0.02
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (64 bp):
TCAAATAATTTCGGTTCGATTAATGGTTAAAGAAAAATAATTGATTTGATTCGGTTAATAATTT
Found at i:41490 original size:159 final size:159
Alignment explanation
Indices: 41195--41886 Score: 1044
Period size: 159 Copynumber: 4.3 Consensus size: 159
41185 TTATTTGTTT
* * * *
41195 AAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATTTGGTTAATTTGATTCAGTTAATAAT
1 AAAT-AATTTCGGTTCGATTAATGGTTAAAGAAAAAAA-TCGGTTGATTTGGTTCGGTTAATAAT
* * *
41260 TTGCAAATAAATTTTGGTTCGTTTAACGGTTAAGGAAAAATAATTTATTTTATTCGGTTAATAAT
64 TTTCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAAT
* * * *
41325 TTTCAAATAAATTTCGATACGATTAACGATC
129 TTTCAAATAAATTTGGGTTCGATTAACGGTC
41356 AAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAATTT
1 AAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAATTT
* *
41421 TCAAATATATTTTGGTTCGATTAACGGTTAAAGAAAAATAATTGATTTTATTCGGTTAATAATTT
66 TCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTT
*
41486 TCAAATAAATTTGGGTTCGATTAATGGTC
131 TCAAATAAATTTGGGTTCGATTAACGGTC
* *
41515 AAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAAAAAATT
1 AAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAATTT
*
41580 TCAAATAAATTTCT-GTTCGATTAACGGTTAAAGAAAATTAATTTATTTTATTCGGTTAATTCGG
66 TCAAATAAATTT-TGGTTCGATTAACGGTTAAAG-AAA--AA--TAATTTATT---TT-ATTCGG
41644 TTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTC
121 TTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTC
*
41683 AAATAATTTTGGTTCGATTAATGGTTAAAGAGAAAAAATCGGTTGATTTGGTTCGGTTAATAATT
1 AAATAATTTCGGTTCGATTAATGGTTAAAGA-AAAAAATCGGTTGATTTGGTTCGGTTAATAATT
**
41748 TTCAAATAAATTTTGGTTTAATTAACGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATT
65 TTCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATT
*
41813 TTCAAATAAATTTGGGTTCGTTTAACGGTC
130 TTCAAATAAATTTGGGTTCGATTAACGGTC
* *
41843 AAATAATTTTGGTTCGATTAATGGTTAAAGAAACAAATTCGGTT
1 AAATAATTTCGGTTCGATTAATGGTTAAAGAAA-AAAATCGGTT
41887 AATAATTTTC
Statistics
Matches: 490, Mismatches: 28, Indels: 27
0.90 0.05 0.05
Matches are distributed among these distances:
159 203 0.41
160 121 0.25
161 6 0.01
162 2 0.00
164 15 0.03
166 2 0.00
167 2 0.00
168 78 0.16
169 61 0.12
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.40
Consensus pattern (159 bp):
AAATAATTTCGGTTCGATTAATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAATTT
TCAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAATAATTTATTTTATTCGGTTAATAATTT
TCAAATAAATTTGGGTTCGATTAACGGTC
Found at i:41529 original size:26 final size:27
Alignment explanation
Indices: 41486--41539 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
41476 TTAATAATTT
*
41486 TCAAATAAATTTGGGTTCGATTAATGG
1 TCAAATAAATTTCGGTTCGATTAATGG
41513 TCAAAT-AATTTCGGTTCGATTAATGG
1 TCAAATAAATTTCGGTTCGATTAATGG
41539 T
1 T
41540 TAAAGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
TCAAATAAATTTCGGTTCGATTAATGG
Found at i:41598 original size:94 final size:92
Alignment explanation
Indices: 41421--41603 Score: 244
Period size: 94 Copynumber: 2.0 Consensus size: 92
41411 TTAATAATTT
* * * *
41421 TCAAATATATTTTGGTTCGATTAACGGTTAAAGAAAAATAATTGATTTTATTCGGTTAATAATTT
1 TCAAATATATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTGATTTGATTCGGTTAAAAAATT
*
41486 TCAAATAAATTTGGGTTCGATTAATGG
66 TCAAATAAATTTCGGTTCGATTAATGG
* *
41513 TCAAATA-ATTTCGGTTCGATTAATGGTTAAAGAAAAA-AATCGGTTGATTTGGTTCGGTTAAAA
1 TCAAATATATTTCGGTTCGATTAACGGTTAAAGAAAAATAA----TTGATTTGATTCGGTTAAAA
*
41576 AATTTCAAATAAATTTCTGTTCGATTAA
62 AATTTCAAATAAATTTCGGTTCGATTAA
41604 CGGTTAAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
90 2 0.03
91 28 0.35
92 7 0.09
94 42 0.53
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (92 bp):
TCAAATATATTTCGGTTCGATTAACGGTTAAAGAAAAATAATTGATTTGATTCGGTTAAAAAATT
TCAAATAAATTTCGGTTCGATTAATGG
Found at i:41838 original size:65 final size:67
Alignment explanation
Indices: 41681--41841 Score: 204
Period size: 65 Copynumber: 2.4 Consensus size: 67
41671 CGATTAACGG
* *
41681 TCAAAT-AATTTTGGTTCGATTAATGGTTAAAGAGAAAAAATCGGTTGATTTGGTTCGGTTAATA
1 TCAAATAAATTTTGGTTCGATTAACGGTTAAAGAGAAAAAAT--GTTGATTTGATTCGGTTAATA
41745 ATTT
64 ATTT
** *
41749 TCAAATAAATTTTGGTTTAATTAACGGTTAAAGA-AAAATAAT-TT-ATTTTATTCGGTTAATAA
1 TCAAATAAATTTTGGTTCGATTAACGGTTAAAGAGAAAA-AATGTTGATTTGATTCGGTTAATAA
41811 TTT
65 TTT
* *
41814 TCAAATAAATTTGGGTTCGTTTAACGGT
1 TCAAATAAATTTTGGTTCGATTAACGGT
41842 CAAATAATTT
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
65 43 0.52
66 2 0.02
68 10 0.12
69 27 0.33
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (67 bp):
TCAAATAAATTTTGGTTCGATTAACGGTTAAAGAGAAAAAATGTTGATTTGATTCGGTTAATAAT
TT
Found at i:41892 original size:81 final size:80
Alignment explanation
Indices: 41798--41955 Score: 262
Period size: 81 Copynumber: 2.0 Consensus size: 80
41788 AATTTATTTT
* * *
41798 ATTCGGTTAATAATTTTCAAATAAATTTGGGTTCGTTTAACGGTCAAATAATTTTGGTTCGATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGCCAAATAATTTCGGTTCGATTA
41863 ATGGTTAAAGAAACAA
66 AT-GTTAAAGAAACAA
* *
41879 ATTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACGGCCAAATAATTTCGGTTTGATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGCCAAATAATTTCGGTTCGATTA
41944 ATGTTAAAGAAA
66 ATGTTAAAGAAA
41956 AAAAATCGAT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
80 10 0.14
81 62 0.86
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (80 bp):
ATTCGGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGCCAAATAATTTCGGTTCGATTA
ATGTTAAAGAAACAA
Found at i:43208 original size:21 final size:19
Alignment explanation
Indices: 43160--43216 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
43150 TCATACTTTT
*
43160 AAATAAAT-TTTTTACATA
1 AAATAAATATTTTTAAATA
*
43178 AAATATATATTTTTAAATGA
1 AAATAAATATTTTTAAAT-A
43198 AAATAAAATATTTTTAAAT
1 AAAT-AAATATTTTTAAAT
43217 TAATTTGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 5 0.15
21 13 0.39
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
AAATAAATATTTTTAAATA
Found at i:46288 original size:10 final size:10
Alignment explanation
Indices: 46266--46321 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
46256 TAAATAGTCA
*
46266 TTATTATAGT
1 TTATTATATT
*
46276 TTATCATATT
1 TTATTATATT
46286 TTATTATTATT
1 TTATTA-TATT
*
46297 ATGATTATATT
1 -TTATTATATT
*
46308 TAATTATATT
1 TTATTATATT
46318 TTAT
1 TTAT
46322 AATTTCTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
10 25 0.66
11 8 0.21
12 5 0.13
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (10 bp):
TTATTATATT
Found at i:46961 original size:19 final size:20
Alignment explanation
Indices: 46937--46975 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
46927 AAGTTTTTTA
*
46937 ATTTTTAATT-TTAGAAAAT
1 ATTTTTAATTATTAAAAAAT
*
46956 ATTTTTTATTATTAAAAAAT
1 ATTTTTAATTATTAAAAAAT
46976 TTAAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTTTTAATTATTAAAAAAT
Found at i:53211 original size:21 final size:21
Alignment explanation
Indices: 53186--53279 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
53176 GTTTTCAGAT
*
53186 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGAATTTGGACTA
*
53207 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAATTTGGACTA
* * * *
53228 TCACAATGCGAATATGTA-AA
1 TCGCAATGCGAATTTGGACTA
*
53248 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAATTTGGACTA
*
53269 TCGCATTGCGA
1 TCGCAATGCGA
53280 TTTATATATT
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGACTA
Found at i:53936 original size:6 final size:6
Alignment explanation
Indices: 53915--53951 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
53905 TTCCGTCTCG
53915 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
53952 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:54121 original size:20 final size:21
Alignment explanation
Indices: 54076--54208 Score: 97
Period size: 20 Copynumber: 6.6 Consensus size: 21
54066 ACTATCGCAA
* * *
54076 ATCGCAATGCGATAGTCTAAGT
1 ATCGCATTGCGATAGTC-GACT
54098 -TCGCATT-CGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
*
54117 ATCGCATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
54136 ATTCGCATTGCGATAGTCGACT
1 A-TCGCATTGCGATAGTCGACT
*
54158 AT--CATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
54175 ATTCGCATTGCGATAGTCGACT
1 A-TCGCATTGCGATAGTCGACT
*
54197 ATCGCAATGCGA
1 ATCGCATTGCGA
54209 ATCTGGAAAC
Statistics
Matches: 89, Mismatches: 8, Indels: 29
0.71 0.06 0.23
Matches are distributed among these distances:
16 2 0.02
17 3 0.03
18 3 0.03
19 14 0.16
20 36 0.40
21 21 0.24
22 6 0.07
23 4 0.04
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (21 bp):
ATCGCATTGCGATAGTCGACT
Found at i:54121 original size:41 final size:41
Alignment explanation
Indices: 54097--54208 Score: 185
Period size: 39 Copynumber: 2.8 Consensus size: 41
54087 ATAGTCTAAG
*
54097 TTCGCATT-CGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCAATGCGATTTACATA
*
54137 TTCGCATTGCGATAGTCGACTAT--CATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCAATGCGATTTACATA
54176 TTCGCATTGCGATAGTCGACTATCGCAATGCGA
1 TTCGCATTGCGATAGTCGACTATCGCAATGCGA
54209 ATCTGGAAAC
Statistics
Matches: 68, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
39 39 0.57
40 8 0.12
41 21 0.31
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (41 bp):
TTCGCATTGCGATAGTCGACTATCGCAATGCGATTTACATA
Done.