Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007714.1 Hibiscus syriacus cultivar Beakdansim tig00109941_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: 79963
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:44 original size:24 final size:22
Alignment explanation
Indices: 11--65 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
1 GGTTTTCTTC
*
11 TTTATTCCATTGTAGAAAAGACAT
1 TTTATGCCA-TGT-GAAAAGACAT
* *
35 TTTATGCCATGTGCAATGACAT
1 TTTATGCCATGTGAAAAGACAT
57 TTTATGCCA
1 TTTATGCCA
66 AGTAAACCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 17 0.61
23 3 0.11
24 8 0.29
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (22 bp):
TTTATGCCATGTGAAAAGACAT
Found at i:906 original size:2 final size:2
Alignment explanation
Indices: 899--952 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
889 GAAAAAGTCA
899 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
941 AT AT AT AT AT AT
1 AT AT AT AT AT AT
953 GAGTATTCGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12072 original size:60 final size:60
Alignment explanation
Indices: 12008--12177 Score: 189
Period size: 60 Copynumber: 2.8 Consensus size: 60
11998 CAATGATCCA
* * * *
12008 CATTCTAAATTAGTCCCTAAACTTTTGAATATTCTAATTTCATCTTCAAACTATGATAAT
1 CATTCTAAATTAGTCCCTAAACTTTTGAAAATTCCAATTTCATCCTCAAACTATGACAAT
* * * * **
12068 CATTCTAAATTAGTCCTTATACTTCTGAAAATTCCAATTTCATCCTCAAACTATTACCTT
1 CATTCTAAATTAGTCCCTAAACTTTTGAAAATTCCAATTTCATCCTCAAACTATGACAAT
* * * * *
12128 TATTCTAAATTGGTCCCTAAACTTTT-AAACCTACCAATTTCATCCCCAAA
1 CATTCTAAATTAGTCCCTAAACTTTTGAAA-ATTCCAATTTCATCCTCAAA
12178 TTCATCCAAA
Statistics
Matches: 91, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
59 3 0.03
60 88 0.97
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.39
Consensus pattern (60 bp):
CATTCTAAATTAGTCCCTAAACTTTTGAAAATTCCAATTTCATCCTCAAACTATGACAAT
Found at i:14163 original size:18 final size:18
Alignment explanation
Indices: 14140--14174 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
14130 GGTGTGGAGA
*
14140 TAATTTTTTTTTTAATTT
1 TAATTTTTTATTTAATTT
14158 TAATTTTTTATTTAATT
1 TAATTTTTTATTTAATT
14175 GCATTTATAT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TAATTTTTTATTTAATTT
Found at i:15171 original size:21 final size:20
Alignment explanation
Indices: 15145--15212 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 20
15135 TGGGAGTGAT
15145 GATGATGACGAGAACGAGGAG
1 GATGATGACGAGAA-GAGGAG
* *
15166 GATGATGATGAGGATA-AGGAC
1 GATGATGACGA-GA-AGAGGAG
15187 GATGATGACGAGGAAGAGGAG
1 GATGATGACGA-GAAGAGGAG
15208 GATGA
1 GATGA
15213 CAATGATAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 1 0.03
21 36 0.90
22 2 0.05
23 1 0.03
ACGTcount: A:0.38, C:0.06, G:0.43, T:0.13
Consensus pattern (20 bp):
GATGATGACGAGAAGAGGAG
Found at i:15530 original size:26 final size:27
Alignment explanation
Indices: 15479--15530 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
15469 GGTATACTTC
*
15479 ATGTCATGTTTAATAGTTTGTTGTTTA
1 ATGTAATGTTTAATAGTTTGTTGTTTA
*
15506 ATGTAATGTTT-ATGGTTTGTTGTTT
1 ATGTAATGTTTAATAGTTTGTTGTTT
15531 TTATAGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (27 bp):
ATGTAATGTTTAATAGTTTGTTGTTTA
Found at i:16546 original size:83 final size:83
Alignment explanation
Indices: 16404--16558 Score: 292
Period size: 83 Copynumber: 1.9 Consensus size: 83
16394 ATGTCATAGT
* *
16404 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCTGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
16469 GTGCGTTCCAGAGGAAGC
66 GTGCGTTCCAGAGGAAGC
16487 GTTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
1 GTTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
16552 GTGCGTT
66 GTGCGTT
16559 TAGATAATCT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (83 bp):
GTTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
GTGCGTTCCAGAGGAAGC
Found at i:18954 original size:16 final size:17
Alignment explanation
Indices: 18930--18962 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
18920 TGAGGTGTCA
18930 CATTGACTTTT-CAAAG
1 CATTGACTTTTACAAAG
*
18946 CATTTACTTTTACAAAG
1 CATTGACTTTTACAAAG
18963 TGACTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (17 bp):
CATTGACTTTTACAAAG
Found at i:26926 original size:32 final size:32
Alignment explanation
Indices: 26867--26928 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
26857 ACGGGGCATA
* *
26867 GGAGGCACATTCCTTACGATGCACCATTCAAG
1 GGAGGCACATTCCATACGACGCACCATTCAAG
* * *
26899 GGAGGCACGTTCCATAGGACGCCCCATTCA
1 GGAGGCACATTCCATACGACGCACCATTCA
26929 TAAAAACCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.19
Consensus pattern (32 bp):
GGAGGCACATTCCATACGACGCACCATTCAAG
Found at i:29527 original size:23 final size:23
Alignment explanation
Indices: 29495--29539 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29485 AAACAAAATG
29495 TCCAGAGGGTACAGATACCCCCC
1 TCCAGAGGGTACAGATACCCCCC
* * *
29518 TCCAGGGGGTACCGATTCCCCC
1 TCCAGAGGGTACAGATACCCCC
29540 TGTGTAACGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (23 bp):
TCCAGAGGGTACAGATACCCCCC
Found at i:37264 original size:15 final size:15
Alignment explanation
Indices: 37244--37272 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
37234 AATCCCAGTG
37244 AATATTAAGTGAGAA
1 AATATTAAGTGAGAA
37259 AATATTAAGTGAGA
1 AATATTAAGTGAGA
37273 TGAAAGAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.28
Consensus pattern (15 bp):
AATATTAAGTGAGAA
Found at i:38340 original size:29 final size:29
Alignment explanation
Indices: 38295--38352 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
38285 GTGTTGGCCG
*
38295 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* * *
38324 TAGGTCGTCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
38353 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.34, G:0.28, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:38417 original size:14 final size:14
Alignment explanation
Indices: 38395--38461 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 14
38385 CGCTGAGCAT
38395 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
38409 CCGATGCCATCCGAGA
1 CCGAGGCCATCC--GA
*
38425 GCATCTGAGACCATCCGA
1 -C--C-GAGGCCATCCGA
38443 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
38457 ACGAG
1 CCGAG
38462 CTATGCGAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
14 26 0.62
15 1 0.02
16 2 0.05
17 2 0.05
18 2 0.05
19 1 0.02
20 8 0.19
ACGTcount: A:0.25, C:0.37, G:0.27, T:0.10
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:38427 original size:34 final size:34
Alignment explanation
Indices: 38389--38456 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
38379 CCAACACGCT
* *
38389 GAGCATCCGAGGCCATCCGACCGATGCCATCCGA
1 GAGCATCCGAGACCATCCGACCGAGGCCATCCGA
*
38423 GAGCATCTGAGACCATCCGACCGAGGCCATCCGA
1 GAGCATCCGAGACCATCCGACCGAGGCCATCCGA
38457 ACGAGCTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.25, C:0.37, G:0.26, T:0.12
Consensus pattern (34 bp):
GAGCATCCGAGACCATCCGACCGAGGCCATCCGA
Found at i:38503 original size:23 final size:23
Alignment explanation
Indices: 38444--38503 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
38434 ACCATCCGAC
* * *
38444 CGAGGCCATCCGAACGAGCTATG
1 CGAGGGCAACCGAGCGAGCTATG
38467 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCAACCGAGCGAGCTATG
38490 CGAGGGCAACCGAG
1 CGAGGGCAACCGAG
38504 GGAAGCCGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.28, G:0.37, T:0.08
Consensus pattern (23 bp):
CGAGGGCAACCGAGCGAGCTATG
Found at i:39379 original size:20 final size:20
Alignment explanation
Indices: 39354--39392 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
39344 AAATAATGTA
39354 ATAATAATATG-ATTTGTATC
1 ATAATAA-ATGCATTTGTATC
39374 ATAATAAATGCATTTGTAT
1 ATAATAAATGCATTTGTAT
39393 GATTATTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (20 bp):
ATAATAAATGCATTTGTATC
Found at i:40136 original size:7 final size:7
Alignment explanation
Indices: 40124--40176 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
40114 AATTAGATTA
40124 AGGGTTT
1 AGGGTTT
40131 AGGGTTT
1 AGGGTTT
40138 A-GGTTT
1 AGGGTTT
* *
40144 AGTGTTA
1 AGGGTTT
40151 AGGGTTT
1 AGGGTTT
**
40158 ATAGTTT
1 AGGGTTT
*
40165 ATGGTTT
1 AGGGTTT
40172 AGGGT
1 AGGGT
40177 GTAATCTAAC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
6 6 0.16
7 31 0.84
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.45
Consensus pattern (7 bp):
AGGGTTT
Found at i:40153 original size:27 final size:28
Alignment explanation
Indices: 40121--40173 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
40111 CATAATTAGA
*
40121 TTAAGGGTTTAGGGTTTA-GGTTTAGTG
1 TTAAGGGTTTAGAGTTTATGGTTTAGTG
*
40148 TTAAGGGTTTATAGTTTATGGTTTAG
1 TTAAGGGTTTAGAGTTTATGGTTTAG
40174 GGTGTAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (28 bp):
TTAAGGGTTTAGAGTTTATGGTTTAGTG
Found at i:40315 original size:11 final size:11
Alignment explanation
Indices: 40299--40356 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
40289 GCATTATAGA
40299 ATTTTTAATAT
1 ATTTTTAATAT
40310 ATTTTTAA-A-
1 ATTTTTAATAT
40319 ATTTTATAAT-T
1 ATTTT-TAATAT
** *
40330 ATTAATAATGT
1 ATTTTTAATAT
40341 ATTTTTAATA-
1 ATTTTTAATAT
40351 ATTTTT
1 ATTTTT
40357 TTATAATGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
9 5 0.13
10 14 0.37
11 19 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:40350 original size:14 final size:14
Alignment explanation
Indices: 40331--40373 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
40321 TTTATAATTA
40331 TTAATAATGTATTT
1 TTAATAATGTATTT
40345 TTAATAAT-T-TTT
1 TTAATAATGTATTT
*
40357 TT-ATAATGTAATT
1 TTAATAATGTATTT
40370 TTAA
1 TTAA
40374 AAATTCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
11 5 0.20
12 6 0.24
13 5 0.20
14 9 0.36
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
TTAATAATGTATTT
Found at i:43989 original size:36 final size:36
Alignment explanation
Indices: 43948--44023 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
43938 ATTTTCGGGA
*
43948 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
43984 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
44020 TTTT
1 TTTT
44024 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:44466 original size:15 final size:15
Alignment explanation
Indices: 44446--44475 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
44436 TATCACAATC
44446 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
44461 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
44476 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:48990 original size:36 final size:36
Alignment explanation
Indices: 48949--49024 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
48939 ATTTTCGGGA
*
48949 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
48985 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
49021 TTTT
1 TTTT
49025 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:53100 original size:22 final size:20
Alignment explanation
Indices: 53075--53124 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
53065 TTTTCTGTGC
53075 TATTTTCTGCTATGATTGTTGG
1 TATTTT-TGCTATGATT-TTGG
*
53097 TATTGTTTGTTATGATTTTGG
1 TATT-TTTGCTATGATTTTGG
53118 T-TTTTTG
1 TATTTTTG
53125 TTTGCTAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 2 0.08
21 5 0.19
22 13 0.50
23 2 0.08
ACGTcount: A:0.12, C:0.04, G:0.22, T:0.62
Consensus pattern (20 bp):
TATTTTTGCTATGATTTTGG
Found at i:53126 original size:19 final size:22
Alignment explanation
Indices: 53085--53126 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
53075 TATTTTCTGC
53085 TATGATTGTTGGTATTGTTTGT
1 TATGATTGTTGGTATTGTTTGT
53107 TATGATT-TTGGT-TT-TTTGT
1 TATGATTGTTGGTATTGTTTGT
53126 T
1 T
53127 TGCTAGAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 5 0.25
22 7 0.35
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.64
Consensus pattern (22 bp):
TATGATTGTTGGTATTGTTTGT
Found at i:53734 original size:141 final size:143
Alignment explanation
Indices: 53398--53725 Score: 416
Period size: 141 Copynumber: 2.3 Consensus size: 143
53388 AGTATTGTAA
* * *
53398 ATTGAATTTATTAGTTTCGTGTTTCATTCTTTAATTCTTCATTATGTTGTGTCCATTCTTCTTTC
1 ATTGAATTTATTAGTTTGGTGTTTCATT-ATTAATTCTTCATTATGTTGCGTCCA-T-TTCTTTC
* *
53463 TCTTTCAAGGCAGAAGAGTTCACGTTATTATTTAAAAATCATTATTAATTAAATTTATTATTTTG
63 TCTTTCAAGGCAGAAGAGTTCACGCTATTATTTAAAAATC--TATTAATTAAATTTATTAGTTTG
53528 GTGCTTCATTATGTGCTC
126 GTGCTTCATTATGTGCTC
* * *
53546 ATTGAATTTATTAGTTTGGTGTTTTAATATTCAGTTCTTCATTATGTTGCGTCCA-TTCTTTCTC
1 ATTGAATTTATTAGTTTGGTGTTTCATTATT-AATTCTTCATTATGTTGCGTCCATTTCTTTCTC
53610 TTTCAAGGCAGCAA-AG-TCTACGCTATTATTTAAAAATC-ATT-ATTAAATTTATTAGTTTGGT
65 TTTCAAGGCAG-AAGAGTTC-ACGCTATTATTTAAAAATCTATTAATTAAATTTATTAGTTTGGT
* * * *
53671 GCTTTATTTTTTGTTC
128 GCTTCATTATGTGCTC
*
53687 ATTGAATTTATTAGTTTGGTGCTTCATTATGT-ATTCTTC
1 ATTGAATTTATTAGTTTGGTGTTTCATTAT-TAATTCTTC
53726 TGCTATGTTT
Statistics
Matches: 160, Mismatches: 16, Indels: 16
0.83 0.08 0.08
Matches are distributed among these distances:
140 6 0.04
141 58 0.36
142 4 0.03
144 2 0.01
145 40 0.25
146 2 0.01
147 2 0.01
148 46 0.29
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (143 bp):
ATTGAATTTATTAGTTTGGTGTTTCATTATTAATTCTTCATTATGTTGCGTCCATTTCTTTCTCT
TTCAAGGCAGAAGAGTTCACGCTATTATTTAAAAATCTATTAATTAAATTTATTAGTTTGGTGCT
TCATTATGTGCTC
Found at i:64289 original size:30 final size:31
Alignment explanation
Indices: 64254--64311 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
64244 AGTAAAATTT
*
64254 TGAT-AAACTTAATAAATGTTTTATAAAATA
1 TGATAAAACTTAATAAATATTTTATAAAATA
* *
64284 TGATAAAATTTAATAATTATTTTATAAA
1 TGATAAAACTTAATAAATATTTTATAAA
64312 TTCTAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (31 bp):
TGATAAAACTTAATAAATATTTTATAAAATA
Found at i:64310 original size:21 final size:21
Alignment explanation
Indices: 64286--64372 Score: 70
Period size: 21 Copynumber: 4.1 Consensus size: 21
64276 ATAAAATATG
*
64286 ATAAAATTTAATAATTATTTT
1 ATAAAATTTAATAATAATTTT
*
64307 AT-AAATTCTAATAA-AATTTA
1 ATAAAATT-TAATAATAATTTT
*** *
64327 ATGGTTATTTAACAATAATTTT
1 AT-AAAATTTAATAATAATTTT
* *
64349 TTAAAATTTAATAATTATTTT
1 ATAAAATTTAATAATAATTTT
64370 ATA
1 ATA
64373 CTAATAATTT
Statistics
Matches: 49, Mismatches: 13, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
20 11 0.22
21 29 0.59
22 9 0.18
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATAAAATTTAATAATAATTTT
Found at i:64321 original size:31 final size:30
Alignment explanation
Indices: 64262--64372 Score: 96
Period size: 31 Copynumber: 3.6 Consensus size: 30
64252 TTTGATAAAC
* * * *
64262 TTAATAAATGTTTTATAAAATATGATAAAAT
1 TTAATAATTATTTTAT-AAATTTAATAAAAT
64293 TTAATAATTATTTTATAAATTCTAATAAAAT
1 TTAATAATTATTTTATAAATT-TAATAAAAT
** * * **
64324 TTAATGGTTATTTAACAATAATTTTTTAAAAT
1 TTAATAATTATTTTA-TA-AATTTAATAAAAT
64356 TTAATAATTATTTTATA
1 TTAATAATTATTTTATA
64373 CTAATAATTT
Statistics
Matches: 63, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
30 4 0.06
31 35 0.56
32 20 0.32
33 4 0.06
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (30 bp):
TTAATAATTATTTTATAAATTTAATAAAAT
Found at i:64367 original size:32 final size:32
Alignment explanation
Indices: 64286--64403 Score: 107
Period size: 31 Copynumber: 3.7 Consensus size: 32
64276 ATAAAATATG
* *
64286 ATAAAATTTAATAATTATTTTA-TA-AATTCTA
1 ATAAAATTTAATAATTATTTAACAATAATT-TA
** *
64317 ATAAAATTTAATGGTTATTTAACAATAATTTT
1 ATAAAATTTAATAATTATTTAACAATAATTTA
*
64349 TTAAAATTTAATAATTATTTTATACTAATAATTTA
1 ATAAAATTTAATAATTA-TTTA-AC-AATAATTTA
* *
64384 AT-AAACTTAATAGTTATTTA
1 ATAAAATTTAATAATTATTTA
64404 TAATTTTTAA
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
31 19 0.27
32 16 0.23
33 12 0.17
34 14 0.20
35 9 0.13
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (32 bp):
ATAAAATTTAATAATTATTTAACAATAATTTA
Found at i:70735 original size:23 final size:22
Alignment explanation
Indices: 70682--70764 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
70672 CAGAACCCGT
* *
70682 GGGGGTATCGATTCCC-T-AAA
1 GGGGGAATCGGTTCCCTTCAAA
70702 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGGTTCCC-TTCAAA
70726 GGGGGAATCGGTTCGCCTTC-AA
1 GGGGGAATCGGTTC-CCTTCAAA
* *
70748 GGGGGTATCGATTCCCT
1 GGGGGAATCGGTTCCCT
70765 CTGCACCAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
20 2 0.04
21 15 0.28
22 14 0.26
23 16 0.30
24 7 0.13
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTTCAAA
Found at i:79916 original size:98 final size:103
Alignment explanation
Indices: 79764--79963 Score: 347
Period size: 98 Copynumber: 2.0 Consensus size: 103
79754 GTAGAGGGTC
79764 TATGTGGTCCTTCGGGGACATATATGTATTCTTTGGAACAGGTTGTGAGGTCTGTTGAGACACAT
1 TATGTGGTCCTT--GGGACATATATGTATTCTTTGGAACAGGTTGTGAGGTCTGTTGAGACACAT
79829 ACTTGATCTTTGGCATATGTATATGATT-TTAAGGAATGA
64 ACTTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
79868 TATGTGGTCCTT-GGACATATAT-TATTC-TTGGAACAGG-TGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTGGGACATATATGTATTCTTTGGAACAGGTTGTGAGGTCTGTTGAGACACATAC
79929 TTGATCTTTGGCATATGTATATGATTCTTAAGGAA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAA
Statistics
Matches: 95, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
98 50 0.53
99 18 0.19
100 5 0.05
101 10 0.11
104 12 0.13
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTGGGACATATATGTATTCTTTGGAACAGGTTGTGAGGTCTGTTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Done.