Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001246.1 Hibiscus syriacus cultivar Beakdansim tig00002448_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: 86982
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:856 original size:30 final size:30
Alignment explanation
Indices: 814--897 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
804 AATGTTTGTG
* *
814 ATTTTAGCTATTTTAGTCATTTAAGTTTCT
1 ATTTTAGATATTTTAGTCATTTAACTTTCT
* * *
844 ATTTTTGTTATTTTAGTCCTTTAACTTTCT
1 ATTTTAGATATTTTAGTCATTTAACTTTCT
* *
874 GTTTTAGATATTTTAGTCTTTTAA
1 ATTTTAGATATTTTAGTCATTTAA
898 ATTTGTTTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.60
Consensus pattern (30 bp):
ATTTTAGATATTTTAGTCATTTAACTTTCT
Found at i:7787 original size:3 final size:3
Alignment explanation
Indices: 7779--7816 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
7769 ATTGGGCTTG
7779 TTA TTA TTA -TA TTA TTA TTA TTA -TA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
7817 ATACTATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:7795 original size:11 final size:11
Alignment explanation
Indices: 7780--7813 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
7770 TTGGGCTTGT
7780 TATTATTA-TA
1 TATTATTATTA
7790 TTATTATTATTA
1 -TATTATTATTA
7802 TATTATTATTA
1 TATTATTATTA
7813 T
1 T
7814 TATATACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 20 0.91
12 2 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTATTATTA
Found at i:7796 original size:14 final size:14
Alignment explanation
Indices: 7779--7818 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
7769 ATTGGGCTTG
7779 TTATTATTATATTA
1 TTATTATTATATTA
7793 TTATTATTATATTA
1 TTATTATTATATTA
7807 TTATTATTATAT
1 TTATTATTATAT
7819 ACTATAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:9289 original size:28 final size:28
Alignment explanation
Indices: 9228--9294 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
9218 ACGTAAGTAT
*
9228 ATAAAATTATTTTTTGTCAAAATAGATAC
1 ATAAAA-TATTTTTTATCAAAATAGATAC
* *
9257 TTAAAATATTTTTTATTAAAATATG-TAC
1 ATAAAATATTTTTTATCAAAATA-GATAC
*
9285 ATAAAGTATT
1 ATAAAATATT
9295 CAATTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 26 0.81
29 6 0.19
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (28 bp):
ATAAAATATTTTTTATCAAAATAGATAC
Found at i:9474 original size:33 final size:30
Alignment explanation
Indices: 9402--9458 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
9392 TAATTTTAAC
9402 TTAAGTACTTAAATAAAGAAGAAAATAATT
1 TTAAGTACTTAAATAAAGAAGAAAATAATT
*
9432 TTAAATACTTAAATAAAGAAGAAAATA
1 TTAAGTACTTAAATAAAGAAGAAAATA
9459 TACTTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.28
Consensus pattern (30 bp):
TTAAGTACTTAAATAAAGAAGAAAATAATT
Found at i:14756 original size:111 final size:105
Alignment explanation
Indices: 14615--14838 Score: 270
Period size: 111 Copynumber: 2.1 Consensus size: 105
14605 AAGTTAAATT
* * * * *
14615 ATTTTTATTTTATTATTTGGATTCTCTAAATAATTTTAATACAATTTTATTTTTTTAATATAATT
1 ATTTTTATCTTGTGATTTGAATTCTATAAATAATTTTAATACAATTTTA---TTTTAATAT-ATT
*
14680 T-ATATATTATTATTTAAAAAATAATTTAAATAAAAATCTTAAACTC
62 TGATATATTATTATTT-AAAAATAA-TTAAA-AAAAATATTAAACTC
* * * *
14726 GTTTTTATCTTGTGATTTGAATTCTATAAATAATTTTAATATAATTTTATTTTCATATATTTGGT
1 ATTTTTATCTTGTGATTTGAATTCTATAAATAATTTTAATACAATTTTATTTTAATATATTTGAT
* *
14791 ATATTATTATTTTAAAATAATTATAAAAAATATTAAACTC
66 ATATTATTATTTAAAAATAATTAAAAAAAATATTAAACTC
14831 ATTTTTAT
1 ATTTTTAT
14839 TTTTGAGTTT
Statistics
Matches: 99, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
105 21 0.21
106 4 0.04
107 11 0.11
108 21 0.21
111 42 0.42
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (105 bp):
ATTTTTATCTTGTGATTTGAATTCTATAAATAATTTTAATACAATTTTATTTTAATATATTTGAT
ATATTATTATTTAAAAATAATTAAAAAAAATATTAAACTC
Found at i:18025 original size:25 final size:25
Alignment explanation
Indices: 17997--18053 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
17987 AATTGATTTG
17997 ATCG-GGCAAGATAATAACCTATCAA
1 ATCGAGGCAA-ATAATAACCTATCAA
**
18022 ATCGAGGTGAATAATAACCTATCAA
1 ATCGAGGCAAATAATAACCTATCAA
*
18047 GTCGAGG
1 ATCGAGG
18054 TGAAATAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (25 bp):
ATCGAGGCAAATAATAACCTATCAA
Found at i:18035 original size:22 final size:23
Alignment explanation
Indices: 18009--18067 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 23
17999 CGGGCAAGAT
18009 AATAACCTATCAAATCGAGGTGAA
1 AATAACCTATCAAATCGAGGTG-A
*
18033 TAATAACCTATCAAGTCGAGGTGA
1 -AATAACCTATCAAATCGAGGTGA
18057 AATAACC-ATCA
1 AATAACCTATCA
18068 CTAATTTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 4 0.12
23 7 0.21
24 1 0.03
25 21 0.64
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (23 bp):
AATAACCTATCAAATCGAGGTGA
Found at i:18054 original size:25 final size:25
Alignment explanation
Indices: 18007--18057 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
17997 ATCGGGCAAG
18007 ATAATAACCTATCAAATCGAGGTGA
1 ATAATAACCTATCAAATCGAGGTGA
*
18032 ATAATAACCTATCAAGTCGAGGTGA
1 ATAATAACCTATCAAATCGAGGTGA
18057 A
1 A
18058 ATAACCATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.24
Consensus pattern (25 bp):
ATAATAACCTATCAAATCGAGGTGA
Found at i:27395 original size:13 final size:14
Alignment explanation
Indices: 27370--27398 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
27360 TTGACTTTTT
27370 GGTCAACAGTCAAC
1 GGTCAACAGTCAAC
27384 GGTCAA-AGTCAAC
1 GGTCAACAGTCAAC
27397 GG
1 GG
27399 GTTGACTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.24, G:0.28, T:0.14
Consensus pattern (14 bp):
GGTCAACAGTCAAC
Found at i:35350 original size:26 final size:26
Alignment explanation
Indices: 35304--35353 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
35294 AACTAAACAA
* *
35304 TCAACTTTTTCTTTCTCTTTTTTTTT
1 TCAACTTTTTCTTTATATTTTTTTTT
35330 TCAA-TTTTTCTTTAATATTTTTTT
1 TCAACTTTTTCTTT-ATATTTTTTT
35354 CTGTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (26 bp):
TCAACTTTTTCTTTATATTTTTTTTT
Found at i:46085 original size:81 final size:81
Alignment explanation
Indices: 45869--46602 Score: 1087
Period size: 81 Copynumber: 9.1 Consensus size: 81
45859 AATTCTAAAA
* *
45869 TAAAAGATTAATGGTCTAGCTGTGCATTTGGCAGAAATGTGT-TATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
45933 CTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
45949 T-AAAGATTAATGACCTAGCTGTGCATTTGCCATAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
46013 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* **
46029 TAAAAGATTAATGGCCTAACTGTGCATTTGGCAGAAATGTGTCAATTATGTTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
46094 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
46110 TAAAAGATTAATGGCCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
46175 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
46191 TAAAAGATTAATGGCCTAGCTATGCATTTGGTAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
46256 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
46272 TAAAAGATTAATGGCCTAGCTGTGCATTTGGAAGAAATGTGTCAATTATGCCAATTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
46337 GTTAAATACATTTGAG
66 GTTAAATACCTTTGAG
* *
46353 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAA-GATGTCAATTATACCAGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATG-TGTCAATTATGCCAGTTAGATGAAA
*
46417 GGTTAAATACCTTTGAA
65 GGTTAAATACCTTTGAG
* * * *** * *
46434 TAAAAGATTAATGGCCTATCTGTGCATTTGGTAGAAATGTGTCAAGTATGTTGGTTAGACGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
46499 GTTAAATACCTCTGAG
66 GTTAAATACCTTTGAG
* * * * **
46515 TAAAAGATTAATGGTCTAGCTGTGCATTTGGCAGAAAAGTGTCAATCATGCAAGTTATTTGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* * *
46580 GCTAAATGCCTTTGTG
66 GTTAAATACCTTTGAG
46596 TAAAAGA
1 TAAAAGA
46603 CTAAAGGATT
Statistics
Matches: 587, Mismatches: 63, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
79 35 0.06
80 39 0.07
81 512 0.87
82 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:51274 original size:81 final size:81
Alignment explanation
Indices: 51173--51988 Score: 1150
Period size: 81 Copynumber: 10.1 Consensus size: 81
51163 AATCCTTTTG
* * * ** * * * * *
51173 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTTCATGATTAACACTTTTCTACCAATTGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGC
51238 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* *
51254 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGC
*
51319 ACAGCTAGGCAATTAA
66 ACAGCTAGGCCATTAA
* * * *
51335 TCTTTTACTCAAAGGTATTCAACCTTTCATCTAACTGGCATAATTGACACATTTATGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGC
51400 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
51416 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GTTATAATTGACACCTTTTTTCCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAG-CATAATTGACACCTTTCTGCCAAATG
*
51480 CGCAGCTAGGCCATTAA
65 CACAGCTAGGCCATTAA
* * *
51497 TCTTTTACTCAAAGGTATTT-ATCTTTCATCTAACTAGCATAATTTACACCTTTATGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGC
* *
51561 ATAGCTAGGCCTTTAA
66 ACAGCTAGGCCATTAA
* * *
51577 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACCTTTCTGCAAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGC
* *
51642 ATAGCTAGTCCATTAA
66 ACAGCTAGGCCATTAA
* *
51658 TCTTTTACTCAAAGTTATTTAACCTTTCATCTAACTAGCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGC
* *
51723 ACAACTAGGGCATTAA
66 ACAGCTAGGCCATTAA
* * *
51739 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTATCTTCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGC
51804 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * ** * * *
51820 TCTTTTACTTAAAGGTATTTAACTTTTTTTCTAACAACCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGC
*
51885 ACAGCTACGCCATTAA
66 ACAGCTAGGCCATTAA
* * *
51901 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAACATAATTGACACCATTATGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGC
*
51966 ACAACTAGGCCATTAA
66 ACAGCTAGGCCATTAA
*
51982 TATTTTA
1 TCTTTTA
51989 TTTAGAACAG
Statistics
Matches: 656, Mismatches: 76, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
80 71 0.11
81 585 0.89
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATAATTGACACCTTTCTGCCAAATGC
ACAGCTAGGCCATTAA
Found at i:51784 original size:323 final size:323
Alignment explanation
Indices: 51173--51988 Score: 1209
Period size: 323 Copynumber: 2.5 Consensus size: 323
51163 AATCCTTTTG
* * * ** * * * *
51173 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTTCATGATTAACACTTTTCTACCAATTGC
1 TCTTTTACTCAAAGGTATTTA-ACTTTCATCTAACTACCATAATTAACACATTTCTGCCAAATGC
51238 ACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA
65 ACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA
* *
51303 CCTTTCTACCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTCAACCTTTCATCTA
130 CCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTCAACCTTTCATCTA
* *
51368 ACTGGCATAATTGACACATTTATGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTA
195 ACTAGCATAATTGACACATTTATGCCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTA
** * * *
51433 TTTAACCTTTCATCTAACTGTTATAATTGACACCTTTTTTCCAAATGCGCAGCTAGGCCATTAA
260 TTTAACCTTTCATCTAACTGGCATAATTGACACCTATCTTCCAAATGCACAGCTAGGCCATTAA
* * * * *
51497 TCTTTTACTCAAAGGTATTTATCTTTCATCTAACTAGCATAATTTACACCTTTATGCCAAATGCA
1 TCTTTTACTCAAAGGTATTTAACTTTCATCTAACTACCATAATTAACACATTTCTGCCAAATGCA
* * *
51562 TAGCTAGGCCTTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACAC
66 CAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC
* * * * *
51627 CTTTCTGCAAAATGCATAGCTAGTCCATTAATCTTTTACTCAAAGTTATTTAACCTTTCATCTAA
131 CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTCAACCTTTCATCTAA
* *
51692 CTAGCATAATTGACACATTTCTGCCAAATGCACAACTAGGGCATTAATCTTTTACTCAAAGGTAT
196 CTAGCATAATTGACACATTTATGCCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTAT
51757 TTAACCTTTCATCTAACTGGCATAATTGACACCTATCTTCCAAATGCACAGCTAGGCCATTAA
261 TTAACCTTTCATCTAACTGGCATAATTGACACCTATCTTCCAAATGCACAGCTAGGCCATTAA
* ** * *
51820 TCTTTTACTTAAAGGTATTTAACTTTTTTTCTAACAACCATAATTGACACATTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAAC-TTTCATCTAACTACCATAATTAACACATTTCTGCCAAATGC
* **
51885 ACAGCTACGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAACATAATTGACA
65 ACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACA
* * * *
51950 CCATTATGCCAAATGCACAACTAGGCCATTAATATTTTA
130 CCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTA
51989 TTTAGAACAG
Statistics
Matches: 439, Mismatches: 52, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
323 295 0.67
324 144 0.33
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (323 bp):
TCTTTTACTCAAAGGTATTTAACTTTCATCTAACTACCATAATTAACACATTTCTGCCAAATGCA
CAGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACAC
CTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACTCAAAGGTATTCAACCTTTCATCTAA
CTAGCATAATTGACACATTTATGCCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTAT
TTAACCTTTCATCTAACTGGCATAATTGACACCTATCTTCCAAATGCACAGCTAGGCCATTAA
Found at i:63806 original size:26 final size:27
Alignment explanation
Indices: 63754--63807 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
63744 AAAATAAAAA
*
63754 AAATGCAAATCAAACAATTTTTTTATT
1 AAATGCAAATCAAACAATTTTTGTATT
*
63781 AAAT-CAAA-CAAATAATTATTTGTATT
1 AAATGCAAATCAAACAATT-TTTGTATT
63807 A
1 A
63808 TTTGAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 12 0.50
27 4 0.17
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (27 bp):
AAATGCAAATCAAACAATTTTTGTATT
Found at i:85174 original size:29 final size:30
Alignment explanation
Indices: 85141--85213 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 30
85131 AAAATTTATG
*
85141 TTAGTGACCAAAATATAAAG-TTTGAAAGT
1 TTAGTGACCAAAATATAAAGATTAGAAAGT
* *
85170 TTAGTGGCCAAAGTATAAAGATTAGAAAGT
1 TTAGTGACCAAAATATAAAGATTAGAAAGT
* *
85200 TTAGGGATCAAAAT
1 TTAGTGACCAAAAT
85214 GGTAATTTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 18 0.50
30 18 0.50
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.29
Consensus pattern (30 bp):
TTAGTGACCAAAATATAAAGATTAGAAAGT
Found at i:86652 original size:12 final size:13
Alignment explanation
Indices: 86635--86664 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
86625 TATCAAAAGA
86635 ATTTTAG-AAATT
1 ATTTTAGAAAATT
86647 ATTTTAGAAAATT
1 ATTTTAGAAAATT
86660 ATTTT
1 ATTTT
86665 CTATTGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
ATTTTAGAAAATT
Done.