Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000410.1 Hibiscus syriacus cultivar Beakdansim tig00000756_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: 90420
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:11804 original size:31 final size:31
Alignment explanation
Indices: 11769--11834 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
11759 GTTTTAAAAA
**
11769 TAACAAATTAATCACTAATGTTAT-TGATTTG
1 TAACAAATTAATCACTAACATTATCT-ATTTG
11800 TAACAAATTAATCACTAACATTATCTATTTG
1 TAACAAATTAATCACTAACATTATCTATTTG
11831 TAAC
1 TAAC
11835 GAATCAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (31 bp):
TAACAAATTAATCACTAACATTATCTATTTG
Found at i:20893 original size:13 final size:13
Alignment explanation
Indices: 20875--20901 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20865 TTTGACTTCG
20875 CAATGTTCTTTTT
1 CAATGTTCTTTTT
20888 CAATGTTCTTTTT
1 CAATGTTCTTTTT
20901 C
1 C
20902 CTAGATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.19, G:0.07, T:0.59
Consensus pattern (13 bp):
CAATGTTCTTTTT
Found at i:28215 original size:31 final size:31
Alignment explanation
Indices: 28177--28242 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
28167 GTTTTAAAAA
**
28177 TAACAAATTAATCACTAATGTTAT-TGATTTG
1 TAACAAATTAATCACTAACATTATCT-ATTTG
28208 TAACAAATTAATCACTAACATTATCTATTTG
1 TAACAAATTAATCACTAACATTATCTATTTG
28239 TAAC
1 TAAC
28243 GAATCAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (31 bp):
TAACAAATTAATCACTAACATTATCTATTTG
Found at i:32218 original size:40 final size:40
Alignment explanation
Indices: 32163--32244 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
32153 TGCAGGTTTA
*
32163 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
32203 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
32243 TA
1 TA
32245 GCACTACGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:32443 original size:47 final size:45
Alignment explanation
Indices: 32349--32474 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
32339 GTAACCATGC
* * *
32349 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * *
32393 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
* *
32440 AAATAAGCTTACGAGATTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
32475 AGATTTATAT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 37 0.52
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:33373 original size:30 final size:30
Alignment explanation
Indices: 33337--33499 Score: 281
Period size: 30 Copynumber: 5.4 Consensus size: 30
33327 TCCGAAGGAC
* *
33337 CTATCCAGAGGTCATAAAGATCTTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
33367 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
33397 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
33427 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
33457 CTATCAAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
33487 CTGTCCATAGGTC
1 CTATCCAGAGGTC
33500 CCGAAGAACC
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 127 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:33516 original size:90 final size:91
Alignment explanation
Indices: 33337--33524 Score: 279
Period size: 90 Copynumber: 2.1 Consensus size: 91
33327 TCCGAAGGAC
* * *
33337 CTATCCAGAGGTCATAAAGATCTTTGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCAAGAGGTCATAAAGATCCTCGGTAACTATC
* * *
33402 CAGAGGTCATAAAGATCCTCGGT-AA
66 CAGAGGTCACAAAGAACCTAGGTAAA
*
33427 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCAAGAGGTCATAAAGATCCTCGGTAACTGTC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCAAGAGGTCATAAAGATCCTCGGTAACTATC
* * *
33492 CATAGGTCCCGAAGAACCTAGGTAAA
66 CAGAGGTCACAAAGAACCTAGGTAAA
33518 CTATCCA
1 CTATCCA
33525 TATATTCCTT
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 78 0.90
91 9 0.10
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (91 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCAAGAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCACAAAGAACCTAGGTAAA
Found at i:33663 original size:4 final size:4
Alignment explanation
Indices: 33654--34959 Score: 2591
Period size: 4 Copynumber: 327.2 Consensus size: 4
33644 TTTAACTTAT
33654 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
33702 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
33750 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
33798 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
33846 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC-
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
33893 -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
33940 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
33988 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34036 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34084 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34132 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34180 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34228 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34276 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34324 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34372 TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34419 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34467 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34515 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34563 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34611 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34659 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34707 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34755 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34803 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34851 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34899 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
34947 TACA TACA TACA T
1 TACA TACA TACA T
34960 GTCATCATTT
Statistics
Matches: 1299, Mismatches: 0, Indels: 6
1.00 0.00 0.00
Matches are distributed among these distances:
2 2 0.00
3 3 0.00
4 1294 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:35307 original size:2 final size:2
Alignment explanation
Indices: 35295--35366 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
35285 TACACAACTC
35295 AT AT A- 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
35336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35367 CTGTAACATG
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35907 original size:19 final size:20
Alignment explanation
Indices: 35870--35907 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35860 TTTTTCATTA
*
35870 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
35890 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
35908 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:35959 original size:21 final size:21
Alignment explanation
Indices: 35935--35977 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
35925 TCATATTCGT
* *
35935 TTGAGGGGGAATCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
* *
35956 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
35977 T
1 T
35978 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGAACCGATTCCCC
Found at i:41702 original size:21 final size:21
Alignment explanation
Indices: 41678--41721 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
41668 AGAAGATAGA
41678 ACAATTGTCATGTGACAGATT
1 ACAATTGTCATGTGACAGATT
41699 ACAATTGTCATGTGACAGATT
1 ACAATTGTCATGTGACAGATT
41720 AC
1 AC
41722 TGCCTTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (21 bp):
ACAATTGTCATGTGACAGATT
Found at i:43500 original size:17 final size:17
Alignment explanation
Indices: 43478--43531 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
43468 AATATTAATA
43478 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
43495 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
43512 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
43529 TTT
1 TTT
43532 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:45093 original size:21 final size:21
Alignment explanation
Indices: 45063--45106 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
45053 GTAAGGGTAC
* * *
45063 ATGCCCAGCCCTCCATTTCAT
1 ATGCCAAGCCCACCAGTTCAT
45084 ATGCCAAGCCCACCAGTTCAT
1 ATGCCAAGCCCACCAGTTCAT
45105 AT
1 AT
45107 ACCATCTCCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.39, G:0.11, T:0.25
Consensus pattern (21 bp):
ATGCCAAGCCCACCAGTTCAT
Found at i:45140 original size:21 final size:21
Alignment explanation
Indices: 45114--45228 Score: 160
Period size: 21 Copynumber: 5.5 Consensus size: 21
45104 TATACCATCT
45114 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
45135 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
45156 CCGCAGGGTTACATTTCGAGC
1 CCGCAGGGTTACATTCCGAGC
* * *
45177 CCGCGGGGTTATATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
45198 CCGCTA-GGTTACATGCCTAGC
1 CCGC-AGGGTTACATTCCGAGC
45219 CCGCAGGGTT
1 CCGCAGGGTT
45229 TTATACCATA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
20 1 0.01
21 83 0.99
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:45810 original size:33 final size:34
Alignment explanation
Indices: 45751--45847 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
45741 AAATGTTTTT
* *
45751 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* *
45785 AAAATAAAAATAATATTATTC-AAATTTAAAATT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* *
45818 AAAATATAAATTATAGTATTCAAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
45848 CATTAAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 29 0.52
34 27 0.48
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:45853 original size:34 final size:33
Alignment explanation
Indices: 45749--45854 Score: 140
Period size: 34 Copynumber: 3.2 Consensus size: 33
45739 ATAAATGTTT
*
45749 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTC-AAATTTAAAA
* *
45783 TAAAAATAAAAATAATATTATTCAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCAAATTTAAAA
* * *
45816 TTAAAATATAAATTATAGTATTCAAAATTTAACA
1 TTAAAATAAAAATTATATTATTC-AAATTTAAAA
45850 TTAAA
1 TTAAA
45855 TTTCAACTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 29 0.46
34 34 0.54
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCAAATTTAAAA
Found at i:46478 original size:128 final size:128
Alignment explanation
Indices: 46250--46605 Score: 640
Period size: 128 Copynumber: 2.8 Consensus size: 128
46240 ACAATCCATC
* *
46250 TAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATAAT
* *
46315 GGAAGGTGCGCCCCCGGGAACACGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
46378 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATAAT
* * *
46443 GGAAGGCGCCCCCCCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTATTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
46506 TAGTGTCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATAAT
46571 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCC
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCC
46606 TGAATAGTGT
Statistics
Matches: 218, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 218 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:46682 original size:104 final size:104
Alignment explanation
Indices: 46502--46709 Score: 380
Period size: 104 Copynumber: 2.0 Consensus size: 104
46492 GGTATTGATA
*
46502 TGAATAGTGTCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAA
1 TGAATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAA
*
46567 TAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCC
66 TAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCAAGTCC
*
46606 TGAATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAA
1 TGAATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAA
*
46671 TAATGGAAGGCGCGCCCCCAGGAACGCGTCTTCAAGTCC
66 TAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCAAGTCC
46710 CCTGAGAAAT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 100 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (104 bp):
TGAATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAA
TAATGGAAGGCGCGCCCCCAGGAACGCGCCTTCAAGTCC
Found at i:46780 original size:232 final size:232
Alignment explanation
Indices: 46374--46832 Score: 828
Period size: 232 Copynumber: 2.0 Consensus size: 232
46364 GGTACTGATA
46374 TGAATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAA
1 TGAATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAA
* *
46439 TAATGGAAGGCGCCCCCCCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTATTGATATG
66 TAATGGAAGGCGCCCCCCCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATACGTACTGATATG
* *
46504 AATAGTGTCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAATA
131 AATAGTGTCCCCGAGGGACATGAGTGACATAACAGGGCAATGATAACATATTCTCTAACAAAATA
46569 ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCC
196 ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCC
*
46606 TGAATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAA
1 TGAATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAA
* *
46671 TAATGGAAGGCGCGCCCCCAGGAACGCGTCTTCAAGTCCCCTGAGAAATAATACGTACTGATATG
66 TAATGGAAGGCGCCCCCCCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATACGTACTGATATG
* *
46736 AATAGTGTCCCCGAGGGACATGAGTGACATAACAGGGCAATGATAATATATTCTCTGACAAAATA
131 AATAGTGTCCCCGAGGGACATGAGTGACATAACAGGGCAATGATAACATATTCTCTAACAAAATA
*
46801 ATGGAAGGTGCGCCCCCGGGAACGCGCCTTCA
196 ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCA
46833 TGTGAATAGT
Statistics
Matches: 217, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
232 217 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (232 bp):
TGAATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTAACAAAA
TAATGGAAGGCGCCCCCCCAGGAACGCGCCTTCAAGTCCCCTGAGAAATAATACGTACTGATATG
AATAGTGTCCCCGAGGGACATGAGTGACATAACAGGGCAATGATAACATATTCTCTAACAAAATA
ATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCC
Found at i:46926 original size:8 final size:8
Alignment explanation
Indices: 46913--46953 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
46903 TCACAAGCTT
46913 TCAAATTC
1 TCAAATTC
46921 TCAAATTC
1 TCAAATTC
* *
46929 CCAAACTC
1 TCAAATTC
46937 T-AAATTC
1 TCAAATTC
46944 TCAAATTC
1 TCAAATTC
46952 TC
1 TC
46954 TAAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:61296 original size:15 final size:16
Alignment explanation
Indices: 61258--61298 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
61248 ACAGAGCCTC
*
61258 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
61274 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
61290 T-AATCATTC
1 TGAATCATTC
61299 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:61449 original size:3 final size:3
Alignment explanation
Indices: 61441--61465 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
61431 TGTTTTATAT
61441 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
61466 CAATCAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:77956 original size:2 final size:2
Alignment explanation
Indices: 77949--77973 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
77939 GAATAAAAAC
77949 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
77974 CACACATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:81499 original size:30 final size:31
Alignment explanation
Indices: 81445--81526 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 31
81435 ACTTTTAAAA
* * *
81445 TTGCAATATAATCCCCCAATATTTAGTCTGT
1 TTGCAATATGATCCCCCAACATTTAGTCCGT
* *
81476 TTGTAATATGGT-CCCCAACATTTAGTCCGT
1 TTGCAATATGATCCCCCAACATTTAGTCCGT
81506 TTGCAATATGATCCCCCAACA
1 TTGCAATATGATCCCCCAACA
81527 GTTACGTCGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 26 0.60
31 17 0.40
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (31 bp):
TTGCAATATGATCCCCCAACATTTAGTCCGT
Found at i:85262 original size:32 final size:31
Alignment explanation
Indices: 85191--85253 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
85181 TTACGTAGGA
**
85191 GACCATATTGCAAACAGACTAAATGTTGGGG
1 GACCATATTTTAAACAGACTAAATGTTGGGG
*
85222 GACCATATTTTAAACGGACTAAATGTTGGGG
1 GACCATATTTTAAACAGACTAAATGTTGGGG
85253 G
1 G
85254 GATTATATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.25
Consensus pattern (31 bp):
GACCATATTTTAAACAGACTAAATGTTGGGG
Done.