Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002429.1 Hibiscus syriacus cultivar Beakdansim tig00004967_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: 68163
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1388 original size:21 final size:21
Alignment explanation
Indices: 1364--1410 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1354 AGTATCGCGT
1364 TGCGATTTTCCCAATTCGCAA
1 TGCGATTTTCCCAATTCGCAA
*
1385 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTTCCCAATTCGCAA
1406 TGCGA
1 TGCGA
1411 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TGCGATTTTCCCAATTCGCAA
Found at i:1443 original size:21 final size:20
Alignment explanation
Indices: 1400--1448 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1390 TTTTCCTAAT
*
1400 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
1420 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
1441 TCGCAATG
1 TCGCAATG
1449 TGATAATGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1507 original size:20 final size:20
Alignment explanation
Indices: 1482--1577 Score: 158
Period size: 20 Copynumber: 4.8 Consensus size: 20
1472 TAATACAAAA
* *
1482 TCGCAACGCGATACTGACTT
1 TCGCAACGAGATTCTGACTT
1502 TCGCAACGAGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
*
1522 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
1542 TCGCAACGAGATT-TGACTT
1 TCGCAACGAGATTCTGACTT
1561 TCGCAACGAGATTCTGA
1 TCGCAACGAGATTCTGA
1578 AAATCAATCA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.27
20 52 0.73
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:1878 original size:14 final size:14
Alignment explanation
Indices: 1859--1912 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1849 GAAAATCGCA
1859 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1873 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
1890 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
1906 TTGCGAT
1 TTGCGAT
1913 AATCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1878 original size:33 final size:33
Alignment explanation
Indices: 1841--1911 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
1831 AAAATCGCAA
1841 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
1874 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1907 TGCGA
1 TGCGA
1912 TAATCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:3383 original size:21 final size:21
Alignment explanation
Indices: 3359--3436 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
3349 GTGGGGGGAA
3359 ACTCTTGAGGGATGATAGGGG
1 ACTCTTGAGGGATGATAGGGG
3380 ACTCTTGAGGGATGATAGGGG
1 ACTCTTGAGGGATGATAGGGG
* ** *
3401 CCTCTTGAACGATTG-GAGGGG
1 ACTCTTGAGGGA-TGATAGGGG
3422 ACTCTTGAGGGATGA
1 ACTCTTGAGGGATGA
3437 CAGGTGAGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.23, C:0.13, G:0.40, T:0.24
Consensus pattern (21 bp):
ACTCTTGAGGGATGATAGGGG
Found at i:3803 original size:20 final size:20
Alignment explanation
Indices: 3778--3816 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3768 GAAGAATAGT
3778 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
*
3798 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
3817 ATGACCATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:3827 original size:20 final size:19
Alignment explanation
Indices: 3804--3870 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
3794 AAACTTACTT
*
3804 TCGCAACGCGAAAATGACCA
1 TCGCAACGCG-AAATGACAA
* *
3824 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACAA
* *
3844 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACAA
3863 TCGCAACG
1 TCGCAACG
3871 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 14 0.36
20 24 0.62
21 1 0.03
ACGTcount: A:0.37, C:0.25, G:0.24, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGACAA
Found at i:3878 original size:14 final size:14
Alignment explanation
Indices: 3859--3917 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
3849 ATGCGAAATG
3859 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3873 AAAATCGCAATGCGAAATA
1 AAAATCGCAA--CG--A-C
3892 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3906 AAAATCGCAACG
1 AAAATCGCAACG
3918 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3885 original size:33 final size:33
Alignment explanation
Indices: 3843--3933 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 33
3833 GGAAATGGCT
*
3843 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
3876 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
* * *
3909 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATAAAAATCGCA
3934 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATAAAAATCGCAACGACAAA
Found at i:3931 original size:19 final size:17
Alignment explanation
Indices: 3843--3933 Score: 68
Period size: 19 Copynumber: 5.4 Consensus size: 17
3833 GGAAATGGCT
*
3843 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAA-CAAA
3862 ATCGCAA-CG--ACAAA
1 ATCGCAAGCGAAACAAA
*
3876 ATCGCAATGCGAAATAAAA
1 ATCGCAA-GCGAAA-CAAA
3895 ATCGCAA-CG--ACAAA
1 ATCGCAAGCGAAACAAA
3909 ATCGCAACGCGAAACACAA
1 ATCGCAA-GCGAAACA-AA
3928 ATCGCA
1 ATCGCA
3934 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 4 0.07
17 4 0.07
18 4 0.07
19 25 0.42
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.11
Consensus pattern (17 bp):
ATCGCAAGCGAAACAAA
Found at i:3951 original size:19 final size:19
Alignment explanation
Indices: 3929--3981 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
3919 GAAACACAAA
3929 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3948 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3967 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
3982 GTCGTTACGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:4564 original size:18 final size:18
Alignment explanation
Indices: 4541--4588 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
4531 CGGGTCGATC
4541 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
4559 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
4577 AGGTGATGGCTC
1 AGGTGATGGCTC
4589 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:5954 original size:20 final size:20
Alignment explanation
Indices: 5906--5964 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
5896 AATAGTTTCT
* *
5906 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
5926 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
5946 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
5965 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:6555 original size:41 final size:41
Alignment explanation
Indices: 6436--6573 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
6426 CGCTTTGAAA
* * *
6436 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * ** * * *
6477 ATTGCGTTGCAAAATT-AAGTATCGCGTTGTGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
6517 ATCGAGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
6558 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
6574 CCAAATTCGC
Statistics
Matches: 76, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 31 0.41
41 45 0.59
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:6570 original size:20 final size:20
Alignment explanation
Indices: 6456--6569 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
6446 GATTATGTAT
*
6456 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * * *
6476 TATTGCGTTGCAAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
6496 TATCGCGTTGTGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
6516 TATCGAGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
6537 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
6557 TATCGCGTTGCGA
1 TATCGCGTTGCGA
6570 TTTTCCAAAT
Statistics
Matches: 73, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
19 3 0.04
20 55 0.75
21 13 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:6588 original size:21 final size:20
Alignment explanation
Indices: 6559--6610 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
6549 ATAGTCAGTA
* *
6559 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
**
6580 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
6600 TCGCATTGCGA
1 TCGCATTGCGA
6611 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:6589 original size:41 final size:41
Alignment explanation
Indices: 6496--6591 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
6486 CAAAATTAAG
* * * ** *
6496 TATCGCGTTGTGAAAGTCAGTATCGAGTTGCGATTTTGTAT
1 TATCGCATTGCGATAGTCAGTATCGAGTTGCGATTTTCAAA
* *
6537 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAA
1 TATCGCATTGCGATAGTCAGTATCGAGTTGCGATTTT-CAAA
6579 T-TCGCATTGCGAT
1 TATCGCATTGCGAT
6592 TTACTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (41 bp):
TATCGCATTGCGATAGTCAGTATCGAGTTGCGATTTTCAAA
Found at i:6652 original size:21 final size:22
Alignment explanation
Indices: 6600--6652 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
6590 ATTTACTTAT
*
6600 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGAAAAA
**
6621 TCGCAACGCGAAATT-GAAAAA
1 TCGCATTGCGAAATTGGAAAAA
6642 TCGCATTGCGA
1 TCGCATTGCGA
6653 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGAAAAA
Found at i:12943 original size:44 final size:44
Alignment explanation
Indices: 12915--13001 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
12905 GAATTTAAAT
*
12915 TTTAGAGTTTAAAGTTCAAATAAATAAAATAATATAATTAAAGA
1 TTTAAAGTTTAAAGTTCAAATAAATAAAATAATATAATTAAAGA
* *
12959 TTTAAATTTTAAAGTTTAAATAAATAAAA-ATATATAAATTAAA
1 TTTAAAGTTTAAAGTTCAAATAAATAAAATA-ATAT-AATTAAA
13002 CAGTAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 1 0.03
44 30 0.79
45 7 0.18
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (44 bp):
TTTAAAGTTTAAAGTTCAAATAAATAAAATAATATAATTAAAGA
Found at i:13009 original size:44 final size:44
Alignment explanation
Indices: 12922--13011 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
12912 AATTTTAGAG
* *
12922 TTTAAAGTTCAAATAAATAAAATAATATAATTAAAGATTTAAAT
1 TTTAAAGTTCAAATAAATAAAATAATATAATTAAACATGTAAAT
*
12966 TTTAAAGTTTAAATAAATAAAA-ATATATAAATTAAACA-GTAAAT
1 TTTAAAGTTCAAATAAATAAAATA-ATAT-AATTAAACATGTAAAT
13010 TT
1 TT
13012 AAATATATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 32 0.78
45 8 0.20
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (44 bp):
TTTAAAGTTCAAATAAATAAAATAATATAATTAAACATGTAAAT
Found at i:22486 original size:12 final size:11
Alignment explanation
Indices: 22479--22536 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 11
22469 ACCTGAATTT
22479 TGTTCTGATTTC
1 TGTTCTGA-TTC
*
22491 TGATCTGGATTC
1 TGTTCT-GATTC
22503 TGTTCTGATATC
1 TGTTCTGAT-TC
*
22515 TGTTCTGAATTA
1 TGTTCTG-ATTC
*
22527 TGTTTTGATT
1 TGTTCTGATT
22537 TCTGATATCT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 6 0.15
12 29 0.74
13 4 0.10
ACGTcount: A:0.16, C:0.12, G:0.19, T:0.53
Consensus pattern (11 bp):
TGTTCTGATTC
Found at i:22506 original size:24 final size:24
Alignment explanation
Indices: 22448--22542 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
22438 ATTTCCGACT
* * *
22448 TGAATTATGCTCTGA-TACATGACC
1 TGAATTATGTTCTGATTTC-TGATC
*
22472 TGAATTTTGTTCTGATTTCTGATC
1 TGAATTATGTTCTGATTTCTGATC
* * * *
22496 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTATGTTCTGATTTCTGATC
*
22520 TGAATTATGTTTTGATTTCTGAT
1 TGAATTATGTTCTGATTTCTGAT
22543 ATCTCCGTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
24 55 0.96
25 2 0.04
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTATGTTCTGATTTCTGATC
Found at i:29211 original size:137 final size:132
Alignment explanation
Indices: 29023--29293 Score: 391
Period size: 137 Copynumber: 2.0 Consensus size: 132
29013 TGGTCAAGTT
* * *
29023 AAGAGTTTCTTGTAAGACCTTTTATTCAGGGTTGTGTCTAAATCCACAGCCAGCAGCTTTTAAGT
1 AAGAGTTTCTTGTAAGACCTTTTATTCAGGGTTGTGCCTAAACCCACAGCCAACAGCTTTTAAGT
* * *
29088 TGGAT-CAGAGCAACCACCATGCCAATACATAATTTTATAAATGCAGCCACTTTTAATGAAAACA
66 TGGATCCA-AGCAACCACCACG-CAATACATAATTATATAAATGCA--C-C-TCTAATGAAAACA
*
29152 CTTTCGTG
125 CTTTCATG
*
29160 AAGAGTTTCTTGTAAGACCTTTTATTCAGGGTTGTGCCTAAACCCACAGCCAATAGCTTTTAAGT
1 AAGAGTTTCTTGTAAGACCTTTTATTCAGGGTTGTGCCTAAACCCACAGCCAACAGCTTTTAAGT
* *
29225 TGGATCCAAGCAACCACCACGCAATATATAATTATGTAAATGCACCTCTAATGAAAACACTTTCA
66 TGGATCCAAGCAACCACCACGCAATACATAATTATATAAATGCACCTCTAATGAAAACACTTTCA
29290 TG
131 TG
29292 AA
1 AA
29294 CGGATGCTCA
Statistics
Matches: 123, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
132 21 0.17
133 1 0.01
134 1 0.01
136 20 0.16
137 78 0.63
138 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (132 bp):
AAGAGTTTCTTGTAAGACCTTTTATTCAGGGTTGTGCCTAAACCCACAGCCAACAGCTTTTAAGT
TGGATCCAAGCAACCACCACGCAATACATAATTATATAAATGCACCTCTAATGAAAACACTTTCA
TG
Found at i:35487 original size:13 final size:14
Alignment explanation
Indices: 35451--35491 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
35441 TAAACCCCCA
35451 AAATCTCTAAA-CTC
1 AAATCTCTAAATC-C
35465 AAATCTCTAAATCC
1 AAATCTCTAAATCC
35479 AAA-CTCTAAATCC
1 AAATCTCTAAATCC
35492 TTAATTTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.38
14 15 0.58
15 1 0.04
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATCTCTAAATCC
Found at i:37277 original size:23 final size:23
Alignment explanation
Indices: 37232--37278 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
37222 AACTATCTTT
* * *
37232 ATAATATAACAATGATATATAAA
1 ATAAAATAACAATAAAATATAAA
*
37255 ATAAAATAACAATAAAATTTAAA
1 ATAAAATAACAATAAAATATAAA
37278 A
1 A
37279 CCTAATATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (23 bp):
ATAAAATAACAATAAAATATAAA
Found at i:38948 original size:18 final size:19
Alignment explanation
Indices: 38905--38948 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
38895 GTGGTTATGA
**
38905 TGTGTGTGAGGTTGTTGAG
1 TGTGTGTGAGGAAGTTGAG
38924 TGT-TGTGAGGAAG-TGAG
1 TGTGTGTGAGGAAGTTGAG
38941 TGTGTGTG
1 TGTGTGTG
38949 TGTGAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 7 0.32
18 12 0.55
19 3 0.14
ACGTcount: A:0.14, C:0.00, G:0.48, T:0.39
Consensus pattern (19 bp):
TGTGTGTGAGGAAGTTGAG
Found at i:44179 original size:17 final size:17
Alignment explanation
Indices: 44154--44196 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
44144 ATATATTTTT
*
44154 AATTAAAAATATA-AAA
1 AATTTAAAATATATAAA
44170 ATATTTAAAATATATAAA
1 A-ATTTAAAATATATAAA
44188 AATTTAAAA
1 AATTTAAAA
44197 CTTTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 19 0.79
18 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTAAAATATATAAA
Found at i:44569 original size:25 final size:25
Alignment explanation
Indices: 44503--44572 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
44493 GAGCGGTGAT
*
44503 TAGTATCATTATAAATATTTTTTCA
1 TAGTATCATTATAAATGTTTTTTCA
44528 TAGTATCATTATAAATGTTTTTTCA
1 TAGTATCATTATAAATGTTTTTTCA
44553 TAGTATCATTATAAATGTTT
1 TAGTATCATTATAAATGTTT
44573 AAAATATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (25 bp):
TAGTATCATTATAAATGTTTTTTCA
Found at i:52960 original size:17 final size:17
Alignment explanation
Indices: 52940--53000 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
52930 TTCCTGTATC
52940 GTTCCTTTTACTGTACT
1 GTTCCTTTTACTGTACT
* *
52957 GTTCATTTTTCTGTACT
1 GTTCCTTTTACTGTACT
52974 GATT--TATTTACTGTACCT
1 G-TTCCT-TTTACTGTA-CT
52992 -TTCCTTTTA
1 GTTCCTTTTA
53001 TTACAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 3 0.08
17 28 0.78
18 5 0.14
ACGTcount: A:0.15, C:0.20, G:0.10, T:0.56
Consensus pattern (17 bp):
GTTCCTTTTACTGTACT
Found at i:52982 original size:18 final size:17
Alignment explanation
Indices: 52940--52989 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
52930 TTCCTGTATC
*
52940 GTTCCTTTTACTGTACT
1 GTTCATTTTACTGTACT
*
52957 GTTCATTTTTCTGTACT
1 GTTCATTTTACTGTACT
*
52974 GATTTA-TTTACTGTAC
1 G-TTCATTTTACTGTAC
52990 CTTTCCTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 25 0.89
18 3 0.11
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.54
Consensus pattern (17 bp):
GTTCATTTTACTGTACT
Found at i:53003 original size:333 final size:331
Alignment explanation
Indices: 52399--53030 Score: 998
Period size: 333 Copynumber: 1.9 Consensus size: 331
52389 TAATACTATA
52399 CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAGTTATTTGGTTGTTATCTAC
1 CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAGTTATTTGGTTGTTATCTAC
* * * * * **
52464 CGTCACACGACCTCCCACTGATTTACACTATGTTTATAATATTTTATTGTAAAATGCATTTTTAA
66 CGCCACACGACCTCCCACTAATTTACACTATGTTTATAACATTTTACTGTAAAATGAATAATTAA
* * * *
52529 ACTTATACAGTTTTTTATCATATACTTACTCTTTTTACTGTACTAATCTTTTCACTATATTATTC
131 ACTTATACAGTTCTTTATAATATACTTACTATTTTTACTGTACTAATATTTTCACTATATTATTC
**
52594 TTTTTCCTATATCGTTCCTTTCACTGTACTGTTTCTTTTTCTATACTGATTTATTTACTGTTTCT
196 TTTTTCCTATATCGTTCCTTTCACTGTACTGTTTCTTTTTCTATACTGATTTATTTACTGTACCT
* *
52659 TTCCTTTTATTACACTATTTCTCTTATTGTATTATATCTTTTACTGTTATGTATCTGACGTTGTA
261 TTCCTTTTATTACAATATTTCTCTTATTATATTATATCTTTTACTGTTATGTATCTGACGTTGTA
52724 CTATTT
326 CTATTT
* * *
52730 CATAAAATATATGTAACATCTATAATCAGATTTATTCTAAAACATGTTTATTTGGTTGTTGTCTA
1 CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAG-TTATTTGGTTGTTATCTA
52795 CCGCCACACGACCTCCCACTAATTTACACTATGTTTATAACATTTTACTGTAAAATGTAATAATT
65 CCGCCACACGACCTCCCACTAATTTACACTATGTTTATAACATTTTACTGTAAAATG-AATAATT
* *
52860 AAACTTGTGCAGTTCTTTATAATATACTTACTATTTTT-CATGTACTAATATTTTCACTATATTA
129 AAACTTATACAGTTCTTTATAATATACTTACTATTTTTAC-TGTACTAATATTTTCACTATATTA
* * *
52924 TTCTTTTTCCTGTATCGTTCCTTTTACTGTACTG-TTCATTTTTCTGTACTGATTTATTTACTGT
193 TTCTTTTTCCTATATCGTTCCTTTCACTGTACTGTTTC-TTTTTCTATACTGATTTATTTACTGT
*
52988 ACCTTTCCTTTTATTACAATATTTCTCTTATTATATTGTATCT
257 ACCTTTCCTTTTATTACAATATTTCTCTTATTATATTATATCT
53031 GATGTTGTAC
Statistics
Matches: 273, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
331 44 0.16
332 74 0.27
333 155 0.57
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (331 bp):
CATAAAATATATGTAACATCTATAATCAAATTTATTCTAAAACAAGTTATTTGGTTGTTATCTAC
CGCCACACGACCTCCCACTAATTTACACTATGTTTATAACATTTTACTGTAAAATGAATAATTAA
ACTTATACAGTTCTTTATAATATACTTACTATTTTTACTGTACTAATATTTTCACTATATTATTC
TTTTTCCTATATCGTTCCTTTCACTGTACTGTTTCTTTTTCTATACTGATTTATTTACTGTACCT
TTCCTTTTATTACAATATTTCTCTTATTATATTATATCTTTTACTGTTATGTATCTGACGTTGTA
CTATTT
Found at i:53257 original size:65 final size:63
Alignment explanation
Indices: 53151--53338 Score: 223
Period size: 65 Copynumber: 2.9 Consensus size: 63
53141 GACTTTTACA
* * * *
53151 ATATTCAATTATTATTTCACCTCATGCACCATAAATGTACATGATTCATATGACTGATATGTACT
1 ATATTCAATTATCATCT-ACCTCATGCACCACAAA-GTACATGAGTCATATGACTGATATGTACT
* * *
53216 ATATTCAATTATCACTCTACCTCATGTACCACAAAGATACATGAGTCATATGAGTGATTTGTACT
1 ATATTCAATTATCA-TCTACCTCATGCACCACAAAG-TACATGAGTCATATGACTGATATGTACT
* * * *
53281 GTATACAATTATCATTCCACCTCATGCACCACAAAGGTACATGAGTCATATTACTGAT
1 ATATTCAATTATCA-TCTACCTCATGCACCACAAA-GTACATGAGTCATATGACTGAT
53339 CTGCACCACA
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
64 1 0.01
65 102 0.96
66 3 0.03
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (63 bp):
ATATTCAATTATCATCTACCTCATGCACCACAAAGTACATGAGTCATATGACTGATATGTACT
Found at i:53351 original size:35 final size:35
Alignment explanation
Indices: 53305--53376 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
53295 TTCCACCTCA
53305 TGCACCACAAAGGTACATGAGTCATATTACTGATC
1 TGCACCACAAAGGTACATGAGTCATATTACTGATC
*
53340 TGCACCACAAAGGTACATGAGTCATATTATTGATC
1 TGCACCACAAAGGTACATGAGTCATATTACTGATC
53375 TG
1 TG
53377 TATTGTATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (35 bp):
TGCACCACAAAGGTACATGAGTCATATTACTGATC
Found at i:53416 original size:100 final size:100
Alignment explanation
Indices: 53243--53431 Score: 288
Period size: 100 Copynumber: 1.9 Consensus size: 100
53233 TACCTCATGT
* * *
53243 ACCACAAAGATACATGAGTCATATGAGTGATTTGTACTGTATACAATTATCATTCCACCTCATGC
1 ACCACAAAGATACATGAGTCATATGAGTGATCTGTACTGTATACAATTATCACTCCACCCCATGC
*
53308 ACCACAAAGGTACATGAGTCATATTACTGATCTGC
66 ACCACAAAGGTACATGAATCATATTACTGATCTGC
* * * * * *
53343 ACCACAAAGGTACATGAGTCATATTATTGATCTGTATTGTATTCAATTATCACTCTACCCCATGC
1 ACCACAAAGATACATGAGTCATATGAGTGATCTGTACTGTATACAATTATCACTCCACCCCATGC
53408 ACCACAAAGGTACATGAATCATAT
66 ACCACAAAGGTACATGAATCATAT
53432 GAATGATATG
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (100 bp):
ACCACAAAGATACATGAGTCATATGAGTGATCTGTACTGTATACAATTATCACTCCACCCCATGC
ACCACAAAGGTACATGAATCATATTACTGATCTGC
Found at i:53447 original size:165 final size:165
Alignment explanation
Indices: 53175--53495 Score: 480
Period size: 165 Copynumber: 1.9 Consensus size: 165
53165 TTTCACCTCA
* * * *
53175 TGCACCATAAATGTACATGATTCATATGACTGATATGTACTATATTCAATTATCACTCTACCTCA
1 TGCACCACAAAGGTACATGAGTCATATGACTGATATGTACTATATTCAATTATCACTCTACCCCA
* * * * *
53240 TGTACCACAAAGATACATGAGTCATATGAGTGATTTGTACTGTATACAATTATCATTCCACCTCA
66 TGCACCACAAAGATACATGAATCATATGAATGATATGTACTGTATACAATTATCACTCCACCTCA
*
53305 TGCACCACAAAGGTACATGAGTCATATTACTGATC
131 TGCACCAAAAAGGTACATGAGTCATATTACTGATC
* * * * *
53340 TGCACCACAAAGGTACATGAGTCATATTATTGATCTGTATTGTATTCAATTATCACTCTACCCCA
1 TGCACCACAAAGGTACATGAGTCATATGACTGATATGTACTATATTCAATTATCACTCTACCCCA
* **
53405 TGCACCACAAAGGTACATGAATCATATGAATGATATGTACTGTATTTAATTATCACTCCACCTCA
66 TGCACCACAAAGATACATGAATCATATGAATGATATGTACTGTATACAATTATCACTCCACCTCA
53470 TGCACCAAAAAGGTACATGAGTCATA
131 TGCACCAAAAAGGTACATGAGTCATA
53496 GGAGTAATAT
Statistics
Matches: 138, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
165 138 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.31
Consensus pattern (165 bp):
TGCACCACAAAGGTACATGAGTCATATGACTGATATGTACTATATTCAATTATCACTCTACCCCA
TGCACCACAAAGATACATGAATCATATGAATGATATGTACTGTATACAATTATCACTCCACCTCA
TGCACCAAAAAGGTACATGAGTCATATTACTGATC
Found at i:53506 original size:65 final size:65
Alignment explanation
Indices: 53340--53495 Score: 231
Period size: 65 Copynumber: 2.4 Consensus size: 65
53330 ATTACTGATC
* * * * *
53340 TGCACCACAAAGGTACATGAGTCATATTATTGATCTGTATTGTATTCAATTATCACTCTACCCCA
1 TGCACCACAAAGGTACATGAGTCATATGAATGATATGTACTGTATTCAATTATCACTCCACCCCA
* * *
53405 TGCACCACAAAGGTACATGAATCATATGAATGATATGTACTGTATTTAATTATCACTCCACCTCA
1 TGCACCACAAAGGTACATGAGTCATATGAATGATATGTACTGTATTCAATTATCACTCCACCCCA
*
53470 TGCACCAAAAAGGTACATGAGTCATA
1 TGCACCACAAAGGTACATGAGTCATA
53496 GGAGTAATAT
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 81 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (65 bp):
TGCACCACAAAGGTACATGAGTCATATGAATGATATGTACTGTATTCAATTATCACTCCACCCCA
Found at i:55529 original size:18 final size:18
Alignment explanation
Indices: 55505--55548 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
55495 ATAATATGTT
*
55505 AACACATATACTCATG-CA
1 AACACATA-AATCATGACA
*
55523 CACACATAAATCATGACA
1 AACACATAAATCATGACA
55541 AACACATA
1 AACACATA
55549 CTTCTATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.50, C:0.27, G:0.05, T:0.18
Consensus pattern (18 bp):
AACACATAAATCATGACA
Found at i:61321 original size:132 final size:132
Alignment explanation
Indices: 60990--61383 Score: 738
Period size: 132 Copynumber: 3.0 Consensus size: 132
60980 GCCTGGTTCA
*
60990 TTTCATTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
1 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
* *
61055 AGCGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTAAGCGTTC
66 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
61120 -T
131 TT
61121 TTT-TTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
1 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
61185 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
66 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
61250 TT
131 TT
61252 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
1 TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
*
61317 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGTGTTC
66 AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
61382 TT
131 TT
61384 CTGACAATAA
Statistics
Matches: 257, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
130 123 0.48
131 7 0.03
132 127 0.49
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (132 bp):
TTTCTTTTTCTGATTCTAAATGGTCTGGACCCTTCATCATCTCCCTGCTAGTTTGATCTTCAGCA
AGTGGTTTAAGTTTAAGGGGAAGTGGAGAATCTTCCTCAGCCTCAGTATGAAGGTTTACGCGTTC
TT
Found at i:63078 original size:32 final size:33
Alignment explanation
Indices: 63041--63106 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
63031 TAAAAGTTAT
63041 AAATTATCAT-TAAATTTTATCAAACTATTACA
1 AAATTATCATATAAATTTTATCAAACTATTACA
***
63073 AAATTATCATATTTTTTTTATCAAACTATTACA
1 AAATTATCATATAAATTTTATCAAACTATTACA
63106 A
1 A
63107 TCTATATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 10 0.33
33 20 0.67
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (33 bp):
AAATTATCATATAAATTTTATCAAACTATTACA
Found at i:65045 original size:26 final size:28
Alignment explanation
Indices: 65016--65074 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
65006 GTCATGTATG
*
65016 TGAGATTGATA-T-TCAGCTCATCAAAA
1 TGAGACTGATACTCTCAGCTCATCAAAA
*
65042 TGAGACTGATACCTCTCAGGTCATCAAAA
1 TGAGACTGATA-CTCTCAGCTCATCAAAA
65071 -GAGA
1 TGAGA
65075 GAAAAATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 10 0.36
28 5 0.18
29 13 0.46
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (28 bp):
TGAGACTGATACTCTCAGCTCATCAAAA
Found at i:66066 original size:41 final size:41
Alignment explanation
Indices: 66009--66090 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
65999 CGTGTAGCGC
66009 TAGACAAGGTTGGCAAGGTTTTAACTTTTAAGTTTTAACCT
1 TAGACAAGGTTGGCAAGGTTTTAACTTTTAAGTTTTAACCT
66050 TAGACAAGGTTGGCAAGGTTTTAACTTTTAAGTTTTAACCT
1 TAGACAAGGTTGGCAAGGTTTTAACTTTTAAGTTTTAACCT
66091 CTAAGTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (41 bp):
TAGACAAGGTTGGCAAGGTTTTAACTTTTAAGTTTTAACCT
Found at i:66086 original size:14 final size:14
Alignment explanation
Indices: 66067--66108 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
66057 GGTTGGCAAG
*
66067 GTTTTAACTTTTAA
1 GTTTTAACCTTTAA
*
66081 GTTTTAACCTCTAA
1 GTTTTAACCTTTAA
66095 GTTTTAACCTTTAA
1 GTTTTAACCTTTAA
66109 TTGTAGACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
GTTTTAACCTTTAA
Done.