Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004931.1 Hibiscus syriacus cultivar Beakdansim tig00011095_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: 72085
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:948 original size:22 final size:22
Alignment explanation
Indices: 923--988 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
913 GAACTGAAAA
* *
923 GGTGTTCAAATAATCGGTTTGG
1 GGTGTTCAAACAACCGGTTTGG
**
945 GGTGTTTGAACAACCGGTTTGG
1 GGTGTTCAAACAACCGGTTTGG
**
967 GGTGTTTGAACAACCGGTTTGG
1 GGTGTTCAAACAACCGGTTTGG
989 AGGGTTCGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.20, C:0.12, G:0.35, T:0.33
Consensus pattern (22 bp):
GGTGTTCAAACAACCGGTTTGG
Found at i:2126 original size:44 final size:42
Alignment explanation
Indices: 2062--2269 Score: 213
Period size: 43 Copynumber: 4.9 Consensus size: 42
2052 ATAGTGGCAT
* * *
2062 TTTTTTCCATAAACGCCGCTAATTTTCTTGTCTTTAGTGGTG
1 TTTTTTGCACAAACGCCGCTAATTCTCTTGTCTTTAGTGGTG
* * *
2104 TTTTTTTGCCACAGACACCGCTAATTCTCTTATCTTTAGTGGTG
1 -TTTTTTG-CACAAACGCCGCTAATTCTCTTGTCTTTAGTGGTG
** * * *
2148 TTTTCGGCAACAAACGCCTCTAATTTTCTTGTCTTTAGTGGCG
1 TTTTTTGC-ACAAACGCCGCTAATTCTCTTGTCTTTAGTGGTG
* *
2191 TTTTTT--ACAAACGCCGCTAATTCACTTGTCTTTAGTGGTA
1 TTTTTTGCACAAACGCCGCTAATTCTCTTGTCTTTAGTGGTG
* * * *
2231 TTTTTTGCTACAAACGTCGTTAATTCTATTGTTTTTAGT
1 TTTTTTGC-ACAAACGCCGCTAATTCTCTTGTCTTTAGT
2270 TGCATTTGTA
Statistics
Matches: 134, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
40 35 0.26
42 1 0.01
43 68 0.51
44 30 0.22
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (42 bp):
TTTTTTGCACAAACGCCGCTAATTCTCTTGTCTTTAGTGGTG
Found at i:2255 original size:83 final size:84
Alignment explanation
Indices: 2053--2269 Score: 213
Period size: 83 Copynumber: 2.5 Consensus size: 84
2043 TTATGATTTA
* * * * * * *
2053 TAGTGGCATTTTTTTCCATAAACGCCGCTAATTTTCTTGTCTTTAGTGGTGTTTTTTTGCCACAG
1 TAGTGGTATTTTTTGCAACAAACG-CGTTAATTTTCTTGTCTTTAGTGGCGTTTTTTT--CACAA
*
2118 ACACCGCTAATTCTCTTATCTT
63 ACACCGCTAATTCACTTATCTT
* ** *
2140 TAGTGGTGTTTTCGGCAACAAACGCCTCTAATTTTCTTGTCTTTAGTGGCG-TTTTTT-ACAAAC
1 TAGTGGTATTTTTTGCAACAAACGCGT-TAATTTTCTTGTCTTTAGTGGCGTTTTTTTCACAAAC
* *
2203 GCCGCTAATTCACTTGTCTT
65 ACCGCTAATTCACTTATCTT
* * * *
2223 TAGTGGTATTTTTTGCTACAAACGTCGTTAATTCTATTGTTTTTAGT
1 TAGTGGTATTTTTTGCAACAAACG-CGTTAATTTTCTTGTCTTTAGT
2270 TGCATTTGTA
Statistics
Matches: 106, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
83 58 0.55
84 2 0.02
86 7 0.07
87 39 0.37
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (84 bp):
TAGTGGTATTTTTTGCAACAAACGCGTTAATTTTCTTGTCTTTAGTGGCGTTTTTTTCACAAACA
CCGCTAATTCACTTATCTT
Found at i:4850 original size:22 final size:22
Alignment explanation
Indices: 4809--4858 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
4799 TAATTGTAAC
* *
4809 AAATTTATTTAATCACAATAAT
1 AAATTAATTTAATCAAAATAAT
* *
4831 ATATTAATTTAGTCAAAATAAT
1 AAATTAATTTAATCAAAATAAT
4853 AAATTA
1 AAATTA
4859 TGTCAAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATTAATTTAATCAAAATAAT
Found at i:4893 original size:44 final size:44
Alignment explanation
Indices: 4843--4926 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
4833 ATTAATTTAG
* ** * *
4843 TCAAAATAATAAATTATGTCAAATTTATTTAGTCATAATATTTC
1 TCAAAATAATAAATGATGAAAAAATTATTTAGTCAAAATATTTC
4887 TCAAAATAATAAATGATGAAAAAATTATTTAGTCAAAATA
1 TCAAAATAATAAATGATGAAAAAATTATTTAGTCAAAATA
4927 AAAATCAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (44 bp):
TCAAAATAATAAATGATGAAAAAATTATTTAGTCAAAATATTTC
Found at i:5155 original size:197 final size:197
Alignment explanation
Indices: 4800--5213 Score: 532
Period size: 197 Copynumber: 2.1 Consensus size: 197
4790 ATTTGTAACT
*
4800 AATTGTAACAAATTTATTTAATCACAATAATATATTAATTTAGTCAAAATAATAAATTATGTCAA
1 AATTGTAACAAATTTATTTAATCACAATAACATATTAATTTAGTCAAAATAATAAATTATGTCAA
* *
4865 ATTTATTTAGTCATAATATTTCTCAAAATAATAAATGATGAAAAAATTATTTAGTCAAAATAAAA
66 ATTTATTTAGTCACAATATTTCTCAAAATAAAAAATGATGAAAAAATTATTTAGTCAAAATAAAA
* *
4930 ATCAATAACAAAAATTAATTTATCAATATAA-AAATTTACGATAAATAACATTTTTTTCACAATA
131 ATCAATAACAAAAATTAATTTATCAATATAACAAA-TTACGACAAATAACATTGTTTTCACAATA
4994 ATA
195 ATA
* * * * *
4997 AATTGAAACAAACTTATTTAGTCACAATACCATATTAAATTTAGTCAAAAT-A-AAATTATTTCA
1 AATTGTAACAAATTTATTTAATCACAATAACATATT-AATTTAGTCAAAATAATAAATTATGTCA
* * * * * *
5060 AATTTATTTTGTTACAATATTTTCTCAAAATAAAAACAT-TTGACAAATTTATTTAGTCATAATA
65 AATTTATTTAGTCACAATA-TTTCTCAAAATAAAAA-ATGATGAAAAAATTATTTAGTCAAAAT-
* ** * * * *
5124 AAAAAT-TATAACAAATGTTAATTTCTCAATATAACGAATTATGACAAATAATATTGTTTTCACA
127 AAAAATCAATAACAAAAATTAATTTATCAATATAACAAATTACGACAAATAACATTGTTTTCACA
*
5188 ATAATG
192 ATAATA
5194 AATTGTAACAAATTTATTTA
1 AATTGTAACAAATTTATTTA
5214 TTAAAAAAAA
Statistics
Matches: 186, Mismatches: 26, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
196 26 0.14
197 136 0.73
198 24 0.13
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (197 bp):
AATTGTAACAAATTTATTTAATCACAATAACATATTAATTTAGTCAAAATAATAAATTATGTCAA
ATTTATTTAGTCACAATATTTCTCAAAATAAAAAATGATGAAAAAATTATTTAGTCAAAATAAAA
ATCAATAACAAAAATTAATTTATCAATATAACAAATTACGACAAATAACATTGTTTTCACAATAA
TA
Found at i:5369 original size:19 final size:20
Alignment explanation
Indices: 5329--5369 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5319 TTTAAGTTAA
* *
5329 TTGTGATAAAATTTACTTTT
1 TTGTGATAAAATTAAATTTT
5349 TTGTGATAAAA-TAAATTTT
1 TTGTGATAAAATTAAATTTT
5368 TT
1 TT
5370 ATTTCAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (20 bp):
TTGTGATAAAATTAAATTTT
Found at i:5814 original size:22 final size:23
Alignment explanation
Indices: 5773--5830 Score: 100
Period size: 22 Copynumber: 2.6 Consensus size: 23
5763 TAATTTCAAC
*
5773 GTGATTCATGCCATGCAGCACAA
1 GTGATTCATACCATGCAGCACAA
5796 GTGATTCATACC-TGCAGCACAA
1 GTGATTCATACCATGCAGCACAA
5818 GTGATTCATACCA
1 GTGATTCATACCA
5831 AACAAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 22 0.67
23 11 0.33
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (23 bp):
GTGATTCATACCATGCAGCACAA
Found at i:6130 original size:14 final size:14
Alignment explanation
Indices: 6111--6137 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6101 TATTAATATT
6111 TAATGATTTAATAC
1 TAATGATTTAATAC
6125 TAATGATTTAATA
1 TAATGATTTAATA
6138 ATGATTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (14 bp):
TAATGATTTAATAC
Found at i:6187 original size:19 final size:19
Alignment explanation
Indices: 6126--6194 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
6116 ATTTAATACT
6126 AATGATTTAATAATGATTA
1 AATGATTTAATAATGATTA
* * *
6145 AATAAAATTATAATAATTACTA
1 AAT--GATT-TAATAATGATTA
*
6167 AATGATTCAATAATGATTA
1 AATGATTTAATAATGATTA
6186 AAT-ATTTAA
1 AATGATTTAA
6195 GAATTTATTC
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
18 5 0.13
19 15 0.38
20 3 0.08
21 3 0.08
22 13 0.33
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (19 bp):
AATGATTTAATAATGATTA
Found at i:6236 original size:15 final size:16
Alignment explanation
Indices: 6216--6254 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
6206 ATTTAAATCA
*
6216 AATTTATAA-TAGTTG
1 AATTTATAACTAGTCG
6231 AATTTATAACTAGTCG
1 AATTTATAACTAGTCG
6247 AATTTATA
1 AATTTATA
6255 TTAATATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (16 bp):
AATTTATAACTAGTCG
Found at i:7348 original size:11 final size:11
Alignment explanation
Indices: 7343--7405 Score: 72
Period size: 11 Copynumber: 5.4 Consensus size: 11
7333 ATATTTAATC
7343 ATTATTAAATA
1 ATTATTAAATA
7354 ATTATTAGTAATA
1 ATTATTA--AATA
7367 ATTATTAAATA
1 ATTATTAAATA
*
7378 ATTATTACTAATC
1 ATTATTA--AATA
*
7391 ATTATTAAATC
1 ATTATTAAATA
7402 ATTA
1 ATTA
7406 GTTGTAACTA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
11 26 0.55
13 21 0.45
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (11 bp):
ATTATTAAATA
Found at i:7365 original size:24 final size:24
Alignment explanation
Indices: 7338--7467 Score: 113
Period size: 24 Copynumber: 5.4 Consensus size: 24
7328 TTTAAATATT
*
7338 TAATCATTATTAAATAATTATTAG
1 TAATCATTATTAAATAATTATTAC
*
7362 TAATAATTATTAAATAATTATTAC
1 TAATCATTATTAAATAATTATTAC
* *
7386 TAATCATTATTAAATCATTAGTT-G
1 TAATCATTATTAAATAATTA-TTAC
* *
7410 TAA-CTATTA-TAATTTCATTATTAC
1 TAATC-ATTATTAA-ATAATTATTAC
* * *
7434 TAATTATTATTAAATTATTAGTATC
1 TAATCATTATTAAATAATTATTA-C
*
7459 AAATCATTA
1 TAATCATTA
7468 AATATTAATA
Statistics
Matches: 86, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
23 6 0.07
24 67 0.78
25 13 0.15
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (24 bp):
TAATCATTATTAAATAATTATTAC
Found at i:7389 original size:21 final size:23
Alignment explanation
Indices: 7334--7487 Score: 97
Period size: 24 Copynumber: 6.7 Consensus size: 23
7324 TATATTTAAA
*
7334 TATT-TAATCATTATTAAATAAT
1 TATTATAATAATTATTAAATAAT
7356 TATTAGTAATAATTATTAAATAAT
1 TATTA-TAATAATTATTAAATAAT
* *
7380 TATTACTAATCATTATTAAATCAT
1 TATTA-TAATAATTATTAAATAAT
* * *
7404 TAGTTGTAACT-ATTA-TAATTTCAT
1 TA-TTATAA-TAATTATTAA-ATAAT
* *
7428 TATTACTAATTATTATTAAATTAT
1 TATTA-TAATAATTATTAAATAAT
* * *
7452 TAGTATCA-AATCATTAAAT-AT
1 TATTATAATAATTATTAAATAAT
*
7473 TA--ATAAAAATTATTA
1 TATTATAATAATTATTA
7488 TTAACAATCA
Statistics
Matches: 108, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.03
20 7 0.06
21 4 0.04
22 13 0.12
23 8 0.07
24 67 0.62
25 6 0.06
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.47
Consensus pattern (23 bp):
TATTATAATAATTATTAAATAAT
Found at i:7397 original size:48 final size:48
Alignment explanation
Indices: 7338--7455 Score: 143
Period size: 48 Copynumber: 2.5 Consensus size: 48
7328 TTTAAATATT
7338 TAATCATTATTAAATAATTA-TTAGTAA-TAATTATTAA-ATAATTATTAC
1 TAATCATTATTAAATAATTAGTT-GTAACT-ATTA-TAATATAATTATTAC
* * *
7386 TAATCATTATTAAATCATTAGTTGTAACTATTATAATTTCATTATTAC
1 TAATCATTATTAAATAATTAGTTGTAACTATTATAATATAATTATTAC
* *
7434 TAATTATTATTAAATTATTAGT
1 TAATCATTATTAAATAATTAGT
7456 ATCAAATCAT
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
47 3 0.05
48 56 0.90
49 3 0.05
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (48 bp):
TAATCATTATTAAATAATTAGTTGTAACTATTATAATATAATTATTAC
Found at i:7500 original size:13 final size:15
Alignment explanation
Indices: 7484--7525 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
7474 AATAAAAATT
7484 ATTATTAA-CA-ATC
1 ATTATTAATCATATC
7497 ATTATTAAATCATATC
1 ATTATT-AATCATATC
7513 ATTATTAAATCAT
1 ATTATT-AATCAT
7526 TAAATATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.23
14 2 0.08
15 2 0.08
16 16 0.62
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTATTAATCATATC
Found at i:7513 original size:16 final size:16
Alignment explanation
Indices: 7494--7525 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
7484 ATTATTAACA
7494 ATCATTATTAAATCAT
1 ATCATTATTAAATCAT
7510 ATCATTATTAAATCAT
1 ATCATTATTAAATCAT
7526 TAAATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
ATCATTATTAAATCAT
Found at i:7539 original size:15 final size:15
Alignment explanation
Indices: 7519--7547 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
7509 TATCATTATT
7519 AAATCATTAAATATC
1 AAATCATTAAATATC
7534 AAATCATTAAATAT
1 AAATCATTAAATAT
7548 TAATAATAAA
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:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:7560 original size:26 final size:24
Alignment explanation
Indices: 7456--7560 Score: 52
Period size: 26 Copynumber: 4.2 Consensus size: 24
7446 AATTATTAGT
*
7456 ATCAAATCATTAAATATTAATAAAA
1 ATCAAATCATTAAA-ATCAATAAAA
* * * *
7481 AT--TATTATTAACAATCATTATTAA
1 ATCAAATCATTAA-AATCAATA-AAA
* * *
7505 ATCATATCATTATTAAATCATTAAAT
1 ATCAAATCATTA--AAATCAATAAAA
*
7531 ATCAAATCATTAAATATTAATAATAA
1 ATCAAATCATTAAA-ATCAATAA-AA
7557 ATCA
1 ATCA
7561 TTAATAGTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
23 12 0.20
24 7 0.12
25 8 0.13
26 24 0.40
27 8 0.13
28 1 0.02
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (24 bp):
ATCAAATCATTAAAATCAATAAAA
Found at i:9134 original size:22 final size:23
Alignment explanation
Indices: 9109--9152 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
9099 AATTAAGTTT
9109 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
9131 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
9153 CCGTTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:29212 original size:20 final size:20
Alignment explanation
Indices: 29183--29222 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
29173 TAAAATGAAT
29183 AAATAAAT-AATCAAAAAAG
1 AAATAAATAAATCAAAAAAG
*
29202 AAATAAAATAAATGAAAAAAG
1 AAAT-AAATAAATCAAAAAAG
29223 TTAAAAGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 4 0.22
21 10 0.56
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (20 bp):
AAATAAATAAATCAAAAAAG
Found at i:30433 original size:29 final size:29
Alignment explanation
Indices: 30397--30457 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
30387 TGTCGACTTC
30397 TTTTCCTTGTAATTTTCAGTAGTACTTTT
1 TTTTCCTTGTAATTTTCAGTAGTACTTTT
30426 TTTTCCTTGTAATTTTCAGTAGTACTTTT
1 TTTTCCTTGTAATTTTCAGTAGTACTTTT
30455 TTT
1 TTT
30458 CTTTCTCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.16, C:0.13, G:0.10, T:0.61
Consensus pattern (29 bp):
TTTTCCTTGTAATTTTCAGTAGTACTTTT
Found at i:36504 original size:133 final size:133
Alignment explanation
Indices: 36255--36528 Score: 410
Period size: 133 Copynumber: 2.1 Consensus size: 133
36245 AGTACCTGGT
* * * *
36255 AAAACCCAAGAAACAATGTACCTTAGACACATTCTTGGGTGGTTCCCACTCAACTATGATTTGGA
1 AAAACCCAAGAAACAATGTACCTGAGACACATTCTTGGATGGTTCCCACTCAAATACGATTTGGA
* *
36320 TCTTTTAAGGGTCAATTCAAATGCCATATATTGTTGTTACATGACACAAAATAAAACATCTAACA
66 TCTTTTAAGGGTCAATTCAAATGCCATATATTGTTGTGACATGACAAAAAATAAAACATCTAACA
36385 ACC
131 ACC
* *
36388 AAAACCCAAGAAACAGTGTACC-GAGGACACATTCTTGGATGGTTCCCACTCAAATACGGTTTGG
1 AAAACCCAAGAAACAATGTACCTGA-GACACATTCTTGGATGGTTCCCACTCAAATACGATTTGG
* *
36452 ATCTTTTAAGGGTCAACTT-AAATGCCA-ATATTGTTGTGACATGACATAAAAATAAAACCTCTG
65 ATCTTTTAAGGGTCAA-TTCAAATGCCATATATTGTTGTGACATGACA-AAAAATAAAACATCTA
36515 ACAACC
128 ACAACC
36521 AAAACCCA
1 AAAACCCA
36529 CACTTCCTAT
Statistics
Matches: 128, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
132 19 0.15
133 107 0.84
134 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (133 bp):
AAAACCCAAGAAACAATGTACCTGAGACACATTCTTGGATGGTTCCCACTCAAATACGATTTGGA
TCTTTTAAGGGTCAATTCAAATGCCATATATTGTTGTGACATGACAAAAAATAAAACATCTAACA
ACC
Found at i:46830 original size:16 final size:16
Alignment explanation
Indices: 46806--46844 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
46796 TTTAATAATT
46806 ATAATAATAAA-AATAAA
1 ATAA-AATAAATAAT-AA
46823 ATAAAATAAATAATAA
1 ATAAAATAAATAATAA
46839 ATAAAA
1 ATAAAA
46845 ATCTCAGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
ATAAAATAAATAATAA
Found at i:47081 original size:53 final size:53
Alignment explanation
Indices: 47011--47215 Score: 302
Period size: 53 Copynumber: 3.9 Consensus size: 53
47001 CTTCGACCAG
* *
47011 CGGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGTCTA
1 CGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTCTA
* * * * *
47064 CTGGTTTATTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTA
1 CGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTCTA
* * * * *
47117 CGGGTTCGCTCCCTCTTGCTTCGGGGAGTAGAATTCGAATAATCTTCTGTTTA
1 CGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTCTA
47170 CGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTT
1 CGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTT
47216 ATGGTGTGAT
Statistics
Matches: 133, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 133 1.00
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (53 bp):
CGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTCTA
Found at i:47714 original size:42 final size:41
Alignment explanation
Indices: 47594--47717 Score: 185
Period size: 42 Copynumber: 3.0 Consensus size: 41
47584 GGTCTTATGG
* * * * *
47594 ATGACCCAAAGGATTTATCATCTTGCTCGAGAGACTCACAA
1 ATGACCCGAAGGATTTATCATCATGCTCGAAAGACTTACTA
47635 ATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTA
1 ATGACCCGAAGGATTT-ATCATCATGCTCGAAAGACTTACTA
47677 ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACT
1 ATGACCCGAAGGATTT-ATCATCATGCTCGAAAGACTTACT
47718 GATGGATTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 15 0.20
42 61 0.80
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (41 bp):
ATGACCCGAAGGATTTATCATCATGCTCGAAAGACTTACTA
Found at i:47814 original size:43 final size:43
Alignment explanation
Indices: 47765--47851 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
47755 CAGTTACCCG
** *
47765 AAGGATTTGATCATCATACTCGAAAGACTTACTGATGACACTT
1 AAGGATTACATCATCACACTCGAAAGACTTACTGATGACACTT
* * *
47808 AAGGATTACATCATCACGCTTGAAAGACTTACTGATGGCACTT
1 AAGGATTACATCATCACACTCGAAAGACTTACTGATGACACTT
47851 A
1 A
47852 CTGACAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (43 bp):
AAGGATTACATCATCACACTCGAAAGACTTACTGATGACACTT
Found at i:47967 original size:93 final size:93
Alignment explanation
Indices: 47829--48026 Score: 306
Period size: 93 Copynumber: 2.1 Consensus size: 93
47819 CATCACGCTT
*
47829 GAAAGACTTACTGATGGCACTTACTGACAAATTTACTTCACTACTCTTCCGTGAAGCCTTAAAAA
1 GAAAGACTTACTGATGGCACTTACTAACAAATTTACTTCACTACTCTTCCGTGAAGCCTTAAAAA
* * *
47894 TTACCCGAAGGATTTAATCATCATACTC
66 TTACCCGAAGGACTTAAGCAACATACTC
* ** * *
47922 GAAAGACTTATTGATGGCACTTACTAACGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAAAA
1 GAAAGACTTACTGATGGCACTTACTAACAAATTTACTTCACTACTCTTCCGTGAAGCCTTAAAAA
*
47987 TTACCCGAAGGACTTAAGCAACATTCTC
66 TTACCCGAAGGACTTAAGCAACATACTC
48015 GAAAGACTTACT
1 GAAAGACTTACT
48027 AAGTGCGAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (93 bp):
GAAAGACTTACTGATGGCACTTACTAACAAATTTACTTCACTACTCTTCCGTGAAGCCTTAAAAA
TTACCCGAAGGACTTAAGCAACATACTC
Found at i:48203 original size:42 final size:42
Alignment explanation
Indices: 48140--48238 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
48130 AGGTCTTATG
* ** * *
48140 GATGGCCCGAAGAACTTATCATTTTGCTCTAAAGGCTTAC-A
1 GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACTA
* *
48181 GATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTA
1 GATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACTA
48224 -ATGGCCCGAAGGACT
1 GATGGCCCGAAGGACT
48239 CTAATTGTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
41 14 0.30
42 32 0.68
43 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACTA
Found at i:54567 original size:21 final size:22
Alignment explanation
Indices: 54525--54567 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
54515 CTTTCAATAC
*
54525 GAAGTGGTCTTCGTGTCTTTGT
1 GAAGTGGTCTTCGTGTCCTTGT
* *
54547 GAAG-GGTCTTCTTTTCCTTGT
1 GAAGTGGTCTTCGTGTCCTTGT
54568 TATAACTGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (22 bp):
GAAGTGGTCTTCGTGTCCTTGT
Found at i:55076 original size:47 final size:46
Alignment explanation
Indices: 54988--55077 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 46
54978 ACATTAAAAC
*
54988 CCTAACCGCATGATATCTAATTCGCATACTTGTTCGAGAAAAATAAA
1 CCTAACCGCATGATATCTAATTCGCATACTTATTC-AGAAAAATAAA
* *
55035 CCTAACCGCATTATATCTAGTTCGCATACATTTATTC-GAAAAA
1 CCTAACCGCATGATATCTAATTCGCATAC--TTATTCAGAAAAA
55078 CAAAAATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
47 33 0.87
49 5 0.13
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (46 bp):
CCTAACCGCATGATATCTAATTCGCATACTTATTCAGAAAAATAAA
Found at i:58392 original size:11 final size:10
Alignment explanation
Indices: 58376--58415 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
58366 TAATTATAAT
58376 AATAAAAATA
1 AATAAAAATA
58386 AA-ATAAAATA
1 AATA-AAAATA
58396 AATAATAAATA
1 AATAA-AAATA
58407 AATAAAAAT
1 AATAAAAAT
58416 CCCGGACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 1 0.04
10 15 0.56
11 11 0.41
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AATAAAAATA
Done.