Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005878.1 Hibiscus syriacus cultivar Beakdansim tig00013810_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: 66778
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3446 original size:19 final size:21
Alignment explanation
Indices: 3424--3462 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
3414 CTGAAATATG
3424 TAATAAAACA-ATAA-ATAAA
1 TAATAAAACACATAATATAAA
*
3443 TAATATAACACATAATATAA
1 TAATAAAACACATAATATAA
3463 TATGCTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (21 bp):
TAATAAAACACATAATATAAA
Found at i:4519 original size:164 final size:161
Alignment explanation
Indices: 3980--4696 Score: 722
Period size: 164 Copynumber: 4.4 Consensus size: 161
3970 CTTGCTTTGG
* *
3980 GCTATGTTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGACAGAT
1 GCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT--TGGCAGAT
* * * * *
4045 AACCCTCCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCG
64 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCG
* * *
4110 GGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
129 GAGGTCTTTGGCAGATAACCCTTCTAGACTTAA
* * * *
4143 GCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTGGAA
1 GCTATGCTGTAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC---T-TTGGCA
* * * * * *
4207 GACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAAC
61 GATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAAC
* *
4271 TCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTGA
126 TCGGAGGTCTTT-G-G-CAGATAACCCTTCTAGACTTAA
* * * * * * * * * *
4310 GTTATACTGTGAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTC-AGGGGTCTTTGGCAGAT
1 GCTATGCTGTAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGA-AGGTCTTTGGCAGAT
* * * * * * * * *
4374 AGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTG-AGCTGAGCGTAATCGAACTCA
64 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCG
*
4438 GAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAA
129 GAGGTC---T-TTGGCAGATAACCCTTCTAGACTTAA
* * *
4475 GTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
1 GCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-G-G-CAGA
* ** * *
4540 TAACCCTTCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAACCTGAGTGTAATCGAACTC
63 TAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTC
* * * *
4605 GGGGGTCTTTGGCAGATAGCTCTTCTCGACTTAA
128 GGAGGTCTTTGGCAGATAACCCTTCTAGACTTAA
* * *
4639 GCTATGCTGCAAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGG
1 GCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
4697 TTGGCAAATA
Statistics
Matches: 450, Mismatches: 83, Indels: 43
0.78 0.14 0.07
Matches are distributed among these distances:
162 1 0.00
163 47 0.10
164 193 0.43
165 82 0.18
166 4 0.01
167 76 0.17
168 47 0.10
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (161 bp):
GCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAA
CCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGGA
GGTCTTTGGCAGATAACCCTTCTAGACTTAA
Found at i:4702 original size:248 final size:248
Alignment explanation
Indices: 3987--4702 Score: 1229
Period size: 248 Copynumber: 2.9 Consensus size: 248
3977 TGGGCTATGT
*
3987 TGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGGTGACAGATAACCCT
1 TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
* * *
4051 CCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
66 TCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
* *
4116 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
131 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAG
* * *
4181 TCAAACTCAAAGGTCTTTTGTTGGAAGACAACCCTTCTAGACTTAAGTTGTAC
196 TCGAACTTAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTAC
*
4234 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
1 TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
* * *
4299 TCTAGACTTGAGTTATACTGTGAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTCAGGGGTC
66 TCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
*
4364 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAA
131 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAG
* * *
4429 TCGAACTCAGAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
196 TCGAACTTAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTAC
4482 TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
1 TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
*
4547 TCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAACCTGAGTGTAATCGAACTCGGGGGTC
66 TCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
4612 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTC-TTGGAGCTGAGCGTA
131 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTT-GAGCTGAGCGTA
* *
4676 GTCGAACTTGAAGGTCTTTGGTTGGCA
195 GTCGAACTTAAAGGTCTTTTGTTGGCA
4703 AATAGCCCTT
Statistics
Matches: 442, Mismatches: 25, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
247 46 0.10
248 396 0.90
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (248 bp):
TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
TCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAG
TCGAACTTAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTAC
Found at i:4726 original size:84 final size:84
Alignment explanation
Indices: 3980--4737 Score: 647
Period size: 84 Copynumber: 9.2 Consensus size: 84
3970 CTTGCTTTGG
* * * *
3980 GCTATGTTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGG-TGACAG
1 GCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
* * *
4043 ATAACCCTCCTAGCCTTGA
66 ATAACCCTTCTAGACTTAA
* * * * * * **
4062 GTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCA
1 GCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCA
* *
4123 GATAGCCCTTCTCGACTTAA
65 GATAACCCTTCTAGACTTAA
* * * * *
4143 GCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTGGAA
1 GCTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCA
*
4207 GACAACCCTTCTAGACTTAA
65 GATAACCCTTCTAGACTTAA
* * * *
4227 GTTGTACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAG
1 GCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
*
4291 ATAACCCTTCTAGACTTGA
66 ATAACCCTTCTAGACTTAA
* * ** * * * * * *
4310 GTTATACTGTGAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTC-AGGGGTC--T--TTGGC
1 GCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGA-AGGTCTTTGGTTGGC
* * *
4370 AGATAGCTCTTCTCGACTTAA
64 AGATAACCCTTCTAGACTTAA
* * * *
4391 GCTATGCTGCAAATGATGTGTCGTT-GAGCTGAGCGTAATCGAACTC-AGAGGTCTTTTGTTGGC
1 GCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGA-AGGTCTTTGGTTGGC
*
4454 AGACAACCCTTCTAGACTTAA
64 AGATAACCCTTCTAGACTTAA
* * * *
4475 GTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAG
1 GCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
*
4539 ATAACCCTTCTAGACTTGA
66 ATAACCCTTCTAGACTTAA
* ** * * * * * **
4558 GTTATGCTGTGAATGATATGCCCTCGAACCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCA
1 GCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCA
* * *
4619 GATAGCTCTTCTCGACTTAA
65 GATAACCCTTCTAGACTTAA
* * * *
4639 GCTATGCTGCAAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGGTTGGCAA
1 GCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
* * * *
4704 ATAGCCCTTCTTGTCTTGA
66 ATAACCCTTCTAGACTTAA
**
4723 GCTATATTGCAAATG
1 GCTATGCTGCAAATG
4738 TTGTCTTAAA
Statistics
Matches: 538, Mismatches: 115, Indels: 44
0.77 0.16 0.06
Matches are distributed among these distances:
80 71 0.13
81 110 0.20
82 23 0.04
83 111 0.21
84 222 0.41
85 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (84 bp):
GCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
ATAACCCTTCTAGACTTAA
Found at i:9181 original size:20 final size:21
Alignment explanation
Indices: 9145--9184 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
9135 ATAAATACTG
9145 AATAAATTGAAGAGAAAAATA
1 AATAAATTGAAGAGAAAAATA
*
9166 AATAAATTG-TGAGAAAAAT
1 AATAAATTGAAGAGAAAAAT
9185 GTTAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (21 bp):
AATAAATTGAAGAGAAAAATA
Found at i:17556 original size:23 final size:23
Alignment explanation
Indices: 17525--17583 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
17515 TCTAGGCTGG
* *
17525 ACCATTGCCAGCTGCCCAGCAGC
1 ACCACTGCCAGCTGCCCAACAGC
17548 ACCACTGCCAGCTGCCCAACAGC
1 ACCACTGCCAGCTGCCCAACAGC
17571 ACCACTGCCAGCT
1 ACCACTGCCAGCT
17584 CTGCCCGATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.24, C:0.46, G:0.19, T:0.12
Consensus pattern (23 bp):
ACCACTGCCAGCTGCCCAACAGC
Found at i:20675 original size:150 final size:150
Alignment explanation
Indices: 20402--20691 Score: 386
Period size: 150 Copynumber: 1.9 Consensus size: 150
20392 ACAACCAATA
* * * **
20402 AAGGTGAATCCCTATTCTTAATCATACCGAAAGACGTCAGCAGGTCTGGAAAATCAAATGAACAA
1 AAGGTGAATCCCTATTCTTAATCAGACCGAAAGACATCAGCAGGCCTAAAAAATCAAATGAACAA
*
20467 GAAGCTGATATGAACGAAACAGAAACAATTGAAAGCGACTATACAAGAATTGTTGAAAGTGAAAA
66 GAAGCTGATATGAACGAAACAGAAACAATTGAAAGCGACTATACAAGAATTGTCGAAAGTGAAAA
20532 AGAAAGAGAGACAGTTAATG
131 AGAAAGAGAGACAGTTAATG
** * * *
20552 AAGGTGAATCTGTATTCTTAATCAGACCGGAAGACATCATC-GTGCCTAAAAAATCAAATGAAGA
1 AAGGTGAATCCCTATTCTTAATCAGACCGAAAGACATCAGCAG-GCCTAAAAAATCAAATGAACA
* * * * * *
20616 ATAAGCTGATATG-ACTGAAACAGAAACAATTGGAAGTGATTATACAAGCATTGTCGAAAGTGCA
65 AGAAGCTGATATGAAC-GAAACAGAAACAATTGAAAGCGACTATACAAGAATTGTCGAAAGTGAA
*
20680 ATAGAAAGAGAG
129 AAAGAAAGAGAG
20692 GTAAATACAT
Statistics
Matches: 120, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
149 3 0.03
150 117 0.98
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (150 bp):
AAGGTGAATCCCTATTCTTAATCAGACCGAAAGACATCAGCAGGCCTAAAAAATCAAATGAACAA
GAAGCTGATATGAACGAAACAGAAACAATTGAAAGCGACTATACAAGAATTGTCGAAAGTGAAAA
AGAAAGAGAGACAGTTAATG
Found at i:22129 original size:8 final size:8
Alignment explanation
Indices: 22116--22247 Score: 255
Period size: 8 Copynumber: 16.5 Consensus size: 8
22106 ACTTAGTTAT
22116 GTATGTAC
1 GTATGTAC
22124 GTATGTAC
1 GTATGTAC
22132 GTATGTAC
1 GTATGTAC
22140 GTATGTAC
1 GTATGTAC
22148 GTATGTAC
1 GTATGTAC
22156 GTATGTAC
1 GTATGTAC
22164 GTATGTAC
1 GTATGTAC
22172 GTATGTAC
1 GTATGTAC
22180 GTATGTAC
1 GTATGTAC
22188 GTATGTAC
1 GTATGTAC
22196 GTATGTAC
1 GTATGTAC
22204 GTATGTAC
1 GTATGTAC
22212 GTATGTAC
1 GTATGTAC
22220 GTATGTAC
1 GTATGTAC
22228 GTATGTAC
1 GTATGTAC
*
22236 GTATGTAT
1 GTATGTAC
22244 GTAT
1 GTAT
22248 ACATGAAAAC
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
8 123 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (8 bp):
GTATGTAC
Found at i:23166 original size:20 final size:19
Alignment explanation
Indices: 23141--23182 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
23131 ATGAAATTAG
*
23141 TAAAAAAATCTACAATATTT
1 TAAAAAAAT-TAAAATATTT
23161 TAAAAAAAATTAAAATATTT
1 T-AAAAAAATTAAAATATTT
23181 TA
1 TA
23183 CACAGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAAAATTAAAATATTT
Found at i:26258 original size:13 final size:13
Alignment explanation
Indices: 26240--26264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26230 GATTAAATGA
26240 ATTTAAATAATTT
1 ATTTAAATAATTT
26253 ATTTAAATAATT
1 ATTTAAATAATT
26265 AGATGATAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTAAATAATTT
Found at i:35350 original size:138 final size:137
Alignment explanation
Indices: 35141--35409 Score: 317
Period size: 138 Copynumber: 2.0 Consensus size: 137
35131 ACACGGTTTC
* * * ** *
35141 TACGTGATGAGGAAATCCGATTATCTAAGGGTGACACTGCTCCTACGTGATGAAGAGATCTAGTC
1 TACGCGATGAGGAAATCCGACTATCTAAGGATGACACAACTCCTACGTGATGAAGAGACCTAGTC
** * ** * *
35206 GATGGATGACATTGTTCTTACGTGATGAAGATGTCTGGCCATCTTTAAGGG-TAAATGGAGATAA
66 GATGGATGACACAGTTCATACGTGATGAAGACATCTGGCAATCTTT-AGGGAT-AATAGAGATAA
35270 CATGGTTCT
129 CATGGTTCT
* * * * * *
35279 TACGCGATGAGGAAGTCTGACTATCTAAGGATGACGCAACTCCTACGTGATGAGGAGGCCTGGTC
1 TACGCGATGAGGAAATCCGACTATCTAAGGATGACACAACTCCTACGTGATGAAGAGACCTAGTC
*
35344 -AGTGGATGACACAGTTCATACGTGATGAGGACATCTGGCAATCTTTAGGGATAATAGAGATAAC
66 GA-TGGATGACACAGTTCATACGTGATGAAGACATCTGGCAATCTTTAGGGATAATAGAGATAAC
35408 AT
130 AT
35410 AGCTATCTAA
Statistics
Matches: 109, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
137 18 0.17
138 91 0.83
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (137 bp):
TACGCGATGAGGAAATCCGACTATCTAAGGATGACACAACTCCTACGTGATGAAGAGACCTAGTC
GATGGATGACACAGTTCATACGTGATGAAGACATCTGGCAATCTTTAGGGATAATAGAGATAACA
TGGTTCT
Found at i:35538 original size:113 final size:113
Alignment explanation
Indices: 35299--35521 Score: 284
Period size: 113 Copynumber: 2.0 Consensus size: 113
35289 GGAAGTCTGA
* * *
35299 CTATCTAAGGATGACGCAACTCCTACGTGATGAGGAGGCCTGGTCAGTGGATGACACAGTTCATA
1 CTATCTAAGGATGACGCAACTCCTACGTGATGAGAAGACCTGGTCAGTGAATGACACAGTTCATA
* * *
35364 CGTGATGAGGACATCTGGCAATCTTTAGGGATAATAGAGATAACATAG
66 CATGATAAGGACATCTGACAATCTTTAGGGATAATAGAGATAACATAG
* * * * ** *
35412 CTATCTAAGGATGACGCGACTCCTACTTGATGAGAAGATCTGGTCATTGAATGACATGGTTCCTA
1 CTATCTAAGGATGACGCAACTCCTACGTGATGAGAAGACCTGGTCAGTGAATGACACAGTTCATA
** * * *
35477 CATGATAAGGATGTCTGACCATTTTTAGGGATAATGGAGATAACA
66 CATGATAAGGACATCTGACAATCTTTAGGGATAATAGAGATAACA
35522 CGGTTCCTAC
Statistics
Matches: 92, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
113 92 1.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (113 bp):
CTATCTAAGGATGACGCAACTCCTACGTGATGAGAAGACCTGGTCAGTGAATGACACAGTTCATA
CATGATAAGGACATCTGACAATCTTTAGGGATAATAGAGATAACATAG
Found at i:35618 original size:250 final size:251
Alignment explanation
Indices: 35162--35656 Score: 576
Period size: 250 Copynumber: 2.0 Consensus size: 251
35152 GAAATCCGAT
* * * *
35162 TATCTAAGGGTGACACTGCTCCTACGTGATGAAGAGATCTAGTCGATGGATGACATTGTTCTTAC
1 TATCTAAGGATGACACTGCTCCTACGTGATGAAGAGATCTAGTCGATGAATGACATGGTTCCTAC
* * * *
35227 GTGATGAAGATGTCTGGCCATCTTTAAGGGTAAATGGAGATAACATGGTTCTTACGCGATGAGGA
66 ATGATGAAGATGTCTGACCATCTTTAAGGGTAAATGGAGATAACACGGTTCCTACGCGATGAGGA
* * **
35292 AGTCTGACTATCTAAGGATGACGCAACTCCTACGTGATGAGGAGGCCTGGTCAGTGGATGACACA
131 AGTCTGACTATCTAA-GATGACGCAACTCCTACGTGATGAGGAGACCTGGTCAGTAGACAACACA
35357 GTTCATACGTGATGAGGACATCTGG-CAATCTTTAGGGAT-AATAGAGATAACATAGC
195 GTTCATACGTGATGAGGACATCTGGTC-ATCTTTAGGGATAAATAGAGATAACATAGC
* * *
35413 TATCTAAGGATGACGC-GACTCCTACTTGATG-AGAAGATCTGGTC-ATTGAATGACATGGTTCC
1 TATCTAAGGATGACACTG-CTCCTACGTGATGAAG-AGATCTAGTCGA-TGAATGACATGGTTCC
*
35475 TACATGAT-AAGGATGTCTGACCAT-TTTTAGGG-ATAATGGAGATAACACGGTTCCTACGCGAT
63 TACATGATGAA-GATGTCTGACCATCTTTAAGGGTA-AATGGAGATAACACGGTTCCTACGCGAT
** * ** *
35537 GAGGAAGTCTGGTTATCTAA-ATGTAACGCTACTCCTACGTGATGAGGAGATTTGGTCGGTAGAC
126 GAGGAAGTCTGACTATCTAAGATG--ACGCAACTCCTACGTGATGAGGAGACCTGGTCAGTAGAC
* ** * * * * *
35601 AATATTGTTCCTACGTGATTAGGACGTTTGGTCATCTTTAGGGATAAATGGAGATA
189 AACACAGTTCATACGTGATGAGGACATCTGGTCATCTTTAGGGATAAATAGAGATA
35657 TCACGGTTCC
Statistics
Matches: 205, Mismatches: 30, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
248 3 0.01
249 1 0.00
250 124 0.60
251 77 0.38
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (251 bp):
TATCTAAGGATGACACTGCTCCTACGTGATGAAGAGATCTAGTCGATGAATGACATGGTTCCTAC
ATGATGAAGATGTCTGACCATCTTTAAGGGTAAATGGAGATAACACGGTTCCTACGCGATGAGGA
AGTCTGACTATCTAAGATGACGCAACTCCTACGTGATGAGGAGACCTGGTCAGTAGACAACACAG
TTCATACGTGATGAGGACATCTGGTCATCTTTAGGGATAAATAGAGATAACATAGC
Found at i:35693 original size:138 final size:138
Alignment explanation
Indices: 35413--35923 Score: 535
Period size: 138 Copynumber: 3.7 Consensus size: 138
35403 ATAACATAGC
* * * * * ** * * *
35413 TATCTAAGGATGACGC-GACTCCTACTTGATGAGAAGATCTGGTCATTGAATGACATGGTTCCTA
1 TATCTAAGGGTAACGCTG-CTCCTACGTGATGAGGAGATTTGGTCGGTGGATGATATTGTTCCTA
* * * * * * *
35477 CATGATAAGGATGTCT-GACCATTTTTAGGGAT-AATGGAGATAACACGGTTCCTACGCGATGAG
65 CGTGATGAGGACGTTTGGA-CATCTTTAGGGATAAATGGAGATATCACGGTTCCTACGTGATGAG
35540 GAAGTCTGGT
129 GAAGTCTGGT
** * * **
35550 TATCTAAATGTAACGCTACTCCTACGTGATGAGGAGATTTGGTCGGTAGACAATATTGTTCCTAC
1 TATCTAAGGGTAACGCTGCTCCTACGTGATGAGGAGATTTGGTCGGTGGATGATATTGTTCCTAC
* *
35615 GTGATTAGGACGTTTGGTCATCTTTAGGGATAAATGGAGATATCACGGTTCCTACGTGATGAGGA
66 GTGATGAGGACGTTTGGACATCTTTAGGGATAAATGGAGATATCACGGTTCCTACGTGATGAGGA
*
35680 AGTTTGGT
131 AGTCTGGT
* * * * * ** * *
35688 CATCTAAGGGTAACACTGCTCTTACGTGATGAAGAGATCTGGTTTGTGGATGATATTATTTCTAC
1 TATCTAAGGGTAACGCTGCTCCTACGTGATGAGGAGATTTGGTCGGTGGATGATATTGTTCCTAC
* * * * *
35753 GTGATGAGGAC-TTCTGGAAATATTTAGGGATAAATGGAGATATTATGGTTCCTACATGATGAGG
66 GTGATGAGGACGTT-TGGACATCTTTAGGGATAAATGGAGATATCACGGTTCCTACGTGATGAGG
*
35817 AAGCCTGGT
130 AAGTCTGGT
* * * *
35826 TATCTAAGGGTGACGCTGCTCCTACGTGATAAGGAGATTTGGTCGGTGGATGACACTGTTCCTAC
1 TATCTAAGGGTAACGCTGCTCCTACGTGATGAGGAGATTTGGTCGGTGGATGATATTGTTCCTAC
* * *
35891 ATGATGAGGACGTCTGGCCATCTTTAGGGATAA
66 GTGATGAGGACGTTTGGACATCTTTAGGGATAA
35924 TTTTTTCAAG
Statistics
Matches: 302, Mismatches: 67, Indels: 9
0.80 0.18 0.02
Matches are distributed among these distances:
137 73 0.24
138 228 0.75
139 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (138 bp):
TATCTAAGGGTAACGCTGCTCCTACGTGATGAGGAGATTTGGTCGGTGGATGATATTGTTCCTAC
GTGATGAGGACGTTTGGACATCTTTAGGGATAAATGGAGATATCACGGTTCCTACGTGATGAGGA
AGTCTGGT
Found at i:36098 original size:36 final size:35
Alignment explanation
Indices: 36057--36171 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 35
36047 AAAATGTGCA
36057 TGTTTCAAGAGAAAGTGTCTCAAGAGATACAAAATT
1 TGTTTCAAGAGAAA-TGTCTCAAGAGATACAAAATT
*
36093 TGTTTCAAGAGAAATAATCTCAA-AG-T------TT
1 TGTTTCAAGAGAAAT-GTCTCAAGAGATACAAAATT
* *
36121 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
1 -TGTTTCAAGAGAAA-TGTCTCAAGAGATACAAAATT
36158 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
36172 CAATCTCAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
28 2 0.03
29 20 0.31
30 3 0.05
34 1 0.02
35 3 0.05
36 34 0.53
37 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGAGAAATGTCTCAAGAGATACAAAATT
Found at i:36145 original size:65 final size:65
Alignment explanation
Indices: 35927--36180 Score: 339
Period size: 66 Copynumber: 3.9 Consensus size: 65
35917 GGGATAATTT
* * * * *
35927 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCGAGGGAATTAATCTCAAAGATTTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAATCTCAAAG-TTTAT
35992 G
65 G
* * * * **
35993 TTTTAAGAGAAACTGTCTCAAAAGAGATAAAATTTGTTTCAAG-GAAAATAATCTAAAATGTGCA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAG-AAATAATCTCAAA-GTTTA
36057 TG
64 TG
* *
36059 TTTCAAGAGAAAGTGTCTCAAGAGATACAAAATTTGTTTCAAGAGAAATAATCTCAAAGTTTATG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAATCTCAAAGTTTATG
* *
36124 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTCAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAATCTCAA
36181 GGGTTTTATG
Statistics
Matches: 163, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
65 59 0.36
66 102 0.63
67 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (65 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAATCTCAAAGTTTATG
Found at i:36166 original size:21 final size:20
Alignment explanation
Indices: 36133--36174 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
36123 GTTTCAAGAG
*
36133 AAACTGTCTCAAGAGAGACA
1 AAACTGTCTCAAGAGAAACA
*
36153 AAACTTGTTTCAAGAGAAACA
1 AAAC-TGTCTCAAGAGAAACA
36174 A
1 A
36175 TCTCAAGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (20 bp):
AAACTGTCTCAAGAGAAACA
Found at i:36553 original size:36 final size:36
Alignment explanation
Indices: 36509--36617 Score: 146
Period size: 37 Copynumber: 3.0 Consensus size: 36
36499 AAAGGAAAAA
* *
36509 TGTCTCAAGCGAGATGAAATTTGTTTTGAGAGAAAT
1 TGTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAAT
* *
36545 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAT
1 TGTCTCAAGCGAGACGAAATTTG-TTTTAAGAGAAAT
* *
36582 TGTCTCTAGCGAGACGACAATTTGTTTCAAGAGAAA
1 TGTCTCAAGCGAGACGA-AATTTGTTTTAAGAGAAA
36618 CAATCTCAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
36 21 0.33
37 36 0.57
38 6 0.10
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (36 bp):
TGTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAAT
Found at i:58646 original size:32 final size:32
Alignment explanation
Indices: 58603--58673 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
58593 TAACAAAGAC
58603 AAAAAAAAAAGAAAATAAACGACACACCAATA
1 AAAAAAAAAAGAAAATAAACGACACACCAATA
* *
58635 AGAAAATAAAGAAAATAAACGACACACCAATA
1 AAAAAAAAAAGAAAATAAACGACACACCAATA
58667 AAAAAAA
1 AAAAAAA
58674 TAAGTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.72, C:0.14, G:0.07, T:0.07
Consensus pattern (32 bp):
AAAAAAAAAAGAAAATAAACGACACACCAATA
Found at i:64541 original size:20 final size:20
Alignment explanation
Indices: 64512--64557 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
64502 AATTTTCCGG
*
64512 GACACGTCCTAGACTAACCC
1 GACACATCCTAGACTAACCC
64532 GACACATCCTAGACTAACCC
1 GACACATCCTAGACTAACCC
64552 GACACA
1 GACACA
64558 AAGTAGTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.39, G:0.13, T:0.13
Consensus pattern (20 bp):
GACACATCCTAGACTAACCC
Done.