Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001922.1 Hibiscus syriacus cultivar Beakdansim tig00003890_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: 61605
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2313 original size:37 final size:38
Alignment explanation
Indices: 2240--2313 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 38
2230 ATTTCTTATA
* ** *
2240 TTTTTGTTATTTTTTATTATTCTAATTTATTTATTTTC
1 TTTTTGTTATTTTTTAGTATTAAAATTTATTCATTTTC
2278 TTTTTGTTA-TTTTTAGTATTAAAATTT-TTACATTTT
1 TTTTTGTTATTTTTTAGTATTAAAATTTATT-CATTTT
2314 GTTCATATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
36 2 0.06
37 20 0.65
38 9 0.29
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (38 bp):
TTTTTGTTATTTTTTAGTATTAAAATTTATTCATTTTC
Found at i:3638 original size:2 final size:2
Alignment explanation
Indices: 3631--3669 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
3621 TTCCCCGAAT
* *
3631 GA GA GA GA GA TA GA GA GA GA GA TA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3670 TAATAGCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.46, T:0.05
Consensus pattern (2 bp):
GA
Found at i:3648 original size:12 final size:12
Alignment explanation
Indices: 3631--3669 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
3621 TTCCCCGAAT
3631 GAGAGAGAGATA
1 GAGAGAGAGATA
3643 GAGAGAGAGATA
1 GAGAGAGAGATA
*
3655 GAGAGAGAGAGA
1 GAGAGAGAGATA
3667 GAG
1 GAG
3670 TAATAGCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.46, T:0.05
Consensus pattern (12 bp):
GAGAGAGAGATA
Found at i:4029 original size:18 final size:19
Alignment explanation
Indices: 3985--4026 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
3975 TCTCTCTCTC
3985 TCCCCTTTTGAAAAAGGTT
1 TCCCCTTTTGAAAAAGGTT
*
4004 TCCCCTTTTGAAAATGGTT
1 TCCCCTTTTGAAAAAGGTT
4023 TCCC
1 TCCC
4027 TTTCTTTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38
Consensus pattern (19 bp):
TCCCCTTTTGAAAAAGGTT
Found at i:4441 original size:23 final size:24
Alignment explanation
Indices: 4394--4441 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
4384 GTGGATCCTC
*
4394 TTGGGTCGTGCAACTGGGCTCTAG
1 TTGGGTCGTGCAACTGGGCTATAG
* *
4418 TTGGGTC-TGCTATTGGGCTATAG
1 TTGGGTCGTGCAACTGGGCTATAG
4441 T
1 T
4442 CTTGGGCTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.12, C:0.17, G:0.35, T:0.35
Consensus pattern (24 bp):
TTGGGTCGTGCAACTGGGCTATAG
Found at i:4548 original size:3 final size:3
Alignment explanation
Indices: 4533--4582 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
4523 AAATGTAAAT
* *
4533 ATA ATA ATT ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4581 AT
1 AT
4583 TTAAAACCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:5190 original size:138 final size:139
Alignment explanation
Indices: 4789--5489 Score: 600
Period size: 139 Copynumber: 5.1 Consensus size: 139
4779 TTCTACCTGG
* * * * * * * * *
4789 TGAGAAAGTCTGGTTATCTGAGGATGACGTTGTTCATACGTGTTAAGGACATCTGCTCGGTGGAC
1 TGAGGAAGTCTGATTATCTGAGGATGACGTTGCTCCTACGTGTTGAGGAGATCTGATCAGTGGAT
* * * * * *
4854 GGCATTGTTCCTACGTGATGAGGACGTCTAGCCATCTTTAGGGATAATTTGGAGCCAACATGGTT
66 GACATTGTTCCTACGTGATGAGGACTTCTAGTCGTCTTTAAGGATAATTTGGAGACAACATGGTT
4919 CCTACGTA-A
131 CCTACG-AGA
* * * * * * * *
4928 TGAGGAAGTTTGATTATATGAGGATGGCATTGCTCATGCGCGTTAAGGAGATCT-AGTCAGTGGA
1 TGAGGAAGTCTGATTATCTGAGGATGACGTTGCTCCTACGTGTTGAGGAGATCTGA-TCAGTGGA
* * * *
4992 TGGCATTCTTCCTACGTGATGAGGA-TGTCTA-TCCGTCTTTAAAGATAAATTGGAGACAACATG
65 TGACATTGTTCCTACGTGATGAGGACT-TCTAGT-CGTCTTTAAGGATAATTTGGAGACAACATG
5055 GTTCCTACGAGA
128 GTTCCTACGAGA
* * * * *
5067 TGAGGAAGTCTGGTTATCTGATGATGACGCTGCTCCTACGTGTTGAGGAGATGTGATCACT-GAT
1 TGAGGAAGTCTGATTATCTGAGGATGACGTTGCTCCTACGTGTTGAGGAGATCTGATCAGTGGAT
* * * *
5131 GATATTGTTCTTACGTGACGAGGACTTCTAGTCGTCTTTAAGGATAATTTGGAGACAACAAGGTT
66 GACATTGTTCCTACGTGATGAGGACTTCTAGTCGTCTTTAAGGATAATTTGGAGACAACATGGTT
*
5196 CCTA--TGA
131 CCTACGAGA
* * * * *
5203 TAAGGAAGT-TCGATT-TCCTAAGGATGACGTTGCTCCTACGTGTTGAGGAGATATGGTCGGTGG
1 TGAGGAAGTCT-GATTAT-CTGAGGATGACGTTGCTCCTACGTGTTGAGGAGATCTGATCAGTGG
* * * * **
5266 ATGACATTGTTCCTACGTTATTAGGACCTCTAG-CGTCTTTAGGGATAATTTGGAGACAACACAG
64 ATGACATTGTTCCTACGTGATGAGGACTTCTAGTCGTCTTTAAGGATAATTTGGAGACAACATGG
* *
5330 TTCCTATGTGA
129 TTCCTACGAGA
** ** * * * * *
5341 TGACAAAGTCTGATTGCCTAAGGATGACGCTACTCCTACGTGTTGAGGATATCT-AGTCGGTGGA
1 TGAGGAAGTCTGATTATCTGAGGATGACGTTGCTCCTACGTGTTGAGGAGATCTGA-TCAGTGGA
* * * * ** * ** *
5405 CGACATTATTCCTAAC-TGATAAGGACATCTAACCATCTTTCTGGATAATTTGGAGACAACA-CG
65 TGACATTGTTCCT-ACGTGATGAGGACTTCTAGTCGTCTTTAAGGATAATTTGGAGACAACATGG
*
5468 TTCCTACGTGA
129 TTCCTACGAGA
*
5479 TGAGGACGTCT
1 TGAGGAAGTCT
5490 ATCCGTCTTT
Statistics
Matches: 461, Mismatches: 84, Indels: 35
0.79 0.14 0.06
Matches are distributed among these distances:
135 2 0.00
136 84 0.18
137 28 0.06
138 157 0.34
139 189 0.41
140 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (139 bp):
TGAGGAAGTCTGATTATCTGAGGATGACGTTGCTCCTACGTGTTGAGGAGATCTGATCAGTGGAT
GACATTGTTCCTACGTGATGAGGACTTCTAGTCGTCTTTAAGGATAATTTGGAGACAACATGGTT
CCTACGAGA
Found at i:5499 original size:55 final size:55
Alignment explanation
Indices: 5412--5544 Score: 169
Period size: 55 Copynumber: 2.4 Consensus size: 55
5402 GGACGACATT
* * **
5412 ATTCCTAAC-TGATAAGGACATCTAACCATCTTTCTGGATAATTTGGAGACAACAC
1 ATTCCT-ACGTGATGAGGACGTCTAACCATCTTTAGGGATAATTTGGAGACAACAC
* * * *
5467 GTTCCTACGTGATGAGGACGTCTATCCGTCTTTAGGGATAATTTGGAGCCAACAC
1 ATTCCTACGTGATGAGGACGTCTAACCATCTTTAGGGATAATTTGGAGACAACAC
*
5522 ATTCCTACGTGATGAGGAAGTCT
1 ATTCCTACGTGATGAGGACGTCT
5545 GGTTATCTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
54 2 0.03
55 65 0.97
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (55 bp):
ATTCCTACGTGATGAGGACGTCTAACCATCTTTAGGGATAATTTGGAGACAACAC
Found at i:5606 original size:193 final size:193
Alignment explanation
Indices: 5274--5659 Score: 495
Period size: 193 Copynumber: 2.0 Consensus size: 193
5264 GGATGACATT
* * * *
5274 GTTCCTACGTTATTAGGACCTCTAGCGTCTTTAGGGATAATTTGGAGACAACACAGTTCCTATGT
1 GTTCCTACGTGATGAGGACCTCTACCGTCTTTAGGGATAATTTGGAGACAACACAGTTCCTACGT
* * ** * *
5339 GATGACAAAGTCTGATTGCCTAAGGATGACGCTACTCCTACGTGTTGAGGATATCTAGTCGGTGG
66 GATGACAAAGTCTGATTACCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATCTAGTCAGTGG
* * ** *
5404 ACGACATTATTCCTAACTGATAAGGACATCTAACCATCTTTCTGGATAATTTGGAGACAACAC
131 ACAACATTATTCCTAACTAATAAGGACATCTAACCATCTTTAGGGATAATTCGGAGACAACAC
* *
5467 GTTCCTACGTGATGAGGACGTCTATCCGTCTTTAGGGATAATTTGGAGCCAACACA-TTCCTACG
1 GTTCCTACGTGATGAGGACCTCTA-CCGTCTTTAGGGATAATTTGGAGACAACACAGTTCCTACG
** * * * * *
5531 TGATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTATGCATTTAGGAGATCTGGTCAGTG
65 TGATGACAAAGTCTGATTACCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATCTAGTCAGTG
** * * *
5596 GACAACATTATTCCTATGTAATGAGGACATCTAGCCATCTTTAGGGATAATTCGGAGAGAACAC
130 GACAACATTATTCCTAACTAATAAGGACATCTAACCATCTTTAGGGATAATTCGGAGACAACAC
5660 AGTATTTACG
Statistics
Matches: 163, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
193 134 0.82
194 29 0.18
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (193 bp):
GTTCCTACGTGATGAGGACCTCTACCGTCTTTAGGGATAATTTGGAGACAACACAGTTCCTACGT
GATGACAAAGTCTGATTACCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATCTAGTCAGTGG
ACAACATTATTCCTAACTAATAAGGACATCTAACCATCTTTAGGGATAATTCGGAGACAACAC
Found at i:5775 original size:332 final size:330
Alignment explanation
Indices: 5137--5822 Score: 758
Period size: 332 Copynumber: 2.1 Consensus size: 330
5127 TGATGATATT
* * *
5137 GTTCTTACGTGACGAGGACTTCTAGTCGTCTTTAAGGATAATTTGGAGACAACAAGGTTCCTATG
1 GTTCCTACGTGATGAGGACGTCTAGTCGTCTTTAAGGATAATTTGGAGACAACAA-GTTCCTATG
* * * ** *
5202 ATAAGGAAGTTCGATTTCCTAAGGATGACGTTGCTCCTACGTGTTGAGGAGATATGGTCGGTGGA
65 ATAAGGAAGTTCGATTTCCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATATGGTCAGTGGA
** * * * * * *
5267 TGACATTGTTCCTACGTTATTAGGACCTCTAGCGTCTTTAGGGATAATTTGGAGACAACACAGTT
130 CAACATTATTCCTACGTAATGAGGACATCTAGCATCTTTAGGGATAATTCGGAGACAACACAGTT
* * * * * *
5332 CCTATGTGATGACAAAGTCTGATTGCCTAAGGATGACGCTACTCCTACGTGTTGAGGATATCTAG
195 CCTACGTGATAACAAAGTCTGATTACCTAAGGATGACGCTACTCCTACGTGTTAAGGAGATATAG
* ** *
5397 TCGGTGGACGACATTATTCCTAACTGATAAGGACATCTAACCATCTTTCTGGATAATTTGGAGAC
260 TCAGTGGACGACATTATTCCTAACTGATAAGGACATCTAACCATCTTTAGGGATAACTTGGAGAC
5462 AACAC-
325 AACACG
* *
5467 GTTCCTACGTGATGAGGACGTCTA-TCCGTCTTTAGGGATAATTTGGAGCCAACACA-TTCCTAC
1 GTTCCTACGTGATGAGGACGTCTAGT-CGTCTTTAAGGATAATTTGGAGACAACA-AGTTCCTA-
* * * * *
5530 GTGATGAGGAAG-TCTGGTTAT-CTAAGGATGAAGCTACTCCTATGCATTTAGGAGATCTGGTCA
63 -TGATAAGGAAGTTC-GATT-TCCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATATGGTCA
* *
5593 GTGGACAACATTATTCCTATGTAATGAGGACATCTAGCCATCTTTAGGGATAATTCGGAGAGAAC
125 GTGGACAACATTATTCCTACGTAATGAGGACATCTAG-CATCTTTAGGGATAATTCGGAGACAAC
* ** * * * *
5658 ACAGTAT-TTACGTGATAAGGAAGTCTTG-TTATCTGAGGATTACGCTGCTCCTACGTGTTAAGG
189 ACAGT-TCCTACGTGATAACAAAGTC-TGATTACCTAAGGATGACGCTACTCCTACGTGTTAAGG
* * * ** *
5721 AGATATGGTCAGTGGACGACGTTATTCCT-ACATGATGAGGATGTCTAGCCATCTTTAGGGATAA
252 AGATATAGTCAGTGGACGACATTATTCCTAAC-TGATAAGGACATCTAACCATCTTTAGGGATAA
5785 CTTGGAGACAACACG
316 CTTGGAGACAACACG
* *
5800 GTACCTACGTGATGAGGAAGTCT
1 GTTCCTACGTGATGAGGACGTCT
5823 GATTTCCAGG
Statistics
Matches: 294, Mismatches: 51, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
329 7 0.02
330 49 0.17
331 79 0.27
332 135 0.46
333 24 0.08
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (330 bp):
GTTCCTACGTGATGAGGACGTCTAGTCGTCTTTAAGGATAATTTGGAGACAACAAGTTCCTATGA
TAAGGAAGTTCGATTTCCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATATGGTCAGTGGAC
AACATTATTCCTACGTAATGAGGACATCTAGCATCTTTAGGGATAATTCGGAGACAACACAGTTC
CTACGTGATAACAAAGTCTGATTACCTAAGGATGACGCTACTCCTACGTGTTAAGGAGATATAGT
CAGTGGACGACATTATTCCTAACTGATAAGGACATCTAACCATCTTTAGGGATAACTTGGAGACA
ACACG
Found at i:5879 original size:471 final size:469
Alignment explanation
Indices: 5000--5961 Score: 1141
Period size: 471 Copynumber: 2.0 Consensus size: 469
4990 GATGGCATTC
* **
5000 TTCCTACGTGATGAGGATGTCTATCCGTCTTTAAAGATAAATTGGAGACAACATGGTTCCTACGA
1 TTCCTACGTGATGAGGAAGTCTATCCGTCTTTAAAGATAAATTGGAGACAACATCATTCCTACGA
* * * * ** *
5065 GATGAGGAAGTCTGGTTATCTGATGATGACGCTGCTCCTACGTGTTGAGGAGATGTGATCACTGA
66 GATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATCTGATCACTGA
** * * * * * * * *
5130 TGATATTGTTCTTACGTGACGAGGACTTCTAGTCGTCTTTAAGGATAATTTGGAGACAACAAGGT
131 CAACATTATTCCTACGTAACGAGGACATCTAGCCATCTTTAAGGATAATTCGGAGACAACAAGGT
* *
5195 TCCTATGATAAGGAAGTTCGATTTCCTAAGGATGACGTTGCTCCTACGTGTTGAGGAGATATGGT
196 TCCTATGATAAGGAAGTTCGATTTCCTAAGGATGACGCTGCTCCTACGTGTTAAGGAGATATGGT
* * * * * * * *
5260 CGGTGGATGACATTGTTCCTACGTTATTAGGACCTCTAGCGTCTTTAGGGATAATTTGGAGACAA
261 CAGTGGACGACATTATTCCTACATGATGAGGACCTCTAGCATCTTTAGGGATAACTTGGAGACAA
* * *
5325 CACAGTTCCTATGTGATGACAAAGTCTGATTGCCTAAGGATGACGCTACTCCTACGTGTTGAGGA
326 CACAGTACCTACGTGATGACAAAGTCTGATTGCCTAAGGATGACGCTACTCCTACGTGTTAAGGA
* **
5390 TATCTAGTCGGTGGACGACATTATTCCTA-ACTGATAAGGACATCTAACC-ATCTTTCTGGATAA
391 GATCTAGTCGGTGGACGACATTATTCCTACA-TGATAAGGACATCTAACCGA-CTTTAGGGATAA
*
5453 TTTGGAGACAACACG-
454 TTTAGAGACAACACGA
* ** * * *
5468 TTCCTACGTGATGAGGACGTCTATCCGTCTTTAGGGATAATTTGGAGCCAACA-CATTCCTACGT
1 TTCCTACGTGATGAGGAAGTCTATCCGTCTTTAAAGATAAATTGGAGACAACATCATTCCTACGA
* * * *
5532 GATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTATGCATTTAGGAGATCTGGTCAGTGG
66 GATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATCTGATCACT-G
* * * *
5597 ACAACATTATTCCTATGTAATGAGGACATCTAGCCATCTTTAGGGATAATTCGGAGAGAACACA-
130 ACAACATTATTCCTACGTAACGAGGACATCTAGCCATCTTTAAGGATAATTCGGAGACAACA-AG
* * * *
5661 GTAT-TTACGTGATAAGGAAGTCTTG-TTAT-CTGAGGATTACGCTGCTCCTACGTGTTAAGGAG
194 GT-TCCTA--TGATAAGGAAGT-TCGATT-TCCTAAGGATGACGCTGCTCCTACGTGTTAAGGAG
* **
5723 ATATGGTCAGTGGACGACGTTATTCCTACATGATGAGGATGTCTAGCCATCTTTAGGGATAACTT
254 ATATGGTCAGTGGACGACATTATTCCTACATGATGAGGACCTCTAG-CATCTTTAGGGATAACTT
* ** * * *
5788 GGAGACAACACGGTACCTACGTGATGAGGAAGTCTGATTTCC-AGGGGATGACGCTGCTCCTACG
318 GGAGACAACACAGTACCTACGTGATGACAAAGTCTGATTGCCTA-AGGATGACGCTACTCCTACG
* * * *
5852 TGTTAAGGAGATCTAGTCGGTGGACGACATTGTTCGTACATGATGAGGACATCTAGCCGACTTTA
382 TGTTAAGGAGATCTAGTCGGTGGACGACATTATTCCTACATGATAAGGACATCTAACCGACTTTA
5917 GGGATAATTTAGAGACAACACGA
447 GGGATAATTTAGAGACAACACGA
*
5940 TTCCTACATGATGAGGAAGTCT
1 TTCCTACGTGATGAGGAAGTCT
5962 GGTTATCTGA
Statistics
Matches: 413, Mismatches: 69, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
467 60 0.15
468 101 0.24
469 2 0.00
470 81 0.20
471 147 0.36
472 22 0.05
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (469 bp):
TTCCTACGTGATGAGGAAGTCTATCCGTCTTTAAAGATAAATTGGAGACAACATCATTCCTACGA
GATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTACGCATTGAGGAGATCTGATCACTGA
CAACATTATTCCTACGTAACGAGGACATCTAGCCATCTTTAAGGATAATTCGGAGACAACAAGGT
TCCTATGATAAGGAAGTTCGATTTCCTAAGGATGACGCTGCTCCTACGTGTTAAGGAGATATGGT
CAGTGGACGACATTATTCCTACATGATGAGGACCTCTAGCATCTTTAGGGATAACTTGGAGACAA
CACAGTACCTACGTGATGACAAAGTCTGATTGCCTAAGGATGACGCTACTCCTACGTGTTAAGGA
GATCTAGTCGGTGGACGACATTATTCCTACATGATAAGGACATCTAACCGACTTTAGGGATAATT
TAGAGACAACACGA
Found at i:6005 original size:139 final size:139
Alignment explanation
Indices: 5468--6005 Score: 627
Period size: 139 Copynumber: 3.9 Consensus size: 139
5458 AGACAACACG
* * * * *
5468 TTCCTACGTGATGAGGACGTCTATCCGTCTTTAGGGATAATTTGGAGCCAACAC-ATTCCTACGT
1 TTCCTACATGATGAGGACATCTAGCCATCTTTAGGGATAATTTGGAGACAACACGATTCCTACGT
* * * * * * *
5532 GATGAGGAAGTCTGGTTATCTAAGGATGAAGCTACTCCTATGCATTTAGGAGATCTGGTCAGTGG
66 GATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATCTAGTCAGTGG
*
5597 ACAACATTA
131 ACGACATTA
** * * *
5606 TTCCTATGTAATGAGGACATCTAGCCATCTTTAGGGATAATTCGGAGAGAACACAGTATT--TAC
1 TTCCTACATGATGAGGACATCTAGCCATCTTTAGGGATAATTTGGAGACAACAC-G-ATTCCTAC
* * * * * *
5669 GTGATAAGGAAGTCTTGTTATCTGAGGATTACGCTGCTCCTACGTGTTAAGGAGATATGGTCAGT
64 GTGATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATCTAGTCAGT
*
5734 GGACGACGTTA
129 GGACGACATTA
** * * *
5745 TTCCTACATGATGAGGATGTCTAGCCATCTTTAGGGATAACTTGGAGACAACACGGTACCTACGT
1 TTCCTACATGATGAGGACATCTAGCCATCTTTAGGGATAATTTGGAGACAACACGATTCCTACGT
* * * * *
5810 GATGAGGAAGTCTGATT-TCCAGGGGATGACGCTGCTCCTACGTGTTAAGGAGATCTAGTCGGTG
66 GATGAGGAAGTCTGGTTAT-CTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATCTAGTCAGTG
*
5874 GACGACATTG
130 GACGACATTA
* * *
5884 TTCGTACATGATGAGGACATCTAGCCGA-CTTTAGGGATAATTTAGAGACAACACGATTCCTACA
1 TTCCTACATGATGAGGACATCTAGCC-ATCTTTAGGGATAATTTGGAGACAACACGATTCCTACG
* * *
5948 TGATGAGGAAGTCTGGTTATCTGAGGATGATGCTGCTCCTATGCGTTGAGGAGATCTA
65 TGATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATCTA
6006 TTCGATTACC
Statistics
Matches: 335, Mismatches: 57, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
137 1 0.00
138 48 0.14
139 281 0.84
140 2 0.01
141 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (139 bp):
TTCCTACATGATGAGGACATCTAGCCATCTTTAGGGATAATTTGGAGACAACACGATTCCTACGT
GATGAGGAAGTCTGGTTATCTGAGGATGACGCTGCTCCTACGCGTTAAGGAGATCTAGTCAGTGG
ACGACATTA
Found at i:6382 original size:51 final size:51
Alignment explanation
Indices: 6303--6404 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
6293 CGAAACTTTG
* *
6303 TTTCGAGAGAAACGATCTCAAAGATTTATGTTTCAAGAGAAATTGTCTCAA
1 TTTCGAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAA
*
6354 TTTCGAGAGAAACAATCTCAAAGTTTTATGTTTCAAGAGAAACTGTCTCAA
1 TTTCGAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAA
6405 GCGAGACAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (51 bp):
TTTCGAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAA
Found at i:6432 original size:67 final size:67
Alignment explanation
Indices: 6358--6556 Score: 294
Period size: 67 Copynumber: 3.0 Consensus size: 67
6348 TCTCAATTTC
*
6358 GAGAGAAACAATCTCAAAGTTTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTT
1 GAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTT
6423 TA
66 TA
* *
6425 GAGAGAAACAATCTCAAAGATTTATGTTTCAAGTGAAACTGTCTCAAGCGAGACAAAACTTTTTT
1 GAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTT
*
6490 TC
66 TA
* * * * *
6492 GAGAAAAACAATCTCAAAGGTTTATGTTT-ATAGAGAAAATGTCTTAAGCGAGATAAAA-TTTGT
1 GAGAGAAACAATCTCAAAGATTTATGTTTCA-AGAGAAACTGTCTCAAGCGAGACAAAACTTTGT
6555 TT
65 TT
6557 TTAGGGAAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
66 7 0.06
67 113 0.94
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (67 bp):
GAGAGAAACAATCTCAAAGATTTATGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTT
TA
Found at i:6566 original size:36 final size:36
Alignment explanation
Indices: 6516--6592 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
6506 CAAAGGTTTA
*
6516 TGTTTATAGAGAAAATGTCTTAAGCGAGATAAAATT
1 TGTTTATAGAGAAAATGTATTAAGCGAGATAAAATT
* * * * * *
6552 TGTTTTTAGGGAAAATTTATTAAGTGAGATCAATTT
1 TGTTTATAGAGAAAATGTATTAAGCGAGATAAAATT
6588 TGTTT
1 TGTTT
6593 CGAGTGAAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (36 bp):
TGTTTATAGAGAAAATGTATTAAGCGAGATAAAATT
Found at i:6784 original size:99 final size:99
Alignment explanation
Indices: 6620--6950 Score: 342
Period size: 99 Copynumber: 3.3 Consensus size: 99
6610 AAATTTGTGG
* * * * * *
6620 AAAA-TGTCTCAGGCGAGACAAAATTTGTTTTGAGGAAAACAATCTCAATTAAGATAAAATTTGT
1 AAAACTGTCTCAAGTGAGACGAAATTTATTTTGA-G--AACAATCTCAAGTAAGATAAATTTTGT
* *
6684 TTCAAGTGAAACAATTTTAGAATTTGTGTTTCAAAGA
63 TTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAAGA
* * *
6721 AAAACTGTCTCAAGTGAGATGAAATTTATTTTGAGAACAATCCCAAGTGAGATAAATTTTGTTTC
1 AAAACTGTCTCAAGTGAGACGAAATTTATTTTGAGAACAATCTCAAGTAAGATAAATTTTGTTTC
* *** *
6786 AAGTGAAATAATTTCAAAATTTGTGTTTCTTGGG
66 AAGTGAAACAATTTCAAAATTTGTGTTTCAAAGA
* * * * * *
6820 GAAACTGTCTCAAGTTAGACGAAATTTGTTTTGAGAACAATCTTAAGTTAGATAAATTTTGTTTT
1 AAAACTGTCTCAAGTGAGACGAAATTTATTTTGAGAACAATCTCAAGTAAGATAAATTTTGTTTC
* * * *
6885 GAGTGAAACAATTTCAAAATTTGTATTT-ATAGGG
66 AAGTGAAACAATTTCAAAATTTGTGTTTCA-AAGA
* * * *
6919 GAAATTGTCTCAAGTGAGACAAAATTTGTTTT
1 AAAACTGTCTCAAGTGAGACGAAATTTATTTT
6951 TAAGAAAAAA
Statistics
Matches: 196, Mismatches: 32, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
99 167 0.85
101 5 0.03
102 24 0.12
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (99 bp):
AAAACTGTCTCAAGTGAGACGAAATTTATTTTGAGAACAATCTCAAGTAAGATAAATTTTGTTTC
AAGTGAAACAATTTCAAAATTTGTGTTTCAAAGA
Found at i:17665 original size:12 final size:12
Alignment explanation
Indices: 17648--17674 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17638 ATTGAATGTC
17648 CCCCCAGAAGTA
1 CCCCCAGAAGTA
17660 CCCCCAGAAGTA
1 CCCCCAGAAGTA
17672 CCC
1 CCC
17675 GCTGATGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.48, G:0.15, T:0.07
Consensus pattern (12 bp):
CCCCCAGAAGTA
Found at i:19365 original size:21 final size:21
Alignment explanation
Indices: 19329--19408 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
19319 TTAACCACTA
*
19329 TTGACTGGATCGTTGACCGGCG
1 TTGACTGG-CCGTTGACCGGCG
19351 TTGACTGGCCGTTGACCGGCG
1 TTGACTGGCCGTTGACCGGCG
* *
19372 TTGACTGGCCGTTGACCAGCA
1 TTGACTGGCCGTTGACCGGCG
*
19393 TTGACTGGCCATTGAC
1 TTGACTGGCCGTTGAC
19409 TTTTTTTGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
21 46 0.85
22 8 0.15
ACGTcount: A:0.15, C:0.26, G:0.33, T:0.26
Consensus pattern (21 bp):
TTGACTGGCCGTTGACCGGCG
Found at i:19405 original size:11 final size:11
Alignment explanation
Indices: 19329--19409 Score: 69
Period size: 10 Copynumber: 7.5 Consensus size: 11
19319 TTAACCACTA
*
19329 TTGACTGGATCG
1 TTGACTGG-CCG
*
19341 TTGACCGG-CG
1 TTGACTGGCCG
19351 TTGACTGGCCG
1 TTGACTGGCCG
*
19362 TTGACCGG-CG
1 TTGACTGGCCG
19372 TTGACTGGCCG
1 TTGACTGGCCG
** *
19383 TTGACCAG-CA
1 TTGACTGGCCG
*
19393 TTGACTGGCCA
1 TTGACTGGCCG
19404 TTGACT
1 TTGACT
19410 TTTTTTGGGT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
10 25 0.44
11 25 0.44
12 7 0.12
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.27
Consensus pattern (11 bp):
TTGACTGGCCG
Found at i:21321 original size:24 final size:24
Alignment explanation
Indices: 21294--21343 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
21284 AACGAGTTAG
21294 TACATGTAAGATAATCAATAGAAT
1 TACATGTAAGATAATCAATAGAAT
21318 TACATGTAAGATAATCAATAGAAT
1 TACATGTAAGATAATCAATAGAAT
21342 TA
1 TA
21344 AAAGATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (24 bp):
TACATGTAAGATAATCAATAGAAT
Found at i:23117 original size:20 final size:19
Alignment explanation
Indices: 23080--23130 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
23070 CAAACATGGA
* *
23080 TAATAATATTTATTTAATG
1 TAATAATATATATATAATG
23099 TAATACATATATATATAATATG
1 TAATA-ATATATATAT-A-ATG
23121 TAA-AATATAT
1 TAATAATATAT
23131 TCATACATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 14 0.52
21 2 0.07
22 6 0.22
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (19 bp):
TAATAATATATATATAATG
Found at i:40881 original size:20 final size:20
Alignment explanation
Indices: 40858--40901 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
40848 GTCAACTAGT
*
40858 ACCAAACTTAGTCAACCCAA
1 ACCAAACTGAGTCAACCCAA
** *
40878 ACCATCCTGCGTCAACCCAA
1 ACCAAACTGAGTCAACCCAA
40898 ACCA
1 ACCA
40902 TCCTGCGTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.41, G:0.07, T:0.14
Consensus pattern (20 bp):
ACCAAACTGAGTCAACCCAA
Found at i:40902 original size:20 final size:20
Alignment explanation
Indices: 40868--40921 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
40858 ACCAAACTTA
40868 GTCAACCCAAACCATCCTGC
1 GTCAACCCAAACCATCCTGC
40888 GTCAACCCAAACCATCCTGC
1 GTCAACCCAAACCATCCTGC
* *
40908 GTAAACCCGAACCA
1 GTCAACCCAAACCA
40922 GTATGACCCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.43, G:0.11, T:0.13
Consensus pattern (20 bp):
GTCAACCCAAACCATCCTGC
Found at i:40952 original size:18 final size:19
Alignment explanation
Indices: 40929--40978 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
40919 CCAGTATGAC
40929 CCGTTGACTTTGAC-CTGA
1 CCGTTGACTTTGACTCTGA
* *
40947 CCGTTGACTTTGTCTTTGA
1 CCGTTGACTTTGACTCTGA
*
40966 CCGTTGAATTTGA
1 CCGTTGACTTTGA
40979 ACAAAAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (19 bp):
CCGTTGACTTTGACTCTGA
Found at i:45426 original size:12 final size:13
Alignment explanation
Indices: 45409--45443 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
45399 TACATATGTA
45409 ATTTAAGT-ATTT
1 ATTTAAGTGATTT
45421 ATTTAAGTGATTT
1 ATTTAAGTGATTT
*
45434 AATTAAGTGA
1 ATTTAAGTGA
45444 ATCTCTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (13 bp):
ATTTAAGTGATTT
Found at i:49184 original size:26 final size:28
Alignment explanation
Indices: 49155--49212 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
49145 TAATTATTCC
49155 ATTTGTAA-TC-TTTTA-TGCTAAAATGA
1 ATTTGTAATTCATTTTACTGC-AAAATGA
*
49181 ATTTTTAATTCATTTTACTGCAAAATGA
1 ATTTGTAATTCATTTTACTGCAAAATGA
49209 ATTT
1 ATTT
49213 TTGCCCTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 7 0.25
27 2 0.07
28 16 0.57
29 3 0.11
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (28 bp):
ATTTGTAATTCATTTTACTGCAAAATGA
Found at i:51688 original size:62 final size:62
Alignment explanation
Indices: 51614--51791 Score: 198
Period size: 62 Copynumber: 2.9 Consensus size: 62
51604 AAAGGGATCG
* * * ***
51614 ATCTTTTTTCAAATGATTTGACCGTTTCAATAAAGAGACTGATCCTTTAGGGAAAGTGGTCA
1 ATCTTTTTTCAAATAATTTAACCGTTTCAATAAAGAGATTGATCCTTTAGGGAAAGCAATCA
* ** * *
51676 ATCTTTTTTCAAATAATTTCA-TATTTGCAATAAAGAGTTTGATCCTTTAGGGAAAGCAATCG
1 ATCTTTTTTCAAATAATTTAACCGTTT-CAATAAAGAGATTGATCCTTTAGGGAAAGCAATCA
* * *
51738 ATCCTTTCTCAAATAATTTAACCGTTGC-ATGAAAGAGATTGATCCTTTAGGGAA
1 ATCTTTTTTCAAATAATTTAACCGTTTCAAT-AAAGAGATTGATCCTTTAGGGAA
51792 TGGGGTTAGT
Statistics
Matches: 96, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
61 5 0.05
62 89 0.93
63 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (62 bp):
ATCTTTTTTCAAATAATTTAACCGTTTCAATAAAGAGATTGATCCTTTAGGGAAAGCAATCA
Found at i:56393 original size:16 final size:17
Alignment explanation
Indices: 56364--56401 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
56354 TCCCTTTAGG
56364 TATCCATAAATATATGA
1 TATCCATAAATATATGA
56381 TATCCAT-AATATATGA
1 TATCCATAAATATATGA
56397 TATCC
1 TATCC
56402 TTATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (17 bp):
TATCCATAAATATATGA
Found at i:56676 original size:20 final size:20
Alignment explanation
Indices: 56651--56698 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
56641 TTCTAGATTC
*
56651 TTTTTCTTA-AAATTATTTAA
1 TTTTTCTTACAAATCA-TTAA
56671 TTTTTCTTACAAATCATTAA
1 TTTTTCTTACAAATCATTAA
*
56691 TCTTTCTT
1 TTTTTCTT
56699 TCAAGTTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTCTTACAAATCATTAA
Found at i:58912 original size:40 final size:38
Alignment explanation
Indices: 58857--58951 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 38
58847 TAGACAAGGA
58857 GAATCGGTACCCCCTGGGGGGAATCTGTACCCCTGGGGGG
1 GAATCGGTACCCCCTGGGGGGAATCTGTACCCCT--GGGG
58897 GAATCGGTACCCCCTGGGGGGAATCTGTACCCCTGGGG
1 GAATCGGTACCCCCTGGGGGGAATCTGTACCCCTGGGG
* *
58935 GAAACTGTACCCCCTGG
1 GAATCGGTACCCCCTGG
58952 ACAATCTGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
38 19 0.36
40 34 0.64
ACGTcount: A:0.17, C:0.29, G:0.36, T:0.18
Consensus pattern (38 bp):
GAATCGGTACCCCCTGGGGGGAATCTGTACCCCTGGGG
Found at i:58948 original size:19 final size:20
Alignment explanation
Indices: 58857--58951 Score: 133
Period size: 20 Copynumber: 4.8 Consensus size: 20
58847 TAGACAAGGA
*
58857 GAATCGGTACCCCCTGGGGG
1 GAATCTGTACCCCCTGGGGG
58877 GAATCTGTA-CCCCTGGGGGG
1 GAATCTGTACCCCCT-GGGGG
*
58897 GAATCGGTACCCCCTGGGGG
1 GAATCTGTACCCCCTGGGGG
58917 GAATCTGTA-CCCCT-GGGG
1 GAATCTGTACCCCCTGGGGG
*
58935 GAAACTGTACCCCCTGG
1 GAATCTGTACCCCCTGG
58952 ACAATCTGAT
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
18 12 0.18
19 15 0.22
20 35 0.52
21 5 0.07
ACGTcount: A:0.17, C:0.29, G:0.36, T:0.18
Consensus pattern (20 bp):
GAATCTGTACCCCCTGGGGG
Found at i:60407 original size:19 final size:20
Alignment explanation
Indices: 60366--60413 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
60356 TCTAAATCCT
*
60366 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
*
60386 TTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
60405 TTTTCAAAA
1 TTTTCAAAA
60414 GGAAAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Done.